VirtualEscapeRoom

(if: $showFooter)[ =|= (link-reveal-goto: "Instructions", "instructions")[(set:$t to it + time)] =|= (link-reveal-goto: "Go to the library", "Library")[(set:$t to it + time)] =|= (if: $choice is 0)[(link-reveal-goto: "Please choose a difficulty level", "LevelChoice")[(set:$t to it + time)]]\ (if: $choice is 1)[(link-reveal-goto: "Escape the room", "Key1")[(set:$t to it + time)]]\ (if: $choice is 4)[(link-reveal-goto: "Escape the room", "Key4")[(set:$t to it + time)]]\ (if: $choice is 6)[(link-reveal-goto: "Escape the room", "Key6")[(set:$t to it + time)]]\ (if: $choice is 8)[(link-reveal-goto: "Escape the room", "Key8")[(set:$t to it + time)]]\ (if: $choice is 12)[(link-reveal-goto: "Escape the room", "Key12")[(set:$t to it + time)]]\ |==| --- ]

{ (set: $vol1 to (either: 100, 250, 500, 750, 800, 1100, 1500)) (set: $vol2 to (either: 1, 2, 5, 10, 20, 25, 30, 50, 75)) (set: $vol3 to (either: 300, 400, 500, 600, 700, 800)) (set: $vol4 to (either: 200, 400, 600, 800, 1200)) (set: $vol5 to (either: 300, 200, 500, 700, 800, 100, 1500)) (set: $rxn6 to (random: 3, 64)) (set: $vol7 to (either: 1, 3, 5, 15, 12, 25, 30, 40, 50)) (set: $vol8 to (either: 50, 100, 150, 200, 250, 300, 400, 500, 750)) (set: $vol9 to (either: 50, 100, 150, 200, 250, 300, 400, 600)) (set: $vol10 to (either: 500, 150, 250, 350, 450, 700, 900, 1200)) (set: $vol11 to (either: 1, 3, 5, 8, 20, 15, 12, 25, 30, 40, 50)) (set: $vol12 to (either: 500, 1200, 1500, 2000, 2500, 3000)) (set: $vol13 to (either: 100, 250, 400, 750, 800, 1200, 1500)) (set: $vol14 to (either: 600, 500, 250, 400, 750, 800, 1200, 1500)) (set: $vol15 to (either: 500, 100, 150, 200, 250, 300, 400, 600)) (set: $vol16 to (either: 1, 3, 5, 15, 12, 25, 30, 40, 50, 75)) (set: $vol17 to (either: 1, 2, 5, 15, 20, 25, 30, 35, 40, 45, 50)) (set: $vol18 to (either: 500, 150, 250, 350, 450, 700, 900, 1200)) (set: $vol19 to (either: 50, 100, 150, 200, 250, 300, 400, 600)) (set: $vol20 to (either: 100, 250, 300, 750, 900, 1100, 1500)) (set: $vol21 to (either: 1, 3, 5, 15, 20, 25, 30, 40, 50)) (set: $vol22 to (either: 200, 400, 600, 800, 1200, 300, 700)) (set: $vol23 to (either: 100, 150, 200, 250, 300, 400, 500)) (set: $vol24 to (either: 100, 250, 500, 750, 800, 1100, 1500)) (set: $vol25 to (either: 600, 500, 250, 400, 750, 800, 1200, 1500)) (set: $vol26 to (either: 1, 3, 5, 15, 35, 25, 30, 40, 50)) (set: $rxn27 to (random: 5, 70)) (set: $vol28 to (either: 100, 250, 400, 750, 800, 1200, 1500)) (set: $vol29 to (either: 100, 30, 50, 150, 350, 250, 300, 400, 550)) (set: $vol30 to (either: 500, 150, 250, 350, 450, 700, 900, 1200)) (set: $vol31 to (either: 100, 250, 400, 750, 800, 1200, 1500)) (set: $vol32 to (either: 500, 150, 250, 350, 450, 700, 900, 1200)) (set: $vol33 to (either: 100, 250, 400, 750, 800, 1200, 1500)) (set: $vol34 to (either: 100, 30, 50, 150, 350, 250, 300, 400, 550)) (set: $vol35 to (either: 500, 150, 250, 350, 450, 700, 900, 1200)) (set: $vol36 to (either: 100, 30, 50, 150, 350, 250, 300, 400, 550)) (set: $vol37 to (either: 500, 150, 250, 350, 450, 700, 900, 1200)) (set: $vol38 to (either: 500, 150, 250, 350, 450, 700, 900, 1200)) (set: $vol39 to (either: 100, 30, 50, 150, 350, 250, 300, 400, 550)) (set: $vol40 to (either: 1100, 330, 500, 1500, 350, 250, 300, 400, 550)) (set: $vol41 to (either: 1, 3, 5, 15, 12, 25, 30, 40, 50)) (set: $vol42 to (either: 1, 3, 5, 15, 12, 25, 30, 40, 50)) (set: $vol43 to (either: 1, 3, 5, 15, 12, 25, 30, 40, 50)) (set: $vol44 to (either: 1, 3, 5, 15, 12, 25, 30, 40, 50)) (set: $vol45 to (either: 1, 3, 5, 15, 12, 25, 30, 40, 50)) (set: $wt1 to (either: 1, 2, 3, 4, 6, 8, 10)) (set: $16S to 1) (set: $WGS to 1) (set: $choice to 0) (set: $clicks to 0) (set: $hints to 0) (set: $viralseq to 0) (set: $mistakes to 0) (set: $earnedclues to 0) (set: _values to (a: (1 + (random: 1, 29)), (30 + (random: 1, 29)), (60 + (random: 1, 29)), (90 + (random: 1, 29)), (120 + (random: 1, 29)), (150 + (random: 1, 29)), (180 + (random: 1, 29)), (200 + (random: 1, 29)), (230 + (random: 1, 29)), (260 + (random: 1, 29)), (290 + (random: 1, 29)), (320 + (random: 1, 29)), (350 + (random: 1, 29)), (380 + (random: 1, 29)), (410 + (random: 1, 29)), (440 + (random: 1, 29)), (470 + (random: 1, 29)), (500 + (random: 1, 29)), (530 + (random: 1, 29)) )) (set: _values to (shuffled: ..._values)) (set: $C1 to _values's 1) (set: $C2 to _values's 2) (set: $C3 to _values's 3) (set: $C4 to _values's 4) (set: $C5 to _values's 5) (set: $C6 to _values's 6) (set: $C7 to _values's 7) (set: $C8 to _values's 8) (set: $C9 to _values's 9) (set: $C10 to _values's 10) (set: $C11 to _values's 11) (set: $C12 to _values's 12) (set: $C13 to _values's 13) (set: $C14 to _values's 14) (set: $C15 to _values's 15) (set: $F to _values's 16) (set: $F4 to _values's 17) (set: $F6 to _values's 18) (set: $F8 to _values's 19) (set: $C1food to (either: "hamburger", "salami", " Romaine lettuce", "spinach", "sprouts", "iceberg lettuce")) (set: $C2food to (either: "unpasteurised milk", "pork sausage", "hot dogs", "sliced turkey meat", "sliced ham", "ice cream")) (set: $C3food to (either: "peanut butter", "prepackaged salad", "frozen chicken tenders", "ground turkey", "alfalfa sprouts", "potato salad")) (set: $C4food to (either: "unpasteurised milk", "chicken liver", "frozen chicken tenders", "chicken salad")) (set: $C5food to (either: "rice pudding", "macaroni", "oatmeal", "mashed potatoes", "rice and corn salad", "semolina", "rice", "tabbouleh", "spaghetti", "polenta")) (set: $C6food to (either: "oysters", "clams", "shrimp", "cod", "scallops", "mussels")) (set: $C7food to (either: "sliced ham", "apple pastries", "chicken salad sandwiches", "sponge cake", "cream puffs", "sausage rolls", "chocolate eclairs", "ham and cheese sandwiches", "pasta salad")) (set: $C8food to (either: "bean dip", "tossed salad", "fruit salad", "strawberries", "chicken salad", "ham sandwiches", "ground beef", "oysters", "asparagus")) (set: $C9food to (either: "roast beef", "roast turkey", "beef stew", "roast pork", "chicken salad", "beef gravy", "minestrone soup", "sweet and sour pork")) (set: $C10food to (either: "sliced pork", "pork sausages", "pork salami", "minced pork")) (set: $C11food to (either: "honey", "home-canned tuna", "home-canned green beans", "home-canned tomatoes", "canned chili", "nacho cheese sauce", "potato salad")) (set: $C12food to (either: "unpasteurised ('raw') milk", "soft cheese made from unpasteurised milk", "ice cream", "yoghurt made from unpasteurised milk")) (set: $C13food to (either: "raw milk", "soft cheese", "ice cream", "yoghurt")) (set: $C14food to (either: "crab", "shrimp", "oysters", "clams")) (set: $C15food to (either: "powdered milk", "UHT milk", "tofu", "herbal tea", "ground rice", "coconut powder", "dried lentil soup mix")) (set: $Ffood to (either: "fruit salad", "fruit smoothie", "frozen fruit mix", "fruit platter", "Eton mess", "fresh fruit tart", "chocolate-dipped fruits")) (set: $F4food to (either: "maize", "peanuts", "seasame seeds","sunflower seeds", "cocoa beans", "rice", "peanut butter", "pistachios", "millet", "wheat flour", "Brazil nuts")) (set: $F6food to (either: "lettuce", "fresh fruit salad", "sliced strawberries", "lettuce salad")) (set: $F8food to (either: "spinach", "cabbage", "lettuce","rocket")) (set: $final to (either: "A", "B", "C")) (set: $final6 to (either: "A", "B", "C")) (set: $demo to (dm: "Case 1", (str: $C1), )) (set: $easy to (dm: "Case 1", (str: $C1), "Case 3", (str: $C3), "Case 4", (str: $C4), "Case 5", (str: $C5), "Case 7", (str: $C7), "Case 8", (str: $C8), "Case 11", (str: $C11), "Case 14", (str: $C14) )) (set: _possible to (datanames: $easy)) (set: _shuffled to (shuffled: ..._possible)) (set: $medium to (dm: "Case 1", (str: $C1), "Case 2", (str: $C2), "Case 3", (str: $C3), "Case 4", (str: $C4), "Case 5", (str: $C5), "Case 7", (str: $C7), "Case 8", (str: $C8), "Case 10", (str: $C10), "Case 11", (str: $C11), "Case 14", (str: $C14) )) (set: _possible to (datanames: $medium)) (set: _shuffled to (shuffled: ..._possible)) (set: $challenging to (dm: "Case 1", (str: $C1), "Case 2", (str: $C2), "Case 3", (str: $C3), "Case 4", (str: $C4), "Case 5", (str: $C5), "Case 6", (str: $C6), "Case 7", (str: $C7), "Case 8", (str: $C8), "Case 10", (str: $C10), "Case 11", (str: $C11), "Case 14", (str: $C14), "Case 15", (str: $C15) )) (set: _possible to (datanames: $challenging)) (set: _shuffled to (shuffled: ..._possible)) (set: $very to (dm: "Case 1", (str: $C1), "Case 2", (str: $C2), "Case 3", (str: $C3), "Case 4", (str: $C4), "Case 5", (str: $C5), "Case 6", (str: $C6), "Case 7", (str: $C7), "Case 8", (str: $C8), "Case 9", (str: $C9), "Case 10", (str: $C10), "Case 11", (str: $C11), "Case 12", (str: $C12), "Case 13", (str: $C13), "Case 14", (str: $C14), "Case 15", (str: $C15) )) (set: _possible to (datanames: $very)) (set: _shuffled to (shuffled: ..._possible)) (set: $choice to 0) (set: $showFooter to false) (set: $notebookC1 to (a:)) (set: $notebookC2 to (a:)) (set: $notebookC3 to (a:)) (set: $notebookC4 to (a:)) (set: $notebookC5 to (a:)) (set: $notebookC6 to (a:)) (set: $notebookC7 to (a:)) (set: $notebookC8 to (a:)) (set: $notebookC9 to (a:)) (set: $notebookC10 to (a:)) (set: $notebookC11 to (a:)) (set: $notebookC12 to (a:)) (set: $notebookC13 to (a:)) (set: $notebookC14 to (a:)) (set: $notebookC15 to (a:)) (set: $hintsC1 to (a:)) (set: $hintsC2 to (a:)) (set: $hintsC3 to (a:)) (set: $hintsC4 to (a:)) (set: $hintsC5 to (a:)) (set: $hintsC6 to (a:)) (set: $hintsC7 to (a:)) (set: $hintsC8 to (a:)) (set: $hintsC9 to (a:)) (set: $hintsC10 to (a:)) (set: $hintsC11 to (a:)) (set: $hintsC12 to (a:)) (set: $hintsC13 to (a:)) (set: $hintsC14 to (a:)) (set: $hintsC15 to (a:)) (set: $solved to (a:)) (set: $passkey to "") (set: $funfact to (either: "Escherichia coli is named after the German-Austrian pediatrician Theodor Escherich who first discovered it, but it used to be called Bacillus coli based on its cell shape", "Listeria monocytogenes can grow at a range of temperatures from 0-45 degrees Celsius, with some strains having reported minimum growth temperatures as low as -1.5°C - definitely capable of growing in your fridge!", "Listeria monocytogenes is named after Joseph Lister, who worked in the Glasgow Royal Infirmary on the antiseptic principle", "Campylobacter gets its name from the Greek word kampylos, which means curved - reflecting the cell shape of these bacteria", "There are normally 5-6 thousand cases of Campylobacter infections reported in Scotland every year", "Salmonella is named after the American veterinary surgeon Daniel Elmer Salmon, but the first isolate was actually discovered by his assistant, Theobald Smith", "Clostridium botulinum gets its name from the Latin word for sausages - botulus - because the disease was identified in people who had consumed tainted sausages", "The emetic toxin produced by Bacillus cereus, cerulide toxin, is stable up to 121°C", "Yersinia is named after the French bacteriologist Alexandre Yersin - who discovered Y. pestis during an outbreak of plague in Hong Kong in 1894")) (set: $finalorganism to 0) (set: $paths to (shuffled: "Problem1", "Problem2", "Problem3", "Problem4", "Problem5", "Problem6", "Problem7", "Problem8", "Problem9", "Problem10", "Problem11", "Problem12", "Problem13", "Problem14", "Problem15", "Problem16", "Problem17", "Problem18", "Problem19", "Problem20", "Problem21", "Problem22", "Problem23", "Problem24", "Problem25", "Problem26", "Problem27", "Problem28", "Problem29", "Problem30", "Problem31", "Problem32", "Problem33", "Problem34", "Problem35", "Problem36", "Problem37", "Problem38", "Problem39", "Problem40", "Problem41", "Problem42", "Problem43", "Problem44", "Problem45")) (set: $pathcount to 0) }

##Unknown $C1 You have isolated an organism in axenic culture from a sample of $C1food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C1 under the microscope", "microscope1")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C1 on different media", "plates1")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C1", "biochem1")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C1's 16S rRNA gene", "16S1")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C1's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S1-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S1-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C1's entire genome", "WGS1")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C1 is currently unavailable. ] (if: (history:) contains "WGS1-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS1-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C1 notebook (summary of previously obtained results/redeem earned hints)", "notebook1")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C1soln is 0)[(link-reveal-goto: "Identify unknown $C1", "identify1")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C1 - do you want to check your answer again?", "identify1")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you want to earn a hint to help you identify unknown $C1?", "Hint0")[(set:$t to it + time)]]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C1 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C1 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C1 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C1", "Case 1")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C1. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown. You can read a brief description of each test by clicking on its name, or go to the library for more information, before performing a test.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C1", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C1", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C1", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C1", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C1 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C1", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C1", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C1 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C1", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C1", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C1", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C1", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C1", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C1", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C1", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C1", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C1", "Case 1")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C1", "16S1-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C1", "Case 1")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C1", "WGS1-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C1", "Case 1")[(set:$t to it + time)]

###Unknown $C2 You have isolated an organism in axenic culture from a sample of $C2food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C2 under the microscope", "microscope2")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C2 on different media", "plates2")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C2", "biochem2")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C2's 16S rRNA gene", "16S2")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C2's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S2-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S2-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C2's entire genome", "WGS2")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C2 is currently unavailable. ] (if: (history:) contains "WGS2-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS2-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C2 notebook (summary of previously obtained results/redeem earned hints)", "notebook2")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C2soln is 0)[(link-reveal-goto: "Identify unknown $C2", "identify2")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C2 - do you want to check your answer again?", "identify2")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C2?", "Hint0")[(set:$t to it + time)]]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C2 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C2 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C2 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C2", "Case 2")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C2. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C2", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C2", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C2", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C2", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C2 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C2", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C2", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C2 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C2", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C2", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C2", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C2", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C2", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C2", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C2", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C2", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C2", "Case 2")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C2", "16S2-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C2", "Case 2")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C2", "WGS2-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C2", "Case 2")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C1, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C1", "16S1-text")[(set:$t to it + time)]

(set: $clicks to it + 1) (set: $WGS to 0) To sequence the genome of your organism, you purify its genomic DNA, create a library, and send it off for Illumina sequencing. (after: 2s)[= You have to wait for the quality control check to be performed on your library ... (after: time + 2s)[= and for the library to be run on the Illumina machine ... (after: time + 2s)[= and for the sequencing facility to send you the data. (after: time + 2s)[= Then you perform quality control on the raw reads and start processing your data ... (after: time + 2s)[= you align the reads into contigs ... (after: time + 2s)[= assemble your genome, annotate it ... (after: time + 2s)[= and compare it to other sequenced genomes. (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the genome of $C1", "WGS1-Results")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C1 is: `NC_002695.2` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C1 case notes?", "Case 1")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C2, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C2", "16S2-text")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C2 is: `NC_003210.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C2 case notes?", "Case 2")[(set:$t to it + time)]

''Foodborne Pathogens: A Virtual Escape Room'' This is a virtual escape room, designed by Dr. Morgan Feeney (Strathclyde Institute of Pharmacy and Biomedical Sciences). Please contact her if you note any issues with the escape room code or any broken links. ''Instructions:'' A whistleblower has alerted you, a microbiologist working for Public Health Scotland, that there are some dodgy hygiene practices going on in a factory that makes and processes a number of different foods. A number of microbes have been isolated from these foods. Your job is now to identify these microbes. Your goal is to identify as many potential pathogens as you can, as quickly as you can, so that you can recall the contaminated foods before anyone ingests them and becomes ill. Note that you need to identify these organisms to the species level - you will need to provide their binomial name (correctly spelled!) in order to escape the room. (b4r:"solid")+(b4r-size:4)+(b4r-color:red)[''[A note about biosafety:]'' Many of the organisms featured here are ''potentially pathogenic to humans''- including organisms that require BSL-2 or BSL-3 precautions. It is important that they are handled safely and appropriately when working with them in the lab. ] (link-goto: "Click to continue reading the instructions", "About2")

A collection of resources provided for your reference (all links will open in a new window). You may also want to <a href="https://pubmed.ncbi.nlm.nih.gov/" target="_blank">consult the peer-reviewed literature</a>. <a href="https://www.rcpath.org/profession/publications/standards-for-microbiology-investigations.html" target="_blank">UK Standards for Microbiology Investigations</a> <a href="https://bacdive.dsmz.de/" target="_blank">BacDive (Bacterial Diversity database)</a> ###Reference texts The <a href="https://www.strath.ac.uk/professionalservices/library/" target="_blank">Strathclyde library</a> has a number of useful texts for microbial identification that are available online (you will need to be logged in with your university account to access them.) The definitive resource for bacterial identification is Bergey's Manual of Systematic Bacteriology. Information about the various tests, stains, and growth media can also be found on their individual pages, but are the links are also provided here for your convenience. ###Microscopy <a href="https://asm.org/ASM/media/Protocol-Images/Acid-Fast-Stain-Protocols.pdf?ext=.pdf" target="_blank">Acid-fast stain</a> <a href="https://asm.org/ASM/media/Protocol-Images/Capsule-Stain-Protocols.pdf?ext=.pdf" target="_blank">Capsule stain protocols</a> <a href="https://asm.org/ASM/media/Protocol-Images/Endospore-Stain-Protocol.pdf?ext=.pdf"target="_blank">Malachite green stain</a> <a href="https://asm.org/getattachment/5c95a063-326b-4b2f-98ce-001de9a5ece3/gram-stain-protocol-2886.pdf" target="_blank">Gram stain protocol</a> ###Biochemical Tests <a href="https://asm.org/ASM/media/Protocol-Images/Carbohydrate-Fermentation-Protocol.pdf?ext=.pdf" target="_blank">Carbohydrate Fermentation Protocol</a> <a href="https://asm.org/getattachment/72a871fc-ba92-4128-a194-6f1bab5c3ab7/Catalase-Test-Protocol.pdf" target="_blank">Catalase Test</a> <a href="https://asm.org/ASM/media/Protocol-Images/Coagulase-Test-Protocol.pdf?ext=.pdf" target="_blank">Coagulase Test</a> <a href="https://asm.org/ASM/media/Protocol-Images/Decarboxylase-Broth-Protocol.pdf?ext=.pdf" target="_blank">Decarboxylase Broth Protocol</a> <a href="https://asm.org/ASM/media/Protocol-Images/Gelatin-Hydrolysis-Test-Protocol.pdf?ext=.pdf" target="_blank">Gelatin Hydrolysis Test</a> <a href="https://asm.org/getattachment/200d3f34-c75e-4072-a7e6-df912c792f62/indole-test-protocol-3202.pdf" target="_blank">Indole Test</a> <a href="https://asm.org/ASM/media/Protocol-Images/Nitrate-and-Nitrite-Reduction-Test-Protocols.pdf?ext=.pdf" target="_blank">Nitrate and Nitrite Reduction Test</a> <a href="https://asm.org/getattachment/00ce8639-8e76-4acb-8591-0f7b22a347c6/oxidase-test-protocol-3229.pdf" target="_blank">Oxidase Test</a> <a href="https://asm.org/getattachment/0c828061-9d6f-4ae7-aea3-66e1a8624aa0/Methyl-Red-and-Voges-Proskauer-Test-Protocols.pdf" target="_blank">Methyl Red and Voges-Proskauer Test Protocols</a> <a href="https://asm.org/getattachment/ac4fe214-106d-407c-b6c6-e3bb49ac6ffb/urease-test-protocol-3223.pdf" target="_blank">Urease Test</a>

##Unknown $C3 You have isolated an organism in axenic culture from a sample of $C3food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C3 under the microscope", "microscope3")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C3 on different media", "plates3")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C3", "biochem3")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C3's 16S rRNA gene", "16S3")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C3's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S3-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S3-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C3's entire genome", "WGS3")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C3 is currently unavailable. ] (if: (history:) contains "WGS3-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS3-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C3 notebook (summary of previously obtained results/redeem earned hints)", "notebook3")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C3soln is 0)[(link-reveal-goto: "Identify unknown $C3", "identify3")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C3 - do you want to check your answer again?", "identify3")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C3?", "Hint0")[(set:$t to it + time)]]

##Unknown $C4 You have isolated an organism in axenic culture from a sample of $C4food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C4 under the microscope", "microscope4")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C4 on different media", "plates4")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C4", "biochem4")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C4's 16S rRNA gene", "16S4")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C4's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S4-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S4-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C4's entire genome", "WGS4")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C4 is currently unavailable. ] (if: (history:) contains "WGS4-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS4-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C4 notebook (summary of previously obtained results/redeem earned hints)", "notebook4")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C4soln is 0)[(link-reveal-goto: "Identify unknown $C4", "identify4")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C4 - do you want to check your answer again?", "identify4")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C4?", "Hint0")[(set:$t to it + time)]]

##Unknown $C5 You have isolated an organism in axenic culture from a sample of $C5food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C5 under the microscope", "microscope5")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C5 on different media", "plates5")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C5", "biochem5")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C5's 16S rRNA gene", "16S5")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C5's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S5-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S5-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C5's entire genome", "WGS5")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C5 is currently unavailable. ] (if: (history:) contains "WGS5-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS5-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C5 notebook (summary of previously obtained results/redeem earned hints)", "notebook5")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C5soln is 0)[(link-reveal-goto: "Identify unknown $C5", "identify5")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C5 - do you want to check your answer again?", "identify5")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C5?", "Hint0")[(set:$t to it + time)]]

##Unknown $C6 You have isolated an organism in axenic culture from a sample of $C6food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C6 under the microscope", "microscope6")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C6 on different media", "plates6")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C6", "biochem6")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C6's 16S rRNA gene", "16S6")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C6's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S6-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S6-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C6's entire genome", "WGS6")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C6 is currently unavailable. ] (if: (history:) contains "WGS6-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS6-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C6 notebook (summary of previously obtained results/redeem earned hints)", "notebook6")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C6soln is 0)[(link-reveal-goto: "Identify unknown $C6", "identify6")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C6 - do you want to check your answer again?", "identify6")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C6?", "Hint0")[(set:$t to it + time)]]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C3 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C3 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C3 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C3", "Case 3")[(set:$t to it + time)]

Unknown $C3 was isolated from a sample of $C3food. The results from the experiments you have obtained so far are: (if: $notebookC3's length > 0)[\ (for: each _index, ...(range: 1, $notebookC3's length))[_index) (print: $notebookC3's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S3-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S3-text")[(set:$t to it + time)]] (if: (history:) contains "WGS3-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS3-Results")[(set:$t to it + time)]] (if: $C3soln is 0)[(link-reveal-goto: "Identify unknown $C3", "identify3")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C3 - do you want to check your answer again?", "identify3")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C3", "C3hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C3", "Case 3")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C3. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C3", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C3", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C3", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C3", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C3 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C3", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C3", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C3 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C3", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C3", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C3", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C3", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C3", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C3", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C3", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C3", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C3", "Case 3")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C3", "16S3-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C3", "Case 3")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C3", "WGS3-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C3", "Case 3")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C4 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C4 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C4 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C4", "Case 4")[(set:$t to it + time)]

Unknown $C4 was isolated from a sample of $C4food. The results from the experiments you have obtained so far are: (if: $notebookC4's length > 0)[\ (for: each _index, ...(range: 1, $notebookC4's length))[_index) (print: $notebookC4's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S4-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S4-text")[(set:$t to it + time)]] (if: (history:) contains "WGS4-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS4-Results")[(set:$t to it + time)]] (if: $C4soln is 0)[(link-reveal-goto: "Identify unknown $C4", "identify4")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C4 - do you want to check your answer again?", "identify4")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C4", "C4hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C4", "Case 4")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C4. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C4", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C4", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C4", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C4", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C4 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C4", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C4", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C4 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C4", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C4", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C4", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C4", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C4", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C4", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C4", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C4", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C4", "Case 4")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C4", "16S4-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C4", "Case 4")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C4", "WGS4-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C4", "Case 4")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C5 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C5 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C5 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C5", "Case 5")[(set:$t to it + time)]

Unknown $C5 was isolated from a sample of $C5food. The results from the experiments you have obtained so far are: (if: $notebookC5's length > 0)[\ (for: each _index, ...(range: 1, $notebookC5's length))[_index) (print: $notebookC5's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S5-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S5-text")[(set:$t to it + time)]] (if: (history:) contains "WGS5-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS5-Results")[(set:$t to it + time)]] (if: $C5soln is 0)[(link-reveal-goto: "Identify unknown $C5", "identify5")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C5 - do you want to check your answer again?", "identify5")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C5", "C5hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C5", "Case 5")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C5. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C5", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C5", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C5", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C5", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C5 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C5", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C5", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C5 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C5", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C5", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C5", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C5", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C5", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C5", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C5", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C5", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C5", "Case 5")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C5", "16S5-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C5", "Case 5")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C5", "WGS5-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C5", "Case 5")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C6 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C6 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C6 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C6", "Case 6")[(set:$t to it + time)]

Unknown $C6 was isolated from a sample of $C6food. The results from the experiments you have obtained so far are: (if: $notebookC6's length > 0)[\ (for: each _index, ...(range: 1, $notebookC6's length))[_index) (print: $notebookC6's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S6-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S6-text")[(set:$t to it + time)]] (if: (history:) contains "WGS6-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS6-Results")[(set:$t to it + time)]] (if: $C6soln is 0)[(link-reveal-goto: "Identify unknown $C6", "identify6")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C6 - do you want to check your answer again?", "identify6")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C6", "C6hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C6", "Case 6")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C6. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C6", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C6", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C6", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C6", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C6 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C6", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C6", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C6 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C6", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C6", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C6", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C6", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C6", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C6", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C6", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C6", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C6", "Case 6")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C6", "16S6-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C6", "Case 6")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C6", "WGS6-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C6", "Case 6")[(set:$t to it + time)]

The Voges-Proskauer test detects the presence of acetoin (acetylmethyl carbinol) in bacterial cultures. Bacteria are grown overnight in MRVP broth, and then Barrit's reagents A (alpha-napthol) and B (potassium hydroxide) are added, and the culture is mixed well to aerate. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are VP+, a pinkish-red colour will be produced. If the bacteria are VP-, no pinkish-red colour will be produced.] (b4r:"solid")[<center><img alt="example of Voges-Proskauer test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/VP.png"></center> Figure 1. Voges-Proskauer test results. From left to right: a positive test result (indicated by the red colour); a negative test result (indicated by the lack of colour change). ASM Image Gallery: Mary G. Miller, Southeastern Louisiana University, Hammond, LA] <a href="https://asm.org/Protocols/Methyl-Red-and-Voges-Proskauer-Test-Protocols" target="_blank">Read more about the Voges-Proskauer test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform a Voges-Proskauer test on unknown $C1")[Unknown $C1 is ''Voges-Proskauer negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is Voges-Proskauer negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform a Voges-Proskauer test on unknown $C2")[Unknown $C2 is ''Voges-Proskauer positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 is Voges-Proskauer positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform a Voges-Proskauer test on unknown $C3")[Unknown $C3 is ''Voges-Proskauer negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is Voges-Proskauer negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform a Voges-Proskauer test on unknown $C4")[Unknown $C4 is ''Voges-Proskauer negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 is Voges-Proskauer negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform a Voges-Proskauer test on unknown $C5")[Unknown $C5 is ''Voges-Proskauer positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 is Voges-Proskauer positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform a Voges-Proskauer test on unknown $C6")[Unknown $C6 is ''Voges-Proskauer negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is Voges-Proskauer negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform a Voges-Proskauer test on unknown $C7")[Unknown $C7 is ''Voges-Proskauer positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is Voges-Proskauer positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform a Voges-Proskauer test on unknown $C8")[Unknown $C8 is ''Voges-Proskauer negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is Voges-Proskauer negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform a Voges-Proskauer test on unknown $C9")[You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not perform a Voges-Proskauer testt on unknown $C9")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform a Voges-Proskauer test on unknown $C10")[Unknown $C10 is ''Voges-Proskauer negative'' at 37°C, but ''Voges-Proskauer positive'' at 28°C. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is Voges-Proskauer negative at 37°C, but Voges-Proskauer positive at 28°C.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform a Voges-Proskauer test on unknown $C11")[You should consider whether this is the best experiment to identify unknown $C11 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not perform a Voges-Proskauer testt on unknown $C11")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform a Voges-Proskauer test on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not perform a Voges-Proskauer testt on unknown $C12")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform a Voges-Proskauer test on unknown $C13")[Unknown $C13 is ''Voges-Proskauer negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is Voges-Proskauer negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform a Voges-Proskauer test on unknown $C14")[Unknown $C14 is ''Voges-Proskauer positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is Voges-Proskauer positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform a Voges-Proskauer test on unknown $C15")[Unknown $C15 is ''Voges-Proskauer positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is Voges-Proskauer positive")) (set: $clicks to it + 1)]]

The indole test is used to determine whether an organism has the ability to degrade tryptophan to indole. Bacteria are grown for 24-48 hours in tryptone broth, and then 5 drops of Kovac's reagent are added. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are indole+, a cherry-red ring will form in a layer on top of the medium. If the bacteria are indole-, no red colour will be produced (the reagent layer will remain yellow or cloudy).] (b4r:"solid")[<center><img alt="example of indole test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/indole.png"></center> Figure 1. Indole results. From left to right: a positive result (red layer); a negative result (yellow - no colour change). ASM Image Gallery: Mary G. Miller, Southeastern Louisiana University, Hammond] <a href="https://asm.org/Protocols/Indole-Test-Protocol" target="_blank">Read more about the indole test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform an indole test on unknown $C1")[Unknown $C1 is ''indole positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is indole positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform an indole test on unknown $C2")[Unknown $C2 is ''indole negative''.. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 is indole negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform an indole test on unknown $C3")[Unknown $C3 is ''indole negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is indole negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform an indole test on unknown $C4")[Unknown $C4 is ''indole negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 is indole negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform an indole test on unknown $C5")[Unknown $C5 is ''indole negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 is indole negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform an indole test on unknown $C6")[Unknown $C6 is ''indole positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is indole positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform an indole test on unknown $C7")[You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not perform an indole test on unknown $7")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform an indole test on unknown $C8")[Unknown $C8 is ''indole positive''.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is indole positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform an indole test on unknown $C9")[Unknown $C9 is ''indole negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 is indole negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform an indole test on unknown $C10")[Unknown $C10 is ''indole positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is indole positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform an indole test on unknown $C11")[Unknown $C11 is ''indole negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is indole negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform an indole test on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not perform an indole test on unknown $C12")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform an indole test on unknown $C13")[Unknown $C13 is ''indole negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is indole negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform an indole test on unknown $C14")[Unknown $C14 is ''indole positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is indole positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform an indole test on unknown $C15")[Unknown $C15 is ''indole negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is indole negative")) (set: $clicks to it + 1)]]

The oxidase test is used to determine whether an organism has the enzyme cytochrome oxidase. A number of different protocols are used to perform the oxidase test; in your lab, you use strips that contain the oxidase reagent. These strips are touched to a bacterial colony grown on a nutrient agar plate, and then monitored for a colour change. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are oxidase+, a purple colour will form in 5-10 seconds. If the bacteria are oxidase-, no purple colour will form.] (b4r:"solid")[<center><img alt="example of positive and negative oxidase test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/oxidase.png"></center> Figure 1. Oxidase reaction. Example of positive (top) and negative (bottom) oxidase test results.] <a href="https://asm.org/Protocols/Oxidase-Test-Protocol" target="_blank">Read more about the oxidase test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform an oxidase test on unknown $C1")[Unknown $C1 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is oxidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform an oxidase test on unknown $C2")[Unknown $C2 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 is oxidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform an oxidase test on unknown $C3")[Unknown $C3 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is oxidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform an oxidase test on unknown $C4")[Unknown $C4 is ''oxidase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 is oxidase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform an oxidase test on unknown $C5")[Unknown $C5 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 is oxidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform an oxidase test on unknown $C6")[Unknown $C6 is ''oxidase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is oxidase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform an oxidase test on unknown $C7")[Unknown $C7 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is oxidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform an oxidase test on unknown $C8")[Unknown $C8 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is oxidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform an oxidase test on unknown $C9")[Unknown $C9 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 is oxidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform an oxidase test on unknown $C10")[Unknown $C10 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is oxidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform an oxidase test on unknown $C11")[Unknown $C11 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is oxidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform an oxidase test on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 is.....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform an oxidase test on unknown $C13")[Unknown $C13 is ''oxidase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is oxidase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform an oxidase test on unknown $C14")[Unknown $C14 is ''oxidase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is oxidase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform an oxidase test on unknown $C15")[Unknown $C15 is ''oxidase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is oxidase negative")) (set: $clicks to it + 1)]]

The coagulase test can be used to determine whether a bacterial species produces the enzyme coagulase (an enzyme that clots blood plasma). This test can be done using either the slide or the tube procedure (the slide test is simplier and quicker, but can give false negatives). A suspension of bacterial cells are mixed with EDTA-treated rabbit plasma on a glass slide. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are coagulase+, the cells will begin to form visible clumps. If the bacteria are coagulase-, the cells will not clump.] (b4r:"solid")[<center><img alt="example of positive and negative coagulase test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/coagulase.png"></center> Figure 1. Coagulase reaction. Example of positive (top) and negative (bottom) coagulase test results.] <a href="https://asm.org/Protocols/Coagulase-Test-Protocol" target="_blank">Read more about the coagulase test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform a coagulase test on unknown $C1")[You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not perform a coagulase test on unknown $C1.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform a coagulase test on unknown $C2")[You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not perform a coagulase test on unknown $C2.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[ (link: "Click to perform a coagulase test on unknown $C3")[You should consider whether this is the best experiment to identify unknown $C3 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not perform a coagulase test on unknown $C3.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform a coagulase test on unknown $C4")[You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not perform a coagulase test on unknown $C4.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform a coagulase test on unknown $C5")[You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not perform a coagulase test on unknown $C5.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform a coagulase test on unknown $C6")[You should consider whether this is the best experiment to identify unknown $C6 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not perform a coagulase test on unknown $C6.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform a coagulase test on unknown $C7")[Unknown $C7 is ''coagulase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is coagulase positive.")) (set: $clicks to it + 1)]] Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform a coagulase test on unknown $C8")[You should consider whether this is the best experiment to identify unknown $C8 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not perform a coagulase test on unknown $C8.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform a coagulase test on unknown $C9")[You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not perform a coagulase test on unknown $C9.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform a coagulase test on unknown $C10")[You should consider whether this is the best experiment to identify unknown $C10 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not perform a coagulase test on unknown $C10.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform a coagulase test on unknown $C11")[You should consider whether this is the best experiment to identify unknown $C11 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not perform a coagulase test on unknown $C11.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform a coagulase test on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not perform a coagulase test on unknown $C12.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform a coagulase test on unknown $C13")[You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not perform a coagulase test on unknown $C13.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform a coagulase test on unknown $C14")[You should consider whether this is the best experiment to identify unknown $C14 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not perform a coagulase test on unknown $C14.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform a coagulase test on unknown $C15")[You should consider whether this is the best experiment to identify unknown $C15 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not perform a coagulase test on unknown $C15.")) (set: $clicks to it + 1)]]

The catalase test is used to determine whether an organism has the enzyme catalase, which neutralises hydrogen peroxide. A number of different protocols are used to perform the catalase test; in your lab, you generally use the slide catalase test. A small amount of the organism is transferred to a glass microscope slide, and a drop of hydrogen peroxide is added. The slide is then monitored for the appearance of bubbles (production of oxygen from the decomposition of hydrogen peroxide). (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are catalase+, bubbles will rapidly begin to form. If the bacteria are catalase-, no bubbles will form.] (b4r:"solid")[<center><img alt="example of positive and negative catalase reactions" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/catalase.png"></center> Figure 1. Catalase reaction. Example of positive (top) and negative (bottom) catalase test results.] <a href="https://asm.org/Protocols/Catalase-Test-Protocol" target="_blank">Read more about the catalase test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform a catalase test on unknown $C1")[Unknown $C1 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform a catalase test on unknown $C2")[Unknown $C2 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform a catalase test on unknown $C3")[Unknown $C3 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform a catalase test on unknown $C4")[Unknown $C4 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C2 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform a catalase test on unknown $C5")[Unknown $C5 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform a catalase test on unknown $C6")[Unknown $C6 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform a catalase test on unknown $C7")[Unknown $C7 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform a catalase test on unknown $C8")[Unknown $C8 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform a catalase test on unknown $C9")[Unknown $C9 is ''catalase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 is catalase negative"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform a catalase test on unknown $C10")[Unknown $C10 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform a catalase test on unknown $C11")[Unknown $C11 is ''catalase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is catalase negative"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform a catalase test on unknown $C12")[You performed both a semiquantitative catalase test and a thermostable catalase test, and found that unknown $C12 is ''negative'' for both tests. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 is negative for the semiquantitative and thermostable catalase testts"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform a catalase test on unknown $C13")[Unknown $C13 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform a catalase test on unknown $C14")[Unknown $C14 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is catalase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform a catalase test on unknown $C15")[Unknown $C15 is ''catalase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)]] (else:)[Go back to the (link-reveal-goto: "about page?", "About")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is catalase positive"))(set: $clicks to it + 1)]]

The Gram stain is used to differentiate bacteria based on the composition of their cell wall. Bacteria are fixed to a glass slide, which is first flooded with crystal violet, then treated with a mordant (Gram's iodine), then decolorized with ethanol, and finally counterstained with safranin. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are Gram positive, the cells will stain blue/purple. If the bacteria are Gram negative, the cells will stain pink/red.] ''Note'' that some bacteria may appear Gram variable or may produce an aberrant Gram staining result (e.g., //Mycobacterium// cells cannot readily be stained using this procedure). It is also important to note the ''morphology'' of the cells, as this may give important clues for identification of the unknown (e.g., bacillus, coccus, spirochaete, etc.) (b4r:"solid")[<center><img alt="micrographs of Gram-positive cocci and Gram-negative rods" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/Gram-stain.png"></center> Figure 1.Gram-stained bacterial cells. A)Gram-positive cocci and B)Gram-negative rods. Cells were Gram-stained and visualised at 1000X magnification with a light microscope.] <a href="https://asm.org/Protocols/Gram-Stain-Protocols" target="_blank">Read more about the Gram stain</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "microscope1")[ (link: "Click to perform a Gram stain on unknown $C1")[When you examine a Gram-stained sample of unknown $C1 under the microscope, you observe ''pink rods'' Back to the (link-reveal-goto: "microscope?", "microscope1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "A Gram stain of unknown $C1 revealed pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope2")[ (link: "Click to perform a Gram stain on unknown $C2")[When you examine a Gram-stained sample of unknown $C2 under the microscope, you observe ''purple rods'' Back to the (link-reveal-goto: "microscope?", "microscope2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "A Gram stain of unknown $C2 revealed purple rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope3")[ (link: "Click to perform a Gram stain on unknown $C3")[When you examine a Gram-stained sample of unknown $C3 under the microscope, you observe ''pink rods'' Back to the (link-reveal-goto: "microscope?", "microscope3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "A Gram stain of unknown $C3 revealed pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope4")[ (link: "Click to perform a Gram stain on unknown $C4")[When you examine a Gram-stained sample of unknown $C4 under the microscope, you observe ''pink curved rods'' Back to the (link-reveal-goto: "microscope?", "microscope4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "A Gram stain of unknown $C4 revealed pink curved rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope5")[ (link: "Click to perform a Gram stain on unknown $C5")[When you examine a Gram-stained sample of unknown $C5 under the microscope, you observe ''purple rods'' Back to the (link-reveal-goto: "microscope?", "microscope5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "A Gram stain of unknown $C5 revealed purple rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope6")[ (link: "Click to perform a Gram stain on unknown $C6")[When you examine a Gram-stained sample of unknown $C6 under the microscope, you observe ''pink curved rods'' Back to the (link-reveal-goto: "microscope?", "microscope6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "A Gram stain of unknown $C6 revealed pink curved rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope7")[ (link: "Click to perform a Gram stain on unknown $C7")[When you examine a Gram-stained sample of unknown $C7 under the microscope, you observe ''purple cocci'' Back to the (link-reveal-goto: "microscope?", "microscope7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "A Gram stain of unknown $C7 revealed purple cocci")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope8")[ (link: "Click to perform a Gram stain on unknown $C8")[When you examine a Gram-stained sample of unknown $C8 under the microscope, you observe ''pink rods'' Back to the (link-reveal-goto: "microscope?", "microscope8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "A Gram stain of unknown $C8 revealed pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope9")[ (link: "Click to perform a Gram stain on unknown $C9")[When you examine a Gram-stained sample of unknown $C9 under the microscope, you observe ''a mix of pink and purple rods'' Back to the (link-reveal-goto: "microscope?", "microscope9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "A Gram stain of unknown $C9 revealed a mix of pink and purple rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope10")[ (link: "Click to perform a Gram stain on unknown $C10")[When you examine a Gram-stained sample of unknown $C10 under the microscope, you observe ''short pink rods'' Back to the (link-reveal-goto: "microscope?", "microscope10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "A Gram stain of unknown $C10 revealed short pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope11")[ (link: "Click to perform a Gram stain on unknown $C11")[When you examine a Gram-stained sample of unknown $C11 under the microscope, you observe ''purple rods'' Back to the (link-reveal-goto: "microscope?", "microscope11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "A Gram stain of unknown $C11 revealed purple rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope12")[ (link: "Click to perform a Gram stain on unknown $C12")[When you examine a Gram-stained sample of unknown $C12 under the microscope, you observe ''extremely pale purple rods'' Back to the (link-reveal-goto: "microscope?", "microscope12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "A Gram stain of unknown $C12 revealed extremely pale purple rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope13")[ (link: "Click to perform a Gram stain on unknown $C13")[When you examine a Gram-stained sample of unknown $C13 under the microscope, you observe ''small pink coccobacilli'' Back to the (link-reveal-goto: "microscope?", "microscope13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "A Gram stain of unknown $C13 revealed small pink coccobacilli")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope14")[ (link: "Click to perform a Gram stain on unknown $C14")[When you examine a Gram-stained sample of unknown $C14 under the microscope, you observe ''pink curved rods'' Back to the (link-reveal-goto: "microscope?", "microscope14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "A Gram stain of unknown $C14 revealed pink curved rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope15")[ (link: "Click to perform a Gram stain on unknown $C15")[When you examine a Gram-stained sample of unknown $C15 under the microscope, you observe ''pink rods'' Back to the (link-reveal-goto: "microscope?", "microscope15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "A Gram stain of unknown $C15 revealed pink rods")) (set: $clicks to it + 1)]]

Blood agar is a general purpose medium, often helpful for the growth of fastidious organisms. It can also be used to differentiate organisms based on their haemolytic abilities. Your lab routinely uses sheep's blood to make blood agar plates (results may differ compared to, e.g., horse's blood). (b4r:"solid")[<center><img alt="example of haemolysis on blood agar" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//blood-agar.png"></center> Figure 1. Examples of haemolytic colonies on a blood agar plate. A (left): alpha haemolysis, indicated by the transmitted light; B (right): beta haemolysis. ASM Image Gallery: Rebecca Buxton, University of Utah, Salt Lake City, UT] (link: "Click to see the blood agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Peptone</td> <td>23.0</td> </tr> <tr> <td>Starch</td> <td>1.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Agar</td> <td>10.0</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C 5% sterile defibrinated blood added after autoclaving.] <a href="http://www.oxoid.com/uk/blue/prod_detail/prod_detail.asp?pr=CM0331&org=153&c=uk&lang=en" target="_blank">Read more about blood agar...</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from streaking unknown $C1 on blood agar")[Unknown $C1 grows on blood agar, and produces colonies with ''gamma haemolysis''. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 grows on blood agar, and produces colonies with gamma haemolysis")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from streaking unknown $C2 on blood agar")[Unknown $C2 grows on blood agar, and produces colonies with ''beta haemolysis''. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 grows on blood agar, and produces colonies with beta haemolysis")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from streaking unknown $C3 on blood agar")[Unknown $C3 grows on blood agar, and produces colonies with ''gamma haemolysis''. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 grows on blood agar, and produces colonies with gamma haemolysis")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from streaking unknown $C4 on blood agar")[Unknown $C4 does not grow on blood agar under normal atmospheric oxygen levels. Unknown $C4 grew on blood agar (pH 6.0) with ''alpha haemolysis'' when the plates were incubated at 5% oxygen and 10% carbon dioxide; and was able to grow at 37°C and 42°C, but not 25°C. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 does not grow on blood agar under normal atmospheric oxygen levels. Unknown $C4 grew on blood agar (pH 6.0) with alpha haemolysis when the plates were incubated at 5% oxygen and 10% carbon dioxide; and was able to grow at 37°C and 42°C, but not 25°C.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from streaking unknown $C5 on blood agar")[Unknown $C5 grows on blood agar, and produces waxy-looking colonies with ''beta haemolysis''. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 grows on blood agar, and produces colonies with beta haemolysis")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from streaking unknown $C6 on blood agar")[Unknown $C6 grows on blood agar, and produces colonies with ''beta haemolysis''. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 grows on blood agar, and produces colonies with beta haemolysis")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from streaking unknown $C7 on blood agar")[Unknown $C7 grows on blood agar, and produces colonies with ''beta haemolysis''. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 grows on blood agar, and produces colonies with gamma haemolysis")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from streaking unknown $C8 on blood agar")[Unknown $C8 grows on blood agar, and produces large grey colonies with feathered edges. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 grows on blood agar, and produces large grey colonies with feathered edges")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from streaking unknown $C9 on blood agar")[Unknown $C9 does not grow on blood agar under normal atmospheric oxygen levels. Unknown $C9 grew on blood agar when the plates were incubated in an anaerobic chamber; and was able to grow at 25°C, 37°C and 45°C. Colonies of unknown $C9 on blood agar were round with entire margins; gray; and surrounded by a narrow zone of complete haemolysis within a larger zone of partial haemolysis. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 does not grow on blood agar under normal atmospheric oxygen levels. Unknown $C9 grew on blood agar when the plates were incubated in an anaerobic chamber; and was able to grow at 25°C, 37°C and 45°C. Colonies of unknown $C9 on blood agar were round with entire margins; gray; and surrounded by a narrow zone of complete haemolysis within a larger zone of partial haemolysis.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from streaking unknown $C10 on blood agar")[Unknown $C10 grows on blood agar, and produces colonies with ''gamma haemolysis''. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 grows on blood agar, and produces colonies with gamma haemolysis")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from streaking unknown $C11 on blood agar")[Unknown $C11 does not grow on blood agar under normal atmospheric oxygen levels. Unknown $C11 grew on blood agar when the plates were incubated in an anaerobic chamber; and was able to grow at 25°C, 37°C and 45°C. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 does not grow on blood agar under normal atmospheric oxygen levels. Unknown $C11 grew on blood agar when the plates were incubated in an anaerobic chamber; and was able to grow at 25°C, 37°C and 45°C. Unknown $C11 does not grow on blood agar under normal atmospheric oxygen levels. Unknown $C11 grew on blood agar when the plates were incubated in an anaerobic chamber; and was able to grow at 25°C, 37°C and 45°C.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from streaking unknown $C12 on blood agar")[Unknown $C12 does not grow on blood agar under the tested conditions. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 does not grow on blood agar under the tested conditions.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from streaking unknown $C13 on blood agar")[Unknown $C13 grows on blood agar: pinpoint-sized colonies appeared after 24 hours, and these were small, white, round colonies after 48 hours. No haemolysis was observed. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 grows on blood agar: pinpoint-sized colonies appeared after 24 hours, and these were small, white, round colonies after 48 hours. No haemolysis was observed.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from streaking unknown $C14 on blood agar")[Unknown $C14 grows on blood agar, and produces colonies with ''beta haemolysis''. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 grows on blood agar, and produces colonies with beta haemolysis")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from streaking unknown $C15 on blood agar")[Unknown $C15 grows on blood agar, and produces yellow-tan coloured colonies. No haemolysis was observed. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 grows on blood agar, and produces yellow-tan coloured colonies. No haemolysis was observed.")) (set: $clicks to it + 1)]]

Bile aesculin agar is a differential and selective medium often used to differentiate enterococci and non-group D streptococci. Enterococci are capable of growth at the concentration of bile salts in this medium (the selective aspect of this medium), and of hydrolyzing esculin, leading to the production of black halos around the colonies (the differential aspect). (b4r:"solid")[<center><img alt="example of growth on Bile aesculin agar" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/bile-aesculin-agar.png"></center> Figure 1. An organism grown on a Bile Aesculin agar plate that exhibits aesculin hydrolysis (production of dark brown/black halo around the colonies). Image credit: Oyinloye et al (2021).] (link: "Click to see the bile aesculin agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Peptone</td> <td>14.0</td> </tr> <tr> <td>Bile salts</td> <td>15.0</td> </tr> <tr> <td>Ferric citrate</td> <td>0.5</td> </tr> <tr> <td>Aesculins</td> <td>1.0</td> </tr> <tr> <td>Agar</td> <td>15.0</td> </tr> </table> pH 7.1 ± 0.2 @ 25°C] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0888&c=UK&lang=EN" target="_blank">Read more about Bile aesculin agar</a>(link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from streaking unknown $C1 on bile aesculin agar")[You should consider whether streaking unknown $C1 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not grow unknown $C1 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from streaking unknown $C2 on bile aesculin agar")[Unknown $C2 grows on bile aesculin agar, and forms minute black colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 grows on bile aesculin agar, and forms minute black colonies.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from streaking unknown $C3 on bile aesculin agar")[You should consider whether streaking unknown $C3 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not grow unknown $C3 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from streaking unknown $C4 on bile aesculin agar")[You should consider whether streaking unknown $C4 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from streaking unknown $C5 on bile aesculin agar")[You should consider whether streaking unknown $C5 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C55 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from streaking unknown $C6 on bile aesculin agar")[You should consider whether streaking unknown $C6 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from streaking unknown $C7 on bile aesculin agar")[Unknown $C7 is able to grow on bile aesculin agar, but does not hydrolyse aesculin. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is able to grow on bile aesculin agar, but does not hydrolyse aesculin. ")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from streaking unknown $C8 on bile aesculin agar")[You should consider whether streaking unknown $C8 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not grow unknown $C8 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from streaking unknown $C9 on bile aesculin agar")[You should consider whether streaking unknown $C9 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from streaking unknown $C10 on bile aesculin agar")[You should consider whether streaking unknown $C10 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from streaking unknown $C11 on bile aesculin agar")[You should consider whether streaking unknown $C11 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from streaking unknown $C12 on bile aesculin agar")[You should consider whether streaking unknown $C12 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from streaking unknown $C13 on bile aesculin agar")[You should consider whether streaking unknown $C13 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from streaking unknown $C14 on bile aesculin agar")[You should consider whether streaking unknown $C14 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on bile aesculin agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from streaking unknown $C15 on bile aesculin agar")[You should consider whether streaking unknown $C15 on bile aesculin agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not grow unknown $C15 on bile aesculin agar")) (set: $clicks to it + 1)]]

Fluid thioglycollate medium can be used to test the aerotolerance of bacteria, or in the recovery of anaerobes from clinical specimens. (b4r:"solid")[<center><img alt="examples of growth in thioglycollate medium" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/thioglycollate.png"></center> Figure 1. Organisms grown in thioglycollate medium. From left to right: A) a facultative anaerobe; B) an obligate anaerobe; C) a facultative anaerobe; D) a microaerophile; E) an obligate aerobe. ASM Image Gallery: Tasha Sturm, Cabrillo College, Aptos, CA] (link: "Click to see the thioglycollate medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>5.0</td> </tr> <tr> <td>Tryptone</td> <td>15.0</td> </tr> <tr> <td>Glucose</td> <td>5.5</td> </tr> <tr> <td>Sodium thioglycollate</td> <td>0.5</td> </tr> <tr> <td>Sodium chloride</td> <td>2.5</td> </tr> <tr> <td>Resazurin</td> <td>0.001</td> </tr> <tr> <td>Agar</td> <td>0.75</td> </tr> </table> pH 7.1 ± 0.2 @ 25°C] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0173&c=UK&lang=EN" target="_blank">Read more about Thioglycollate Medium</a>(link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 in thioglycollate medium")[Unknown $C1 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "When grown in thioglycollate medium, unknown $C1 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 in thioglycollate medium")[Unknown $C2 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "When grown in thioglycollate medium, unknown $C2 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 in thioglycollate medium")[Unknown $C3 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "When grown in thioglycollate medium, unknown $C3 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 in thioglycollate medium")[Unknown $C4 grows in a thin strip just below the surface of the medium (not at the top of the medium). Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "When grown in thioglycollate medium, unknown $C4 grows a thin strip just below the surface of the medium (not at the top of the medium).")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 in thioglycollate medium")[Unknown $C5 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "When grown in thioglycollate medium, unknown $C5 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 in thioglycollate medium")[Unknown $C6 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "When grown in thioglycollate medium, unknown $C6 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 in thioglycollate medium")[Unknown $C7 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "When grown in thioglycollate medium, unknown $C7 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 in thioglycollate medium")[Unknown $C8 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "When grown in thioglycollate medium, unknown $C8 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 in thioglycollate medium")[Unknown $C9 grows only at the bottom of the tube of thioglycollate medium. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "When grown in thioglycollate medium, unknown $C9 grows only at the bottom of the tube.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 in thioglycollate medium")[Unknown $C10 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "When grown in thioglycollate medium, unknown $C10 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 in thioglycollate medium")[Unknown $C11 grows only at the bottom of the tube of thioglycollate medium. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "When grown in thioglycollate medium, unknown $C11 grows only at the bottom of the tube.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 in thioglycollate medium")[Unknown $C12 did not grow on thioglycollate medium under the tested conditions. Try (link-reveal-goto: "another semi-solid growth medium?", "7H9")[(set:$t to it + time)] Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 did not grow in thioglycollate medium.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 in thioglycollate medium")[Unknown $C13 grows only at the top of the tube. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "When grown in thioglycollate medium, unknown $C13 grows only at the top of the tube.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 in thioglycollate medium")[Unknown $C14 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "When grown in thioglycollate medium, unknown $C14 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 in thioglycollate medium")[Unknown $C15 grows throughout the tube of thioglycollate medium, with slightly denser growth near the top. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "When grown in thioglycollate medium, unknown $C15 grows throughout the tube, with slightly denser growth near the top.")) (set: $clicks to it + 1)]]

Mannitol Salt Agar (MSA) is a commonly used selective and differential growth medium containing a relatively high concentration of sodium chloride (which selects against the growth of most Gram-negative and some Gram-positive bacteria). Phenol red is used as a pH indicator to detect mannitol fermentation. (b4r:"solid")[<center><img alt="example of growth on Mannitol Salt Agar" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/MSA.png"></center> Figure 1. Organisms grown on a Mannitol Salt Agar plate. A and C) growth and mannitol fermentation (indicated by the yellow halo). B) growth but no mannitol fermentation (no colour change). D) no growth. ASM Image Gallery: Tasha Sturm, Cabrillo College, Aptos, CA] (link: "Click to see the Mannitol Salt agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Lab-Lemco powder</td> <td>1.0</td> </tr> <tr> <td>Peptone</td> <td>10.0</td> </tr> <tr> <td>Mannitol</td> <td>10.0</td> </tr> <tr> <td>Sodium chloride</td> <td>75.0</td> </tr> <tr> <td>Phenol red</td> <td>0.025</td> </tr> <tr> <td>Agar</td> <td>15.0</td> </tr> </table> pH 7.5 ± 0.2 @ 25°C] <a href="https://asm.org/Protocols/Mannitol-Salt-Agar-Plates-Protocols" target="_blank">Read more about Mannitol Salt agar</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from streaking unknown $C1 on Mannitol Salt agar")[Unknown $C1 does not grow on MSA. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 does not grow on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from streaking unknown $C2 on Mannitol Salt agar")[You should consider whether streaking unknown $C2 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from streaking unknown $C3 on Mannitol Salt agar")[Unknown $C3 does not grow on MSA. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 does not grow on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from streaking unknown $C4 on Mannitol Salt agar")[Unknown $C4 does not grow on MSA. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C4 does not grow on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from streaking unknown $C5 on Mannitol Salt agar")[You should consider whether streaking unknown $C5 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from streaking unknown $C6 on Mannitol Salt agar")[Unknown $C6 does not grow on MSA. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 does not grow on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from streaking unknown $C7 on Mannitol Salt agar")[Unknown $C7 grows on mannitol salt agar; it produces yellow colonies with a yellow halo. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 grows on mannitol salt agar;; it produces yellow colonies with a yellow halo.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from streaking unknown $C8 on Mannitol Salt agar")[You should consider whether streaking unknown $C8 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not grow unknown $C8 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from streaking unknown $C9 on Mannitol Salt agar")[You should consider whether streaking unknown $C9 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from streaking unknown $C10 on Mannitol Salt agar")[You should consider whether streaking unknown $C10 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from streaking unknown $C11 on Mannitol Salt agar")[You should consider whether streaking unknown $C11 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from streaking unknown $C12 on Mannitol Salt agar")[You should consider whether streaking unknown $C12 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from streaking unknown $C13 on Mannitol Salt agar")[You should consider whether streaking unknown $C13 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from streaking unknown $C14 on Mannitol Salt agar")[You should consider whether streaking unknown $C14 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from streaking unknown $C15 on Mannitol Salt agar")[You should consider whether streaking unknown $C15 on mannitol salt agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not grow unknown $C15 on Mannitol Salt Agar (MSA)")) (set: $clicks to it + 1)]]

The urease test is used to determine whether an organism can break down urea, producing ammonia and carbon dioxide. Different media and commercial kits can be used to detect urease activity. These tests detect the increase in pH caused by the production of ammonia. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are urease+, a pink colour will form. If the bacteria are urease-, no pink colour will form.] (b4r:"solid")[<center><img alt="example of urease test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/urease.png"></center> Figure 1. Urease test results. From left to right: a positive test result (indicated by the bright pink colour); a negative test result (indicated by the yellow colour). ASM Image Gallery: Anne Hanson, University of Maine, Orono, ME] <a href="https://asm.org/getattachment/ac4fe214-106d-407c-b6c6-e3bb49ac6ffb/urease-test-protocol-3223.pdf" target="_blank">Read more about the urease test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform a urease test on unknown $C1")[Unknown $C1 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is urease negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform a urease test on unknown $C2")[Unknown $C2 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 is urease negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform a urease test on unknown $C3")[Unknown $C3 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is urease negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform a urease test on unknown $C4")[Unknown $C4 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 is urease negaive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform a urease test on unknown $C5")[You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not perform a urease test on unknown $C5")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform a urease test on unknown $C6")[Unknown $C6 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is urease negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform a urease test on unknown $C7")[Unknown $C7 is ''urease positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is urease positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform a urease test on unknown $C8")[Unknown $C8 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is urease negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform a urease test on unknown $C9")[Unknown $C9 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 is urease negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform a urease test on unknown $C10")[Unknown $C10 is ''urease positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is urease positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform a urease test on unknown $C11")[Unknown $C11 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is urease negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform a urease test on unknown $C12")[Unknown $C12 is ''urease positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 is urease positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform a urease test on unknown $C13")[Unknown $C13 is ''urease positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is urease positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform a urease test on unknown $C14")[Unknown $C14 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is urease negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform a urease test on unknown $C10")[Unknown $C15 is ''urease negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is urease negative")) (set: $clicks to it + 1)]]

The nitrate test is used to determine whether an organism produces the enzyme nitrate reductase, which reduces nitrate to nitrite. Tests for nitrate and nitrite reduction are based on the Griess reaction. (b4r:"solid")[<center><img alt="example of nitrate reduction test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/nitrate.png"></center> Figure 1. Nitrate reduction test results. Between the two reagent bottles, from left to right: an organism with a positive reaction; an organism with a negative reaction to the nitrate reduction test. ASM Image Gallery: Ken Van Horn, Focus Diagnostics, Inc., Cypress, CA] <a href="https://asm.org/Protocols/Nitrate-and-Nitrite-Reduction-Test-Protocols" target="_blank">Read more about the nitrate reduction test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to test the nitrate reduction ability of unknown $C1")[Unknown $C1 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to test the nitrate reduction ability of unknown $C2")[Unknown $C2 is ''not able to reduce nitrate''. OR You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 is ....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to test the nitrate reduction ability of unknown $C3")[Unknown $C3 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to test the nitrate reduction ability of unknown $C4")[Unknown $C4 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to test the nitrate reduction ability of unknown $C5")[Unknown $C5 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to test the nitrate reduction ability of unknown $C6")[Unknown $C6 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to test the nitrate reduction ability of unknown $C7")[Unknown $C7 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to test the nitrate reduction ability of unknown $C8")[Unknown $C8 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to test the nitrate reduction ability of unknown $C9")[Unknown $C9 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to test the nitrate reduction ability of unknown $C10")[Unknown $C10 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to test the nitrate reduction ability of unknown $C11")[Unknown $C11 is ''not able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is not able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to test the nitrate reduction ability of unknown $C12")[Unknown $C12 is ''not able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 is not able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to test the nitrate reduction ability of unknown $C13")[Unknown $C13 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to test the nitrate reduction ability of unknown $C14")[Unknown $C14 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is able to reduce nitrate")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to test the nitrate reduction ability of unknown $C15")[Unknown $C15 is ''able to reduce nitrate''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is able to reduce nitrate")) (set: $clicks to it + 1)]]

The ornithine decarboxylase test is used to determine whether an organism can decarboxylate ornithine (producing putrescine and carbon dioxide). Similar tests can be done for arginine or lysine decarboxylation. pH indicators are used to detect glucose fermentation and amino acid decarboxylation. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the colour of the medium does not change, or if it changes to yellow, the bacteria are decarboxylase -. If the medium changes to purple, the bacteria are decarboxylase +.] (b4r:"solid")[<center><img alt="example of amino acid decarboxylase test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/decarboxylase.png"></center> Figure 1. Decarboxylase test results. From left to right: A) uninoculated medium; B) inoculated base medium; C-E) arginine, lysine, and ornithine media inoculated with the test organism. ASM Image Gallery: Archana Lal, Independence Community College, Independence, KS] <a href="https://asm.org/ASM/media/Protocol-Images/Decarboxylase-Broth-Protocol.pdf?ext=.pdf" target="_blank">Read more about the decarboxylase tests</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform decarboxylase tests on unknown $C1")[Unknown $C1 is ''arginine dihydrolase negative'', ''ornithine decarboxylase positive'' and ''lysine decarboxylase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is arginine dihydrolase negative, ornithine decarboxylase positive, and lysine decarboxylase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform decarboxylase tests on unknown $C2")[Unknown $C2 is ''arginine dihydrolase negative'', ''ornithine decarboxylase negative'' and ''lysine decarboxylase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 is arginine dihydrolase negative, ornithine decarboxylase negative, and lysine decarboxylase negative"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform decarboxylase tests on unknown $C3")[Unknown $C3 is ''arginine dihydrolase positive'', ''ornithine decarboxylase positive'' and ''lysine decarboxylase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is arginine dihydrolase positive, ornithine decarboxylase positive, and lysine decarboxylase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform decarboxylase tests on unknown $C4")[You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not perform any decarboxylase tests on unknown $C4"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform decarboxylase tests on unknown $C5")[You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not perform any decarboxylase tests on unknown $C5"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform decarboxylase tests on unknown $C6")[Unknown $C6 is ''arginine dihydrolase negative'', ''ornithine decarboxylase positive'' and ''lysine decarboxylase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is arginine dihydrolase negative, ornithine decarboxylase positive, and lysine decarboxylase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform decarboxylase tests on unknown $C7")[Unknown $C7 is ''arginine dihydrolase positive'', ''ornithine decarboxylase negative'' and ''lysine decarboxylase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is arginine dihydrolase positive, ornithine decarboxylase negative, and lysine decarboxylase negative"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform decarboxylase tests on unknown $C8")[Unknown $C8 is ''arginine dihydrolase negative'', ''ornithine decarboxylase negative'' and ''lysine decarboxylase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is arginine dihydrolase negative, ornithine decarboxylase negative, and lysine decarboxylase negative"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform decarboxylase tests on unknown $C9")[You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not perform any decarboxylase tests on unknown $C9"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform decarboxylase tests on unknown $C10")[Unknown $C10 is ''arginine dihydrolase negative'', ''ornithine decarboxylase positive'' and ''lysine decarboxylase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is arginine dihydrolase negative, ornithine decarboxylase positive, and lysine decarboxylase negative"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform decarboxylase tests on unknown $C11")[You should consider whether this is the best experiment to identify unknown $C11 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not perform any decarboxylase tests on unknown $C11"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform decarboxylase tests on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not perform any decarboxylase tests on unknown $C12"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform decarboxylase tests on unknown $C13")[You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not perform any decarboxylase tests on unknown $C13"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform decarboxylase tests on unknown $C14")[Unknown $C14 is ''arginine dihydrolase negative'', ''ornithine decarboxylase positive'' and ''lysine decarboxylase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is arginine dihydrolase negative, ornithine decarboxylase positive, and lysine decarboxylase positive"))(set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform decarboxylase tests on unknown $C15")[Unknown $C15 is ''arginine dihydrolase positive'', ''ornithine decarboxylase positive'' and ''lysine decarboxylase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is arginine dihydrolase positive, ornithine decarboxylase positive, and lysine decarboxylase negative"))(set: $clicks to it + 1)]] *Note that the unknown organism was tested only for decarboxylation of the amino acid(s) listed. If an amino acid is not listed here, you should not assume that the test result was negative.

The gelatinase test is used to determine whether an organism can break down gelatin. Different gelatinase test methods are used; the simple and convenient method used in your laboratory, is to inoculate a stab tube containing gelatin with your unknown organism, and checked regularly for gelatin liquefaction. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are gelatinase+, the nutrient medium will be liquid (even after immersion in an ice bath for 15-30 minutes). If the bacteria are gelatinase-, the nutrient medium will not liquefy (even after prolonged incubation).] (b4r:"solid")[<center><img alt="example of gelatinase test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/gelatinase.png"></center> Figure 1. Gelatinase test results. A (top): an organism with a positive gelatinase result (indicated by the liquid medium; the red colour is incidental to the test). B (bottom): an organism with a negative gelatinase result (indicated by the solid medium). ASM Image Gallery: Janie Sigmon, York Technical College, Rock Hill, SC] <a href="https://asm.org/Protocols/Gelatin-Hydrolysis-Test-Protocol" target="_blank">Read more about the gelatinase test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform a gelatinase test on unknown $C1")[Unknown $C1 is ''gelatinase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is gelatinase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform a gelatinase test on unknown $C2")[You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not perform a gelatinase test on unknown $C2")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform a gelatinase test on unknown $C3")[Unknown $C3 is ''gelatinase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is gelatinase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform a gelatinase test on unknown $C4")[Unknown $C4 is ''gelatinase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 is gelatinase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform a gelatinase test on unknown $C5")[Unknown $C5 is ''gelatinase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 is gelatinase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform a gelatinase test on unknown $C6")[Unknown $C6 is ''gelatinase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is gelatinase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform a gelatinase test on unknown $C7")[Unknown $C7 is ''gelatinase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is gelatinase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform a gelatinase test on unknown $C8")[Unknown $C8 is ''gelatinase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is gelatinase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform a gelatinase test on unknown $C9")[Unknown $C9 is ''gelatinase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C1 is gelatinase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform a gelatinase test on unknown $C10")[Unknown $C10 is ''gelatinase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is gelatinase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform a gelatinase test on unknown $C11")[Unknown $C11 is ''gelatinase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is gelatinase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform a gelatinase test on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not perform a gelatinase test on unknown $C12")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform a gelatinase test on unknown $C13")[Unknown $C13 is ''gelatinase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is gelatinase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform a gelatinase test on unknown $C14")[Unknown $C14 is ''gelatinase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is gelatinase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform a gelatinase test on unknown $C15")[Unknown $C15 is ''gelatinase negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is gelatinase negative")) (set: $clicks to it + 1)]]

The alkaline phosphatase test is used to determine whether an organism produces the enzyme alkaline phosphatase. This test uses a chromogenic substrate and can be included as part of the miniaturized API test strips used to identify unknown organisms. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are alkaline phosphatase+, the test will turn bright yellow. If the bacteria are alkaline phosphatase-, the test will remain colourless/pale yellow.] <a href="https://www.abcam.com/products/assay-kits/alkaline-phosphatase-assay-kit-colorimetric-ab83369.html" target="_blank">Read more about the alkaline phosphatase test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform an alkaline phosphatase test on unknown $C1")[You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not perform an alkaline phosphatase test on unknown $C1")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform an alkaline phosphatase test on unknown $C2")[You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not perform an alkaline phosphatase test on unknown $C2")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform an alkaline phosphatase test on unknown $C3")[You should consider whether this is the best experiment to identify unknown $C3 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not perform an alkaline phosphatase test on unknown $C3")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform an alkaline phosphatase test on unknown $C4")[You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not perform an alkaline phosphatase test on unknown $C4")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform an alkaline phosphatase test on unknown $C5")[You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not perform an alkaline phosphatase test on unknown $C5")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform an alkaline phosphatase test on unknown $C6")[You should consider whether this is the best experiment to identify unknown $C6 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is alkaline phosphatase....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform an alkaline phosphatase test on unknown $C7")[Unknown $C7 is ''alkaline phosphatase positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is alkaline phosphatase positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform an alkaline phosphatase test on unknown $C8")[You should consider whether this is the best experiment to identify unknown $C8 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is alkaline phosphatase....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform an alkaline phosphatase test on unknown $C9")[You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 is alkaline phosphatase....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform an alkaline phosphatase test on unknown $C10")[You should consider whether this is the best experiment to identify unknown $C10 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is alkaline phosphatase....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform an alkaline phosphatase test on unknown $C11")[You should consider whether this is the best experiment to identify unknown $C11 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is alkaline phosphatase....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform an alkaline phosphatase test on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 is alkaline phosphatase....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform an alkaline phosphatase test on unknown $C13")[You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is alkaline phosphatase....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform an alkaline phosphatase test on unknown $C14")[You should consider whether this is the best experiment to identify unknown $C14 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is alkaline phosphatase....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform an alkaline phosphatase test on unknown $C15")[You should consider whether this is the best experiment to identify unknown $C15 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is alkaline phosphatase....")) (set: $clicks to it + 1)]]

Carbohydrate fermentation tests are performed to determine whether an organism has the ability to ferment particular carbohydrates. Depending on the method used, these may detect fermentation based on a colour change (a pH indicator changing colour in the presence of acid produced as a consequence of fermentation), or they may detect this colour change and the production of gas (using a Durham tube). (b4r:"solid")[<center><img alt="example of carbohydrate fermentation test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/carbohydrate-fermentation.png"></center> Figure 1. Carbohydrate fermentation test results. Example using Durham tubes to detect gas production. positive (top) and negative (bottom) oxidase test results. a) acid-gas production indicated by the yellow colour and production of bubbles (arrow). b) a negative reaction (K) with alkaline conditions indicated by the red colour. ASM Image Gallery: Kim Finer, Kent State University at Stark, N. Canton, OH.] <a href="https://asm.org/ASM/media/Protocol-Images/Carbohydrate-Fermentation-Protocol.pdf?ext=.pdf" target="_blank">Read more about the carbohydrate fermentation tests</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C1")[Unknown $C1 is able to ferment: L-arabinose; melibiose; L-rhamnose; D-mannitol; D-mannose. Unknown $C1 produces both acid and gas when it ferments D-glucose. Unknown $C1 is not able to ferment: inositol; sucrose; sorbitol. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is able to ferment: L-arabinose; melibiose; L-rhamnose; D-mannitol; D-mannose. Unknown $C1 produces both acid and gas when it ferments D-glucose. Unknown $C1 is not able to ferment: inositol; sucrose; sorbitol")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C2")[Unknown $C2 produces acid from the fermentation of glucose. Unknown $C2 is also able to ferment: L-Rhamnose and α-Methyl-D-mannoside. Unknown $C2 is not able to ferment: D-Xylose and D-Mannitol. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 produces acid from the fermentation of glucose. Unknown $C2 is also able to ferment: L-Rhamnose and α-Methyl-D-mannoside. Unknown $C2 is not able to ferment: D-Xylose and D-Mannitol. ")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to test the carbohydrate fermentation abilities of unknown $C3")[Unknown $C3 is able to ferment: L-arabinose, L-rhamnose, melibiose, sorbitol, D-mannose, D-glucose. Unknown $C3 produces both acid and gas when it ferments D-glucose. Unknown $C3 is not able to ferment: sucrose, amygdalin. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is able to ferment: L-arabinose, L-rhamnose, melibiose, sorbitol, D-mannose, D-glucose. Unknown $C3 produces both acid and gas when it ferments D-glucose. Unknown $C3 is not able to ferment: sucrose, amygdalin.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C4")[Unknown $C4 is not able to ferment: D-glucose. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 is not able to ferment: D-glucose.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C5")[Unknown $C5 is able to ferment: D-glucose, glycogen, and starch. Unknown $C5 is not able to ferment: L-arabinose, D-mannitol, D-mannose, and D-xylose. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 is able to ferment: D-glucose, glycogen, and starch. Unknown $C5 is not able to ferment: L-arabinose, D-mannitol, D-mannose, and D-xylose.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C6")[Unknown $C6 is able to ferment: D-glucose (producing acid, but not gas), D-mannitol, D-mannose, L-arabinose, fructose, and maltose. Unknown $C6 is not able to ferment: sucrose, salicin, cellobiose, lactose, and myo-inositol. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is able to ferment: D-glucose (producing acid, but not gas), D-mannitol, D-mannose, L-arabinose, fructose, and maltose. Unknown $C6 is not able to ferment: sucrose, salicin, cellobiose, lactose, and myo-inositol.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C7")[Unknown $C7 is able to ferment: glucose, fructose, maltose, mannose, mannitol, trehalose, lactose, and sucrose. Unknown $C7 is not able to ferment: raffinose, ribose, cellobiose, and arabinose. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is able to ferment: glucose, fructose, maltose, mannose, mannitol, trehalose, lactose, and sucrose. Unknown $C7 is not able to ferment: raffinose, ribose, cellobiose, and arabinose. ")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C8")[Unknown $C8 is able to ferment: glucose, D-mannitol, L-arabinose, melibiose. Unknown $C8 is not able to ferment: lactose, sucrose, D-xylose, dulcitol, inositol, sorbitol, L-rhamnose. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is able to ferment: glucose, D-mannitol, L-arabinose, melibiose. Unknown $C8 is not able to ferment: lactose, sucrose, D-xylose, dulcitol, inositol, sorbitol, L-rhamnose.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C9")[Unknown $C9 is able to ferment: inositol, lactose, maltose, mannose, sucrose, and sorbitol. Unknown $C9 is not able to ferment: arabinose, mannitol, rhamnose, salicin, and xylose. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 is able to ferment: inositol, lactose, maltose, mannose, sucrose, and sorbitol. Unknown $C9 is not able to ferment: arabinose, mannitol, rhamnose, salicin, and xylose.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C10")[Unknown $C10 is able to ferment: L-arabinose, D-mannitol, D-glucose, sucrose, sorbitol. Unknown $C10 is not able to ferment: mucate, raffinose, L-rhamnose, melibiose. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is able to ferment: L-arabinose, D-mannitol, D-glucose, sucrose, sorbitol. Unknown $C10 is not able to ferment: mucate, raffinose, L-rhamnose, melibiose.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C11")[Unknown $C11 is not able to ferment: arabinose, inositol, lactose, maltose, mannose, mannitol, rhamnose, salicin, sucrose, sorbitol, and xylose. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is not able to ferment: arabinose, inositol, lactose, maltose, mannose, mannitol, rhamnose, salicin, sucrose, sorbitol, and xylose.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 is .....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C13")[You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is ....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C14")[Unknown $C14 is able to ferment: D-glucose, D-galactose, maltose, D-mannitol, and sucrose. Unknown $C14 is not able to ferment: myo-inositol, L-arabinose, L-rhamnose, or lactose. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is able to ferment: D-glucose, D-galactose, maltose, D-mannitol, and sucrose. Unknown $C14 is not able to ferment: myo-inositol, L-arabinose, L-rhamnose, or lactose.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to test the carbohydrate fermentation abilities of unknown $C15")[Unknown $C15 is able to ferment: D-glucose, inositol, L-arabinose, D-galactose, lactose, D-maltose, D-mannitol, D-mannose, D-melibiose, salicin, D-sucrose, D-trehalose, xylose, D-rhamnose. Unknown $C15 is not able to ferment: sorbitol, D-adonitol, dulcitol, D-arabitol. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C15 is able to ferment: D-glucose, inositol, L-arabinose, D-galactose, lactose, D-maltose, D-mannitol, D-mannose, D-melibiose, salicin, D-sucrose, D-trehalose, xylose, D-rhamnose. Unknown $C15 is not able to ferment: sorbitol, D-adonitol, dulcitol, D-arabitol.")) (set: $clicks to it + 1)]] *Note that the unknown organism was tested only for fermentation of the carbohydrate(s) listed. If a carbohydrate is not listed here, you should not assume that the test result was negative.

Unknown $C1 was isolated from a sample of $C1food. The results from the experiments you have obtained so far are: (if: $notebookC1's length > 0)[\ (for: each _index, ...(range: 1, $notebookC1's length))[_index) (print: $notebookC1's (_index)) ] ] (else:)[You have not yet performed any experiments.] The hints you have redeemed for this organism are: (if: $hintsC1's length > 0)[\ (for: each _index, ...(range: 1, $hintsC1's length))[_index) (print: $hintsC1's (_index)) ] ] (else:)[You have not yet redeemed any hints for this organism.] { (if: (history:) contains "16S1-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S1-text")[(set:$t to it + time)]] (if: (history:) contains "WGS1-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS1-Results")[(set:$t to it + time)]] (if: $C1soln is 0)[(link-reveal-goto: "Identify unknown $C1", "identify1")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C1 - do you want to check your answer again?", "identify1")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C1", "C1hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C1", "Case 1")[(set:$t to it + time)]

Unknown $C2 was isolated from a sample of $C2food. The results from the experiments you have obtained so far are: (if: $notebookC2's length > 0)[\ (for: each _index, ...(range: 1, $notebookC2's length))[_index) (print: $notebookC2's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S2-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S2-text")[(set:$t to it + time)]] (if: (history:) contains "WGS2-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS2-Results")[(set:$t to it + time)]] (if: $C2soln is 0)[(link-reveal-goto: "Identify unknown $C2", "identify2")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C2 - do you want to check your answer again?", "identify2")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C2", "C2hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C2", "Case 2")[(set:$t to it + time)]

MacConkey agar is a selective and differential medium commonly supplemented with lactose. Other sugars are sometimes used. The crystal violet and bile salts inhibit growth of Gram-positive bacteria and some fastidious Gram negative bacteria. Phenol red is used as a pH indicator to detect lactose fermentation. (b4r:"solid")[<center><img alt="examples of growth on MacConkey agar" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/macconkey.png"></center> Figure 1. Organisms grown on a MacConkey/lactose plate. A) a strong lactose fermenter showing bile precipitation; B and D) no lactose fermentation; C) a moderate lactose fermenter (no bile precipitation). ASM Image Gallery: Tasha Sturm, Cabrillo College, Aptos, CA] (link: "Click to see the MacConkey agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Peptone</td> <td>20.0</td> </tr> <tr> <td>Lactose</td> <td>10.0</td> </tr> <tr> <td>Bile salts</td> <td>5.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Neutral red</td> <td>0.075</td> </tr> <tr> <td>Agar</td> <td>12.0</td> </tr> </table> pH 7.4 ± 0.2 @ 25°C] <a href="http://www.oxoid.com/uk/blue/prod_detail/prod_detail.asp?pr=CM0007" target="_blank">Read more about MacConkey medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from streaking unknown $C1 on MacConkey agar")[Unknown $C1 grows on MacConkey/lactose agar, producing dark pink colonies surrounded by a ring of precipitated bile salts. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 grows on MacConkey/lactose agar, producing dark pink colonies surrounded by a ring of precipitated bile salts.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from streaking unknown $C2 on MacConkey agar")[You should consider whether streaking unknown $C2 on MacConkey agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on MacConkey/lactose agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from streaking unknown $C3 on MacConkey agar")[Unknown $C3 grows on MacConkey/lactose agar, producing clear/white colonies. The medium around the colonies appears yellow. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 grows on MacConkey/lactose agar, producing clear/white colonies. The medium around the colonies appears yellow.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from streaking unknown $C4 on MacConkey agar")[You should consider whether streaking unknown $C4 on MacConkey agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on MacConkey/lactose agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from streaking unknown $C5 on MacConkey agar")[You should consider whether streaking unknown $C5 on MacConkey agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on MacConkey/lactose agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from streaking unknown $C6 on MacConkey agar")[Unknown $C6 grows slowly on MacConkey/lactose agar, producing small white/clear colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 grows slowly on MacConkey/lactose agar, producing small white/clear colonies.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from streaking unknown $C7 on MacConkey agar")[You should consider whether streaking unknown $C7 on MacConkey agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on MacConkey/lactose agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from streaking unknown $C8 on MacConkey agar")[Unknown $C8 grows on MacConkey/lactose agar, producing transparent (colourless) colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 grows on MacConkey/lactose agar, producing transparent (colourless) colonies.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from streaking unknown $C9 on MacConkey agar")[You should consider whether streaking unknown $C9 on MacConkey agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on MacConkey/lactose agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from streaking unknown $C10 on MacConkey agar")[Unknown $C10 grows on MacConkey/lactose agar, producing small colourless colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on MacConkey/lactose agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from streaking unknown $C11 on MacConkey agar")[You should consider whether streaking unknown $C11 on MacConkey agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on MacConkey/lactose agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from streaking unknown $C12 on MacConkey agar")[You should consider whether streaking unknown $C12 on MacConkey agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on MacConkey/lactose agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from streaking unknown $C13 on MacConkey agar")[Unknown $C13 ''does not grow'' on MacConkey/lactose agar. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 ''does not grow'' on MacConkey/lactose agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from streaking unknown $C14 on MacConkey agar")[Unknown $C14 grows slowly on MacConkey/lactose agar, producing small white/clear colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 grows slowly on MacConkey/lactose agar, producing small white/clear colonies.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from streaking unknown $C15 on MacConkey agar")[Unknown $C15 grows on MacConkey/lactose agar, producing pink colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 grows on MacConkey/lactose agar, producing pink colonies.")) (set: $clicks to it + 1)]]

Simmons citrate agar is a differential medium for testing an organism's ability to use citrate as a sole carbon source that contains the pH indicator bromothymol blue. (b4r:"solid")[<center><img alt="examples of growth on Simmons Citrate Agar" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/simmons-citrate-agar.png"></center> Figure 1. Organisms grown on Simmons Citrate Agar (slant tubes). A (left): no growth and no colour change. B) a positive result, indicated by the blue colour change. ASM Image Gallery: Anne Hanson, University of Maine, Orono] (link: "Click to see the Simmons Citrate agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Magnesium sulphate</td> <td>0.2</td> </tr> <tr> <td>Ammonium dihydrogen phosphate</td> <td>0.2</td> </tr> <tr> <td>Sodium ammonium phosphate</td> <td>0.8</td> </tr> <tr> <td>Sodium citrate, tribasic</td> <td>2.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Bromothymol blue</td> <td>0.08</td> </tr> <tr> <td>Agar</td> <td>12.0</td> </tr> </table> pH 7.0 ± 0.2 @ 25°C] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0155&c=UK&lang=EN" target="_blank">Read more about Simmons Citrate medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from streaking unknown $C1 on Simmons Citrate agar")[Unknown $C1 does not grow on Simmons citrate agar. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 does not grow on Simmons citrate agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from streaking unknown $C2 on Simmons Citrate agar")[Unknown $C2 does not grow on Simmons citrate agar. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 does not grow on Simmons citrate agar.")) (set: $clicks to it + 1)]] Unknown $C3 grows on Simmons citrate agar, and turns the medium blue. (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from streaking unknown $C3 on Simmons Citrate agar")[Unknown $C3 grows on Simmons citrate agar, and turns the medium blue. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 grows on Simmons citrate agar, and turns the medium blue.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from streaking unknown $C4 on Simmons Citrate agar")[You should consider whether streaking unknown $C4 on Simmons Citrate agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on Simmons citrate agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[(link: "Click to see the results from streaking unknown $C4 on Simmons Citrate agar")[Unknown $C5 grows on Simmons citrate agar, and turns the medium blue. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 grows on Simmons citrate agar, and turns the medium blue.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from streaking unknown $C6 on Simmons Citrate agar")[Unknown $C6 does not grow on Simmons citrate agar. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 does not grow on Simmons citrate agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from streaking unknown $C7 on Simmons Citrate agar")[You should consider whether streaking unknown $C7 on Simmons Citrate agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on Simmons citrate agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from streaking unknown $C8 on Simmons Citrate agar")[Unknown $C8 does not grow on Simmons citrate agar. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 does not grow on Simmons citrate agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from streaking unknown $C9 on Simmons Citrate agar")[You should consider whether streaking unknown $C9 on Simmons Citrate agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on Simmons citrate agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from streaking unknown $C10 on Simmons Citrate agar")[Unknown $C10 does not grow on Simmons citrate agar. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 does not grow on Simmons citrate agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from streaking unknown $C11 on Simmons Citrate agar")[You should consider whether streaking unknown $C11 on Simmons Citrate agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on Simmons citrate agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from streaking unknown $C12 on Simmons Citrate agar")[You should consider whether streaking unknown $C12 on Simmons Citrate agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on Simmons citrate agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from streaking unknown $C13 on Simmons Citrate agar")[Unknown $C13 does not grow on Simmons citrate agar. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 does not grow on Simmons citrate agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from streaking unknown $C14 on Simmons Citrate agar")[Unknown $C14 grows on Simmons citrate agar, and turns the medium blue. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 grows on Simmons citrate agar, and turns the medium blue.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from streaking unknown $C15 on Simmons Citrate agar")[Unknown $C15 grows on Simmons citrate agar, and turns the medium blue. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 grows on Simmons citrate agar, and turns the medium blue.")) (set: $clicks to it + 1)]]

The Acid-fast stain is used to identify acid-fast organisms; your lab uses the Ziehl-Neelsen stain to test for acid-fastness. Cells are fixed to a glass slide, stained with carbol fuchsin, decolorized, and then counter-stained with methylene blue. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are Acid-fast, the cells will stain red. If the bacteria are not Acid-fast, the cells will stain blue.] (b4r:"solid")[<center><img alt="micrographs of Ziehl-Nielsen stained cells" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/ZNstain.jpg"></center> Figure 1. Ziehl-Nielsen stained bacterial cells. Cells were imaged at 1000X magnification using a light microscope. Image credit <a href="https://phil.cdc.gov/Details.aspx?pid=16485" target="_blank CDC PHIL</a>] <a href="https://asm.org/ASM/media/Protocol-Images/Acid-Fast-Stain-Protocols.pdf?ext=.pdf" target="_blank">Read more about the acid fast stain</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "microscope1")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C1")[When you examine a Ziehl-Neelsen stained sample of unknown $C1 under the microscope, you observe ''blue rods'' Back to the (link-reveal-goto: "microscope?", "microscope1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "A Ziehl-Neelsen stain of unknown $C1 revealed blue rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope2")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C2")[When you examine a Ziehl-Neelsen stained sample of unknown $C2 under the microscope, you observe ''blue rods'' Back to the (link-reveal-goto: "microscope?", "microscope2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "A Ziehl-Neelsen stain of unknown $C2 revealed blue rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope3")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C3")[When you examine a Ziehl-Neelsen stained sample of unknown $C3 under the microscope, you observe ''blue rods'' Back to the (link-reveal-goto: "microscope?", "microscope3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "A Ziehl-Neelsen stain of unknown $C3 revealed blue rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope4")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C4")[When you examine a Ziehl-Neelsen stained sample of unknown $C4 under the microscope, you observe ''blue curved rods'' Back to the (link-reveal-goto: "microscope?", "microscope4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "A Ziehl-Neelsen stain of unknown $C4 revealed blue curved rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope5")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C5")[When you examine a Ziehl-Neelsen stained sample of unknown $C5 under the microscope, you observe ''blue rods'' Back to the (link-reveal-goto: "microscope?", "microscope5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "A Ziehl-Neelsen stain of unknown $C5 revealed blue rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope6")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C6")[When you examine a Ziehl-Neelsen stained sample of unknown $C6 under the microscope, you observe ''blue curved rods'' Back to the (link-reveal-goto: "microscope?", "microscope6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "A Ziehl-Neelsen stain of unknown $C6 revealed blue curved rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope7")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C7")[When you examine a Ziehl-Neelsen stained sample of unknown $C7 under the microscope, you observe ''blue cocci'' Back to the (link-reveal-goto: "microscope?", "microscope7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "A Ziehl-Neelsen stain of unknown $C7 revealed blue cocci")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope8")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C8")[When you examine a Ziehl-Neelsen stained sample of unknown $C8 under the microscope, you observe ''blue rods'' Back to the (link-reveal-goto: "microscope?", "microscope8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "A Ziehl-Neelsen stain of unknown $C8 revealed blue rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope9")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C9")[When you examine a Ziehl-Neelsen stained sample of unknown $C9 under the microscope, you observe ''blue rods'' Back to the (link-reveal-goto: "microscope?", "microscope9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "A Ziehl-Neelsen stain of unknown $C9 revealed blue rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope10")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C10")[When you examine a Ziehl-Neelsen stained sample of unknown $C10 under the microscope, you observe ''short blue rods'' Back to the (link-reveal-goto: "microscope?", "microscope10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "A Ziehl-Neelsen stain of unknown $C10 revealed short blue rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope11")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C11")[When you examine a Ziehl-Neelsen stained sample of unknown $C11 under the microscope, you observe ''blue rods'' Back to the (link-reveal-goto: "microscope?", "microscope11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "A Ziehl-Neelsen stain of unknown $C11 revealed blue rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope12")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C12")[When you examine a Ziehl-Neelsen stained sample of unknown $C12 under the microscope, you observe ''short red rods'' Back to the (link-reveal-goto: "microscope?", "microscope12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "A Ziehl-Neelsen stain of unknown $C12 revealed short red rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope13")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C13")[When you examine a Ziehl-Neelsen stained sample of unknown $C13 under the microscope, you observe ''weakly red coccobacilli'' Back to the (link-reveal-goto: "microscope?", "microscope13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "A Ziehl-Neelsen stain of unknown $C13 revealed weakly red coccobacilli")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope14")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C14")[When you examine a Ziehl-Neelsen stained sample of unknown $C14 under the microscope, you observe ''blue curved rods'' Back to the (link-reveal-goto: "microscope?", "microscope14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "A Ziehl-Neelsen stain of unknown $C14 revealed blue curved rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope15")[ (link: "Click to perform a Ziehl-Neelsen stain on unknown $C15")[When you examine a Ziehl-Neelsen stained sample of unknown $C15 under the microscope, you observe ''blue rods'' Back to the (link-reveal-goto: "microscope?", "microscope15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "A Ziehl-Neelsen stain of unknown $C15 revealed blue rods")) (set: $clicks to it + 1)]]

Motility test agar contains a low concentration of agar and an indicator (triphenyltetrazolium chloride) that is reduced to an insoluble red pigment in the presence of bacterial growth. (b4r:"solid")[<center><img alt="examples of growth on motility agar" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/motility.png"></center> Figure 1. Organisms grown in motility agar. On the left: a motile organism (indicated by diffuse growth and red pigment throughout the tube). On the right: a non-motile organism (red colour appears only along the line where the organism was inoculated). ASM Image Gallery: Laura Cathcart, Deanna Swartzfager, Patricia Shields, University of Maryland, College Park, MD] (link: "Click to see the motility agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>amount/litre</th> </tr> <tr> <td>Beef extract</td> <td>3.0 g</td> </tr> <tr> <td>Pancreatic digest of casein</td> <td>10.0 g</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0 g</td> </tr> <tr> <td>Agar</td> <td>4.0 g</td> </tr> <tr> <td>1% triphenyltetrazolium chloride solution </td> <td>5 mL</td> </tr> </table>] <a href="https://asm.org/Protocols/Motility-Test-Medium-Protocol" target="_blank">Read more about motility test medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 in motility agar")[A red turbid area has formed throughout the tube where unknown $C1 was inoculated. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "In motility agar, a red turbid area formed throughout the tube where unknown $C1 was inoculated.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 in motility agar")[Unknown $C2 was motile only when tested at 25°C - not at 37°C. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 was motile only when tested at 25°C - not at 37°C.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 in motility agar")[A red turbid area has formed throughout the tube where unknown $C3 was inoculated. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "In motility agar, a red turbid area formed throughout the tube where unknown $C3 was inoculated.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 in motility agar")[Unknown $C4 did not grow in this experiment. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 did not grow in motility agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 in motility agar")[A red turbid area has formed throughout the tube where unknown $C5 was inoculated. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "In motility agar, a red turbid area formed throughout the tube where unknown $C5 was inoculated.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 in motility agar")[A red turbid area has formed throughout the tube where unknown $C6 was inoculated. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "In motility agar, a red turbid area formed throughout the tube where unknown $C6 was inoculated.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 in motility agar")[A red colour appears only along the line where unknown $C7 was inoculated in the tube. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "In motility agar, a red turbid area formed throughout the tube where unknown $C7 was inoculated.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 in motility agar")[A red colour appears only along the line where unknown $C8 was inoculated in the tube. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "In motility agar, a red colour appears only along the line where unknown $C8 was inoculated in the tube")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 in motility agar")[A red colour appears only along the line where unknown $C9 was inoculated in the tube Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "In motility agar, a red colour appears only along the line where unknown $C9 was inoculated in the tube")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 in motility agar")[Unknown $C10 was motile only when tested at 25°C - not at 37°C. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 was motile only when tested at 25°C - not at 37°C.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 in motility agar")[A red colour appears only along the line where unknown $C11 was inoculated in the tube. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "In motility agar, a red colour appears only along the line where unknown $C11 was inoculated in the tube")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 in motility agar")[Unknown $C12 did not grow in motility agar under the conditions tested. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 did not grow in motility agar under the conditions tested.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 in motility agar")[A red colour appears only along the line where unknown $C13 was inoculated in the tube. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "In motility agar, a red colour appears only along the line where unknown $C13 was inoculated in the tube")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 in motility agar")[A red turbid area has formed throughout the tube where unknown $C14 was inoculated. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "In motility agar, a red turbid area formed throughout the tube where unknown $C14 was inoculated.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 in motility agar")[A red turbid area has formed throughout the tube where unknown $C15 was inoculated. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "In motility agar, a red turbid area formed throughout the tube where unknown $C15 was inoculated.")) (set: $clicks to it + 1)]]

The closest match in the NCBI database to unknown $C3 is: `NC_003197.2` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C3 case notes?", "Case 3")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C3, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C3", "16S3-text")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C4, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C4", "16S4-text")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C4 is: `NC_002163.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C4 case notes?", "Case 4")[(set:$t to it + time)]

(set: $clicks to it + 1) King's B medium is well-suited for the detection of certain fluorescent pigment molecules. <img alt="example of growth on King's Medium B" src="escape02-images/KingsB.jpg"> Figure 1. An organism grown on a King's Medium B plate that appears fluorescent when examined under UV light. Image credit: Carrie Lapaire Harmon, Southern Plant Diagnostic Network (link: "Click to see the King's Medium B recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>amount/litre</th> </tr> <tr> <td>Proteose peptone</td> <td>20.0 g</td> </tr> <tr> <td>Dipotassium hydrogen phosphate/td> <td>1.5 g</td> </tr> <tr> <td>Magnesium sulphate heptahydrate</td> <td>1.5 g</td> </tr> <tr> <td>Agar</td> <td>12.0 g</td> </tr> <tr> <td>Glycerol</td> <td>15 mL</td> </tr> </table> pH 7.2 ± 0.2 @ 25°C] (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from streaking unknown $C1 on King's Medium B")[You should consider whether streaking unknown $C1 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from streaking unknown $C2 on King's Medium B agar")[You should consider whether streaking unknown $C2 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from streaking unknown $C3 on King's Medium B agar")[You should consider whether streaking unknown $C3 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from streaking unknown $C4 on King's Medium B agar")[Unknown $C4 grows on King's Medium B, and the colonies are (colour). These colonies (appear/do not appear) fluorescent when examined under UV light. OR You should consider whether streaking unknown $C4 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from streaking unknown $C5 on King's Medium B agar")[Unknown $C5 grows on King's Medium B, and the colonies are (colour). These colonies (appear/do not appear) fluorescent when examined under UV light. OR You should consider whether streaking unknown $C5 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from streaking unknown $C6 on King's Medium B agar")[Unknown $C6 grows on King's Medium B, and the colonies are (colour). These colonies (appear/do not appear) fluorescent when examined under UV light. OR You should consider whether streaking unknown $C6 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from streaking unknown $C7 on King's Medium B agar")[Unknown $C7 grows on King's Medium B, and the colonies are (colour). These colonies (appear/do not appear) fluorescent when examined under UV light. OR You should consider whether streaking unknown $C7 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from streaking unknown $C8 on King's Medium B agar")[Unknown $C8 grows on King's Medium B, and the colonies are (colour). These colonies (appear/do not appear) fluorescent when examined under UV light. OR You should consider whether streaking unknown $C8 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from streaking unknown $C9 on King's Medium B agar")[Unknown $C9 grows on King's Medium B, and the colonies are (colour). These colonies (appear/do not appear) fluorescent when examined under UV light. OR You should consider whether streaking unknown $C9 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from streaking unknown $C10 on King's Medium B agar")[Unknown $C10 grows on King's Medium B, and the colonies are (colour). These colonies (appear/do not appear) fluorescent when examined under UV light. OR You should consider whether streaking unknown $C10 on King's Medium B agar is the best experiment in light of what you know about this growth medium and the other data available about this organism.] Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)]]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C5, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C5", "16S5-text")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C5 is: `NC_004722.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C5 case notes?", "Case 5")[(set:$t to it + time)]

The Methyl Red test detects the presence of acid produced from glucose fermentation in bacterial cultures. Bacteria are grown overnight in MRVP broth, and then the methyl red reagent is added and the culture is observed for a colour change (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are Methyl Red +, the medium will be red (because of a pH at/below 4.4) If the bacteria are Methyl Red -, the medium will be yellow (because less acid is produced from glucose fermentation).] (b4r:"solid")[<center><img alt="example of methyl red test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/methyl-red.png"></center> Figure 1. Methyl Red test results. From left to right: a positive result (red colour); a negative result (yellow - no colour change). ASM Image Gallery: Mary G. Miller, Southeastern Louisiana University, Hammond] <a href="https://asm.org/Protocols/Methyl-Red-and-Voges-Proskauer-Test-Protocols" target="_blank">Read more about the Methyl Red test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform a methyl red test on unknown $C1")[Unknown $C1 is ''Methyl Red positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is methyl red positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform a methyl red test on unknown $C2")[Unknown $C2 is ''Methyl Red positive''.. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 is methyl red positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform a methyl red test on unknown $C3")[Unknown $C3 is ''Methyl Red positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is methyl red positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform a methyl red test on unknown $C4")[You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not perform a methyl red test on unknown $C4")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform a methyl red test on unknown $C5")[Unknown $C5 is ''Methyl Red negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 is methyl red negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform a methyl red test on unknown $C6")[Unknown $C6 is ''Methyl Red positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is methyl red positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform a methyl red test on unknown $C7")[You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not perform a methyl red test on unknown $C7")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform a methyl red test on unknown $C8")[Unknown $C8 is ''Methyl Red positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is methyl red positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform a methyl red test on unknown $C9")[You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not perform a methyl red test on unknown $C9")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform a methyl red test on unknown $C10")[Unknown $C10 is ''Methyl Red positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is methyl red positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform a methyl red test on unknown $C11")[You should consider whether this is the best experiment to identify unknown $C11 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not perform a methyl red test on unknown $C11")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform a methyl red test on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not perform a methyl red test on unknown $C12")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform a methyl red test on unknown $C13")[Unknown $C13 is ''Methyl Red negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is methyl red negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform a methyl red test on unknown $C14")[Unknown $C14 is ''Methyl Red positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is methyl red positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform a methyl red test on unknown $C15")[Unknown $C15 is ''Methyl Red negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is methyl red negative")) (set: $clicks to it + 1)]]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C6, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C6", "16S6-text")[(set:$t to it + time)]

The closest match in the NCBI database to the first contig sequenced from unknown $C6 is: `NZ_CP014046.2` The closest match in the NCBI database to the second contig sequenced from unknown $C6 is: `NZ_CP014047.2` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C6 case notes?", "Case 6")[(set:$t to it + time)]

(set: $orchid to (prompt: "What is the binomial name of unknown organism $C1?", "correctly spelled and appropriately capitalised") ) (if: $orchid is "Escherichia coli")[(set:$C1soln to it + 1)(set: $solved to it + (a: "Escherichia coli"))You have correctly identified unknown $C1, very well done! //Escherichia coli // is a Gram-negative, rod-shaped facultative anaerobe often found as a commensal in mammalian guts - but some strains can cause serious food poisoning. The isolate found in the $C1food sample is an O157 strain (notable for its inability to ferment sorbitol) - not what you want to find in your food! --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] if you would like to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C1?", "Hint0")[(set:$t to it + time)]]

If you think that you have correctly identified an unknown, but you are getting an message indicating that your identification is incorrect: 1. Double check that the organism's name is correctly spelled and capitalized. The binomial name should be spelled out in full (for example, Legionella pneumophila would be a correct key, while L. pneumophila or legionella pneumophila would be incorrect.) 2. Work your way through the identification again, making sure that you have ruled out all of the alternatives and used the available evidence logically. If you are still struggling to identify this unknown, you can earn some hints by solving some calculations (similar to the types of problems that you might have to solve in a clinical microbiology lab.) Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

(set: $grace to (prompt: "What is the binomial name of unknown organism $C2?", "correctly spelled and appropriately capitalised") ) (if: $grace is "Listeria monocytogenes")[(set:$C2soln to it + 1)(set: $solved to it + (a: "Listeria monocytogenes"))You have correctly identified unknown $C2, very well done! //Listeria monocytogenes // is a Gram-positive, rod-shaped, facultative anaerobe that can cause listeriosis (which is particularly serious for pregnant women, newborns, and the elderly, as well as any adults with weakened immune systems). //Listeria// can be found in a range of foods, but most commonly is associated with unpasteurized soft cheeses, deli meat, and other meat and unpasteurised dairy products. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] if you would like to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C2?", "Hint0")[(set:$t to it + time)]]

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC2 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the results of the malachite green stain (set: $hintsC2 to it + (a: "Consider the results of the malachite green stain."))] (else-if: visits is 3)[ Hint: Consider the results of the methyl red and Voges Proskauer tests (set: $hintsC2 to it + (a: "Consider the results of the methyl red and Voges Proskauer tests "))] (else-if: visits is 4)[ Hint: Consider the ability of this organism to ferment different carbohydrates. (set: $hintsC2 to it + (a: "Consider the ability of this organism to ferment different carbohydrates."))] (else-if: visits is 5)[ Hint: Consider the results of the urease test (set: $hintsC2 to it + (a: "Consider the results of the urease test."))] (else-if: visits is 5)[ Hint: Consider the growth of this unknown on PALCAM medium. (set: $hintsC2 to it + (a: "Consider the growth of this unknown on PALCAM medium."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C2", "Case 2")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

(set: $polar to (prompt: "What is the binomial name of unknown organism $C3?", "correctly spelled and appropriately capitalised") ) (if: $polar is "Salmonella enterica")[(set:$C3soln to it + 1)(set: $solved to it + (a: "Salmonella enterica"))You have correctly identified unknown $C3, very well done! //Salmonella enterica // is a Gram-negative, rod-shaped facultative anaerobe that can cause diarrhoeal disease (some serovars can cause typhoid fever). Although it is most commonly contracted by consuming contaminated foods, it can also be spread by contact with animals, for example turtles or lizards. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] if you would like to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C3?", "Hint0")[(set:$t to it + time)]]

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC3 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the phenotype of this organism on MacConkey agar. (set: $hintsC3 to it + (a: "Consider the phenotype of this organism on MacConkey agar. "))] (else-if: visits is 3)[ Hint: The IMViC tests (indole, methyl red, Voges Proskauer, and citrate) are often helpful for identifying this type of unknown. (set: $hintsC3 to it + (a: "The IMViC tests (indole, methyl red, Voges Proskauer, and citrate) are often helpful for identifying this type of unknown. "))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC3 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on Simmons Citrate agar. (set: $hintsC3 to it + (a: "Consider the phenotype of this organism on Simmons Citrate agar."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on Hektoen Enteric agar. (set: $hintsC3 to it + (a: "Consider the phenotype of this organism on Hektoen Enteric agar."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C3", "Case 3")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

(set: $telescope to (prompt: "What is the binomial name of unknown organism $C4?", "correctly spelled and appropriately capitalised") ) (if: $telescope is "Campylobacter jejuni")[(set: $C4soln to it + 1)(set: $solved to it + (a: "Campylobacter jejuni"))You have correctly identified unknown $C4, very well done! //Campylobacter jejuni// is a Gram-negative, motile, curved or comma-shaped bacterium that typically grows best in a microaerophilic environment. //Campylobacter// can be contracted via eating contaminated foods - most commonly poultry. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C4?", "Hint0")[(set:$t to it + time)].]

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the oxidase test result for this organism (set: $hintsC4 to it + (a: "Consider the oxidase test result for this organism"))] (else-if: visits is 2)[ Hint: Consider the ability of this organism to ferment carbohydrates. (set: $hintsC4 to it + (a: "Consider the ability of this organism to ferment carbohydrates."))] (else-if: visits is 3)[ Hint: Consider the growth of this organism in motility agar. (set: $hintsC4 to it + (a: "Consider the growth of this organism in motility agar."))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC4 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the oxygen requirements of this organism. (set: $hintsC4 to it + (a: "Consider the oxygen requirements of this organism."))] (else-if: visits is 5)[ Hint: Consider the cell shape of this unknown. (set: $hintsC4 to it + (a: "Consider the cell shape of this unknown."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C4", "Case 4")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

(set: $capillary to (prompt: "What is the binomial name of unknown organism $C5?", "correctly spelled and appropriately capitalised") ) (if: $capillary is "Bacillus cereus")[(set: $C5soln to it + 1)(set: $solved to it + (a: "Bacillus cereus"))You have correctly identified unknown $C5, very well done! //Bacillus cereus // is a Gram-positive, endospore-forming, rod shaped bacterium often food in the soil, but which can sometimes be found in starchy foods such as rice. Some strains of //B. cereus// produce a cerulide toxin which is incredibly stable (even when heated). --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C5?", "Hint0")[(set:$t to it + time)]]

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC5 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the gelatinase activity of this organism. (set: $hintsC5 to it + (a: "Consider the gelatinase activity of this organism."))] (else-if: visits is 3)[ Hint: Consider the ability of this organism to reduce nitrate. (set: $hintsC5 to it + (a: "Consider the ability of this organism to reduce nitrate."))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC5 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the malachite green stain results for this organism. (set: $hintsC5 to it + (a: "Consider the malachite green stain results for this organism."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on MYP agar. (set: $hintsC5 to it + (a: "Consider the phenotype of this organism on MYP agar."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C5", "Case 5")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

(set: $greengrocer to (prompt: "What is the binomial name of unknown organism $C6?", "correctly spelled and appropriately capitalised") ) (if: $greengrocer is "Vibrio parahaemolyticus")[(set: $C6soln to it + 1)(set: $solved to it + (a: "Vibrio parahaemolyticus"))You have correctly identified unknown $C6, very well done! //Vibrio parahaemolyticus // is a Gram-negative, curved, facultative aerobe that can cause gastrointesteritis in humans. //V. parahaemolyticus// is generally found in marine environments and associated with seafood such as oysterrs, shrimp, and some types of fish. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C6?", "Hint0")[(set:$t to it + time)]]

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC6 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the oxygen requirement of this organism. (set: $hintsC6 to it + (a: "Consider the oxygen requirement of this organism."))] (else-if: visits is 3)[ Hint: Consider the results of the Voges-Proskauer test. (set: $hintsC6 to it + (a: "Consider the results of the Voges-Proskauer test. "))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC6 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the cell shape of this unknown. (set: $hintsC6 to it + (a: "Consider the cell shape of this unknown."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on TCBS agar. (set: $hintsC6 to it + (a: "Consider the phenotype of this organism on TCBS agar."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C6", "Case 6")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

The FASTA file containing the sequence of the 16S rRNA gene from $C1 has the following sequence: (font:"Courier New")[AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGT AACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGAT GGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTC GGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGAC GATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAG GCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCT TCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCC GCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAA TTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAA CTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCG TAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGC GTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCC CTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAAC TCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACC TTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTG CTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCT TTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATG ACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCG ACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCAT GAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACC GCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACT TTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCT TA] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C1 case notes?", "Case 1")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C2 has the following sequence: (font:"Courier New")[TAAAGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGT CGAACGAACGGAGGAAGAGCTTGCTCTTCCAAAGTTAGTGGCGGACGGGTGAGTAACACG TGGGCAACCTGCCTGTAAGTTGGGGATAACTCCGGGAAACCGGGGCTAATACCGAATGAT AAAGTGTGGCGCATGCCACGCTTTTGAAAGATGGTTTCGCTATCGCTTACAGATGGGCCC GCGGTGCATTAGCTAGTTGGTAGGGTAATGGCCTACCAAGGCAACGATGCATAGCCGACC TGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC AGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGTATGAAGAA GGTTTTCGGATCGTAAAGTACTGTTGTTAGAGAAGAACAAGGATAAGAGTAACTGCTNGT CCCTTGACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATA CGTAGGTGGCNAGCGTNGTCCGGATGGATTGGGCGTNAAGCGCGCGCAGGCGGTCTTTTA AGTCTNATGTGAAAGCCCCCGGCTGAACCGGGNNGGGTCATTGGAAACTGGAAGACTNGA GTGCNGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGATATGTGGAGGA ACACCAGTGGCGAAGGCGACTCTCTGGTCTGTNACTGACGCTGAGGCGCGAAAGCGTGGG GAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTA GGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACG ACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCGCACAAGCGGTGGAGCATGTGGT TTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCTTTGACCACTCTGGAG ACAGAGCTTTCCCTTCGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGT CGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGATTTTAGTTGCCAGCATT TAGTTGGGCACTCTAAAGTGACTGCCGGTGCAAGCCGGAGGAAGGTGGGGATGACGTCAA ATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGATAGTACAAAGGGTC GCGAAGCCGCGAGGTGGAGCTAATCCCATAAAACTATTCTCAGTTCGGATTGTAGGCTGC AACTCGCCTACATGAAGCCGGAATCGCTAGTAATCGTGGATCAGCATGCCACGGTGAATA CGTTCCCGGGCCTNGTACACACCGCNCGTCACACCACGAGAGTTNGTAACACCCGAAGTC GGTAGGGTCACCTTTATGGAGCCAGCCGC] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C2 case notes?", "Case 2")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C3 has the following sequence: (font:"Courier New")[ATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGC TGCTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGG GATAACTACTGGAAACGGTGGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACC TTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTTGTTGGTGAGGTAACGGC TCACCAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGA CACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCT GATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGG AGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGC TAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGG GCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGG GAACTGCATTCGAAACTGGCAGGCTTGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTA GCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAA GACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCA CGCCGTAAACGATGTCTACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACG CGTTAAGTAGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGG GGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTG GTCTTGACATCCACAGAANNNTCCAGAGATGGATTNGTGCCTTCGGGAACTGTGAGACAG GTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGC GCAACCCTTATCCTTTGTTGCCAGCGATTAGGTCGGGAACTCAAAGGAGACTGCCAGTGA TAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACA CACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATA AAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAG TAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTC ACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACC ACTTTGTGATTCATGACTGGGGTGAAG] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C3 case notes?", "Case 3")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C4 has the following sequence: (font:"Courier New")[TTATGGAGAGTTTGATCCTGGCTCAGAGTGAACGCTGGCGGCGTGCCTAATACATGCAAG TCGNACGATGAAGCTTCTAGCTTGCTAGAAGTGGATTAGTGGCGCACGGGTGAGTAAGGT ATAGTTAATCTGCCCTACACAAGAGGACAACAGTTGGAAACGACTGCTNATACTCTATAC TCCTGCTTAACACAAGTTGAGTAGGGAAAGTTTTTCGGTGTAGGATGAGACTATATAGTA TCAGCTAGTTGGTAAGGTAATGGCTTACCAAGGCTATGACGCTTAACTGGTCTGAGAGGA TGATCAGTCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGA ATATTGCGCAATGGGGGAAACCCTGACGCAGCAACGCCGCGTGGAGGATGACACTTTTCG GAGCGTAAACTCCNTTTCTTAGGGAAGAATTCTGACGGTACCTAAGGAATAAGCACCGGC TAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTACTCGGAATCACTGG GCGTAAAGGGCGCGTAGGCGGATTATCAAGTCTCTTGTGAAATCTAATGGCTTAACCATT AAACTGCTTGGGAAACTGATAGTCTAGAGTGAGGGAGAGGCAGATGGAATTGGTGGTGTA GGGGTAAAATCCGTAGATATCACCAAGAATACCCATTGCGAAGGCGATCTGCTGGAACTC AACTGACGCTAAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCA CGCCCTNAACGATGTACACTAGTTGTTGGGGTGCTAGTCATCTCAGTAATGCAGCTAACG CATTAAGTGTACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATAGACGGG GACCCGCACAAGCGGTGGAGCATGTGGTTTNNNNCGAAGATACGCGAAGAACCTTACCTG GGCTTGATATCCTAAGAACCTTATAGAGATATGAGGGTGCTAGCTTGCTAGAACTTAGAG ACAGGTGCTGCACGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTNAGTCCCGCAAC GAGCGCAACCCACGTATTTAGTTGCTAACGGTTCGGCCGAGCACTCTAAATAGACTGCCT TCGTAAGGAGGAGGAAGGTGTGGACGACGTCAAGTCATCATGGCCCTTATGCCCAGGGCG ACACACGTGCTACAATGGCATATACAATGAGACGCAATACCGCGAGGTGGAGCAAATCTA TAAAATATGTCCCAGTTCGGATTGTTCTCTGCAACTCGAGAGCATGAAGCCGGAATCGCT AGTAATCGTAGATCAGCCATGCTACGGTGAATACGTTCCCGGGTCTTGTACTCACCGCCC GTCACACCATGGGAGTTGATTTCACTCGAAGCCGGAATACTAAACTAGTTACCGTCCACA GTGGAATCAGCGACTGGGG] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C4 case notes?", "Case 4")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C5 has the following sequence: (font:"Courier New")[CCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAATGGATTA AGAGCTTGCTCTTATGAAGTTAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCCA TAAGACTGGGATAACTCCGGGAAACCGGGGCTAATACCGGATAACATTTTGAACCGCATG GTTCGAAATTGAAAGGCGGCTTCGGCTGTCACTTATGGATGGACCCGCGTCGCATTAGCT AGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCG GCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTC CGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGT AAAACTCTGTTGTTAGGGAAGAACAAGTGCTAGTTGAATAAGCTGGCACCTTGACGGTAC CTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAG CGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAA AGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGA AAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGA AGGCGACTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGGAT TAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGAGGGTTTCCGCC CTTTAGTGCTGAAGTTAACGCATTAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTGA AACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGC AACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGAAAACCCTAGAGATAGGGCTTCTC CTTCGGGAGCAGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTG GGTTAAGTCCCGCAACGAGCGCAACCCTTGATCTTAGTTGCCATCATTAAGTTGGGCACT CTAAGGTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCC CCTTATGACCTGGGCTACACACGTGCTACAATGGACGGTACAAAGAGCTGCAAGACCGCG AGGTGGAGCTAATCTCATAAAACCGTTCTCAGTTCGGATTGTAGGCTGCAACTCGCCTAC ATGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGC CTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTCGGTGGGGTAAC CTTTTTGGAGCCAGCCGCCTAAGGTGGGACAGATGATTGGGG] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C5 case notes?", "Case 5")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C6 has the following sequence: (font:"Courier New")[AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGC GGAAACGAGTTATCTGAACCTTCGGGGAACGATAACGGCGTCGAGCGGCGGACGGGTGAG TAATGCCTAGGAAATTGCCCTGATGTGGGGGATAACCATTGGAAACGATGGCTAATACCG CATGATGCCTACGGGCCAAAGAGGGGGACCTTCGGGCCTCTCGCGTCAGGATATGCCTAG GTGGGATTAGCTAGTTGGTGAGGTAAGGGCTCACCAAGGCGACGATCCCTAGCTGGTCTG AGAGGATGATCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAG TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGG CCTTCGGGTTGTAAAGCACTTTCAGTCGTGAGGAAGGCGGGTACGTTAATAGCGTATTCG TTTGACGTTAACGACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACG GAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCATGCAGGTGGTTTGTTAAG TCAGATGTGAAAGCCCGGGGCTCAACCTCGGAATTGCATTTGAAACTGGCAGACTAGAGT GCTGTAGAGGGGGGTAGAATTTCAGGTGTAGCGGTGAAATGCGTAGAGATCTGAAGGAAT ACCGGTGGCGAAGGCGGCCCCCTGGACAGATACTGACACTCAGATGCGAAAGCGTGGGGA GCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCTACTTGGAGGTTGT GGCCTTGAGCCGTGGCTTTCGGAGCTAACGCGTTAAGTAGACCGCCTGGGGAGTACGGTC GCAAGATTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTT AATTCGATGCAACGCGAAGAACCTTACCTACTCTTGACATCCAGAGAACTTTCCAGAGAT GGATTGGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTG TGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTGTTTGCCAGCGAGTA ATGTCGGGAACTCCAGGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGACGACGTCA AGTCATCATGGCCCTTACGAGTAGGGCTACACACGTGCTACAATGGCGCATACAGAGGGC AGCCAACTTGCGAAAGTGAGCGAATCCCAAAAAGTGCGTCGTAGTCCGGATTGGAGTCTG CAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAAT ACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGCTGCAAAAGAAGT AGGTAGTTTAACCTTCGGGGGGACGCTTACCACTTTGTGGTTCATGACTGGGGTGAAGTC GTAACAAGGTAACC] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C6 case notes?", "Case 6")[(set:$t to it + time)]

1. Rename this passage to the name of the growth medium 2. ADD this code to each of the plates1, plates2, etc. passages: (link-reveal-goto: "Grow organism $C4 on/in (medium name)", "(name of THIS passage")[(set:$t to it + time)] 3. Edit the code for this passage as appropriate: Insert brief description of medium here <img alt="insert alt text here" src="insert image link here"> Figure 1. Add figure legend and image credit (link: "Click to see the (insert name here) medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>insert name of component here </td> <td>insert amount in grams </td> </tr> <tr> <td>add as many/td> <td>rows as necessary</td> </tr> </table> pH (specify) ± (value) @ 25°C, or add any additional instructions here] <a href="link" target="_blank">Read more about X medium (Oxoid)</a> {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 in/on (medium name)")[Unknown $C1 (phenotype) Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 in/on (medium name)")[Unknown $C2 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 in/on (medium name)")[Unknown $C3 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 in/on (medium name)")[Unknown $C4 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 in/on (medium name)")[Unknown $C5 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 in/on (medium name)")[Unknown $C6 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 in/on (medium name)")[Unknown $C7 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 in/on (medium name)")[Unknown $C8 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 in/on (medium name)")[Unknown $C9 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 in/on (medium name)")[Unknown $C10 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 in/on (medium name)")[Unknown $C11 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 in/on (medium name)")[Unknown $C12 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 in/on (medium name)")[Unknown $C13 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 in/on (medium name)")[Unknown $C14 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 in/on (medium name)")[Unknown $C15 (phenotype). Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 (phenotype)")) (set: $clicks to it + 1)]]

1. Rename this passage to the name of the biochemical test 2. ADD this code to each of the biochem1, biochem2, etc. passages: (link-reveal-goto: "Perform an (test) on organism $C1", "(name of THIS passage)")[(set:$t to it + time)] 3. Edit the code for this passage as appropriate: (set: $clicks to it + 1) Insert a brief description of test here. If the bacteria are test+, (describe result) If the bacteria are test-, (describe result) <img alt="(insert image alt text)" src="insert image location"> Figure 1. (Add figure legend and image credit). <a href="link" target="_blank">Read more about the (name) test</a> {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to see the (name) test results for unknown $C1")[Unknown $C1 is test ''positive/negative''.OR You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to see the (name) test results for unknown $C2")[Unknown $C2 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to see the (name) test results for unknown $C3")[Unknown $C3 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C3 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to see the (name) test results for unknown $C4")[Unknown $C4 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 (phenotype)")) (set: $clicks to it + 1)] (else-if: _lastPassage is "biochem5")[ (link: "Click to see the (name) test results for unknown $C5")[Unknown $C5 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to see the (name) test results for unknown $C6")[Unknown $C6 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C6 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to see the (name) test results for unknown $C7")[Unknown $C7 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to see the (name) test results for unknown $C8")[Unknown $C8 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C8 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to see the (name) test results for unknown $C9")[Unknown $C8 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to see the (name) test results for unknown $C10")[Unknown $C10 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C10 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to see the (name) test results for unknown $C11")[Unknown $C11 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C11 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to see the (name) test results for unknown $C12")[Unknown $C12 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to see the (name) test results for unknown $C13")[Unknown $C13 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to see the (name) test results for unknown $C14")[Unknown $C14 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C14 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 (phenotype)")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to see the (name) test results for unknown $C15")[Unknown $C15 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C15 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 (phenotype)")) (set: $clicks to it + 1)]]

##Unknown $C7 You have isolated an organism in axenic culture from a sample of $C7food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C7 under the microscope", "microscope7")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C7 on different media", "plates7")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C7", "biochem7")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C7's 16S rRNA gene", "16S7")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C7's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S7-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S7-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C7's entire genome", "WGS7")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C7 is currently unavailable. ] (if: (history:) contains "WGS7-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS7-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C7 notebook (summary of previously obtained results/redeem earned hints)", "notebook7")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C7soln is 0)[(link-reveal-goto: "Identify unknown $C7", "identify7")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C7 - do you want to check your answer again?", "identify7")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C7?", "Hint0")[(set:$t to it + time)]]

Unknown $C7 was isolated from a sample of $C7food. The results from the experiments you have obtained so far are: (if: $notebookC7's length > 0)[\ (for: each _index, ...(range: 1, $notebookC7's length))[_index) (print: $notebookC7's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S7-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S7-text")[(set:$t to it + time)]] (if: (history:) contains "WGS7-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS7-Results")[(set:$t to it + time)]] (if: $C7soln is 0)[(link-reveal-goto: "Identify unknown $C7", "identify7")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C7 - do you want to check your answer again?", "identify7")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C7", "C7hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C7", "Case 7")[(set:$t to it + time)]

##Unknown $C8 You have isolated an organism in axenic culture from a sample of $C8food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C8 under the microscope", "microscope8")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C8 on different media", "plates8")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C8", "biochem8")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C8's 16S rRNA gene", "16S8")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C8's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S8-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S8-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C8's entire genome", "WGS8")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C8 is currently unavailable. ] (if: (history:) contains "WGS8-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS8-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C8 notebook (summary of previously obtained results/redeem earned hints)", "notebook8")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C8soln is 0)[(link-reveal-goto: "Identify unknown $C8", "identify8")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C8 - do you want to check your answer again?", "identify8")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C8?", "Hint0")[(set:$t to it + time)]]

Unknown $C8 was isolated from a sample of $C8food. The results from the experiments you have obtained so far are: (if: $notebookC8's length > 0)[\ (for: each _index, ...(range: 1, $notebookC8's length))[_index) (print: $notebookC8's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S8-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S8-text")[(set:$t to it + time)]] (if: (history:) contains "WGS8-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS8-Results")[(set:$t to it + time)]] (if: $C8soln is 0)[(link-reveal-goto: "Identify unknown $C8", "identify8")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C8 - do you want to check your answer again?", "identify8")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C8", "C8hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C8", "Case 8")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C7", "16S7-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C7", "Case 7")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C8", "16S8-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C8", "Case 8")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C7, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C7", "16S7-text")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C8, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C8", "16S8-text")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C7 has the following sequence: (font:"Courier New")[TGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTA GGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTC TGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGC AGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACAC CAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATC AAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGG GTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCG CAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTA ATTCGAAGCAACGCGAAGAACCTTACCAAATCTTGACATCCTTTGACAACTCTAGAGATA GAGCCTTCCCCTTCGGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTC GTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTA AGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAA ATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACAAAGGGCA GCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGC AACTCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATA CGTTCCCGGGTCTTGTACACACCGCCCGTCACACCACG] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C7 case notes?", "Case 7")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C8 has the following sequence: (font:"Courier New")[TGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAG CAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGA TGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGA GGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGG GTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGG AACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGC GCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTT CAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAA GCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGA ATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCT CAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTC CAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCC TGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTG GTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGG AGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAA TTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAAC CTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCG TGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCG CAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACT GCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCA GGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGG ACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGA ATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACAC CGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGG CGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTA] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C8 case notes?", "Case 8")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C7", "WGS7-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C7", "Case 7")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C8", "WGS8-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C8", "Case 8")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C7 is: `NC_007795.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C7 case notes?", "Case 7")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C8 is: `NC_004337.2` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C8 case notes?", "Case 8")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C7. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C7", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C7", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C7", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C7", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C7 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C7", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C7", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C7 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C7", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C7", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C7", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C7", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C7", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C7", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C7", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C7", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C7", "Case 7")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C8. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C8", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C8", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C8", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C8", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C8 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C8", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C8", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C8 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C8", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C8", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C8", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C8", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C8", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C8", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C8", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C8", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C8", "Case 8")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C7 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C7 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C7 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C7", "Case 7")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C8 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C8 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C8 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C8", "Case 8")[(set:$t to it + time)]

(set: $armchair to (prompt: "What is the binomial name of unknown organism $C7?", "correctly spelled and appropriately capitalised") ) (if: $armchair is "Staphylococcus aureus")[(set: $C7soln to it + 1)(set: $solved to it + (a: "Staphylococcus aureus"))You have correctly identified unknown $C7, very well done! //Staphylococcus aureus // is a Gram-positive coccus-shaped facultative anaerobe. Some strains produce enterotoxins, which are usually encoded on accessory genetic elements (such as plasmids or prophages), Food poisoning caused by //S. aureus// is usually characterised by nausea, vomiting, stomach cramps, and diarrhea, and typically has a very rapid onset after consumption of the contaminated food (1-6 hours). --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C7?", "Hint0")[(set:$t to it + time)]]

(set: $begonia to (prompt: "What is the binomial name of unknown organism $C8?", "correctly spelled and appropriately capitalised") ) (if: $begonia is "Shigella flexneri")[(set: $C8soln to it + 1)(set: $solved to it + (a: "Shigella flexneri"))You have correctly identified unknown $C8, very well done! //Shigella flexneri// is a Gram-negative, rod-shaped, facultative anaerobe, that can cause shigellosis. //Shigella// has a very low infectious dose, sometimes as low as 10-50 organisms. Patients infected with //Shigella// may sometimes develop secondary complications, such as haemolytic uremic syndrome (HUS). --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer.(link-reveal-goto: "Do you need a hint to help you identify unknown $C8?", "Hint0")[(set:$t to it + time)]]

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC7 to it + (a: "Consider the results of the oxidase and catalase tests."))] (else-if: visits is 2)[ Hint: Consider the oxygen requirements of this organism. (set: $hintsC7 to it + (a: "Consider the oxygen requirements of this organism."))] (else-if: visits is 3)[ Hint: Consider the Voges-Proskauer test result for this organism. (set: $hintsC7 to it + (a: "Consider the Voges-Proskauer test result for this organism. "))] (else-if: visits is 4)[ Hint: Consider the phenotype of this organism on blood agar. (set: $hintsC7 to it + (a: "Consider the phenotype of this organism on blood agar."))] (else-if: visits is 5)[ Hint: Consider the coagulase test result for this organism. (set: $hintsC7 to it + (a: "Consider the coagulase test result for this organism."))] (else-if: visits is 5)[ Hint: Consider the growth of this organism on MSA. (set: $hintsC7 to it + (a: "Consider the growth of this organism on MSA."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C7", "Case 7")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC8 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the phenotype of this organism on MacConkey agar. (set: $hintsC8 to it + (a: "Consider the phenotype of this organism on MacConkey agar. "))] (else-if: visits is 3)[ Hint: The IMViC tests (indole, methyl red, Voges Proskauer, and citrate) are often helpful for identifying this type of unknown. (set: $hintsC8 to it + (a: "The IMViC tests (indole, methyl red, Voges Proskauer, and citrate) are often helpful for identifying this type of unknown. "))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC8 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on Simmons Citrate agar. (set: $hintsC8 to it + (a: "Consider the phenotype of this organism on Simmons Citrate agar."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on Hektoen Enteric Agar. (set: $hintsC8 to it + (a: "Consider the phenotype of this organism on Hektoen Enteric Agar."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C8", "Case 8")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

##Unknown $C9 You have isolated an organism in axenic culture from a sample of $C9food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C9 under the microscope", "microscope9")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C9 on different media", "plates9")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C9", "biochem9")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C9's 16S rRNA gene", "16S9")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C9's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S9-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S9-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C9's entire genome", "WGS9")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C9 is currently unavailable. ] (if: (history:) contains "WGS9-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS9-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C9 notebook (summary of previously obtained results/redeem earned hints)", "notebook9")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C9soln is 0)[(link-reveal-goto: "Identify unknown $C9", "identify9")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C9 - do you want to check your answer again?", "identify9")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C9?", "Hint0")[(set:$t to it + time)]]

Unknown $C9 was isolated from a sample of $C9food. The results from the experiments you have obtained so far are: (if: $notebookC9's length > 0)[\ (for: each _index, ...(range: 1, $notebookC9's length))[_index) (print: $notebookC9's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S9-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S9-text")[(set:$t to it + time)]] (if: (history:) contains "WGS9-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS9-Results")[(set:$t to it + time)]] (if: $C9soln is 0)[(link-reveal-goto: "Identify unknown $C9", "identify9")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C9 - do you want to check your answer again?", "identify9")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C9", "C9hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C9", "Case 9")[(set:$t to it + time)]

##Unknown $C10 You have isolated an organism in axenic culture from a sample of $C10food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C10 under the microscope", "microscope10")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C10 on different media", "plates10")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C10", "biochem10")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C10's 16S rRNA gene", "16S10")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C10's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S10-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S10-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C10's entire genome", "WGS10")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C10 is currently unavailable. ] (if: (history:) contains "WGS10-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS10-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C10 notebook (summary of previously obtained results/redeem earned hints)", "notebook10")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C10soln is 0)[(link-reveal-goto: "Identify unknown $C10", "identify10")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C10 - do you want to check your answer again?", "identify10")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C10?", "Hint0")[(set:$t to it + time)]]

Unknown $C10 was isolated from a sample of $C10food. The results from the experiments you have obtained so far are: (if: $notebookC10's length > 0)[\ (for: each _index, ...(range: 1, $notebookC10's length))[_index) (print: $notebookC10's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S10-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S10-text")[(set:$t to it + time)]] (if: (history:) contains "WGS10-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS10-Results")[(set:$t to it + time)]] (if: $C10soln is 0)[(link-reveal-goto: "Identify unknown $C10", "identify10")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C10 - do you want to check your answer again?", "identify10")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C10", "C10hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C10", "Case 10")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C9", "16S9-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C9", "Case 9")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C10", "16S10-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C10", "Case 10")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C9, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C9", "16S9-text")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C10, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C10", "16S10-text")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C9 has the following sequence: (font:"Courier New")[ACGCTGGCGGCGTGCTTAACACATGCAAGTCGAGCGATGAAGTTTCTTCGGGAAACGGAT TAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCTCATAGAGTGGAATAGCCTTCC GAAAGGAAGATTAATACCGCATAATGTTGAAAGATGGCATCATCATTCAACCAAAGGAGC AATCCGCTATGAGATGGACCCGCGGCGCATTAGCTAGTTGGTGGGGTAACGGCCTACCAA GGCGACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCC CAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAG CAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTCTTTGGGGAAGATAA TGACGGTACCCAAGGAGGAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTA GGTGGCGAGCGTTATCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGATGATTAAGTG GGATGTGAAATACCCGGGCTCAACTTGGGTGCTGCATTCCAAACTGGTTATCTAGAGTGC AGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACAC CAGTGGCGAAGGCGACTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGC AAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATACTAGGTGTGGGGGT TTCAACACCTCCGTGCCGCCGCTAACGCATTAAGTATTCCGCCTGGGGAGTACGGTCGCA AGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGTAGCGGAGCATGTGGTTTAAT TCGAAGCAACGCGAAGAACCTTACCTACACTTGACATCCCTTGCATTACTCTTAATCGAG GAAATCCCTTCGGGGACAAGGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGA GATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCGTTAGTTACTACCATTAAGTT GAGGACTCTAGCGAGACTGCCTGGGTTAACCAGGAGGAAGGTGGGGATGACGTCAAATCA TCATGCCCCTTATGTGTAGGGCTACACACGTGCTACAATGGCTGGTACAGAGAGATGCAA TACCGCGAGGTGGAGCCAAACTTAAAAACCAGTCTCAGTTCGGATTGTAGGCTGAAACTC GCCTACATGAAGCTGGAGTTACTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTC CCGGGTCTTGTACACACCGCCCGTCACACCATGAGAGTTGGCAATACCCGAAGTCCGTGA GCTAACCGCAAGAGGCAGCGGCCGYAGTAGGGTCAGCGATTGGGGTGAAGTCGTAACAAG GTAGCCGTAGAGAACCTGCG] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C9 case notes?", "Case 9")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C10 has the following sequence: (font:"Courier New")[ATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGGCAGCGGGAAGTAGTTTAC TACTTTGCCGGCGAGCGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGG GATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCTTCGGACCAAAGTGGGGGACC TTAGGGCCTCACGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAATGGC TCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGA CACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCT GATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGCGAGG AGGAAGGCCAATAACTTAATACGTTGTTGGATTGACGTTACTCGCAGAAGAAGCACCGGC TAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGG GCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGCGCTTAACGTGG GAACTGCATTTGAAACTGGCAAGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTA GCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAA GACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCA CGCTGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACG CGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGG GGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTA CTCTTGACATCCACGGAATTTAGCAGAGATGCTTTAGTGCCTTCGGGAACCGTGAGACAG GTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGC GCAACCCTTATCCTTTGTTGCCAGCACGTAATGGTGGGAACTCAAAGGAGACTGCCGGTG ATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAGGGCTAC ACACGTGCTACAATGGCAGATACAAAGTGAAGCGAACTCGCGAGAGCAAGCGGACCACAT AAAGTCTGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTA GTAATCGTAGATCAGAATGCTACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGT CACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTAC CACTTTGTGATTCATGACTGG] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C10 case notes?", "Case 10")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C9", "WGS9-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C9", "Case 9")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C10", "WGS10-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C10", "Case 10")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C9 is: `NZ_CP075979.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C9 case notes?", "Case 9")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C10 is: `NZ_CP016937.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C10 case notes?", "Case 10")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C9. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C9", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C9", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C9", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C9", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C9 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C9", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C9", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C9 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C9", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C9", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C9", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C9", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C9", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C9", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C9", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C9", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C9", "Case 9")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C10. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C10", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C10", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C10", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C10", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C10 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C10", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C10", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C10 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C10", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C10", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C10", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C10", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C10", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C10", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C10", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C10", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C10", "Case 10")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C9 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C9 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C9 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C9", "Case 9")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C10 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C10 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C10 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C10", "Case 10")[(set:$t to it + time)]

(set: $prosecco to (prompt: "What is the binomial name of unknown organism $C9?", "correctly spelled and appropriately capitalised") ) (if: $prosecco is "Clostridium perfringens")[(set: $C9soln to it +1)(set: $solved to it + (a: "Clostridium perfringens"))You have correctly identified unknown $C9, very well done! //Clostridium perfringens // is a Gram-positive, rod-shaped, anaerobic bacterium capable of forming spores. Food poisoning caused by //C. perfringens// is usually characterised by diarrhea and stomach cramps, but not vomiting. Foods that are cooked in large batches and kept at unsafe temperatures are most commonly associated with food poisoning by //C. perfringens//. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C9?", "Hint0")[(set:$t to it + time)]]

(set: $pendulum to (prompt: "What is the binomial name of unknown organism $C10?", "correctly spelled and appropriately capitalised") ) (if: $pendulum is "Yersinia enterocolitica")[(set: $C10soln to it + 1)(set: $solved to it + (a: "Yersinia enterocolitica"))You have correctly identified unknown $C10, very well done! //Yersinia enterocolitica // is a Gram-negative, rod-shaped , facultative anaerobe capable of causing yersiniosis. //Y. enterocolitica// infection is most commonly associated with raw or undercooked pork products. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C10?", "Hint0")[(set:$t to it + time)]]

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the ability of this organism to ferment carbohydrates. (set: $hintsC9 to it + (a: "Consider the ability of this organism to ferment carbohydrates."))] (else-if: visits is 2)[ Hint: Consider the phenotype of this organism on blood agar. (set: $hintsC9 to it + (a: "Consider the phenotype of this organism on blood agar."))] (else-if: visits is 3)[ Hint: Consider the indole test result for this organism. (set: $hintsC9 to it + (a: "Consider the indole test result for this organism. "))] (else-if: visits is 4)[ Hint: Consider the malachite green stain of this organism. (set: $hintsC9 to it + (a: "Consider the malachite green stain of this organism."))] (else-if: visits is 5)[ Hint: "Consider the phenotype of this organism on TSC medium. (set: $hintsC9 to it + (a: "Consider the phenotype of this organism on TSC medium."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on DRCM medium. (set: $hintsC9 to it + (a: "Consider the phenotype of this organism on DRCM medium."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C9", "Case 9")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC10 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the ability of this organism to ferment carbohydrates. (set: $hintsC10 to it + (a: "Consider the ability of this organism to ferment carbohydrates. "))] (else-if: visits is 3)[ Hint: Consider the ability of this organism to reduce nitrate. (set: $hintsC10 to it + (a: "Consider the ability of this organism to reduce nitrate. "))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC10 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the urease test result for this organism. (set: $hintsC10 to it + (a: "Consider the urease test result for this organism."))] (else-if: visits is 5)[ Hint: Consider tthe growth of this organism on CIN agar. (set: $hintsC10 to it + (a: "Consider tthe growth of this organism on CIN agar."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C10", "Case 10")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

Unknown $C11 was isolated from a sample of $C11food. The results from the experiments you have obtained so far are: (if: $notebookC11's length > 0)[\ (for: each _index, ...(range: 1, $notebookC11's length))[_index) (print: $notebookC11's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S11-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S11-text")[(set:$t to it + time)]] (if: (history:) contains "WGS11-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS11-Results")[(set:$t to it + time)]] (if: $C11soln is 0)[(link-reveal-goto: "Identify unknown $C11", "identify11")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C11 - do you want to check your answer again?", "identify11")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C11", "C11hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C11", "Case 11")[(set:$t to it + time)]

MacConkey agar is a selective and differential medium commonly supplemented with lactose. Other sugars are sometimes used. For sorbitol MacConkey agar (SMAC), the lactose is replaced with sorbitol. The crystal violet and bile salts inhibit growth of Gram-positive bacteria and some fastidious Gram negative bacteria. Phenol red is used as a pH indicator to detect sorbitol fermentation. (link: "Click to see the MacConkey/sorbitol agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Peptone</td> <td>20.0</td> </tr> <tr> <td>Sorbitol</td> <td>10.0</td> </tr> <tr> <td>Bile salts</td> <td>5.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Neutral red</td> <td>0.075</td> </tr> <tr> <td>Agar</td> <td>12.0</td> </tr> </table> pH 7.4 ± 0.2 @ 25°C] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0813&c=UK&lang=EN" target="_blank">Read more about MacConkey/sorrbitol medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from streaking unknown $C1 on SMAC agar")[Unknown $C1 grows on MacConkey/sorbitol agar, producing colourless colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 grows on MacConkey/sorbitol agar, producing colourless colonies")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from streaking unknown $C2 on SMAC agar")[You should consider whether streaking unknown $C2 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from streaking unknown $C3 on SMAC agar")[Unknown $C3 grows on SMAC agar, producing pink colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 grows on MacConkey/sorbitol agar, producing pink colonies")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from streaking unknown $C4 on SMAC agar")[You should consider whether streaking unknown $C4 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from streaking unknown $C5 on SMAC agar")[You should consider whether streaking unknown $C5 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from streaking unknown $C6 on SMAC agar")[You should consider whether streaking unknown $C6 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from streaking unknown $C7 on SMAC agar")[You should consider whether streaking unknown $C7 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from streaking unknown $C8 on SMAC agar")[Unknown $C8 grows on SMAC agar, producing colourless colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 grows on SMAC agar, producing colourless colonies")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from streaking unknown $C9 on SMAC agar")[You should consider whether streaking unknown $C9 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from streaking unknown $C10 on SMAC agar")[You should consider whether streaking unknown $C10 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from streaking unknown $C11 on SMAC agar")[You should consider whether streaking unknown $C11 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from streaking unknown $C12 on SMAC agar")[You should consider whether streaking unknown $C12 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from streaking unknown $C13 on SMAC agar")[Unknown $C13 ''does not grow'' on SMAC agar. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 does not grow on SMAC agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from streaking unknown $C14 on SMAC agar")[You should consider whether streaking unknown $C14 on SMAC agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on MacConkey/sorbitol agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from streaking unknown $C15 on SMAC agar")[Unknown $C15 grows on SMAC agar, producing colourless colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 grows on SMAC agar, producing colourless colonies.")) (set: $clicks to it + 1)]]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C1", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C1", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C1", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C1", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C1", "Case 1")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C2", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C2", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C2", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C2", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C2", "Case 2")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C3", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C3", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C3", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C3", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C3", "Case 3")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C4", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C4", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C4", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C4", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C4", "Case 4")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C5", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C5", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C5", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C5", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C5", "Case 5")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C6", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C6", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C6", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C6", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C6", "Case 6")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C7", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C7", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C7", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C7", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C7", "Case 7")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C8", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C8", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C8", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C8", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C8", "Case 8")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C9", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C9", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C9", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C9", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C9", "Case 1")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C10", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C10", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C10", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C10", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C10", "Case 10")[(set:$t to it + time)]

Many different protocols are available to stain and visualise bacterial capsules. Your lab uses the simple India ink stain, a negative stain that highlights capsules around the cells. The cells are mixed with India ink on a glass slide, and visualised under the microscope. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria produce a capsule, a white halo will appear around the cells. If the bacteria are do not produce a capsule, no halo will appear around the cells.] (b4r:"solid")[<center><img alt="encapsulated bacterial cells" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/capsule.jpg"></center> Figure 1. India ink-stained encapsulated bacilli. Cells were stained and visualised at 1000X magnification with a light microscope. Image credit: <a href="https://phil.cdc.gov/Details.aspx?pid=1882" target="_blank">CDC PHIL</a>] <a href="https://asm.org/ASM/media/Protocol-Images/Capsule-Stain-Protocols.pdf?ext=.pdf" target="_blank">Read more about the capsule stain</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "microscope1")[ (link: "Click to see the India ink stain results for unknown $C1")[When you examine a India ink-stained sample of unknown $C1 under the microscope, you observe ''rods surrounded by white halos'' Back to the (link-reveal-goto: "microscope?", "microscope1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "A capsule stain of unknown $C1 revealed rods with white halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope2")[ (link: "Click to see the India ink stain results for unknown $C2")[When you examine a India ink-stained sample of unknown $C2 under the microscope, you observe ''rods with no halos'' Back to the (link-reveal-goto: "microscope?", "microscope2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "A capsule stain of unknown $C2 revealed rods with no halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope3")[ (link: "Click to see the India inkstain results for unknown $C3")[When you examine a India ink-stained sample of unknown $C3 under the microscope, you observe ''rods with no halo'' Back to the (link-reveal-goto: "microscope?", "microscope3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "A capsule stain of unknown $C3 revealed rods with no halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope4")[ (link: "Click to see the India ink stain results for unknown $C4")[When you examine a India ink-stained sample of unknown $C4 under the microscope, you observe ''curved rods with no halo'' Back to the (link-reveal-goto: "microscope?", "microscope4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "A capsule stain of unknown $C4 revealed curved rods with no halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope5")[ (link: "Click to see the India ink stain results for unknown $C5")[When you examine a India ink-stained sample of unknown $C5 under the microscope, you observe ''rods with no halo'' Back to the (link-reveal-goto: "microscope?", "microscope5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "A capsule stain of unknown $C5 revealed rods with white halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope6")[ (link: "Click to see the India ink stain results for unknown $C6")[When you examine a India ink-stained sample of unknown $C6 under the microscope, you observe ''curved rods with halos'' Back to the (link-reveal-goto: "microscope?", "microscope6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "A capsule stain of unknown $C6 revealed curved rods with white halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope7")[ (link: "Click to see the India ink stain results for unknown $C7")[When you examine a India ink-stained sample of unknown $C7 under the microscope, you observe ''cocci with no halos'' Back to the (link-reveal-goto: "microscope?", "microscope7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "A capsule stain of unknown $C7 revealed cocci with no halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope8")[ (link: "Click to see the India ink stain results for unknown $C8")[When you examine a India ink-stained sample of unknown $C8 under the microscope, you observe ''rods with no halos'' Back to the (link-reveal-goto: "microscope?", "microscope8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "A capsule stain of unknown $C8 revealed rods with no halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope9")[ (link: "Click to see the India ink stain results for unknown $C9")[When you examine a India ink-stained sample of unknown $C9 under the microscope, you observe ''rods with halos'' Back to the (link-reveal-goto: "microscope?", "microscope9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "A capsule stain of unknown $C9 revealed rods with white halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope10")[ (link: "Click to see the India ink stain results for unknown $C10")[When you examine a India ink-stained sample of unknown $C10 under the microscope, you observe ''rods with no halos'' Back to the (link-reveal-goto: "microscope?", "microscope10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "A capsule stain of unknown $C10 revealed rods with no halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope11")[ (link: "Click to see the India ink stain results for unknown $C11")[When you examine a India ink-stained sample of unknown $C11 under the microscope, you observe ''rods with no halos'' Back to the (link-reveal-goto: "microscope?", "microscope11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "A capsule stain of unknown $C11 revealed rods with no halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope12")[ (link: "Click to see the India ink stain results for unknown $C12")[When you examine a India ink-stained sample of unknown $C12 under the microscope, you observe ''rods with no halos'' Back to the (link-reveal-goto: "microscope?", "microscope12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "A capsule stain of unknown $C12 revealed rods with no halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope13")[ (link: "Click to see the India ink stain results for unknown $C13")[When you examine a India ink-stained sample of unknown $C13 under the microscope, you observe ''coccobacilli with no halos'' Back to the (link-reveal-goto: "microscope?", "microscope13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "A capsule stain of unknown $C13 revealed coccobacilli with no halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope14")[ (link: "Click to see the India ink stain results for unknown $C14")[When you examine a India ink-stained sample of unknown $C14 under the microscope, you observe ''curved rods with halos'' Back to the (link-reveal-goto: "microscope?", "microscope14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "A capsule stain of unknown $C14 revealed curved rods with white halos")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope15")[ (link: "Click to see the India ink stain results for unknown $C15")[When you examine a India ink-stained sample of unknown $C15 under the microscope, you observe ''rods with halos'' Back to the (link-reveal-goto: "microscope?", "microscope15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "A capsule stain of unknown $C15 revealed rods with white halos")) (set: $clicks to it + 1)]]

Many different protocols are available to stain and visualise bacterial endospores. Your lab uses the Schaeffer-Fulton method, sometimes called a malachite green stain. The cells are fixed on a glass slide, and stained with malachite green (steamed over a container of boiling water), then counter-stained with safranin and visualised under the microscope. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[Vegetative cells will appear pink/red. Endospores will appear bright green.] (b4r:"solid")[<center><img alt="encapsulated bacterial cells" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/malachite.jpg"></center> Figure 1. Malachite green-stained endospore-forming bacteria. Cells were stained and visualised at 1000X magnification with a light microscope. Image credit: <a href="https://phil.cdc.gov/Details.aspx?pid=1931" target="_blank">CDC PHIL</a>] <a href="https://asm.org/ASM/media/Protocol-Images/Endospore-Stain-Protocol.pdf?ext=.pdf" target="_blank">Read more about this stain</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "microscope1")[ (link: "Click to see the Malachite green stain results for unknown $C1")[When you examine a Malachite green-stained sample of unknown $C1 under the microscope, you observe ''pink rods''. Back to the (link-reveal-goto: "microscope?", "microscope1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "A Malachite green stain of unknown $C1 revealed pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope2")[ (link: "Click to see the Malachite green stain results for unknown $C2")[When you examine a Malachite green-stained sample of unknown $C2 under the microscope, you observe ''pink rods''. Back to the (link-reveal-goto: "microscope?", "microscope2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "A Malachite green stain of unknown $C2 revealed pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope3")[ (link: "Click to see the Malachite green stain results for unknown $C3")[When you examine a Malachite green-stained sample of unknown $C3 under the microscope, you observe ''pink rods''. Back to the (link-reveal-goto: "microscope?", "microscope3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "A Malachite green stain of unknown $C3 revealed pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope4")[ (link: "Click to see the Malachite green stain results for unknown $C4")[When you examine a Malachite green-stained sample of unknown $C4 under the microscope, you observe ''pink curved rods''. Back to the (link-reveal-goto: "microscope?", "microscope4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "A Malachite green stain of unknown $C4 revealed pink curved rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope5")[ (link: "Click to see the Malachite green stain results for unknown $C5")[When you examine a Malachite green-stained sample of unknown $C5 under the microscope, you observe ''pink rods and bright green circles''. Back to the (link-reveal-goto: "microscope?", "microscope5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "A Malachite green stain of unknown $C5 revealed pink rods and bright green circles")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope6")[ (link: "Click to see the Malachite green stain results for unknown $C6")[When you examine a Malachite green-stained sample of unknown $C6 under the microscope, you observe ''pink curved rods''. Back to the (link-reveal-goto: "microscope?", "microscope6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "A Malachite green stain of unknown $C6 revealed pink curved rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope7")[ (link: "Click to see the Malachite green stain results for unknown $C7")[When you examine a Malachite green-stained sample of unknown $C7 under the microscope, you observe ''pink cocci''. Back to the (link-reveal-goto: "microscope?", "microscope7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "A Malachite green stain of unknown $C7 revealed pink cocci")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope8")[ (link: "Click to see the Malachite green stain results for unknown $C8")[When you examine a Malachite green-stained sample of unknown $C8 under the microscope, you observe ''pink rods''. Back to the (link-reveal-goto: "microscope?", "microscope8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "A Malachite green stain of unknown $C8 revealed pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope9")[ (link: "Click to see the Malachite green stain results for unknown $C9")[When you examine a Malachite green-stained sample of unknown $C9 under the microscope, you observe ''pink rods''. Back to the (link-reveal-goto: "microscope?", "microscope9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "A Malachite green stain of unknown $C9 revealed pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope10")[ (link: "Click to see the Malachite green stain results for unknown $C10")[When you examine a Malachite green-stained sample of unknown $C10 under the microscope, you observe ''short pink rods''. Back to the (link-reveal-goto: "microscope?", "microscope10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "A Malachite green stain of unknown $C10 revealed short pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope11")[ (link: "Click to see the Malachite green stain results for unknown $C11")[When you examine a Malachite green-stained sample of unknown $C11 under the microscope, you observe ''pink rods; some pink rods with green circles''. Back to the (link-reveal-goto: "microscope?", "microscope11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "A Malachite green stain of unknown $C11 revealed pink rods, and some pink rods with green circles")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope12")[ (link: "Click to see the Malachite green stain results for unknown $C12")[When you examine a Malachite green-stained sample of unknown $C12 under the microscope, you observe ''pink rods''. Back to the (link-reveal-goto: "microscope?", "microscope12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "A Malachite green stain of unknown $C12 revealed pink rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope13")[ (link: "Click to see the Malachite green stain results for unknown $C13")[When you examine a Malachite green-stained sample of unknown $C13 under the microscope, you observe ''pink coccobacilli''. Back to the (link-reveal-goto: "microscope?", "microscope13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "A Malachite green stain of unknown $C13 revealed pink coccobacilli")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope14")[ (link: "Click to see the Malachite green stain results for unknown $C14")[When you examine a Malachite green-stained sample of unknown $C14 under the microscope, you observe ''pink curved rods''. Back to the (link-reveal-goto: "microscope?", "microscope14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "A Malachite green stain of unknown $C14 revealed pink curved rods")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "microscope15")[ (link: "Click to see the Malachite green stain results for unknown $C15")[When you examine a Malachite green-stained sample of unknown $C15 under the microscope, you observe ''pink rods''. Back to the (link-reveal-goto: "microscope?", "microscope15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "A Malachite green stain of unknown $C15 revealed pink rods")) (set: $clicks to it + 1)]]

Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar is a selective and differential medium. The selective elements are Polymyxin, Acriflavin, Lithium chloride, and Ceftazidime. The differential elements to this medium are indicators for aesculin hydrolysis (aesculin and ferrous iron) and mannitol fermentation (mannitol and phenol red). This medium is commonly used for the isolation of Listeria monocytogenes. (link: "Click to see the PALCAM agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Columbia Blood Agar base</td> <td>39.0</td> </tr> <tr> <td>Yeast extract</td> <td>3.0</td> </tr> <tr> <td>Glucose</td> <td>0.5</td> </tr> <tr> <td>Aesculin</td> <td>0.8</td> </tr> <tr> <td>Ferric ammonium citrate</td> <td>0.5</td> </tr> <tr> <td>Mannitol</td> <td>10.0</td> </tr> <tr> <td>Phenol red</td> <td>0.08</td> </tr> <tr> <td>Lithium chloride</td> <td>15.0</td> </tr> </table> pH 7.2 ± 0.2 @ 25°C; PALCAM selective supplement (Polymyxin B, Acriflavine hydrochloride, Ceftazidime) added after autoclaving] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0877&c=UK&lang=EN" target="_blank">Read more about PALCAM medium</a> {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on PALCAM agar")[You should consider whether streaking unknown $C1 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not grow unknown $C1 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on PALCAM agar")[Unknown $C2 grows on PALCAM agar, producing brown/black colonies with a black halo. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 grows on PALCAM agar, producing brown/black colonies with a black halo.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on PALCAM agar")[You should consider whether streaking unknown $C3 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not grow unknown $C3 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on PALCAM agar")[You should consider whether streaking unknown $C4 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on PALCAM agar")[You should consider whether streaking unknown $C5 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on PALCAM agar")[You should consider whether streaking unknown $C6 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 on PALCAM agar")[Unknown $C7 grows poorly on PALCAM agar, producing yellow colonies surrounded by yellow halos. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 grows poorly on PALCAM agar, producing yellow colonies surrounded by yellow halos.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on PALCAM agar")[You should consider whether streaking unknown $C8 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not grow unknown $C8 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on PALCAM agar")[You should consider whether streaking unknown $C9 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on PALCAM agar")[You should consider whether streaking unknown $C10 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 on PALCAM agar")[You should consider whether streaking unknown $C11 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on PALCAM agar")[You should consider whether streaking unknown $C12 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on PALCAM agar")[You should consider whether streaking unknown $C13 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on PALCAM agar")[You should consider whether streaking unknown $C14 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on PALCAM agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on PALCAM agar")[You should consider whether streaking unknown $C15 on PALCAM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not grow unknown $C15 on PALCAM agar.")) (set: $clicks to it + 1)]]

Various tests can be used to detect whether bacteria can produce hydrogen sulphide (H2S) - most are based on the fact that H2S will react with certain heavy metal salts to produce an insoluble black precipitate. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are H2S)+, a black precipitate will be observed. If the bacteria are H2S)-, no precipitate will be observed (no colour change).] (b4r:"solid")[<center><img alt="example of positive and negative oxidase test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/TSI.jpg"></center> Figure 1. Hydrogen sulphide production. Example of positive (left) and negative (right) hydrogen sulphide test results. Bacteria were grown on Triple Sugar Iron Agar, which also tests for sugar fermentation. CDC Public Health Image Library (5158).] <a href="link" target="_blank">Read more about the (name) test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform a H2S production test on unknown $C1")[Unknown $C1 is H2S ''negative''.OR You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 is....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform a H2S production test on unknown $C2")[Unknown $C2 is H2S ''negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "Unknown $C2 is H2S negative.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform a H2S production test on unknown $C3")[Unknown $C3 is H2S ''positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 is H2S positive.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform a H2S production test on unknown $C4")[Unknown $C4 is H2S ''negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 is H2S negative.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform a H2S production test on unknown $C5")[You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 is H2S ....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform a H2S production test on unknown $C6")[Unknown $C6 is H2S ''negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 is H2S negative.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform a H2S production test on unknown $C7")[You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 is H2S ...")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform a H2S production test on unknown $C8")[Unknown $C8 is H2S ''negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 is H2S negative.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform a H2S production test on unknown $C9")[Unknown $C9 is H2S ''positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 is H2S positive.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform a H2S production test on unknown $C10")[Unknown $C10 is H2S''negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 is H2S negative.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform a H2S production test on unknown $C11")[Unknown $C11 is H2S''positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C11 is H2S positive.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform a H2S production test on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 is H2S .....")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform a H2S production test on unknown $C13")[Unknown $C13 is H2S''positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 is H2S positive.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform a H2S production test on unknown $C14")[Unknown $C14 is H2S''negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 is H2S negative.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform a H2S production test on unknown $C15")[Unknown $C15 is H2S ''negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 is H2S negative.")) (set: $clicks to it + 1)]]

Hektoen enteric agar (HEA) is a selective and differential medium with indicators for sugar fermentation and hydrogen sulphide production (and therefore often used to isolate and differentiate Salmonella and Shigella spp. from clinical samples. Bile salts inhibit the growth of most Gram-positive and some Gram-negative organisms. The sugars lactose, sucrose, and salicin are present, and their fermentation can be detected due to the pH indicators bromothymol blue and acid fuchsin. Ferric iron is present for the detection of H2S production. (b4r:"solid")[<center><img alt="example of growth on HEA agar" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/HEA.jpg"></center> Figure 1.Shigella sonnei grown on a Hektoen Enteric Agar (HEA) plate for 48 hours at 37°C. Image credit: <a href="https://phil.cdc.gov/Details.aspx?pid=17186" target="_blank">CDC PHIL</a>] (link: "Click to see the HEA medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Proteose peptone</td> <td>12.0</td> </tr> <tr> <td>Yeast extract</td> <td>3.0</td> </tr> <tr> <td>Lactose</td> <td>12.0</td> </tr> <tr> <td>Sucrose</td> <td>12.0</td> </tr> <tr> <td>Salicin</td> <td>2.0</td> </tr> <tr> <td>Bile salts No. 3</td> <td>9.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Sodium thiosulphate</td> <td>5.0</td> </tr> <tr> <td>Ammonium ferric citrate</td> <td>1.5</td> </tr> <tr> <td>Acid fuchsin</td> <td>0.1</td> </tr> <tr> <td>Bromothymol blue</td> <td>0.065</td> </tr> <tr> <td>Agar</td> <td>14.0</td> </tr> </table> pH 7.5 @ 25°C] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0419&c=UK&lang=EN" target="_blank">Read more about HEA</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on HEA")[Unknown $C1 grows on HEA, producing pinkish-coloured colonies surrounded by a ring of bile precipitation. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 grows on HEA, producing pinkish-coloured colonies surrounded by a ring of bile precipitation.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on HEA")[You should consider whether streaking unknown $C2 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on HEA.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on HEA")[Unknown $C3 grows on HEA, producing blueish-green colonies with black centres. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "Unknown $C3 grows on HEA, producing blueish-green colonies with black centres")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on HEA")[You should consider whether streaking unknown $C4 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on HEA")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on HEA")[You should consider whether streaking unknown $C5 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on HEA.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on HEA")[You should consider whether streaking unknown $C6 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on HEA")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 on HEA")[You should consider whether streaking unknown $C7 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on HEA")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on HEA")[Unknown $C8 grows on HEA, producing green colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 grows on HEA, producing green colonies")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on HEA")[You should consider whether streaking unknown $C9 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on HEA")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on HEA")[Unknown $C10 grows on HEA, producing blueish-greenish coloured colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 grows on HEA, producing blueish-greenish coloured colonies.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 on HEA")[You should consider whether streaking unknown $C11 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on HEA")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on HEA")[You should consider whether streaking unknown $C12 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on HEA")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on HEA")[You should consider whether streaking unknown $C13 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on HEA")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on HEA")[You should consider whether streaking unknown $C14 on HEA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on HEA")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on HEA")[Unknown $C15 grows on HEA, producing pinkish-coloured colonies surrounded by a ring of bile precipitation. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 grows on HEA, producing pinkish-coloured colonies surrounded by a ring of bile precipitation.")) (set: $clicks to it + 1)]]

Mannitol Egg Yolk Polymyxin Agar (MYP agar) is a selective and differential growth medium, useful for detecting mannitol fermentation and lecithinase activity. It is commonly used to detect the presence of Bacillus cereus associated with food poisoning outbreaks. (link: "Click to see the MYP agar medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Meat extract</td> <td>1.0</td> </tr> <tr> <td>Peptone</td> <td>10.0</td> </tr> <tr> <td>Mannitol</td> <td>10.0</td> </tr> <tr> <td>Sodium chloride</td> <td>10.0</td> </tr> <tr> <td>Phenol Red</td> <td>0.025</td> </tr> <tr> <td>Agar</td> <td>12.0</td> </tr> </table> pH 7.2 ± 0.2 @ 25°C, polymyxin added after autoclaving.] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0929&c=UK&lang=EN" target="_blank">Read more about MYP agar</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on MYP agar")[You should consider whether streaking unknown $C1 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not grow unknown $C1 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on MYP agar")[You should consider whether streaking unknown $C2 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on MYP agar")[You should consider whether streaking unknown $C3 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not grow unknown $C3 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on MYP agar")[You should consider whether streaking unknown $C4 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on MYP agar")[Unknown $C5 grows on MYP agar and produces bright pink, rough, dry-looking colonies surrounded by a ring of precipitation (opaque zone surrounding the colonies). Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "Unknown $C5 grows on MYP agar and produces bright pink, rough, dry-looking colonies surrounded by a ring of precipitation (opaque zone surrounding the colonies).")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on MYP agar")[You should consider whether streaking unknown $C6 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 on MYP agar")[Unknown $C7 grows on MYP agar and produces yellow colonies surrounded by a ring of precipitation (opaque zone surrounding the colonies). Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "Unknown $C7 grows on MYP agar and produces yellow colonies surrounded by a ring of precipitation (opaque zone surrounding the colonies).")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on MYP agar")[You should consider whether streaking unknown $C8 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not grow unknown $C8 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on MYP agar")[You should consider whether streaking unknown $C9 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on MYP agar")[You should consider whether streaking unknown $C10 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 on MYP agar")[You should consider whether streaking unknown $C11 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on MYP agar")[You should consider whether streaking unknown $C12 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on MYP agar")[You should consider whether streaking unknown $C13 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on MYP agar")[You should consider whether streaking unknown $C14 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on MYP agar.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on MYP agar")[You should consider whether streaking unknown $C15 on MYP agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not grow unknown $C15 on MYP agar.")) (set: $clicks to it + 1)]]

Thiosulfate-citrate-bile salts-sucrose is a selective and differential medium. The bile salts inhibit the growth of Gram positive bacteria, and the relatively high pH and high sodium chloride concentration help to inhibit the growth of most non-Vibrio species. Sucrose fermentation can be detected because of the bromothymol blue pH indicator. H2S production can be detected due to the presence of thiosulphate and ferric iron. (link: "Click to see the TCBS agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>5.0</td> </tr> <tr> <td>Peptone</td> <td>10.0</td> </tr> <tr> <td>Sodium thiosulphate</td> <td>10.0</td> </tr> <tr> <td>Sodium citrate</td> <td>10.0</td> </tr> <tr> <td>Ox Bile</td> <td>8.0</td> </tr> <tr> <td>Sucrose</td> <td>20.0</td> </tr> <tr> <td>Sodium chloride</td> <td>10.0</td> </tr> <tr> <td>Ferric citrate</td> <td>1.0</td> </tr> <tr> <td>Bromothymol blue</td> <td>0.04</td> </tr> <tr> <td>Thymol blue</td> <td>0.04</td> </tr> <tr> <td>Agar</td> <td>14.0</td> </tr> </table> pH 8.6 ± 0.2 @ 25°C] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0333&c=UK&lang=EN" target="_blank">Read more about TCBS</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on TCBS agar")[You should consider whether streaking unknown $C1 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not grow unknown $C1 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on TCBS agar")[You should consider whether streaking unknown $C2 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on TCBS agar)")[You should consider whether streaking unknown $C3 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not grow unknown $C3 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on TCBS agar")[You should consider whether streaking unknown $C4 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on TCBS agar")[You should consider whether streaking unknown $C5 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on TCBS agar")[Unknown $C6 grows on TCBS medium, producing large (>2 mm diameter) ''green'' colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "Unknown $C6 grows on TCBS medium, producing large (>2 mm diameter) green colonies.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 on TCBS agar")[You should consider whether streaking unknown $C7 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on TCBS agar")[You should consider whether streaking unknown $C8 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not grow unknown $C8 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on TCBS agar")[You should consider whether streaking unknown $C9 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on TCBS agar")[You should consider whether streaking unknown $C10 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 on TCBS agar")[You should consider whether streaking unknown $C11 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on TCBS agar")[You should consider whether streaking unknown $C12 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on TCBS agar")[You should consider whether streaking unknown $C13 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on TCBS agar")[Unknown $C14 grows on TCBS medium, producing large (>2 mm diameter) ''yellow'' colonies Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "Unknown $C14 grows on TCBS medium, producing large (>2 mm diameter) yellow colonies")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on TCBS agar")[You should consider whether streaking unknown $C15 on TCBS agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not grow unknown $C15 on Thiosulfate-citrate-bile salts-sucrose (TCBS) agar")) (set: $clicks to it + 1)]]

Reinforced Clostridial Medium (RCM) is a growth medium used for anaerobes. It is made differential (DRCM) by the addition of sodium sulphite and ferric citrate, which allow the detection of sulphite-reducing clostridia. (link: "Click to see the DRCM medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>13.0</td> </tr> <tr> <td>Peptone</td> <td>10.0</td> </tr> <tr> <td>Glucose</td> <td>5.0</td> </tr> <tr> <td>Soluble starch</td> <td>1.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Sodium acetate</td> <td>3.0</td> </tr> <tr> <td>Cysteine hydrochloride</td> <td>0.5</td> </tr> <tr> <td>Agar</td> <td>0.5</td> </tr> </table> pH 6.8 ± 0.2 @ 25°C; filter-sterilised sodium sulphite and ferric citrate are added after autoclaving.] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0149&c=UK&lang=EN" target="_blank">Read more about DRCM</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 in DRCM")[You should consider whether streaking unknown $C1 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not grow unknown $C1 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 in DRCM")[You should consider whether streaking unknown $C2 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 in DRCM")[You should consider whether streaking unknown $C3 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not grow unknown $C3 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 in DRCM")[You should consider whether streaking unknown $C4 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 in DRCM")[You should consider whether streaking unknown $C5 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 in DRCM")[You should consider whether streaking unknown $C6 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 in DRCM")[You should consider whether streaking unknown $C7 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 in DRCM")[You should consider whether streaking unknown $C8 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not grow unknown $C8 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 in DRCM")[Unknown $C9 grows in DRCM; the culture is black. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C1 grows in DRCM; the culture is black.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 in DRCM)")[You should consider whether streaking unknown $C10 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 in DRCM)")[Unknown $C11 grows in DRCM; the culture is black. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C11 grows in DRCM; the culture is black")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 in DRCM)")[You should consider whether streaking unknown $C12 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 in DRCM)")[You should consider whether streaking unknown $C13 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 in DRCM)")[You should consider whether streaking unknown $C14 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on DRCM")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 in DRCM)")[You should consider whether streaking unknown $C15 in DRCM is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not grow unknown $C15 on DRCM")) (set: $clicks to it + 1)]]

Cefsulodin-Irgasan-Novobiocin (CIN) agar is a selective and differential medium used primarily for the isolation of Yersinia enterocolitica. Differentiation is based on mannitol fermentation and often results in a characteristic "bull's eye" appearance to mannitol-fermenting colonies.. Cefsulodin, Irgasan Novobiocin, and crystal violet inhibit the growth of Gram positive and many Gram negative bacteria. Sodium pyruvate helps to stimulate the growth of Yersinia spp. (link: "Click to see the CIN medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Special peptone</td> <td>20.0</td> </tr> <tr> <td>Yeast extract</td> <td>2.0</td> </tr> <tr> <td>Mannitol</td> <td>20.0</td> </tr> <tr> <td>Sodium pyruvate</td> <td>2.0</td> </tr> <tr> <td>Sodium chloride</td> <td>1.0</td> </tr> <tr> <td>Magnesium sulphate</td> <td>0.01</td> </tr> <tr> <td>Sodium desoxycholate</td> <td>0.5</td> </tr> <tr> <td>Neutral red</td> <td>0.03</td> </tr> <tr> <td>Crystal violet</td> <td>0.001</td> </tr> <tr> <td>Agar</td> <td>12.5</td> </tr> </table> pH 7.4 ± 0.2 @ 25°C,with the selective supplement (Cefsulodin, Irgasan, and Novobiocin) added after autoclaving.] <a href="https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/236/018/103871dat-ms.pdf" target="_blank">Read more about CIN medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on CIN agar")[You should consider whether streaking unknown $C1 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not try growing unknown $C1 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on CIN agar")[You should consider whether streaking unknown $C2 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not try growing unknown $C2 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on CIN agar")[You should consider whether streaking unknown $C3 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not try growing unknown $C3 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on CIN agar")[You should consider whether streaking unknown $C4 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not try growing unknown $C4 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on CIN agar")[You should consider whether streaking unknown $C5 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not try growing unknown $C5 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on CIN agar")[You should consider whether streaking unknown $C6 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not try growing unknown $C6 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 in/on (medium name)")[You should consider whether streaking unknown $C7 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not try growing unknown $C7 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on CIN agar")[You should consider whether streaking unknown $C8 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not try growing unknown $C8 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on CIN agar")[You should consider whether streaking unknown $C9 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not try growing unknown $C9 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on CIN agar")[Unknown $C10 grows on CIN agar, producing red "bull's eye" colonies with transparent borders. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "Unknown $C10 grows on CIN agar, producing red bull's eye colonies with transparent borders.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 on CIN agar")[You should consider whether streaking unknown $C11 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not try growing unknown $C1 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on CIN agar")[You should consider whether streaking unknown $C12 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not try growing unknown $C12 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on CIN agar")[You should consider whether streaking unknown $C13 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not try growing unknown $C13 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on CIN agar")[You should consider whether streaking unknown $C14 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not try growing unknown $C14 on CIN agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on CIN agar")[You should consider whether streaking unknown $C15 on CIN agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not try growing unknown $C15 on CIN agar")) (set: $clicks to it + 1)]]

(set: $clicks to it + 1) A lipase test measures the ability of an organism to break down fats (in this case, the triglyceride tributyrin; other oils can be used). Organisms are innoculated onto agar media containing peptone and yeast extract as energy/nutrient sources, and an emulsion of tributyrin. If the bacteria are lipase+, a clear zone (tributyrin degradation) will form around the colonies If the bacteria are lipase-, no clear zones will form <a href="https://himedialabs.com/TD/M157.pdf" target="_blank">Read more about the lipase test (Himedia)</a> {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to see the lipase test results for unknown $C1")[Unknown $C1 is lipase ''positive/negative''.OR You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to see the lipase test results for unknown $C2")[Unknown $C2 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem3")[(link: "Click to see the lipase test results for unknown $C3")[Unknown $C3 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C3 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to see the lipase test results for unknown $C4")[Unknown $C4 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to see the lipase test results for unknown $C5")[Unknown $C5 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to see the lipase test results for unknown $C6")[Unknown $C6 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C6 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to see the lipase test results for unknown $C7")[Unknown $C7 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to see the lipase test results for unknown $C8")[Unknown $C8 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C8 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to see the lipase test results for unknown $C9")[Unknown $C9 is lipase ''negative''. OR You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to see the lipase test results for unknown $C10")[Unknown $C10 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C10 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to see the lipase test results for unknown $C11")[Unknown $C11 is lipase ''positive''.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to see the lipase test results for unknown $C12")[Unknown $C12 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to see the lipase test results for unknown $C13")[Unknown $C13 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to see the lipase test results for unknown $C14")[Unknown $C14 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C14 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to see the lipase test results for unknown $C15")[Unknown $C15 is lipase ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C15 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)]]

Unknown $C12 was isolated from a sample of $C12food. The results from the experiments you have obtained so far are: (if: $notebookC12's length > 0)[\ (for: each _index, ...(range: 1, $notebookC12's length))[_index) (print: $notebookC12's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S12-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S12-text")[(set:$t to it + time)]] (if: (history:) contains "WGS12-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS12-Results")[(set:$t to it + time)]] (if: $C12soln is 0)[(link-reveal-goto: "Identify unknown $C12", "identify12")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C12 - do you want to check your answer again?", "identify12")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C12", "C12hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C12", "Case 12")[(set:$t to it + time)]

Unknown $C13 was isolated from a sample of $C13food. The results from the experiments you have obtained so far are: (if: $notebookC13's length > 0)[\ (for: each _index, ...(range: 1, $notebookC13's length))[_index) (print: $notebookC13's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S13-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S13-text")[(set:$t to it + time)]] (if: (history:) contains "WGS13-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS13-Results")[(set:$t to it + time)]] (if: $C13soln is 0)[(link-reveal-goto: "Identify unknown $C13", "identify13")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C13 - do you want to check your answer again?", "identify13")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C13", "C13hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C13", "Case 13")[(set:$t to it + time)]

Unknown $C14 was isolated from a sample of $C14food. The results from the experiments you have obtained so far are: (if: $notebookC14's length > 0)[\ (for: each _index, ...(range: 1, $notebookC14's length))[_index) (print: $notebookC14's (_index)) ] ] (else:)[You have not yet performed any experiments.] [ (if: (history:) contains "16S14-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S14-text")[(set:$t to it + time)]] (if: (history:) contains "WGS14-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS14-Results")[(set:$t to it + time)]] (if: $C14soln is 0)[(link-reveal-goto: "Identify unknown $C14", "identify14")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C14 - do you want to check your answer again?", "identify14")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C14", "C14hints")[(set:$t to it + time)]] ] (link-reveal-goto: "Go back to study the case overview for organism $C14", "Case 14")[(set:$t to it + time)]

Unknown $C15 was isolated from a sample of $C15food. The results from the experiments you have obtained so far are: (if: $notebookC15's length > 0)[\ (for: each _index, ...(range: 1, $notebookC15's length))[_index) (print: $notebookC15's (_index)) ] ] (else:)[You have not yet performed any experiments.] { (if: (history:) contains "16S15-1")[You have sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S15-text")[(set:$t to it + time)]] (if: (history:) contains "WGS15-1")[You have sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS15-Results")[(set:$t to it + time)]] (if: $C15soln is 0)[(link-reveal-goto: "Identify unknown $C15", "identify15")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C15 - do you want to check your answer again?", "identify15")[(set:$t to it + time)]] (if: $earnedclues > 0)[(link-reveal-goto: "Redeem a hint to help you identify unknown $C15", "C15hints")[(set:$t to it + time)]] } (link-reveal-goto: "Go back to study the case overview for organism $C15", "Case 15")[(set:$t to it + time)]

##Unknown $C11 You have isolated an organism in axenic culture from a sample of $C11food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C11 under the microscope", "microscope11")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C11 on different media", "plates11")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C11", "biochem11")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C11's 16S rRNA gene", "16S11")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C11's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S11-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S11-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C11's entire genome", "WGS11")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C11 is currently unavailable. ] (if: (history:) contains "WGS11-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS11-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C11 notebook (summary of previously obtained results/redeem earned hints)", "notebook11")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C11soln is 0)[(link-reveal-goto: "Identify unknown $C11", "identify11")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C11 - do you want to check your answer again?", "identify11")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C11?", "Hint0")[(set:$t to it + time)]]

##Unknown $C12 You have isolated an organism in axenic culture from a sample of $C12food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C12 under the microscope", "microscope12")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C12 on different media", "plates12")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C12", "biochem12")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C12's 16S rRNA gene", "16S12")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C12's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S12-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S12-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C12's entire genome", "WGS12")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C12 is currently unavailable. ] (if: (history:) contains "WGS12-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS12-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C12 notebook (summary of previously obtained results/redeem earned hints)", "notebook12")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C12soln is 0)[(link-reveal-goto: "Identify unknown $C12", "identify12")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C12 - do you want to check your answer again?", "identify12")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C12?", "Hint0")[(set:$t to it + time)]]

##Unknown $C13 You have isolated an organism in axenic culture from a sample of $C13food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C13 under the microscope", "microscope13")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C13 on different media", "plates13")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C13", "biochem13")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C13's 16S rRNA gene", "16S13")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C13's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S13-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S13-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C13's entire genome", "WGS13")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C13 is currently unavailable. ] (if: (history:) contains "WGS13-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS13-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C13 notebook (summary of previously obtained results/redeem earned hints)", "notebook13")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C13soln is 0)[(link-reveal-goto: "Identify unknown $C13", "identify13")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C13 - do you want to check your answer again?", "identify13")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C13?", "Hint0")[(set:$t to it + time)]]

##Unknown $C14 You have isolated an organism in axenic culture from a sample of $C14food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C14 under the microscope", "microscope14")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C14 on different media", "plates14")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C14", "biochem14")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C14's 16S rRNA gene", "16S14")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C14's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S14-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S14-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C14's entire genome", "WGS14")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C14 is currently unavailable. ] (if: (history:) contains "WGS14-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS1-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C14 notebook (summary of previously obtained results/redeem earned hints)", "notebook14")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C14soln is 0)[(link-reveal-goto: "Identify unknown $C14", "identify14")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C14 - do you want to check your answer again?", "identify14")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C14?", "Hint0")[(set:$t to it + time)]]

##Unknown $C15 You have isolated an organism in axenic culture from a sample of $C15food. Your task is to identify this organism. 🔬 (link-reveal-goto: "Look at unknown $C15 under the microscope", "microscope15")[(set:$t to it + time)] 🧫 (link-reveal-goto: "Grow unknown $C15 on different media", "plates15")[(set:$t to it + time)] 🧪 (link-reveal-goto: "Perform some biochemical tests on unknown $C15", "biochem15")[(set:$t to it + time)] { 🧬 (if: $16S is 1)[ (link-reveal-goto: "Sequence unknown $C15's 16S rRNA gene", "16S15")[ (set:$t to it + time) ] ] (else:)[ 🚫 Sequencing of unknown $C15's 16S rRNA gene is currently unavailable. ] (if: (history:) contains "16S15-1")[ You have already sequenced this unknown's 16S rRNA gene, do you want to (link-reveal-goto: "see the results again?", "16S15-text")[ (set:$t to it + time) ] ] 🧬 (if: $WGS is 1)[ (link-reveal-goto: "Sequence unknown $C15's entire genome", "WGS15")[ (set:$t to it + time) ] ] (else:)[ 🚫 Whole genome sequencing of unknown $C15 is currently unavailable. ] (if: (history:) contains "WGS15-1")[ You have already sequenced this unknown's genome, do you want to (link-reveal-goto: "see the results again?", "WGS15-Results")[ (set:$t to it + time) ] ] } 🕮 (link-reveal-goto: "Look at the unknown $C15 notebook (summary of previously obtained results/redeem earned hints)", "notebook15")[(set:$t to it + time)] (b4r:"solid")+(b4r-size:4)+(b4r-color:green)[(if: $C15soln is 0)[(link-reveal-goto: "Identify unknown $C15", "identify15")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have already identified unknown $C15 - do you want to check your answer again?", "identify15")[(set:$t to it + time)]]] (b4r:"solid")+(b4r-size:4)+(b4r-color:gray)[(link-reveal-goto: "Do you need a hint to help you identify unknown $C15?", "Hint0")[(set:$t to it + time)]]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C11", "16S11-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C11", "Case 11")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C12", "16S12-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C12", "Case 12")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C13", "16S13-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C13", "Case 13")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C14", "16S14-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C14", "Case 14")[(set:$t to it + time)]

Your lab only has enough money budgeted for ''one'' Sanger sequencing reaction. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my Sanger sequencing budget to sequence the 16S rRNA gene from organism $C15", "16S15-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C15", "Case 15")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C11, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C11", "16S11-text")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C12, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C12", "16S12-text")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C13, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C13", "16S13-text")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C14, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C14", "16S14-text")[(set:$t to it + time)]

{ (set: $clicks to it + 1) (set: $16S to 0) } To sequence the 16S rRNA gene from unknown $C15, you purify genomic DNA from this organism ... (after: 2s)[= and you select the universal 16S primers 27F and 1492R, and use these in a PCR with purified genomic DNA as the template. (after: 2s)[= You then run the PCR reaction on an agarose gel, and find that the PCR has produced a band of the expected size. <center><img alt="picture of agarose gel" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images//02-16Sgel.jpg"></center>(after: time + 2s)[= You cut the band out of the gel and purify this PCR product ... (after: time + 2s)[= send it off for Sanger sequencing ... (after: time + 2s)[= You have received confirmation that your samples have arrived at the sequencing facility .... (after: time + 2s)[= you check your e-mail to see if the samples have been sequenced ... (after: time + 2s)[= and finally receive an email from the sequencing facility ... (after: time + 2s)[= (link-reveal-goto: "Click to see the results from sequencing the 16S rRNA gene from unknown $C15", "16S15-text")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C11 has the following sequence: (font:"Courier New")[NNNNNNNGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCA AGTCGAGCGATGAAGCTTCCTTCGGGAAGTGGATTAGCGGCGGACGGGTGAGTAACACGT GGGTAACCTGCCTCAAAGTGGGGGATAGCCTTCCGAAAGGAAGATTAATACCGCATAATA TAAGAGAATCGCATGATTTTCTTATCAAAGATTTATTGCTTTGAGATGGACCCGCGGCGC ATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCAACGATGCGTAGCCGACCTGAGAGG GTGATCGGCCACATTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGG AATATTGCGCAATGGGGGAGACCCTGACGCAGCAACGCCGCGTGGGTGATGAAGGTCTTC GGATTGTAAAGCCCTGTTTTCTAGGACGATAATGACGGTACTAGAGGAGGAAGCCACGGC TAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCGAGCGTTGTCCGGATTTACTGG GCGTAAAGGGTGCGTAGGCGGATGTTTAAGTGGGATGTGAAATCCCCGGGCTTAACCTGG GGGCTGCATTCCAAACTGGATATCTAGAGTGCAGGAGAGGAAAGCGGAATTCCTAGTGTA GCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGT AACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCA CGCCGTAAACGATGGATACTAGGTGTAGGGGGTATCAACTCCCCCTGTGCCGCAGTTAAC ACAATAAGTATCCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGG GGGCCCGCACAAGCAGCGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCT GGACTTGACATCCCTTGCATAGCCTAGAGATAGGTGAAGCCCTTCGGGGCAAGGAGACAG GTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAACGAGC GCAACCCTTGTTATTAGTTGCTACCATTAAGTTGAGCACTCTAATGAGACTGCCTGGGTA ACCAGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCCAGGGCTACACA CGTGCTACAATGGTAGGTACAATAAGACGCAAGACCGTGAGGTGGAGCAAAACTTATAAA ACCTATCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGCTGGAGTTGCTAGTA ATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCCGTCA CACCATGAGAGCTGGTAACACCCGAAGTCCGTGAGGTAACCGTAAGGAGCCAGCGGCCGA AGGTGGGATTAGTGATTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGAGAACCTGCGGCT GGATCACCTCC] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C11 case notes?", "Case 11")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C12 has the following sequence: (font:"Courier New")[GTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACG GGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCT AATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGG ATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGT AGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGG GAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGG GGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTC GGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATA CGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGTGGTTTGTCGC GTTGTTCGTGAAATC] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C12 case notes?", "Case 12")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C13 has the following sequence: (font:"Courier New")[CATGGCTCAGAACGAACGCTGGCGGCAGGCTTAACACATGCAAGTCGAGCGCCCCGCAAGGGGAGCGGCA GACGGGTGAGTAACGCGTGGGAACGTACCATTTGCTACGGAATAACTCAGGGAAACTTGTGCTAATACCG TATGTGCCCTTCGGGGGAAAGATTTATCGGCAAATGATCGGCCCGCGTTGGATTAGCTAGTTGGTGGGGT AAAGGCTCACCAAGGCGACGATCCATAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACG GCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCC GCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCACCGGTGAAGATAATGACGGTAACCGGAGAA GAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGTTCGGATTTACTG GGCGTAAAGCGCACGTAGGCGGACTTTTAAGTCAGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCT TTGATACTGGAAGTCTTGAGTATGGTAGAGGTGAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATA TTCGGAGGAACACCAGTGGCGAAGGCGGCTCACTGGACCATTACTGACGCTGAGGTGCGAAAGCGTGGGG AGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATGTTAGCCGTCGGGGTGTTTACA CTTCGGTGGCGCAGCTAACGCATTAAACATTCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGG AATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGCAGAACCTTACCAG CCCTTGACATCCCGGTCGCGGTTAGTGGAGACACTATCCTTCAGTTAGGCTGGACCGGAGACAGGTGCTG CATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGCCCTTA GTTGCCAGCATTCAGTTGGGCACTCTAAGGGGACTGCCGGTGATAAGCCGAGAGGAAGGTGGGGATGACG TCAAGTCCTCATGGCCCTTACGGGCTGGGCTACACACGTGCTACAATGGTGGTGACAGTGGGCAGCGAGC ACGCGAGTGTGAGCTAATCTCCAAAAGCCATCTCAGTTCGGATTGCACTCTGCAACTCGAGTGCATGAAG TTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCC GTCACACCATGGGAGTTGGTTTTACCCGAAGGCGCTGTGCTAACCGCAAGGAGGCAGGCGACCACGGTAG GGTCAGCGACTGGGGTGAAGTCGTAACAAG] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C13 case notes?", "Case 13")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C14 has the following sequence: (font:"Courier New")[AGAGTTTGATNNTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGC GGCAGCACAGAGGAACTTGTTCCTTGGGTGGCGAGCGGCGGACGGGTGAGTAATGCCTGG GAAATTGCCCGGTAGAGGGGGATAACCATTGGAAACGATGGCTAATACCGCATAACCTCG CAAGAGCAAAGCAGGGGACCTTCGGGCCTTGCGCTACCGGATATGCCCAGGTGGGATTAG CTAGTTGGTGAGGTAAGGGCTCACCAAGGCGACGATCCCTAGCTGGTCTGAGAGGATGAT CAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATAT TGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTT GTAAAGTACTTTCAGTAGGGAGGAAGGTGGTTAAGTTAATACCTTAATCATTTGACGTTA CCTACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAA GCGTTAATCGGAATTACTGGGCGTAAAGCGCATGCAGGTGGTTTGTTAAGTCAGATGTGA AAGCCCTGGGCTCAACCTAGGAATCGCATTTGAAACTGACAAGCTAGAGTACTGTAGAGG GGGGTAGAATTTCAGGTGTAGCGGTGAAATGCGTAGAGATCTGAAGGAATACCGGTGGCG AAGGCGGCCCCCTGGACAGATACTGACACTCAGATGCGAAAGCGTGGGGAGCAAACAGGA TTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCTACTTGGAGGTTGTGCCCTAGAGG CGTGGCTTTCGGAGCTAACGCGTTAAGTAGACCGCCTGGGGAGTACGGTCGCAAGATTAA AACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGC AACGCGAAGAACCTTACCTACTCTTGACATCCAGAGAATCTAGCGGAGACGCTGGAGTGC CTTCGGGAGCTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTG GGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTGTTTGCCAGCACGTAATGGTGGGAA CTCCAGGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGACGACGTCAAGTCATCATG GCCCTTACGAGTAGGGCTACACACGTGCTACAATGGCGTATACAGAGGGCAGCGAATACC GCGAAGGTGGAGCGAATCTCACAAAGTACGTCGTAGTCCGGATTGGAGTCTGCAACTCGA CTCCATGAAGTCGGAATCGCTAGTAATCGCAAATCAGAATGTTGCGGTGAATACGTTCCC GGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGCTGCAAAAGAAGCAGGTAGTT TAACCTTCGGGAGGACGCTTGCCACTTTGTGGTTCATGACTGGGGTGAAGTCGTAACAAG GTAGCGCTAGGGGAACCTGGCGCTGGATCACCTCCTTT] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C14 case notes?", "Case 14")[(set:$t to it + time)]

The FASTA file containing the results from sequencing the 16S rRNA gene from $C15 has the following sequence: (font:"Courier New")[ATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTTCGAACGGTAACAGGGAGCAGCTTG CTGCTCTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGG GGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCTACGGACCAAAGTGGGGGAC CTTCGGGCCTCATGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGG CTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAG ACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCC TGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGG GAGGAAGGTGCTGTGGTTAATAACCACAGCAATTGACGTTACCCGCAGAAGAAGCACCGG CTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTG GGCGTAAAGCGCACGCAGGCGGTCTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTG GGAACTGCATTTGAAACTGGCAGGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGT AGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGA AGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCC ACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAAC GCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGG GGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCT GGTCTTGACATCCAGAGAATCCTGCAGAGATGCGGGAGTGCCTTCGGGAACTCTGAGACA GGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAG CGCAACCCTTATCCTTTGTTGCCAGCGGTTCGGCCGGGAACTCAAAGGAGACTGCCGGTG ATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTAC ACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCAT AAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTA GTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGT CACACCATGGGAGTGGGTTGCAAAAGAAGTARGTAGCTTAACCTTCGGGAGGGGCGCTTA CCACTTTGTGATTCATGACCTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGAA] (link-reveal-goto: "Do you need help interpreting these results?", "16S-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C15 case notes?", "Case 15")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C11", "WGS11-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C11", "Case 11")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C12", "WGS12-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C12", "Case 12")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C13", "WGS13-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C13", "Case 13")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C14", "WGS14-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C14", "Case 14")[(set:$t to it + time)]

Your lab only has enough money budgeted to sequence the whole genome of ''one'' organism. Are you sure you want to proceed? (link-reveal-goto: "Yes, use my WGS sequencing budget to sequence the whole genome of organism $C15", "WGS15-1")[(set:$t to it + time)] (link-reveal-goto: "No, go back to study the other data available for organism $C15", "Case 15")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C11 is: `NC_009495.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C11 case notes?", "Case 11")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C12 is: `NZ_LR699570.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C12 case notes?", "Case 12")[(set:$t to it + time)]

The closest match in the NCBI database to the first contig sequenced from unknown $C13 is: `NC_007618.1` The closest match in the NCBI database to the second contig sequenced from unknown $C13 is: `NC_007624.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C13 case notes?", "Case 13")[(set:$t to it + time)]

The closest match in the NCBI database to the first contig sequenced from unknown $C12 is: `NZ_CP043554.1` The closest match in the NCBI database to the second contig sequenced from unknown $C12 is: `NZ_CP043556.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C14 case notes?", "Case 14")[(set:$t to it + time)]

The closest match in the NCBI database to unknown $C15 is: `NZ_CP027107.1` (link-reveal-goto: "Do you need help interpreting these results?", "WGS-help")[(set:$t to it + time)] (link-reveal-goto: "Go back to the $C15 case notes?", "Case 15")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C11. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C11", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C11", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C11", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C11", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C11 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C11", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C11", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C11 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C11", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C11", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C11", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C11", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C11", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C11", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C11", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C11", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C11", "Case 11")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C12. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C12", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C12", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C12", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C12", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C12 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C12", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C12", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C12 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C12", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C12", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C12", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C12", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C12", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C12", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C12", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C12", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C12", "Case 12")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C13. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C13", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C13", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C13", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C13", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C13 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C13", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C13", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C13 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C13", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C13", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C13", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C13", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C13", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C13", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C13", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C13", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C13", "Case 13")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C14. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C14", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C14", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C14", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C14", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C14 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C14", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C14", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C14 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C14", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C14", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C14", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C14", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C14", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C14", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C14", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C14", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C14", "Case 14")[(set:$t to it + time)]

Your laboratory is set up and ready to perform a number of different biochemical assays that are useful for identifying unknown organisms. Click the appropriate link below to carry out a particular biochemical test on unknown $C15. (b4r:"solid")[Remember to choose your experiments wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform an alkaline phosphatase assay on organism $C15", "Alkaline phosphatase")[(set:$t to it + time)] (link-reveal-goto: "Perform amino acid decarboxylase tests on organism $C15", "Decarboxylase tests")[(set:$t to it + time)] (link-reveal-goto: "Perform a catalase test on organism $C15", "Catalase")[(set:$t to it + time)] (link-reveal-goto: "Perform a coagulase test on organism $C15", "Coagulase")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C15 to ferment different carbohydrates", "Carbohydrate Fermentations")[(set:$t to it + time)] (link-reveal-goto: "Perform a gelatinase test on organism $C15", "Gelatinase")[(set:$t to it + time)] (link-reveal-goto: "Perform a hippurate test on organism $C15", "Hippurate")[(set:$t to it + time)] (link-reveal-goto: "Test the ability of organism $C15 to produce H2S", "H2S production")[(set:$t to it + time)] (link-reveal-goto: "Perform an indole test on organism $C15", "Indole")[(set:$t to it + time)] (link-reveal-goto: "Perform a Methyl Red test on organism $C15", "Methyl Red")[(set:$t to it + time)] (link-reveal-goto: "Perform a niacin test on organism $C15", "Niacin")[(set:$t to it + time)] (link-reveal-goto: "Perform a Nitrate reduction test on organism $C15", "Nitrate reduction")[(set:$t to it + time)] (link-reveal-goto: "Perform an oxidase test on organism $C15", "Oxidase")[(set:$t to it + time)] (link-reveal-goto: "Perform a pyrazinamidase test on organism $C15", "PZase")[(set:$t to it + time)] (link-reveal-goto: "Perform a urease test on organism $C15", "Urease")[(set:$t to it + time)] (link-reveal-goto: "Perform a Voges-Proskauer test on organism $C15", "Voges-Proskauer")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C15", "Case 15")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C11 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C11 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C11 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C11", "Case 11")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C12 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C12 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C12 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C12", "Case 12")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C13 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C13 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C13 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C13", "Case 13")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C14 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C14 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C14 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C14", "Case 14")[(set:$t to it + time)]

Your laboratory is stocked with a number of different bacteriological growth media, including many selective and differential media useful for the identification of unknown organisms. Using correct aseptic technique, you will streak unknown $C15 for single colonies on a set of appropriate media (selected based on other data you have collected about the unknown bacterium). Unless otherwise specified, you can assume that all plates will be incubated aerobically at 37°C. Click the appropriate link below to see some information about the medium and the phenotype(s) of the unknown when grown on that medium. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Grow organism $C15 on Bile Aesculin agar", "Bile aesculin agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Blood agar", "Blood agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Cefsulodin-Irgasan-Novobiocin (CIN)", "CIN")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Differential Reinforced Clostridial Medium (DRCM) agar", "DRCM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Enterobacter Sakazakii Isolation (ESIA)", "ESIA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Farrell's medium (FM)", "SDA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Hektoen Enteric Agar (HEA)", "Hektoen")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Lowenstein-Jensen (LJ) agar", "LJ")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on MacConkey/lactose agar (MAC)", "MacConkey/lactose agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on MacConkey/sorbitol agar (SMAC)", "SMAC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Mannitol Salt Agar (MSA)", "Mannitol Salt Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Motility agar", "Motility agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Mannitol Egg Yolk Polymyxin Agar (MYP) agar", "MYP")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Polymyxin Acriflavin Lithium-chloride Ceftazidime Aesculin Mannitol (PALCAM) agar", "PALCAM")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Simmons Citrate Agar", "Simmons Citrate Agar")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Thiosulfate-citrate-bile salts-sucrose (TCBS)", "TCBS")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Thioglycollate medium", "Thioglycollate medium")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Trypticase Soy Agar (TSA)", "TSA")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Tryptose Sulfite Cycloserine (TSC) agar", "TSC")[(set:$t to it + time)] (link-reveal-goto: "Grow organism $C15 on Xylose Lysine Deoxycholate (XLD) agar", "XLD")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C15", "Case 15")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C11", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C11", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C11", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C11", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C11", "Case 11")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C12", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C12", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C12", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C12", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C12", "Case 12")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C13", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C13", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C13", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C13", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C13", "Case 13")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C14", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C14", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C14", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C14", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C14", "Case 14")[(set:$t to it + time)]

Your laboratory has bright-field, phase contrast, and fluorescence microscopes, and the ability to perform a number of different staining techniques. Click the appropriate link below to see some information about the chosen stain and the phenotype(s) of the unknown when a sample was stained and examined under the microscope. (b4r:"solid")[Remember to make your choices wisely! In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on any experiments that will not help with the identification of your unknown.] (link-reveal-goto: "Perform a Gram stain on organism $C15", "Gram stain")[(set:$t to it + time)] (link-reveal-goto: "Perform an acid fast stain on organism $C15", "Acid fast stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a capsule stain on organism $C15", "Capsule stain")[(set:$t to it + time)] (link-reveal-goto: "Perform a malachite green stain on organism $C15", "Malachite green stain")[(set:$t to it + time)] (link-reveal-goto: "Go back to study the case overview for organism $C15", "Case 15")[(set:$t to it + time)]

(set: $adage to (prompt: "What is the binomial name of unknown organism $C11?", "correctly spelled and appropriately capitalised") ) (if: $adage is "Clostridium botulinum")[(set: $C11soln to it + 1)(set: $solved to it + (a: "Clostridium botulinum"))You have correctly identified unknown $C11, very well done! //Clostridium botulinum // is a Gram-positive, rod-shaped, anaerobic bacterium capable of forming spores. It produces botulinum toxin, a potent neurotoxin. It is most commonly associated with improperly canned or lightly preserved food, particularly foods with low acid content. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C11?", "Hint0")[(set:$t to it + time)]]

(set: $clementine to (prompt: "What is the binomial name of unknown organism $C12?", "correctly spelled and appropriately capitalised") ) (if: $clementine is "Mycobacterium bovis")[(set: $C12soln to it +1)(set: $solved to it + (a: "Mycobacterium bovis"))You have correctly identified unknown $C12, very well done! //Mycobacterium bovis// is an acid-fast, straight or curved rod-shaped bacterium. //M. bovis// can cause bovine tuberculosis, but can also cause tuberculosis-like infections in humans and other mammals. Infections in humans are most commonly associated with consumption of unpasteurized dairy products such as "raw" milk. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C12?", "Hint0")[(set:$t to it + time)]]

(set: $fortitude to (prompt: "What is the binomial name of unknown organism $C13?", "correctly spelled and appropriately capitalised") ) (if: $fortitude is "Brucella abortus")[(set: $C13soln to it +1)(set: $solved to it + (a: "Brucella abortus"))You have correctly identified unknown $C13, very well done! //Brucella abortus // is a Gram-negative, non-spore forming, aerobic bacterium that can cause brucellosis. Humans can contract brucellosis through contact with infected animals (e.g., sheep, cattle), or consumption of contaminated, undercooked meat or unpasteurized dairy products. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C13?", "Hint0")[(set:$t to it + time)]]

(set: $coffeecup to (prompt: "What is the binomial name of unknown organism $C14?", "correctly spelled and appropriately capitalised") ) (if: $coffeecup is "Vibrio cholerae")[(set: $C14soln to it +1)(set: $solved to it + (a: "Vibrio cholerae"))You have correctly identified unknown $C14, very well done! //Vibrio cholerae // is a Gram-negative, typically comma-shaped, facultative anaerobe that can cause cholera. Transmission is typically through the faecal-oral route, e.g. consumption of contaminated food or water. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer. (link-reveal-goto: "Do you need a hint to help you identify unknown $C14?", "Hint0")[(set:$t to it + time)]]

(set: $outrage to (prompt: "What is the binomial name of unknown organism $C15?", "correctly spelled and appropriately capitalised") ) (if: $outrage is "Cronobacter sakazakii")[(set: $C15soln to it +1)(set: $solved to it + (a: "Cronobacter sakazakii"))You have correctly identified unknown $C15, very well done! //Cronobacter sakazakii // is a Gram-negative, rod-shaped bacterium notable for its xerotolerance. //C. sakazakii// infections are typically associated with dried/powdered foods (such as powdered infant formula) and can be especially serious in infants. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else-if: $outrage is "Enterobacter sakazakii")[(set: $C15soln to it +1)You have correctly identified unknown $C15, very well done! //Cronobacter sakazakii // is a Gram-negative, rod-shaped bacterium notable for its xerotolerance. //C. sakazakii// infections are typically associated with dried/powdered foods (such as powdered infant formula) and can be especially serious in infants. --- Please click (link-reveal-goto: "here", "ident1cont")[(set:$t to it + time)] to check your progress toward escaping the room, or select another case to solve from the menu.] (else:)[That is not the correct answer.(link-reveal-goto: "Do you need a hint to help you identify unknown $C15?", "Hint0")[(set:$t to it + time)]]C

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the urease test result for this organism. (set: $hintsC11 to it + (a: "Consider the urease test result for this organism. "))] (else-if: visits is 2)[ Hint: Consider the phenotype of this organism on blood agar. (set: $hintsC11 to it + (a: "Consider the phenotype of this organism on blood agar. "))] (else-if: visits is 3)[ Hint: Consider the oxygen requirements of this organism. (set: $hintsC11 to it + (a: "Consider the oxygen requirements of this organism. "))] (else-if: visits is 4)[ Hint: Consider the malachite green stain results for this organism. (set: $hintsC11 to it + (a: "Consider the malachite green stain results for this organism."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on TSC medium. (set: $hintsC11 to it + (a: "Consider the phenotype of this organism on TSC medium."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on DRCM medium. (set: $hintsC11 to it + (a: "Consider the phenotype of this organism on DRCM medium."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C11", "Case 11")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the ability of this organism to reduce nitrate. (set: $hintsC12 to it + (a: "Consider the ability of this organism to reduce nitrate."))] (else-if: visits is 2)[ Hint: Consider the pyrazinamidase test result for this organism. (set: $hintsC12 to it + (a: "Consider the pyrazinamidase test result for this organism."))] (else-if: visits is 3)[ Hint: Consider the niacin test result for this organism. (set: $hintsC12 to it + (a: "Consider the niacin test result for this organism. "))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC12 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the acid fast stain result for this organism. (set: $hintsC12 to it + (a: "Consider the acid fast stain result for this organism."))] (else-if: visits is 5)[ Hint: Consider the growth of this organism on LJ medium. (set: $hintsC12 to it + (a: "Consider the growth of this organism on LJ medium."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C12", "Case 12")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC13 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the ability of this organism to produce hydrogen sulphide. (set: $hintsC13 to it + (a: "Consider the ability of this organism to produce hydrogen sulphide. "))] (else-if: visits is 3)[ Hint: Consider the urease test result for this organism. (set: $hintsC13 to it + (a: "Consider the urease test result for this organism. "))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC13 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on MacConkey agar and blood agar. (set: $hintsC13 to it + (a: "Consider the phenotype of this organism on MacConkey agar and blood agar."))] (else-if: visits is 5)[ Hint:Consider the growth of this organism on Farrell's medium. (set: $hintsC13 to it + (a: "Consider the growth of this organism on Farrell's medium."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C13", "Case 13")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC14 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the phenotype of this organism in motility agar. (set: $hintsC14 to it + (a: "Consider the phenotype of this organism in motility agar. "))] (else-if: visits is 3)[ Hint: Consider the results of the Voges-Proskauer test. (set: $hintsC14 to it + (a: "Consider the results of the Voges-Proskauer test. "))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC14 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the cell shape of this unknown. (set: $hintsC14 to it + (a: "Consider the cell shape of this unknown."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on TCBS agar. (set: $hintsC14 to it + (a: "Consider the phenotype of this organism on TCBS agar."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C14", "Case 14")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC15 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the ability of this organism to ferment carbohydrates. (set: $hintsC15 to it + (a: "Consider the ability of this organism to ferment carbohydrates. "))] (else-if: visits is 3)[ Hint: The IMViC tests (indole, methyl red, Voges Proskauer, and citrate) are often helpful for identifying this type of unknown. (set: $hintsC15 to it + (a: "The IMViC tests (indole, methyl red, Voges Proskauer, and citrate) are often helpful for identifying this type of unknown. "))] (else-if: visits is 4)[ Hint: Consider the phenotype of this organism on TSA medium. (set: $hintsC15 to it + (a: "Consider the phenotype of this organism on TSA medium."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on Simmons Citrate agar. (set: $hintsC15 to it + (a: "Consider the phenotype of this organism on Simmons Citrate agar."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on ESIA medium. (set: $hintsC15 to it + (a: "Consider the phenotype of this organism on ESIA medium."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C15", "Case 15")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

(b4r:"solid")+(b4r-size:4)+(b4r-color:red)[''Reminder:'' Refreshing or reloading this page in your browser will result in a new set of unknown organisms being chosen for you to identify. ''Only'' refresh the page if you want to start the game over again from the beginning.] You have chosen to play this scenario in $mode mode. Your task is to identify $choice bacteria isolated from different foods in the factory. The cases are linked at the top of this page: you can solve them in any order. You can carry out various tests to determine the identity of the bacteria - for example, you can look at the bacteria under the microscope, carry out some biochemical tests, or grow the bacteria on various selective or differential growth media. Try to think like a detective and use logical reasoning to identify each bacterium. Choose your experiments wisely - only perform an experiment if it will help you identify the organism! (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[''[A note about budgets:]'' In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on experiments that will not help with the identification of your unknown. In the escape room, all the virtual experiments you perform will be counted - try to identify the bacteria with the smallest number of experiments possible. Your lab has a small budget for Sanger sequencing - enough for you to be able to sequence the 16S rRNA gene from one organism. You also have a small budget for next generation sequencing (Illumina) - enough for you to be able to sequence and assemble the genome of one organism. Make sure you spend your budgets wisely - when you have used up your budget, you will not be able to do any more sequencing!] ''Navigation:'' There are a number of resources to help you linked in the "Library" at the top of the page; you can also use your course notes, textbook(s), and any other resources that you can find (remember, however, that not all information on the internet is trustworthy, so choose your sources wisely). You can come back to these instructions at any point by clicking "Instructions" at the top of the page. (b4r:"solid")+(b4r-size:4)+(b4r-color:red)[''[A note about biosafety:]'' Many of the organisms featured here are ''potentially pathogenic to humans''- including organisms that require BSL-2 or BSL-3 precautions. It is important that they are handled safely and appropriately when working with them in the lab. ]

The hippurate hydrolysis test detects the activity of hippuricase, which hydrolyses hippuric acid to benzoic acid and glycine. Your lab performs the rapid version of the test, which uses ninhydrin to detect the glycine. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are hippurate+, the ninhydrin reacts with glycine, turning dark blue/purple. If the bacteria are hippurate-, no colour change occurs.] (b4r:"solid")[<center><img alt="example of hippurate test results" src="https://mafeeney.github.io/Virtual-Escape-Rooms/images/hippurate.png"></center> Figure 1. Hippurate test results. From left to right: a negative test result (indicated by the lack of purple colour); a positive test resul (indicated by the dark purple colour).). Image credit <a href="https://doi.org/10.1007/s40011-015-0565-2" target="_blank>Pallavi et al 2015</a>] <a href="https://www.sigmaaldrich.cn/deepweb/assets/sigmaaldrich/product/documents/115/966/40405dat.pdf" target="_blank">Read more about the hippurate test</a>(link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform the hippurate test on unknown $C1")[You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not perform a hippurate test on unknown $C1")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform the hippurate test on unknown $C2")[You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not perform a hippurate test on unknown $C2")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform the hippurate test on unknown $C3")[You should consider whether this is the best experiment to identify unknown $C3 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not perform a hippurate test on unknown $C3")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform the hippurate test on unknown $C4")[Unknown $C4 is hippurate ''positive''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "Unknown $C4 is hippurate positive")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform the hippurate test on unknown $C5")[You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not perform a hippurate test on unknown $C5")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform the hippurate test on unknown $C6")[You should consider whether this is the best experiment to identify unknown $C6 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not perform a hippurate test on unknown $C6")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform the hippurate test on unknown $C7")[You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not perform a hippurate test on unknown $C7")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform the hippurate test on unknown $C8")[You should consider whether this is the best experiment to identify unknown $C8 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not perform a hippurate test on unknown $C8")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform the hippurate test on unknown $C9")[You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not perform a hippurate test on unknown $C9")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform the hippurate test on unknown $C10")[You should consider whether this is the best experiment to identify unknown $C10 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not perform a hippurate test on unknown $C10")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform the hippurate test on unknown $C11")[You should consider whether this is the best experiment to identify unknown $C11 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not perform a hippurate test on unknown $C11")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform the hippurate test on unknown $C12")[You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not perform a hippurate test on unknown $C12")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform the hippurate test on unknown $C13")[You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not perform a hippurate test on unknown $C13")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform the hippurate test on unknown $C14")[You should consider whether this is the best experiment to identify unknown $C14 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not perform a hippurate test on unknown $C14")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform the hippurate test on unknown $C15")[You should consider whether this is the best experiment to identify unknown $C15 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not perform a hippurate test on unknown $C15")) (set: $clicks to it + 1)]]

{ (set: $soln to $C1soln + $C2soln + $C3soln + $C4soln + $C5soln + $C6soln + $C7soln + $C8soln + $C9soln + $C10soln + $C11soln + $C12soln + $C13soln + $C14soln + $C15soln) (set: $unsolved to (a:)) (if: "Case 1" is in $list and $C1soln < 1)[(set: $unsolved to it + (a: "$C1"))] (if: "Case 2" is in $list and $C2soln < 1)[(set: $unsolved to it + (a: "$C2"))] (if: "Case 3" is in $list and $C3soln < 1)[(set: $unsolved to it + (a: "$C3"))] (if: "Case 4" is in $list and $C4soln < 1)[(set: $unsolved to it + (a: "$C4"))] (if: "Case 5" is in $list and $C5soln < 1)[(set: $unsolved to it + (a: "$C5"))] (if: "Case 7" is in $list and $C7soln < 1)[(set: $unsolved to it + (a: "$C7"))] (if: "Case 8" is in $list and $C8soln < 1)[(set: $unsolved to it + (a: "$C8"))] (if: "Case 10" is in $list and $C10soln < 1)[(set: $unsolved to it + (a: "$C10"))] (if: "Case 11" is in $list and $C11soln < 1)[(set: $unsolved to it + (a: "$C11"))] (if: "Case 14" is in $list and $C14soln < 1)[(set: $unsolved to it + (a: "$C14"))] (if: $soln is >= 6)[Congratulations, you have identified all of your unknown organisms! (link-reveal-goto: "Solve a final puzzle to escape the room", "Final6")[(set:$t to it + time)]] (else:)[You can escape the room after you have identified all of the unknowns. You still need to identify the following unknown(s): (print: (joined: ", ", ...$unsolved)) ] }

{ (set: $soln to $C1soln + $C2soln + $C3soln + $C4soln + $C5soln + $C6soln + $C7soln + $C8soln + $C9soln + $C10soln + $C11soln + $C12soln + $C13soln + $C14soln + $C15soln) (set: $unsolved to (a:)) (if: "Case 1" is in $list and $C1soln < 1)[(set: $unsolved to it + (a: "$C1"))] (if: "Case 2" is in $list and $C2soln < 1)[(set: $unsolved to it + (a: "$C2"))] (if: "Case 3" is in $list and $C3soln < 1)[(set: $unsolved to it + (a: "$C3"))] (if: "Case 4" is in $list and $C4soln < 1)[(set: $unsolved to it + (a: "$C4"))] (if: "Case 5" is in $list and $C5soln < 1)[(set: $unsolved to it + (a: "$C5"))] (if: "Case 6" is in $list and $C6soln < 1)[(set: $unsolved to it + (a: "$C6"))] (if: "Case 7" is in $list and $C7soln < 1)[(set: $unsolved to it + (a: "$C7"))] (if: "Case 8" is in $list and $C8soln < 1)[(set: $unsolved to it + (a: "$C8"))] (if: "Case 10" is in $list and $C10soln < 1)[(set: $unsolved to it + (a: "$C10"))] (if: "Case 11" is in $list and $C11soln < 1)[(set: $unsolved to it + (a: "$C11"))] (if: "Case 14" is in $list and $C14soln < 1)[(set: $unsolved to it + (a: "$C14"))] (if: "Case 15" is in $list and $C15soln < 1)[(set: $unsolved to it + (a: "$C15"))] (if: $soln is >= 8)[Congratulations, you have identified all of your unknown organisms! (link-reveal-goto: "Solve a final puzzle to escape the room", "Final12")[(set:$t to it + time)]] (else:)[You can escape the room after you have identified all of the unknowns. You still need to identify the following unknown(s): (print: (joined: ", ", ...$unsolved))] }

{ (set: $soln to $C1soln + $C2soln + $C3soln + $C4soln + $C5soln + $C6soln + $C7soln + $C8soln + $C9soln + $C10soln + $C11soln + $C12soln + $C13soln + $C14soln + $C15soln) (set: $unsolved to (a:)) (if: "Case 1" is in $list and $C1soln < 1)[(set: $unsolved to it + (a: "$C1"))] (if: "Case 2" is in $list and $C2soln < 1)[(set: $unsolved to it + (a: "$C2"))] (if: "Case 3" is in $list and $C3soln < 1)[(set: $unsolved to it + (a: "$C3"))] (if: "Case 4" is in $list and $C4soln < 1)[(set: $unsolved to it + (a: "$C4"))] (if: "Case 5" is in $list and $C5soln < 1)[(set: $unsolved to it + (a: "$C5"))] (if: "Case 6" is in $list and $C6soln < 1)[(set: $unsolved to it + (a: "$C6"))] (if: "Case 7" is in $list and $C7soln < 1)[(set: $unsolved to it + (a: "$C7"))] (if: "Case 8" is in $list and $C8soln < 1)[(set: $unsolved to it + (a: "$C8"))] (if: "Case 9" is in $list and $C9soln < 1)[(set: $unsolved to it + (a: "$C9"))] (if: "Case 10" is in $list and $C10soln < 1)[(set: $unsolved to it + (a: "$C10"))] (if: "Case 11" is in $list and $C11soln < 1)[(set: $unsolved to it + (a: "$C11"))] (if: "Case 12" is in $list and $C12soln < 1)[(set: $unsolved to it + (a: "$C12"))] (if: "Case 13" is in $list and $C13soln < 1)[(set: $unsolved to it + (a: "$C13"))] (if: "Case 14" is in $list and $C14soln < 1)[(set: $unsolved to it + (a: "$C14"))] (if: "Case 15" is in $list and $C15soln < 1)[(set: $unsolved to it + (a: "$C15"))] (if: $soln is >= 12)[Congratulations, you have identified all of your unknown organisms! (link-reveal-goto: "Solve a final puzzle to escape the room", "Final12")[(set:$t to it + time)]] (else:)[You can escape the room after you have identified all of the unknowns. You still need to identify the following unknown(s): (print: (joined: ", ", ...$unsolved))] }

Enterobacter Sakazakii Isolation Agar (ESIA) is a selective and differential growth medium that contains 5-Bromo-4-chloro-3-indolyl α-D-glucopyranoside, a chromogenic substrate which yields a bright blue colour when cleaved by an α-glucosidase. ESIA is primarily used for the isolation of Cronobacter (formerly Enterobacter) sakazakii. (link: "Click to see the ESIA medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Pancreatic digest of casein</td> <td>7.0</td> </tr> <tr> <td>Yeast extract</td> <td>3.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Sodium deoxycholate</td> <td>0.6</td> </tr> <tr> <td>5-Bromo-4-chloro-3-indolyl α-D-glucopyranoside</td> <td>0.15</td> </tr> <tr> <td>Crystal violet</td> <td>0.002</td> </tr> <tr> <td>Agar</td> <td>12</td> </tr> </table> pH 7.0 ± 0.2 @ 25°C] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM1134&c=UK&lang=EN" target="_blank">Read more about ESIA medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on ESIA")[Unknown $C1 grows on ESIA and produces ''purple'' colonies Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 grows on ESIA agar, and produces purple colonies")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on ESIA")[You should consider whether streaking unknown $C2 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on ESIA")[Unknown $C3 grows on ESIA and produces ''purple'' colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "[Unknown $C3 grows on ESIA and produces purple colonies.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on ESIA")[You should consider whether streaking unknown $C4 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on ESIA")[You should consider whether streaking unknown $C5 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on ESIA")[You should consider whether streaking unknown $C6 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 on ESIA")[You should consider whether streaking unknown $C7 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on ESIA")[You should consider whether streaking unknown $C8 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not grow unknown $C8 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on ESIA")[You should consider whether streaking unknown $C9 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on ESIA")[You should consider whether streaking unknown $C10 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 on ESIA")[You should consider whether streaking unknown $C11 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on ESIA")[You should consider whether streaking unknown $C12 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on ESIA")[You should consider whether streaking unknown $C13 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on ESIA")[You should consider whether streaking unknown $C14 on ESIA is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on ESIA agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on ESIA")[Unknown $C15 grows on ESIA and produces ''blue'' colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C15 grows on ESIA and produces blue colonies.")) (set: $clicks to it + 1)]]

{(set: $seconds to $t/1000) (set: $minutes to $seconds/60) (set: $minutes to (round: $minutes)) (if: $C1hints is not 0)[(set: $hints to $hints + $C1hints's length)] (if: $C2hints is not 0)[(set: $hints to $hints + $C2hints's length)] (if: $C3hints is not 0)[(set: $hints to $hints + $C3hints's length)] (if: $C4hints is not 0)[(set: $hints to $hints + $C4hints's length)] (if: $C5hints is not 0)[(set: $hints to $hints + $C5hints's length)] (if: $C6hints is not 0)[(set: $hints to $hints + $C6hints's length)] (if: $C7hints is not 0)[(set: $hints to $hints + $C7hints's length)] (if: $C8hints is not 0)[(set: $hints to $hints + $C8hints's length)] (if: $C9hints is not 0)[(set: $hints to $hints + $C9hints's length)] (if: $C10hints is not 0)[(set: $hints to $hints + $C10hints's length)] (if: $C11hints is not 0)[(set: $hints to $hints + $C11hints's length)] (if: $C12hints is not 0)[(set: $hints to $hints + $C12hints's length)] (if: $C13hints is not 0)[(set: $hints to $hints + $C13hints's length)] (if: $C14hints is not 0)[(set: $hints to $hints + $C14hints's length)] (if: $C15hints is not 0)[(set: $hints to $hints + $C15hints's length)] (if: $solved contains "Escherichia coli")[ (set: $passkey to $passkey + "1")] (if: $solved contains "Listeria monocytogenes")[ (set: $passkey to $passkey + "2")] (if: $solved contains "Salmonella enterica")[ (set: $passkey to $passkey + "3") ](if: $solved contains "Campylobacter jejuni")[ (set: $passkey to $passkey + "4") ](if: $solved contains "Bacillus cereus")[ (set: $passkey to $passkey + "5") ](if: $solved contains "Vibrio parahaemolyticus")[ (set: $passkey to $passkey + "6") ](if: $solved contains "Staphylococcus aureus")[ (set: $passkey to $passkey + "7") ](if: $solved contains "Shigella flexneri")[ (set: $passkey to $passkey + "8") ](if: $solved contains "Clostridium perfringens")[ (set: $passkey to $passkey + "9") ](if: $solved contains "Yersinia enterocolitica")[ (set: $passkey to $passkey + "10") ](if: $solved contains "Clostridium botulinum")[ (set: $passkey to $passkey + "11") ](if: $solved contains "Mycobacterium bovis")[ (set: $passkey to $passkey + "12") ](if: $solved contains "Brucella abortus")[ (set: $passkey to $passkey + "13") ](if: $solved contains "Vibrio cholerae")[ (set: $passkey to $passkey + "14") ](if: $solved contains "Cronobacter sakazakii")[ (set: $passkey to $passkey + "15") ] } (print: (either: "Hooray! You nailed it!", "Way to go! You're a rock star!", "High-fives all around! You aced it!", "Cheers to your success! Well done!", "Fantastic job! You're a champion!", "Woo-hoo! You've reached the top!", "Bravo! You crushed it!", "Celebrate good times! You did it!", "Hip, hip, hooray! You're a winner!", "Amazing work! You're on fire!", "You're a star! Congratulations!", "Party time! You conquered it!", "Kudos! You've made it happen!", "Smiles and applause! You succeeded!", "To the moon and back! You've achieved greatness!")) { (if: $choice is 4)[Your secret code (to prove you have successfully escaped the room) is: $passkey] (else-if: $choice is 6)[Your secret code (to prove you have successfully escaped the room) is: $passkey] (else-if: $choice is 8)[Your secret code (to prove you have successfully escaped the room) is: $passkey] (else-if: $choice is 12)[Your secret code (to prove you have successfully escaped the room) is: $passkey] } It took you approximately $minutes minutes to escape the room. You played in $mode mode and identified $choice bacteria and 1 sample contaminated with a $finalorganism: very well done! You used $clicks pieces of data, and needed $hints hints to escape the room. (b4r:"solid")+(b4r-size:4)+(b4r-color:red)[''As a reward for escaping the room:'' Here's a fun trivia fact about a foodborne pathogen! $funfact] {= (if: $16S is 1)[You did not use your 16S sequencing budget - good job saving money for future experiments!](else-if: $16S is 0)[You used your 16S sequencing budget, hopefully this helped you to identify one of the unknown organisms correctly.] (if: $WGS is 1)[You did not use your next generation sequencing budget - good job saving money for future experiments!](else-if: $WGS is 0)[You used your next generation sequencing budget, hopefully this helped you to identify one of the unknown organisms correctly.] (if: $choice is >7)[You used money for $viralseq round of virus sequencing, and you made $mistakes mistakes when explaining your sequencing method to your colleague.] (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[''Some things to reflect on:'' What were the most informative tests for identifying each organism? Could you have identified any of the unknowns with less data (performed fewer experiments)? What have you learned that will help you better identify unknown organisms next time?] (link: "Click here if you would like to play again")[(restart:)]

(if: $pathcount >= $paths's length)[ (set: $paths to (shuffled: ...$paths))  (set: $pathcount to 0)  ] (set: _passage to $paths's ($pathcount + 1)) (set: $pathcount to $pathcount + 1) (display: _passage)

(set: $earnedclues to it + 1) (print: (either: "Great job!", "Fantastic work!", "Excellent!", "Outstanding performance!", "Bravo!", "Superb!", "Terrific!", "Impressive!", "Kudos to you!", "Way to go!", "You nailed it!", "Marvelous!", "Splendid!", "Remarkable!", "Top-notch!", "Aces!", "Well calculated!", "Awesome job!", "Thumbs up!", "Gold star for you!", "First-rate!", "Hats off to you!", "You're a star!", "Rockstar performance!", "Champion effort!", "You knocked it out of the park!", "You aced it!", "Impressive work!", "Nicely done!", "Brilliant job!", "You're a pro!", "Stellar!", "You're on fire!", "Top marks!", "Standing ovation!", "You're killing it!", "Well executed!", "You're a legend!", "Cheers to you!", "Hip, hip, hooray!", "Well deserved!", "Sensational!", "You're the best!", "Incredible effort!", "A job well done indeed!", "You're a wizard!", "You're the bee's knees!", "You've outdone yourself!", "Remarkable achievement!", "Magnificent work!", "Excellent job!", "You've excelled!", "Brilliant performance!", "Impressive accomplishment!", "Exceptional effort!", "You're outstanding!", "Phenomenal work!", "Astounding job!", "Superior performance!", "You're a standout!", "Exceptional achievement!", "You're a marvel!", "Skillfully done!", "You're a virtuoso!", "Stupendous!", "A feat to remember!", "Job executed flawlessly!", "Exceptional workmanship!", "You're a maestro!", "First-class performance!", "You're a genius!", "Job well mastered!", "Top-tier effort!", "You've set the bar high!", "You're a sensation!", "Splendidly executed!", "Exemplary job!", "You're remarkable!", "Job well accomplished!", "You're unparalleled!", "Kudos on a superb job!", "You're unmatched!", "Masterstroke!", "You're a sensation!", "Job handled with precision!", "You're extraordinary!", "You're in a league of your own!", "Outshining excellence!", "You're unbeatable!", "You're phenomenal!", "Unsurpassed achievement!", "You're exceptional!", "Job brilliantly done!", "Well done!", "Superstar!")) You have earned a hint. You may redeem this by going to the notebook for the unknown you are trying to identify. Would you like to: (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)], or (link-reveal-goto: "solve another problem to earn another clue", "Problem")[(set:$t to it + time)]?

(go-to: (history:)'s last)[(set:$t to it + time)]

(set: $viralseq to it +1) To sequence the DNA present in your sample, you extract and purify it, create a library, and send it off for Illumina sequencing. (after: 2s)[= You have to wait for the quality control check to be performed on your library ... (after: time + 2s)[= and for the library to be run on the Illumina machine ... (after: time + 2s)[= and for the sequencing facility to send you the data. (after: time + 2s)[= Then you perform quality control on the raw reads ... (after: time + 2s)[= assemble the remaining reads into contigs and ... (after: time + 2s)[= (link-reveal-goto: "Click to see the sequencing results", "dna-sequencing1")[(set:$t to it + time)]

Based on the results from your sequencing experiment, you conclude that unknown $F contains which virus? (dropdown: bind $finalchoice, "Select the correct virus", "rotavirus A", "norovirus", "adenovirus", "poliovirus", "hepatitis A virus", "hepatitis E virus", "astrovirus", "coxsackie A virus", "echovirus", "Aichivirus A") (if: $final is "A")[(link-reveal-goto: "Click to check your answer", "Final-answerA")[(set:$t to it + time)]] (if: $final is "B")[(link-reveal-goto: "Click to check your answer", "Final-answerB")[(set:$t to it + time)]] (if: $final is "C")[(link-reveal-goto: "Click to check your answer", "Final-answerC")[(set:$t to it + time)]]

You have one final unknown to identify before you can escape the room. Sample $F is a portion of $Ffood. No potential bacterial pathogens were isolated from this sample: you suspect it may be contaminated by a virus instead - probably an ''enterovirus'' of some type. To identify this virus, do you want to: (link-reveal-goto: "Prepare a DNA library from sample $F and sequence it using Illumina technology", "Final-seq-DNA")[(set:$t to it + time)] or (link-reveal-goto: "Prepare a cDNA library from sample $F and sequence it using Illumina technology", "Final-seq-cDNA")[(set:$t to it + time)]?

"Interesting," your colleague says. "So why do you use the RTase to transcribe RNA to DNA?" Which explanation do you give to your colleague? (link-reveal-goto: "Most databases only contain DNA sequence information; the RNA needs to be transcribed to DNA so that we can compare our sequences to the database", "cdna-sequencing-reason1a")[(set:$t to it + time)] or (link-reveal-goto: "Most enteric viruses are RNA viruses; their RNA genomes need to be converted to DNA to sequence them", "cdna-sequencing-reason1b")[(set:$t to it + time)] or (link-reveal-goto: "Most pathogens are actively transcribing genes needed for virulence; it's easiest to detect them by detecting their messenger RNAs", "cdna-sequencing-reason1c")[(set:$t to it + time)] or (link-reveal-goto: "The most abundant RNA molecules are ribosomal RNAs; sequencing RNA makes it easier to identify the pathogen", "cdna-sequencing-reason1d")[(set:$t to it + time)]

(set: $mistakes to it + 1) "That's odd," your colleague says. "I thought that was RNA polymerase that transcribed DNA to RNA." You double check the <a href="https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/279/975/m1302bul.pdf" target="_blank">product information sheet</a> for your RTase. "That's right," you say. "(link-reveal-goto: "RTase transcribes ssRNA to DNA", "cdna-sequencing-reason1")[(set:$t to it + time)]."

(set: $viralseq to it +1) Having made your cDNA, you then create a library for Illumina sequencing and send it off to the facility that will sequence it. (after: 2s)[= (after: 2s)[= You have to wait for the quality control check to be performed on your library ... (after: time + 2s)[= and for the library to be run on the Illumina machine ... (after: time + 2s)[= and for the sequencing facility to send you the data. (after: time + 2s)[= Then you perform quality control on the raw reads ... (after: time + 2s)[= filter out the sequences coming from the $F sample ... (after: time + 2s)[= assemble the remaining reads into contigs and ... (after: time + 2s)[= (if: $final is "A")[(link-reveal-goto: "Click to see the results", "Final-ResultsA")[(set:$t to it + time)]] (if: $final is "B")[(link-reveal-goto: "Click to see the results", "Final-ResultsB")[(set:$t to it + time)]] (if: $final is "C")[(link-reveal-goto: "Click to see the results", "Final-ResultsC")[(set:$t to it + time)]]

(set: $dnaseq to it +1) (set: _seq to (random: 1, 6)) Contig #$dnaseq that you obtained from sequencing the DNA from sample $F has the following sequence: {= (if: _seq is 1)[(font:"Courier New")[CGTGCAACGTGATTTCCCAAGGCAACATTTTCCCACGCCGACATTAAAGCGGCCTTGTCGTCGCGTCCGG CAAAAGCTCCAAGCGTACTAACTCATTTGCTTTGGGATCAAAAGGCATCCTAGACGAACACCCCCCTTTC CCGCCGCCCACAAGCTTTCAACCATGAAAACCCAAGCCTTCAACTAATCCAAAGCAAACCCGCCGCGCAA CGTGTTTTTCGAAGAAAGTAATAGGGTAGCATCAAGTACGCACAATGCCCAAACCCCCAATCAAGTAGTA ACTAGTGCATTGAGAGGTAGGTGTCGTTTCCCGTATCCTCCCTCCACTCGCCGCACAAGCTTTCATTGAT TAAGAAATCAAGCACAAAACGAAACCGGCGCCACCGCATTACCCCTCCTCAGCAAACAATAGGTGGCGTC AAGTATGCACTATGCCCAAGCCCCCAATCAAGTACTAACTAGTGCATTGAGAGGTCGGTGTCGTTTCCCG TATCCTCCCTCCCCCTCGCCGCACAAGCTTTCATCGACTAAGAACCAAGCACAAAACAAAACTGACACCA CCGCATTACCCGCTTGCTAGTATTTCTTTTTTCGATCGGGACAAAACCCCCAGGGTGCGGGAAGCAACCC TTTAGAGCACCCTTGGGTGCGGAAAAAGACGCCTGGCCGCGCCCTGGGGTGCGCAAGAGTCTATTTTTTT TTCGATCGGGACAAAACACCCAGGGTGCGGGAAGCAACCCTTTAGAGCCACCTTAGGTGCGGAAAAAAGG CGCCCGGGCGCGCCCTGGGGTGCGGAAGGTACATCTAGGCGCCCCTGGGGTGCGGAGAGGGTCACCGGAG CGCACCCTCGAGTGCCGGCATGGGCGCCACCCTCACACCTTGAGGTGCGGCAAGGGTGCCTGGGCGCGCA CCCTTTCTTCCGAAGGCAACATTCGAGGCAACGACACTCAAATTTGATCAATTTTGATCCGAGGAGGGTC GCCGGAGGTCCGCCGGGGCGCCGCCAGGAATGCCCGGAGGGACGACGGAGCGCACCCTCGGGTGCCGGCG AGGGTGCCTGGCGCGCACCTCGGGTGCGGCAAGGGTGCCTGGGCGCGCACCCTCGGGTGCGGCAGGGGTG]] (if: _seq is 2)[(font:"Courier New")[CGTGCAACGTGATTTCCCAAGGCAACATTTTCCCACGCCGACATTAAAGCGGCCTTGTCGTCGCGTCCGG CAAAAGCTCCAAGCGTACTAACTCATTTGCTTTGGGATCAAAAGGCATCCTAGACGAACACCCCCCTTTC CCGCCGCCCACAAGCTTTCAACCATGAAAACCCAAGCCTTCAACTAATCCAAAGCAAACCCGCCGCGCAA CGTGTTTTTCGAAGAAAGTAATAGGGTAGCATCAAGTACGCACAATGCCCAAACCCCCAATCAAGTAGTA ACTAGTGCATTGAGAGGTAGGTGTCGTTTCCCGTATCCTCCCTCCACTCGCCGCACAAGCTTTCATTGAT TAAGAAATCAAGCACAAAACGAAACCGGCGCCACCGCATTACCCCTCCTCAGCAAACAATAGGTGGCGTC AAGTATGCACTATGCCCAAGCCCCCAATCAAGTACTAACTAGTGCATTGAGAGGTCGGTGTCGTTTCCCG TATCCTCCCTCCCCCTCGCCGCACAAGCTTTCATCGACTAAGAACCAAGCACAAAACAAAACTGACACCA CCGCATTACCCGCTTGCTAGTATTTCTTTTTTCGATCGGGACAAAACCCCCAGGGTGCGGGAAGCAACCC TTTAGAGCACCCTTGGGTGCGGAAAAAGACGCCTGGCCGCGCCCTGGGGTGCGCAAGAGTCTATTTTTTT TTCGATCGGGACAAAACACCCAGGGTGCGGGAAGCAACCCTTTAGAGCCACCTTAGGTGCGGAAAAAAGG CGCCCGGGCGCGCCCTGGGGTGCGGAAGGTACATCTAGGCGCCCCTGGGGTGCGGAGAGGGTCACCGGAG CGCACCCTCGAGTGCCGGCATGGGCGCCACCCTCACACCTTGAGGTGCGGCAAGGGTGCCTGGGCGCGCA CCCTTTCTTCCGAAGGCAACATTCGAGGCAACGACACTCAAATTTGATCAATTTTGATCCGAGGAGGGTC GCCGGAGGTCCGCCGGGGCGCCGCCAGGAATGCCCGGAGGGACGACGGAGCGCACCCTCGGGTGCCGGCG AGGGTGCCTGGCGCGCACCTCGGGTGCGGCAAGGGTGCCTGGGCGCGCACCCTCGGGTGCGGCAGGGGTG]] (if: _seq is 3)[(font:"Courier New")[TCATCATTAGAGAAGGAGCAAGAGGAGAGATTGATCGAAGTTTTGAAGAGACACAAGACGGCCATAGGTT GGACCTTAGCCGACATCAAGGGAATTAGCCCTACAATGTGTGTTCACCGAATTTCGCTTGAAGATGGAGC AAAACCGACCAAGGAGGGTCAACGACGTCTTCATCCACCTATGATGCAAGTTGTGAAGGATGAGGTGACA AAATTGCTCGATTGTGGAGTCATCTACCCAATTTTGGATTCAAGGTGGATTTCACCGGTTCAAGTTGTGC CAAAGAAGAGCGGAATCACGGTGGTGAAGAATGATGAAAACGAGCTTGTGCCGCAAAGGACCGTAACCGG CCACCGAGTGTGTATCGATTATAGGAGGCTCAATGCAACAAGGAAGGATCACATGCCATTGCCATTCATT GATCAAATGCTTGAGAGGTTAGCCGGTCATTCCTTCTATTGTTTTCTTGACGGTTATAGTGGTTACAATC AAATAGGTGTTGCGGAAGAGGATCAAGAGAAGACAACGTTCACATGTCCCTTTGGCACTTTTGCCTACCG CCGCATGCCTTTTGGCTTGTGCAATGCTCCAGGTACGTTTCAAAGATGCATGTACCACATATTTTCTGAA TTCATAGGTTCTAAGATTGAAGTCTTTATGGATGATTTTTCTGTTTATGGTGAGGATTTCGATGCATGTT TAGAAAATGTAGAATTTGTGCTTAGGAGATGTGAGGAAACTAATCTTGTGCTTAATTGGGAAAATGTCAC TTCATGGTTAATCAGGGTATCGTGCTCGGCCACATTGTTAGTTCTAGGGGTATTGAAGTTGATAAATCTA AGATAGATCTTGTGCGTCACTTACCCATCCCCACAAGTGTGAGGGATGTTCGAAGCTTTCTTGGACATGC AGGTTTTTATCGTCGATTTATCAAAGATTTCTCTAAGATAGCTCAGCCCTTAAGTTCTTTGTTGCAAAAG GATGTGCCCTTCCACTTTGATGCCGAATGCAAGGAGGCTTTTGAGCGGTTGAAGACCATGTTGACATCGG CACCGATCATGGCGCCACCGGATTGGTCCTTGCCCTTCGAGTTGATGTGTGACGCCTCAGACTATGCCGT GGGGGCTGTGCTCGGACAGAGAAGAGACAAGCAGCCGTATACCATCTATTATGCCTCTCGGACGCTCAAT GATGCGCAACAGAACTACACCACCACCGAGAAAGAACTTCTTGCCGTGATCTTTGCTTTAGATAAGTTTC GTTCTTACTTACTTCAATCTAAAGTTATTGTTTACATTGACCATGCGGCTTTGAAGTATTTGTTGACAAA GAAGGATGCCAAGCCGAGATTGATAAGGTGGATATTGCTTCTCCAAGAGTTCGATTTGGAAATCAAAGAC AAGAAGGGGTCGGACAACGTTGTTGCCGACCACCTTAGCCGGTTGGTGCGTGACTCGGATCCCGTGGCCA]] (if: _seq is 4)[(font:"Courier New")[AGCCTTTGCCGAAACTCCATCAACCTCCAAACACCACAATCCGATCCCACCTCCAGCACTCGTCCAAAGC ACGTAGCCTAGGACTCCGCGCACTCAAAGAATAGAACACGTAGGGATATTTTGAGAGTGTATTCATCTTC TATTTTCGGATTGCTATGTGTTTGTTCTTGTTTATGTTGTTTTAGGTTTTTGCTTAAGTATGTTTTGATT CTTGTCTATGAGATAGAAACACTTTTGAACCATGTTTTGAATTTAAGTTTTCAATTTTTAATCAATGATT TTAGGTTTTATGCCGTGAGTATTATGTTCTTTATACTTTAAGATTTTCGGTGCATTTTTCCATTATCATG TGTAGTTGATACAAGTAGTTGATATTGCATGTGTTAATCATCCAAAGTTCGACTTTGATACACGTAGTTG ATAGGTTGCATTGTCTTTGTTATTTCACCGATTTTCTGCCTATGTTTGATTTAGGACTAGTACTTAAACA CATCGATTCTTTATGTGATACGTAATTGCATGATTAGTTTATGTGTGACCTATAAGTAGAGCACGTAGCC GAGCTTGTTGTGTCGCGATGTTGAATGAAACCCGTAGTCTAATTCTAAGTTGGTCTATGTCATAGGAACC ACGTAGGAACTTATGTGCATATCAAATTTAGGTTGTATATTTGCTCACGGTGTAGACTTAAATGAGATTA GAAATCGTCTTCTTTATTCTTGCATGGTTGTTTGGTTGAGTTTGCATGATTGTTGGTTGATCACATGTAT ATATGTATAGAAGTAATTTAGGATTTATTTTCATTGTCTATTTCAAAATCATCAAACCTTTAAAACCTAT ATGCTTATTTCGGCACTTATATTAGATTAGATGGATCTACCCTGTAGTTGGATCCCCGATTTAGAACGAT CCCTGCTTGCTTTATACTATAACTGATTTGTTGACAGGGTTAATTGATGCATGTGCAAATACGTCTTATC AATCGTTAGACCAGGGTGTGAGTCATCAAGATCGTACGAGGCAAAACTCACCTTGGCTGAGTACCACAAA TACATTCATTCCACCCGAGAGGAACTTGACCGAGAGTGACATCCCACCGTTCAATACACACCGTGAGCAT GGACTTGGGGGGACTATGGTGGAAGACTATGGTGGGACCCATCCGAGATAGTTCTCTGGTCTACGGGCTT ATTTCAGCCAAGTCCCCACTCAAGATGTGTCTTGAATGAGAACTTGGGGGGACTTGTAGTCGGTTGTGCA]] (if: _seq is 5)[(font:"Courier New")[AGAGCTATGAACTCAAGCTCCAACTGCTCCCTCACTGTAACAGGAAAATACTTCTCCCGAAAGAGCTGAA CAAACCCCTCCCAAGTCAAGGCAGTCACATCTCTGGATCTCTCTACCCCGCTCCACCATACCCGTGCCTC ATCCTTGAGAAGAAACGCAGCGATACGCATCTTCTCAATCTCCGTACACGTGATCATGGTGAAGTATGTC TCAATGCCCTCTATCCAATGATCAGCTACGAGGTAGTCTGTACCTCCCAGAAAAGAAGGCGCTCCTAACC TGATGATACCCTGAGCCAGCCTGGCCAATCGTAGACCATCATCTACAGCAACAGGCACCGGCACCTCCAA CACTACCTCGTCCTCAAAGAAATCATCCACAGGTGGAGCCCTACCTCCGCCTCTGGCCCCACCTGCCCCT CTGGCTCTACCGGCCCCCCTGGCCCTACCGGCCCCTCTGGCCCTACCGGCCCCACTGGCCCTACCTCGGC CTCTAGCTCTCCCTCGTGGAGAATCCATCACCTAAGAATCAAACAAACCTTGGTTAACTCATGCATAAAA CTTAAACCAAAGTATAAGTCAAATGCGACATTTATTAACCAAGGCACTAACTCAAGATGGAACACCAAGA TTTTAAGAAAATAAAATCCACTAACAGAGTACTCTCTACTCTGACATCCTATTAACCTAGAGGCGACACC TACCCTTCACATACCCAATGACAAATCAATACCGAAGAGTTTATGATGGTGATCCGCTGCAGTCGGGCCA TCACTCCGAAGTATTGATTATCACCAAATATGTAACCCTCGCTCTGATACCAACTGTCACGCCCCTATTT TTTTGAAAAATAATTTCAAAAATTTTGGCATGATATATCCTAAAATACTAACATCCCAAAACCTGTTTCA ACAAAACAAACAAGGAAAATAAACTCAATGCGTAAAGTAAATTTACACACAACCCCAAATTGAGTTAGAT ATTACATTTCCTTGTTTTACATAACTTGAGAACAAGAGAGGAAACGCTCACAAGAGTTTAACAATTCATA TCCCCATGAATATAAAAGAATATACAAACACACCCCAAACCCAACAAAAAACCCTGCCACTACGCCTCCA TCTCAACCCTGCTGATCCTCACCTGCAGGTCTAACCCCTACACCAAAATATGGTGCACCGGGTTGTAAAC]] (if: _seq is 6)[(font:"Courier New") [GATTTTTGAGATCGGCCCTCGTGGTTTCTGAGCAGCCCAGCTTTTGAGAAAGCAAGCGCCTCTTCGATTT CTGAGATCGGCCTTCATGGTCTTTGAGCAGCCCAGCTTTTGAGAAAGCAAATGCGTCTTCGATTTCTGAG ATCAGCCCTCGTGGTCTCTGAGCAGCCCAACTTTTGAGAAAGCAAACGCCTCTTCGATTTCCGAAGCTCC GTCGAGTGCAGATTTTTATAGAGGCTGGCATTAAGTTCCAAAGCACACTTGAATCTCCACCAGTAGAATC TCCCTTCTTGCACTTCTAAGATCTTGATTTGTCCGACCTCTTCTCTCTTCAACACCTTTGAAAATGTCTG GCCCTTCCGACCATCGTTTTGACTTGAACCTTGTTGAAGAGGCAGCCACGCCTTCTCCAGACAACATATG GCGCCCATCCTTCTTATCCCCTACTGGTCCTCTTACCGTTAGGGATTCCGTGATGAAGAATGATATGATT GCTGCGGTGGTGACCAGGAACCTTCTCACTCCCAAAGATAACAGACTATTTTCCAAACGGTTTGATGAGT TGGCTGTTAAGGATTCTCTGGCTCTCAGTGTTCAGTGTGCAGGTTCTGTGTCTAATATGGCCCAACGTCT ATTTGCTCGAACCCGCCAAGTTGAATCATTGGCGGCAGAAGTGATGAGTCTCAAACAGGAGATTAGAGGG CTCAAACATGAGAATAAACAGTTGCACCAGCTCGCACATGACCATGCTACAAACATGAAGATGAAGCTTC ACCAGATGAAGGAATTTGATGGTTAAATTTTACTTGATCATCAGAGGTTTGTGGGTTTGTTCCAAAGGTA TTTATTGCCTTCGTCTTCTGGGGCTGTACCACGTAATGAAGCTCCAAATGATCAATCTCCGATGCCTCCT CCTTCTAGGGTTCTATCCAGTACTGAGGCTCCGAACGATCCCCCTCCGGTGCCTTCTCTTTCTGGAGCTC TACCGACTGCTGAGACTTCTCCTAAGCAACCTTTGTGAAGACTCCCTCTTGTTTGTTTATTTTGACTCAT GTATATGTACATATTTGTAACTTATCGGAGATATCAATAAATAAGCTTTGCTTCATTTCAACGTATTGTG TTAAATACACCAAAACCTTCTTCACTAAGTTCTTTGAATTTTTCTTTTGTTGAAGCTTGTATGTTGAAAC TTTGTGAGTGGAGCATGTAGGTTGAGGTAGTATTCCCTTAATTTCCCGAGTGAGGAAAACTTCTCAGTTG GAGACTTGAAAAATCCAAGTCACTGAGTGGGGTCGGCTATATGAATCTTAGAACGCCATTGTGCTGGATC CTGTGTCATGTCCTCCGTTAGATCCAAGTGCTCTAAGTCTTTTCTTAGAGTCTCTTCCAAAATTTTCCTA]] (if: $dnaseq > 4)[(link-reveal-goto: "Chat with a colleague about why you're struggling to identify any pathogens present in unknown $F", "troubleshoot")[(set:$t to it + time)],] (link-reveal-goto: "Identify the pathogen present in unknown $F", "dna-seq-id")[(set:$t to it + time)], (link-reveal-goto: "Look at the sequence of another contig from this sequencing run", "dna-sequencing2")[(set:$t to it + time)], or (link-reveal-goto: "Prepare a new library and repeat the sequencing experiment?", "Final")[(set:$t to it + time)]?

(set: $dnaseq to it +1) (set: _seq to (random: 1, 6)) Contig #$dnaseq that you obtained from sequencing the DNA from sample $F has the following sequence: {= (if: _seq is 1)[(font:"Courier New")[GAATCCGGCCCCTTGCTCAATGGCTAATTGCTATGCTTGCTCGATGGACATTGCACCTTGTGCAACTCCA CCATATCTATAGACAGACTCGGCATCTCCCTCTCTAAGTGACTTGGCATGGCTGCCCTCTTGGTCATTCT CGGCCCTAAAGCTTGGATATTTCATGGTGTTGAAGATGTTGAACTTTATAATCTCCCCATCGAACTCCAT GGTCAAGTTGCCTCCATGCACATCAATGTTTGTCCTTGCGGTTCTCATGAAGGGTCTTCCTAACAAAAGC TGTGTAGAATCATCAACAGACTCCTCCATCTCCAACACATAAAAGTCGGCAGGGAATATCAAGTGGTTAA CCTGCACAAGGACATCCTTCACATACCCCTTAGGGTATTTGCTTGATCGATCCGCCAATTGGATAATCAC GTCGTCATGTTGTAATGGACCAAGACCTAGGGACAAGTAAATAGAGTAGGGCATGACATTAATAGAAGCC CCTAGATCGAGCATCACCTTCTCAAACCTTGTAGTTCCGATGACAACTGGAATGGAAAAACTCCCTGGAT CCTTAAGCTTTGGCGGCATCTTGCGTTGTAGCACGGCGGACACGGTCTCGCTCATGCTCATCACTTTCTT CTCCCTTGTGTGTCTTCTTGTGGTGCAAAGCTCCTTCAAAAACTTTGCATACTTGGGCACTTGCTTGATA CATTCTAACAAGGGGATGTTCACATTCACCTTTCGAAAGACGTCCAACACTTCTTCGTCGGACTTGGCTT GCTTGCTCTTGGTGAAACGTGAGGGGAAGGGGATACAACAAGTGCTCGGCATGGCTGCATCCTTGGCAGC CGAATGTCTTCCTTCCATGGCAGCAGGGTCTTTCTCAAGAGCCCTCTTCTTCATTGCTTCCAAGTCTCCC TTGCTTGGCTTAGCATTCGGTTGTTGCTCGGTACCTTGATCTTGGTGTTGTGTAGGCTCGGCGTCCATGG CAGCCCTCTCGGCAATGTGGCCACAAAGCAAAGTATGTAACTTGGCAATCATTAATAAGTTAAAAGTTGT CACTTAAGCACATATGTCGGCAACCTAAATAAAAGTTGCTAGTTTGTTTTATTAACTCTTAACTTTATGG TACGTGGAGCAGTGAAGACCAGTGTGCGATGTCCTTGTACAGGCCAGTCCGGTGTTTTGCTTGATCCGAT ATACCATTATAAGTTAAGAGGGTAAATTTTCGAACCATAATGTATGATGATTATATATCAAGTTATTTTA CAACGTCTAAAGTAAGGTTTATGCTACGGCCCGAGTATTTGGCTAGGTCGAGCGGATTCCGTGGTTTCAG AAGACGAATGTCACGGAGGGCGAACCCCCTACAGGAATCAGGCAGGACTCGTTTGTGGTCACGGAGGGCG AACCCCCTATCGTCCCCTTCATAGAGAAGAGATGACAGTCAATGACCTTGAGATCCAGTTAGACAAACCT]] (if: _seq is 2)[(font:"Courier New")[GTTGAGCGCATAGCTGAAGGGGTCGTAGTGGAAGCTGAAACGCTGCTTGCTCTCCCTTCCTTTGCCCAGC TGCCTCCTTATCTCCGCCCTGAGCTTCCAGTAGAGGCTCTTGAACCTCCTCTTTCGCGCACCCAGTACCG CTCCGGCCTCTCCCAGAACTGCCACCACTCCGACGGCCACAGCCATCTTCACCGCCACCTCACCACAGAA TGCCAACGGCGCAAGACCTTTTAACCCTGGGGAGATGCAAGACAAGCCCGAGCCTGAGAGGAGTTGTCTT ACTCTAAGCTACCCTACTCTAAGAAGAGAGAGGGGGCAGGTGAGACAGCGAGGCTTGTTGCGCAAGTGTC GAAGGTATAGTGGAAAGTGAAGCTATAGAGGACAGAAGAGGACGGTGGAGACGCTGCTTTCTCTCTCTCC TTTGGCTCTGTTTCAGCCCTTGCTTTCGCAATGTTGCCTTATGCAACAAAGCTTTGGAGCATCAGATGGG ACAGAGCCAGACTCCATCCATTAACTGATGGATATATATGGATGGATGAGATGTTTTTGTTCCTTCGTTT GGAATGTGGTGGGAGATGGCAATATTGTCTTTGGTGCTATGTTTAATATCAACAATAATATTTTTCCAAA TGGAAACCTGTTTACACCTTAAAGATCTACAGAAGAATTCGATGAAGTAGTTGTCGACAACACCGGTGGA ACGTTGATCCATAGGTCGCTGTGAGACAGGCTGAGGTGAGGCCATGGGTCATGGGGATAGCAGCAGTAGC AGAGGTGCAAGTGGAATGTTGAGCCCCGCCACAGAGCAAGCTAATCTTGTCACAGCCTCGGAGCAATTGA TCGAACGACTGGCGGAGGTTGCTGGGATCACCTTTTCGGGTTTTGCCCTGCCTCGGGGACCCAATATTCC CCACTTTTAATGCGGGCGTCGACAGAGATCCTGTCCCTCCTCGTCCTCCGAGCATGTGCTCACCCATTCA ATTCCCAACTCTTCTTCTCTCTTTTACATTTCCATCGTTCGAGCCATTGGAAAGCCATGTTCGTGTCAAA CTTACTTCTCTCGTCCTGTTGCTCAGCCTTTTACCTTGGCGTACAGCTCAGTTCAATTTCGTCTCACCTC TCTCTCTCTCACTGTCTCCTCCCTTTTACTAATATGAACAATTATTAAGGGTCAGCTGATGGCGATTGCA AATGGAAGAGTTGTATCTCGTGGCCTGTTAAGTCAAAAGGCTCACATTGCTCTGTCAGAGAACTGCAGAC TGGGATAAGCCTATATGTCGCGTCCCGCTCACACATCCCTACCCAGTTTCCATGGGCACCTCACTGGTCC ACCAAGCATCACCGTTCTGGGAATATTTTAGGCATAGGAACTGTGTGCGGGGCTCTATAAAGATGTTTCA CGTCTAAGACTTCTTTTTCTTGTTTCCTTCAAATAAGAGTAAAAGCAGATTAGCTTCTGAGCCCAAAACA TACTATTTTCTTTCGCATGTTTCCTCAACACCCCTTCTTGCGGTTAATTCCTTGAATTCCACTGTTTATA]] (if: _seq is 3)[(font:"Courier New")[AATACTATGAAACCTTTGATCCCCACAGACAACTCATATAGCTTAAGCAAAATTATATGGAATGCTGAAG TCTCATTTGAAGTCAGTTGGTCAATCCCTTTGTCACACTACACCTATGGATATGCCGTCAGTCGAGCCAA TATGTAGGTTCATTCCTCTACCTATAGACATGAGTATACTTGATTTCGTCAAAAGACATTGGAACAGTTT GATGTCTTTATAAAGACTTGTTGAAGATGTCAACGAGAAGTTTTGCATCTATTTCGACGTGGATTTTAGA TATTCCTGTTGAATGATGATCCTTAGTCCATCCAGAATTAATTGCCTTGGCCTCGCAATAGAGCACAAGA TGATCATACACATGAGAGCATCCAGCAGCAATACATAATCCTATATGTATTTCTTGATTCCTACCGAGAG CTATCAGTGTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA TATATACATGAAAAGCTGTAAGATAGTGATTTCAGAAAGTTCAATATTGCTTTACACGCTGAAAGAGGTT TTGTCATACAGATGGAGTTGAATGCAGGGAAGTGAACAACAACATTTAGAGATTTTTGAGGAACTTTTCG GTTTGCTAAGTTCCTTAAGCATTTGTTCTCTAAACCTGCATCCCAGTGTTTTAACCATAAGCATATAGAA ACTACAGTGCTAACTACAAGAATTCCCTGTTTTGCTGTTTACTGGGGAAACTCATGCACATAGCTGAATT GGCTATAGCAAATGCATACATAACCACTAAATATAATCGACAACATTCTAGACATTTGGATGCTCCCTAA ACAGAGCAGAAACCAAACAGTTGAGCCAAACTCTCATAGGTTTACAATGACAAAAGCAGATGTTTCATCA AAATGATTATACAATTTCAAGAAACCAGAAAAGTTACATGTATTAACAATACAGTACAAAATAGATGGCC AAAGTCATCAATGGCATGTCATCACCTGTAAAAAAAATACATTATTAAGTGCAGAACCAACCAAATTGTC CATCACAAAACAAAAACAAAACACAAAGTGCCTGATTCTTTATAAACCCTGAGCTGCATCGTTGGAGTCG TATCCCATCATAACCCAGTTTTTAACATCCAGCAACTAATGATTCATTCACAGCCGGAACCTTCATCAAA ATCTTCAATATCCACTAAAAAAAACATATGGACAAAAACTTGTAACCTTTGATTTCTTCTATTTTACTCG CCTAGACTTCTGGTTCAAACTGCATTGTCAAACGTCAATGCAGTTCCAATTTACAAATAACTGCTCCCAT AATTTCCTACCACCAATTGATGTATCAGCTGCTAATTTCTTCATGCTTTGTCAGATATGCCACGGTAGTT CACCATATAAATAGCTAGTATAGTAACTAAAGCACCAACCAACTGCAATGGTGAGAACGTTTCACCAAGG]] (if: _seq is 4)[(font:"Courier New")[AAGAAGCCCAATAACACCAAGTACGAGCCCTGCAACTCCAATGGCACCAATTGATTCTCCAAATAAGATT GCAGCAAGTATAGCAACTGTTAAAGGTTGTGAATCGATTATAACCTGCAATTTATTTTAAAAGCTGAAGT CAACAGCCAAGATGAAAACAAAAGCAAAAAAAGCATCGAATTACATTTTTAATTTATGGACAATTCTTCG TTCTAAACAATTACATTTTCCATATTTGCTAGATATAACCAAAAATAGTTTCCAAGTATCATTTTCGAAG AAGCATACTCTTAATTTACATGATTACCATTTACATGAAACACATGAAACAACTAAATAGAAGCTAACAG TCTTCTACCTTCTTCTATAGAGAGAAAGAGGAAAAATGGAAGATTTATAATTATTCCCAGTTTAGAAATG GCTGCCACTTTGATCAACACCAACCTCAAAAGTCAAACTCAAATCTAAAGTGCTACATACATTAAAATGT TTTTGTTGTAGATTCAGAATGCAAAACCTAGAGATCAGAGAGTGAAAGAAGAGTTGACAAGCACTAATAG CATATGCAGCTATATTTTACTAAAATTTGTGATTTCTAACATTTATAACTTTCTTCTAGAAAATTAATAC AAATCACAGAAAAATATCAAGCAACAGTACTAGAAACGAAGGCTCAGAGAACCCCTAAATCACAATGATA GAAGTATTCCAATCTAACTATGCGCAAACACACAAAGATAACTAAGTGGTAAAATCAATTTCCAATGAAG ACAACAAGAGGAGAATTGATGAACCAAAACCCATAGTGAAGTGGAAAAGAGATGGCCAAAGATATTAGTC ATACACTGCCCAATCCAGCGGCTGTCTTTTGCAATCCTTCGGCAAGAAATCCCTGCCACCACATGGAAAA GGAGATTAGAAAATAACAACAACAAGACACACTCAGGCAGCCTAACAAATCGAATGTTGCTAAAGCTCAA GTATTTTTTATTTTCTTGTTAATCTTTTCATAAACCAGCAATGACGAGTCCGCGCACCTGAAAGCACGCA GCGTCCACAACCCCAAACAAGAAGATGGACAGCCACGCCAGAGAACCCGCCGGCAGCTTCCTTCCCCTGG CCGCGGCAAAACCAATCAAGACCGCCCCAGCGGGGATCAGCCGGACCGCAGAGACGAAGAAAGGCCCCGT CTTGGGAATCACCCCCTTCATGGCCACCATGGCCGTGCCCCAGAAGAAGAAGGGTGACACCAGAAGCGCC CAATCCAGAGCCTTCCCGAGCAACCCGGCGACGGGATCCCCCTCGTCGCCGCCTCGGGCGATCTCGAAGC TCAACGGGGGGTTCTTGGGCGGGGGCAGCAGCTGATCACCCTCATCGGCGGCGTCCACCGCGTAGCACTC AACGTCAGCGCCGGTGCCGACGCAGTCGACGGCGGCGGGGTAGTCCACATCGGGGCGGGGCGGCATGGGG CTCTCCCTGGTGCTGCAGCGGGCGAGGGTTCTTGGGGTAGGAGTCCTAACCCTAACCCTGAGCTTGAGAT GGGAGGAGGAAGAGGAGAAGGCCACATTGGGGTTTGGTGGGGAGGACAGAAGACCGAGATGGGGATGGAG AAGGAAGAACGCGGCCGCTGACATCGCACAGGAGATGTTTAATTTATTGCATGCGCGACTTTGAAACGAG]] (if: _seq is 5)[(font:"Courier New")[AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAAAGAGGAGGAGAAACTGCTGCTGTTTGCTGCTTGAAAG AAAGGGAGGAGATTTGAAATAGTGGAGAAAAAGGGAAGTATTTTAAGTATTGGGGTTGCTGCGTGGGGAA GGAAATGTAGCCGTTGCGAGTAATATTATGCGTATATAATTACGAAGATTCTCATCATTCTCTTTCTTCT GTGTGGGATTTGAATGGCGTAATTCCAAACCTTGCAACGGCTACCTGCACAACGGAATCCAATCCCCCGC CCCCATCTGCCATCTTCTGTCTCTTTATTTTTACTGCTGTCACAATTATAGAATATATGTGATGTAATTA AATGTAAAAAAAAATATCTTTGAGCACAAAGGTACATACCATGTCTTTGATTATGCCAGCAGATATTGGA CAGGATTCATCTTCCTTAGTGCATTATTCCTGCAGTAAATTTGGAACAAAGATGAACATTTATTGGTGCT CTACTTTCTCTAAATTGAACTTGATAAAAATGGATACAAGAAGGGTTGACAAAGGTGAATTGTACACATA TCTTTAGGACAAAGGTGAAAGGAGAGTAAACATACCTTTACGTCAAAAGTAGAGTGGAAGGAACTATGAC GACCACCATCCTGCGAAAAGAAAAGAGAAGCACTTTTCAAGTGGGATTCAAACGATGCACTGAGTCTTAC CTTTGCCCACTTTACATGTGAATATGAGCTACTGTACAGATCAATCACTTGGGTATTACCTGAAAATGCA CAGTATAAAGATGTAGATCCAGACATGTTACTTACAGTTTCTGAGTATGAAGACAGCAGATGAACAAAAT AAGTTTCTTTCTGTTAGTTTCTGAGATACACCAAAACTATTGCTTCCACAAATCCAACCAAAATAACATA AAACTCCTGAACAGTAATATGTCTTGAAGAAGACATCATTAGACTACGCAATAATGCATACTTGTACCGA GTCACGATCCTATGCTGCTGCTCCAAGTGATGAGTTCAACTGATCAACTTATCTTGAATTCCTTGGTAGA AACCAATGGAGCACTGATCAGCCTATCAAATACTCTCAGGATTCGGCAGCATCCCCATGCAATTAATTGC ATAGCCTAGCTAACAACAGATACTCAAAACTCCAAGCTAGCAGACCAAATTAACATGATTGATATCACCA TCATTCATCTTTTGACCTTAATCTAGTAAATCACAAACATATACCCATTAGAAAAACAAGCAGTAAGAAC TTCCCTATAGACTTTCTGTAAATAAGCAAATACAAAGCAATACAATATTCTTGTTACTTGTAAATAGAGA TTGTGAGGTGCAGATCAGTTTAGTAGGGCATAGGGGCACCAAGACATCGCATGAATGAACATCTGCCAAT TTTGTTAGGGCATGAATGAACATCTCAAATACAACAACAAGAATCAGTATGTATTAATCGACAAGAAATT TTAGTATATTAATCTAAAATGAGAAAAAAAAATGATAGGAAAAAGTGAACAATAATTTAGAGAAATTGGA]] (if: _seq is 6)[(font:"Courier New") [CATTAATTTGAACAGCTCAGTCATCAGATGTAAAAGAAAAATGTAGTACATTAAAAGATGTTTCATAACC AACAATAATAACCCAAATCTCCCATGAGTTTAGTGACAAAATTAGCAGATAGGCAGAGCATGATTTTACC TCTATGATAGCACTTTGTTTTGCTTTGAGGACGCGTGGTGTGGTTTTAGAGACCTTTCCAGTCTTCTGGT CCAGCAGTGCTACCATCTTCACCACTCTTCCAGCCTCTTTTGCATGATGTATATGAAATTCAACCTATAT TTTCTCCTTTTCTTAAGAAGTGAAGCTAATTTATACATTTAACAAATTAAATGTAGATTTCCATGCCAAA CCTGGGATCCAGTTAGAATTGGTGTCGTAATGTCCAAGACAAGGATCCTTAGCTCCAAATATGTAGCCAC AGGCACTGCATAATCAGGGTGACAGAGCACCCCACCAGGCATAACATGACTGGACTGGATGCCTTGTAAG GTAACAGCTACATGGTCACCAGCTCTTGCCAAATTGCAGTTGATCGAGTCTCGCTCGATGGACCGTACCG TAGCTAATTCACCAAGTGGCATAACTAAAACCTGCAATAAGCCCAGCTCCCTACCATCAAAGACTACTCC TAAATACAAAAGTAAATGTATACTTGATTAATATCACAATCATGATGGCACAAGCAATGCCAGCCATGAC CAGATAAACAGTGAGATGCATCAAGTAGATTTAATCCAATCAACAACCTCAAAAGAACATGCCTGCTTGA ATGAAAACATACAAAACCTAGTCTAGAAGTTCTCCTAAGCAGTGCCACTCAAATGAAAAAGAACATTGAC AAAGTCAAAAAGCAAATATGTCATCATATTTATAGTTCCAAGATAAATATGGTTCAAATTTTCTGGTATA AGGGCACCCAATTTTTGGCATGAATTTCAAGCATCCAAGTATCTCATGCTACAATGTAGACAAAGGCAAT GCGGAAACTTGACTTAGGATATAGCCAAACAATCCATATCACACTTAAAGAATTAAAAAAGCATGTAAGC ACAAAGCTGTGTGACAATTTAGCACACAGTACTTATGGTAACTTTCCCTTAAAAAAAGGGGTACAGCTGT CGGTTCCTAAAGCTTAAAATAGCAAATAGAAATAGCTACTTCTGTAGACCACAGCTGATACAGGAATCTA ATTACTATCTAGTGTAACAACTTAAGTTAATCTATGTAATTTTTTTTTCATATTCAGATCAGTTCCCCTC CAAGAGCGAACATCAGCATAACAAGATGAAAACACAACATATGAAAAGTAAGCATAGAGATATTCATCCT CAGAGCCTCCCGCCAATTTCCCAACACAAACCGATGGTGACATCGATGAAGTGGAATGTTCTTTCTACAA CTTTGTCCAACATTGGTCTCAAGAAATTAGTCTAAGTGGACGAGTATCCAGACTGCCACTTAATGCCTGA TTTTGTTGGATTACCTTTAGAACTCTTTTTTAGATTGGAAGAGAAGGAAGAGAAGTGGCAGCAATGCATC]] (if: $dnaseq > 4)[(link-reveal-goto: "Chat with a colleague about why you're struggling to identify any pathogens present in unknown $F", "troubleshoot")[(set:$t to it + time)],] (link-reveal-goto: "Identify the pathogen present in unknown $F", "dna-seq-id")[(set:$t to it + time)], (link-reveal-goto: "Look at the sequence of another contig from this sequencing run", "dna-sequencing1")[(set:$t to it + time)], or (link-reveal-goto: "Prepare a new library and repeat the sequencing experiment?", "Final")[(set:$t to it + time)]?

(set: _seq to (random: 1, 5)) The first contig you obtained from sequencing the cDNA from sample $F has the following sequence: {= (if: _seq is 1)[(font:"Courier New")[ATGATGATGGCGTCTAAGGACGCTACATCAAGCGTGGATGGCGCTAGTGGCGCTGGTCAGTTGGTACCGG AGGTTAATGCTTCTGACCCTCTTGCAATGGATCCTGTAGCAGGTTCTTCGACAGCAGTCGCGACTGCTGG ACAAGTTAATCCTATTGATCCCTGGATAATTAATAATTTTGTGCAAGCCCCCCAAGGTGAATTTACTATT TCCCCAAATAATACCCCCGGTGATGTTTTGTTTGATTTGAGTTTGGGTCCCCATCTTAATCCTTTCTTGC TCCATCTATCACAAATGTATAATGGTTGGGTTGGTAACATGAGAGTCAGGATTATGCTAGCTGGTAATGC CTTTACTGCGGGGAAGATAATAGTTTCCTGCATACCCCCTGGTTTTGGTTCACATAATCTTACTATAGCA CAAGCAACTCTCTTTCCACATGTGATTGCTGATGTTAGGACTCTAGACCCCATTGAGGTGCCTTTGGAAG ATGTTAGGAATGTTCTCTTTCATAATAATGATAGAAATCAACAAACCATGCGCCTTGTGTGCATGCTGTA CACCCCCCTCCGCACTGGTGGTGGTACTGGTGATTCTTTTGTAGTTGCAGGGCGAGTTATGACTTGCCCC AGTCCTGATTTTAATTTCTTGTTTTTAGTCCCTCCTACGGTGGAGCAGAAAACCAGGCCCTTCACACTCC CAAATCTGCCATTGAGTTCTCTGTCTAACTCACGTGCCCCTCTCCCAATCAGTAGTATGGGCATTTCCCC AGACAATGTCCAGAGTGTGCAGTTCCAAAATGGTCGGTGTACTCTGGATGGCCGCCTGGTTGGCACCACC CCAGTTTCATTGTCACATGTTGCCAAGATAAGAGGGACCTCCAATGGCACTGTAATCAACCTTACTGAAT TGGATGGCACACCCTTTCACCCTTTTGAGGGCCCTGCCCCCATTGGGTTTCCAGACCTCGGTGGTTGTGA TTGGCATATCAATATGACACAGTTTGGCCATTCTAGCCAGACCCAGTATGATGTAGACACCACCCCTGAC ACTTTTGTCCCCCATCTTGGTTCAATTCAGGCAAATGGCATTGGCAGTGGTAATTATGTTGGTGTTCTTA GCTGGATTTCCCCCCCATCACACCCGTCTGGCTCCCAAGTTGACCTTTGGAAGATCCCCAATTATGGGTC AAGTATTACGGAGGCAACACATCTAGCCCCTTCTGTATACCCCCCTGGTTTCGGAGAGGTATTGGTCTTT TTCATGTCAAAAATGCCAGGTCCTGGTGCTTATAATTTGCCCTGTCTATTACCACAAGAGTACATTTCAC ATCTTGCTAGTGAACAAGCCCCTACTGTAGGTGAGGCTGCCCTGCTCCACTATGTTGACCCTGATACCGG TCGGAATCTTGGGGAATTCAAAGCATACCCTGATGGTTTCCTCACTTGTGTCCCCAATGGGGCTAGCTCG GGTCCACAACAGCTGCCGATCAATGGGGTCTTTGTCTTTGTTTCATGGGTGTCCAGATTTTATCAATTAA AGCCTGTGGGAACTGCCAGCTCGGCAAGAGGTAGGCTTGGTCTGCGCCGATAA]] (if: _seq is 2)[(font:"Courier New")[ATGGCCCAAGCCATAATTGGTGCAATTGCTGCTTCCACAGCAGGTAGTGCTCTGGGAGCGGGCATACAGG TTGGTGGCGAAGCGGCCCTCCAAAGCCAAAGGTATCAACAAAATTTGCAACTGCAAGAAAATTCTTTTAA ACATGACAGGGAAATGATTGGGTATCAGGTTGAAGCTTCAAATCAATTATTGGCTAAAAATTTGGCAACT AGATATTCACTCCTCCGTGCTGGGGGTTTGACCAGTGCTGATGCAGCAAGATCTGTGGCAGGAGCTCCAG TCACCCGCATTGTAGATTGGAATGGCGTGAGAGTGTCTGCTCCCGAGTCCTCTGCTACCACATTGAGATC CGGTGGCTTCATGTCAGTTCCCATACCATTTGCCTCTAAGCAAAAACAGGTTCAATCATCTGGTATTAGT AATCCAAATTATTCCCCTTCATCCATTTCTCGAACCACTAGTTGGGTCGAGTCACAAAACTCATCGAGAT TTGGAAATCTTTCTCCATACCACGCGGAGGCTCTCAATACAGTGTGGTTGACTCCACCCGGTTCAACAGC CTCTTCTACACTGTCTTCTGTGCCACGTGGTTATTTCAATACAGACAGGTTGCCATTATTCGCAAATAAT AGGCGATGA]] (if: _seq is 3)[(font:"Courier New")[ATGATGATGGCGTCTAAGGACGCTACGTCAAACGTGGATGGCGCCAGTGGCGCTGGTCAGTTGGTACCGG AGGCTAACACTTCTGACCCCCTTGCAATGGATCCTGTGGCAGGTTCTTCGACGGCGGTTGCGACTGCTGG ACAAGTAAACCCCATTGACCCTTGGATAATTAATAATTTTGTGCAAGCTCCCCAAGGGGAGTTCACAATC TCTCCAAATAATACCCCCGGTGATGTTTTATTTGATCTGAGTTTAGGTCCCCATCTTAATCCCTTCTTGC TACATCTGTCACAAATGTATAATGGTTGGGTTGGTAATATGAGAGTTAGGATTATGTTGGCCGGCAATGC CTTTACTGCAGGTAAGATCATAGTTTCCTGTATACCTCCTGGTTTTGGGTCGCATAATCTTACTATAGCA CAATCAACTCTATTCCCACATGTGATTGCTGATGTTAGGACTTTAGACCCTATTGAAGTACCTCTGGAAG ATGTTAGGAATGTTCTCTTTCATAATAATGATAGGAACCAACAAACTATGCGCCTTGTGTGCATGTTATA TACCCCTCTCCGCACTGGTGGTGGTACAGGTGATTCCTTTGTTGTGGCGGGGCGAGTCATGACCTGCCCT AGTCCTGATTTTAATTTCTTGTTTTTGGTTCCCCCCACAGTGGAGCAGAAAACTAGGCCTTTCACCCTTC CAAATTTGCCTTTGAGCTCTTTGTCCAACTCACGTGCTCCTCTTCCAATTGGCAGCATGGGCATTTCTCC AGACAATGTTCAGAGTGTACAATTCCAAAATGGTCGGTGTACTTTGGACGGTCGTTTGGTTGGCACCACC CCAGTTTCACTGTCCCAGGTTGGCAAGGTAAGGGGCACTTCCAATGGCACTGTCATCAACCTCACTGAAT TGGATGGTACACCTTTTCACCCTTTTGAAGGCCCTGCCCCCATTGGATTCCCAGATCTCGGTGGTTGTGA CTGGCACATCAACATGACACAATTTGGCCACTCTAGTCAGACACAATTTGATGTGGATACCACCCCTGAA ACCTTTGTCCCTCATTTAGGTTCAATCCAGGCAAATGGTGTTGGTAGTGGCAATTACATTGGTGTTCTCA GTTGGATCTCCCCCCCATCACACCCTTCTGGTTCCCAGGTAGACCTTTGGAAGATCCCCAATTATGGGTC GAGCGTTACTGAGGCAACACACCTGGCCCCATCAGTGTTCCCACCCGGCTTTGGGGAAGTGCTGGTTTTC TTCATGTCGAAGATACCAGGACCTGGCGCCTACAATCTGCCATGCCTGCTGCCACAAGAGTACATCTCAC ACTTTGCAAGTGAGCAAGCCCCCACTGTGGGTGAGGCCGCTCTGCTCCATTATGTTGACCCTGATACAGG GCGGAACCTTGGGGAGTTCAAAGCATACCCCGATGGATTTCTCACTTGTGTCCCCAATGGATCCAGCTCA GGTCCACAACAATTACCAATCAATGGAGTTTTTGTTTTTGTCTCTTGGGTATCTAGGTTCTATCAATTGA AGCCTGTGGGAACTGCCAGTACGGCAAGAGGTAGGCTTGGACTGCGCCGATAA]] (if: _seq is 4)[(font:"Courier New")[ATGGCCCAAGCTATAATTGGTGCAATTGCTGCCTCCACAGTAGGCAGTGCCCTTGGGGCAGGTATACAGG TTGGTGGTGAGGCAGCACTCCAAAGTCAAAGATATCAACAGAATCTGCAATTGCAAGAGAATTCCTTTAA ACATGACAAAGAAATGATTGGATATCAAGTTGAGGCTTCAAATCAACTGCTAGCCAAGAATCTTGCAACC AGATACTCACTCCTTCGTGCTGGAGGTCTATCCAGTGCTGACGCAGCAAGGTCCATCGCGGGAGCCCCAG TGACCCGAATCGTGGATTGGAATGGTGTGAGAGTGTCAGCTCCTGAATCTTCTGCAACTACATTGAGGTC TGGTGGCTTTATGTCAGTGCCAATACCATATGCATCTAAGCAAAAACAGATTCAACCATCTGGTATTAGT AATCCAAATTACTCTCCTTCTTCCATTTCTCGAACCGCTAGTTGGGTTGAATCACAAAATTCATTAAGAT TTGGGAATCTATCCCCATACCATACAGAGGCCCTTAACACAGTGTGGTTGACCCCACCTGGTTCAACAGC ATCCTCCACACTGTCTTCTGTGCCACGTGGTTATTTCAATACAGATAGATTGCCATTGTTCGCAAACAAT AGGCGATAA]] (if: _seq is 5)[(font:"Courier New")[ATGGCTCAGGCTATAATTGGTGCAATTGCCGCCTCCACAGCAGGCAGTGCTTTGGGGGCAGGTATACAGG TTGGTGGTGAGGCGGCCCTTCAGAGTCAGAGATATCAACAAAATCTGCAATTACAAGAAAACTCTTTCAA GCATGATAAGGAGATGATTGGTTATCAAGTTGAGGCTTCAAATCAGTTGCTGGCAAAGAATTTGGCCACC AGGTACTCACTTCTCCGCGCTGGGGGTCTGACCAGTGCTGATGCGGCAAGGTTTGTTGCGGGGGCCCCGG TCACTCGCGTTGTGGACTGGAATGGTGTGAGAGTGTCTGCCCCTGAAACTCCTGCGACCACACTGAGATC TGGCGGCTTCATGTCTGTACCTATGCCATACACTATCAAACAAAAGCAGGCTCAACCATCTGGTATTAGC AATCCAAATTATGCCCCCTCTACTGTTTCTCGTACTACTAGTTGGGTTGAATCACAGAATTCATTAAGAT TTGGTAATTTACCCCCCTACCACACAGAGGCTCTTAATACTGTGTGGTTGACTCCACCTGGTTCAACTGC TTCTTCCACGTTGTCTTCTGTGCCACGTGGTTATTTCAATACAGATAGGTTGCCATTGTTCGCAAACAAT AGGCGAT]] (link-reveal-goto: "Identify unknown $F", "Final-id")[(set:$t to it + time)] , (link-reveal-goto: "Look at the sequence of another contig from this sequencing run", "Final-ResultsA")[(set:$t to it + time)], or (link-reveal-goto: "Prepare a new library and repeat the sequencing experiment?", "Final")[(set:$t to it + time)]?

(set: $mistakes to it + 1) Your colleague frowns. "That seems odd," they say. "I thought that there were RNA databases out there - like Rfam, for example." "Well, I guess," you say. "But it is totally true that you can't sequence RNA." (link-reveal-goto: "Maybe one of the other explanations was correct?", "cdna-sequencing-reason1")[(set:$t to it + time)]

"That's really interesting," your colleague says. "Are you really able to pick out the viral RNAs out of all the other RNAs present in the sample?" "That's a great point," you say. "We do need to remove the ribosomal RNAs first, because they're very abundant - and then we'll use some custom scripts to clean up the data and remove any sequences that come from the $F sample - strawberry RNAs, or whatever." "That's a really cool method," your colleague says. "Good luck identifying the unknown virus!" (link-reveal-goto: "You thank them and carry on preparing your library for Illumina sequencing", "sequencing-method")[(set:$t to it + time)]

(set: $mistakes to it + 1) "That doesn't seem right," your colleague says. "What if the virus isn't actually infecting the cells in your $F sample - it's just present but not transcriptionally active?" "Well," you say, "it's true that a lot of foods do get contaminated by people who handle them ... maybe the virus isn't actually replicating in the food." (link-reveal-goto: "Maybe one of the other explanations was correct?", "cdna-sequencing-reason1")[(set:$t to it + time)]

(set: $mistakes to it + 1) Your colleague frowns. "That can't be right," they say. "I thought you were trying to identify a virus - surely they don't have any ribosomal RNAs?" "Oops," you say, "that's true, isn't it? The virus will use the host ribosomes for translation." (link-reveal-goto: "Maybe one of the other explanations was correct?", "cdna-sequencing-reason1")[(set:$t to it + time)]

(if: $finalchoice is "norovirus")[You have correctly identified unknown $F, well done! (link-reveal-goto: "Click to see a summary of your results", "Final-summary")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have not correctly identified unknown $F - do you want to look at the sequence again?", "Final-ResultsA")[(set:$t to it + time)]]

(if: $finalchoice is "rotavirus A")[You have correctly identified unknown $F, well done! (link-reveal-goto: "Click to see a summary of your results", "Final-summary")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have not correctly identified unknown $F - do you want to look at the sequence again?", "Final-ResultsB")[(set:$t to it + time)]]

(if: $finalchoice is "hepatitis A virus")[You have correctly identified unknown $F, well done! (link-reveal-goto: "Click to see a summary of your results", "Final-summary")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have not correctly identified unknown $F - do you want to look at the sequence again?", "Final-ResultsC")[(set:$t to it + time)]]

(set: _seq to (random: 1, 5)) The file containing the results from sequencing the cDNA from sample $F has the following sequence: {= (if: _seq is 1)[(font:"Courier New")[ATGTATGGTATTGAATATACCGCAATTCTAACCTTTCTGATATCAATAGTTTTATTGAACTATATATTAA AATCACTAACTAGTGCGATGGACTTTATAATTTATAGATTTCTTTTACTTATTGTTATTGTATCACCTTT TGTTAAAACACAAAATTATGGAATTAATTTACCGATAACTGGTTCCATGGATACAGCATATGCAAATTCA TCACAGCAAGAAACATTTTTGACTTCAACGCTATGCTTATATTATCCTACAGAAGCATCAACTCAAATTG GAGATACGGAATGGAAGGATACTCTGTCCCAATTATTCTTGACTAAAGGATGGCCAACTGGATCAGTCTA TTTTAAAGAATACACTGATATCGCTTCATTCTCAATTGATCCACAACTTTATTGTGATTATAATGTTGTA CTGATGAAGTATGATTCAACGTTAGAGCTAGATATGTCTGAATTAGCTGATTTAATTCTAAATGAATGGT TATGTAACCCAATGGATATAACATTATATTATTATCAGCAAACAGATGAAGCGAATAAATGGATATCGAT GGGACAGTCTTGTACCATAAAAGTATGTCCATTGAATACGCAGACTTTAGGAATAGGTTGTATTACCACA AATACAGCGACATTTGAAGAGGTGGCTACAAGTGAAAAATTAGTAATAACCGATGTTGTTGATGGTGTAA ACCATAAACTTGATGTGACTACAAATACCTGTACAATTAGGAATTGTAAGAAGTTAGGACCAAGAGAAAA TGTAGCGATTATACAAGTCGGTGGCTCAGATGTGTTAGATATTACAGCAGATCCAACTACTGCACCACAA ACTGAACGTATGATGCGAGTAAATTGGAAG]] (if: _seq is 2)[(font:"Courier New")[GAAATAAATGATTCAACCACAGTGGAACCAATTTTAGATGGTCCTTATCAACCTACTACATTTACACCAC CTACTGATTACTGGATACTTATTAACTCAAATACAAATGGAGTAGTATACGAAAGTACAAATAATAGTGA CTTTTGGACTGCAGTCATTGCTGTTGAACCGCACGTCGATCCAGTAGATAGACAATATAATGTATTTGGT GAAAATAAACAATTTAATGTAAGAAATGATTCAGATAAATGGAAGTTTTTAGAAATGTTTAGAGGCAGTA GTCAAAATGACTTTTATAATAGACGTACACTAACTTCTGATACTAGACTCGTAGGAATATTAAAATATGG TGGAAGAATATGGACATTTCATGGTGAAACACCGAGGGCTACTACCGATAGCTCAAACACTGCAAATTTG GACGGTATATCAATTACAATTCATTCAGAATTTTATATTATTCCAAGGTCCCAAGAGTCTAAGTGTAATG AATATATTAACAACGGTCTACCACCAATTCAAAATACTAGAAATGTAGTACCATTATCATTATCATCTAG ATCTATACAGTATACGAGAGCACAAGTTAATGAAGACATTACGATTTCAAAGACTTCATTATGG]] (if: _seq is 3)[(font:"Courier New")[ATGGATGTCCTGTATTCCTTGTCAAAAACTCTTAAAGATGCTAGAGACAAGATTGTCGAAGGCACATTAT ACTCTAATGTGAGTGATCTAATTCAACAATTTAACCAAATGATAATTACTATGAATGGAAATGAGTTCCA AACTGGAGGAATTGGTAATCTACCAATTAGAAATTGGAATTTTGATTTTGGATTACTTGGAACAACTCTA CTAAATTTAGACGCTAATTACGTCGAAACAGCCCGCAACACAATTGATTATTTTGTAGATTTTGTAGATA ACGTATGTATGGATGAAATGGTTAGAGAATCACAAAGAAATGGAATTGCACCACAATCAGATTCGCTTAG AAAATTGTCAGGCATTAAGTTCAAAAGAATAAATTTTGATAATTCATCGGAATATATAGAGAATTGGAAT CTGCAAAACAGAAGACAACGAACAGGTTTTACATTTCATAAACCAAATATTTTCCCTTATTCAGCGTCAT TCACACTAAATAGATCACAACCAGCTCATGACAACTTGATGGGTACGATGTGGCTGAACGCAGGATCAGA AATTCAGGTCGCTGGATTCGACTATTCGTGTGCAATTAATGCGCCAGCTAATACGCAACAATTTGAGCAC ATTGTACAGCTCCGAAGAGTTTTAACTACAGCTACAATAACACTTTTACCGGATGCAGAAAGATTCAGTT TTCCAAGAGTGATTAATTCAGCTGACGGAGCAACTACATGGTATTTTAACCCAGTAATTCTTAGACCAAA CAACGTTGAAGTGGAGTTTCTACTAAACGGGCAGATAATAAACACTTACCAGGCTAGATTTGGAACAATC GTAGCTAGAAATTTTGATACAATCAGATTGTCGTTCCAGTTGATGAGACCACCGAATATGACACCAGCAG TAGCAGCATTATTTCCAAACGCGCAACCATTTGAACATCACGCTACAGTAGGACTGACACTGAGAATTGA ATCTGCAGTTTGTGAATCTGTACTTGCCGACGCAAGCGAGACAATGCTAGCAAATGTGACATCTGTTAGA CAAGAATATGCAATACCAGTTGGACCAGTTTTTCCACCAGGTATGAATTGGACTGATTTGATCACTAACT ATTCACCATCCAGAGAGGATAACTTGCAGCGTGTATTTACAGTAGCTTCCATTAGAAGCATGCTTGTCAA ATAA]] (if: _seq is 4)[(font:"Courier New")[TCAACCAATTAGATCCAATAAAGTTAAATGAGGATAGCTATGTTTTGTTGAATTATGAAATAAATTGGAA TGTTATGAATGTATTAATTAATAGTATTGGTAAAGTACCAAAAATATTAACTTTGAGTGACGTTATTTCG ATTTTACGTATAATAATATATGATTGGTTTGACATAAGGTTTATGAGAAATACTCCAATGACTACGTTCA CAGTTAATAAATTGAAGCAATTATATGAAAAAGATAGAACTGCAGAATATGATTCAGATATATCCGATGT TGAATAA]] (if: _seq is 5)[(font:"Courier New")[ATGCTCAAGATGGAGTCTACTCAGCAGATGGCATCTTCTATCATTAACTCTTCTTTTGAAGCTGCAGTTG TCGCTGCAACTTCTACATTGGAATTAATGGGTATTCAATATGATTATAATGAAGTATATACTAGAGTTAA AAGTAAGTTTGATTTTGTAATGGATGATTCTGGCGTTAAGAATAATCTAATAGGTAAAGCAGTTACAATT GATCAGGCTTTGAATGGTAAATTTAGTTCATCTATCAGAAATAGAAATTGGATGACTGATTCAAAAACTG TAGCAAGATTAGATGAAGATGTGAACAAACTCAGATTATTGTTGTCATCGAAAGGAATTGATCAAAAAAT GAGAGTTCTTAATGCGTGCTTTAGAGTTAAGATAGTACCTGGAAAATCGTCATCTATCATTAAATGTACT AGGTTAATGAAAGAGAAAATAGAACGTGGAGAAGTCGAAGTGGATGATGCGTTCATTGAAGAAAAAATGG AAATTGACACTATAGATTGGAAATCCAGATATGATCAACTTGAAAGACGATTTGAGTCATTAAAACAGCG AGTTAATGAAAAGTACAATAATTGGGTTATTAAAGCAAGGAAAGTAAACGAAAACATGAACTCTCTTCAG AATGTTATTTCGCAACAACAAGCTCATATTAATGAATTACAAATATATAATAATAAACTAGAGCGTGATT TACAATCAAAAATAGGATCAGTTATCTCATCCATTGAATGGTACTTACGATCTATGGAACTGTCAGATGA CATTAAATCAGATATTGAACAACAACTCAATTCAATAGATCATATTAATCCAGTTAACGCTTTTGACGAT TTTGAGTCTATTCTTCGTAATTTAATATCTGATTATGATAGAATTTTTATTATGTTTAAAGGATTGTTGC AGCAAAGTAATTACACTTATACCTATGAGTAA]] (link-reveal-goto: "Identify unknown $F", "Final-id")[(set:$t to it + time)] , (link-reveal-goto: "Look at the sequence of another contig from this sequencing run", "Final-ResultsB")[(set:$t to it + time)], or (link-reveal-goto: "Prepare a new library and repeat the sequencing experiment?", "Final")[(set:$t to it + time)]?

(set: _seq to (random: 1, 5)) The file containing the results from sequencing the cDNA from sample $F has the following sequence: {= (if: _seq is 1)[(font:"Courier New")[ATTTAAACCCTCTCCCTTTTGGACTTCTCTAGTCTGGGGAAGTAAAATACCAGACTCCCGTTTGCCTAGG GTATAGGCTATTATTTATGTTTGTTTTGTTATGTTTGTCTTTTAATGTTTTGTAAATATTAATTCCAGCA GGTTCTGGTTTCTGAATTTGTCCTCTTTAAGGCACTCATAATGCTTTCTTTCATCTTCATTTCCCTGGCT CTCACCTTGCCAGATGGACTGACCCATGCGCCCGTGGGGGTTAACCACAGGACTAGCCTGTGGCTGTAGG TTCTGAAAGAGGTGACATTAAGACTATGGTTGTGATTCCACATGTTTTAACTGGTATGATGTAGTAGCAA TTGATCTTTGGTATGGGGTAGGCTACGGGTGAAACCCCATAGGTTAATACTAATATTTAGAGATACCTCC AGTAGGTGAAGTGCACAGGATAAGATTGAGTTATTTTGACAAAAGATCTTCAACTGTGGTGGACACCATC TCACTGGGCCAATGCTTTTGTTATGAAACCATATTGGGCATGTCTCTTGGATGAGCATTCATGGACACTG ATGCCTAGACTAGGGTGAATATTGCCTTAAATCATAGAGTTCTTTGGGATTTTATGGCCTTGCTTCTGTT GAACAGACACTGGGGCTTATGGTATTCACCCTGGCCTCTGGGGTAATCAGGGGCATTTAGGTTTTCCACA TTTATATAATGCTATGATGATGAGTCATAAAGGATTGTTGCAGAGTGTTGGGGAGGGTTTGGATAAAATC CTGACCCTCTCAGATATAGAGGAAGAACAAATGATTCAGTCAGTAGATCGAACAGCAGTAGCTGGTGCTA GTTATTTCACCTCTGTTGATCAATCTAGTGTTCACAGTGCAGAGGTTGGTTCACATCAAAGAGAGAGATT ATTAACTAGTGTAGACTTGCCTGGTTCAAAGAAAACACAGGGTGAAAAGTTTTTCCTGATACATACAGCC]] (if: _seq is 2)[(font:"Courier New")[ATACCCAGTTTGGGAATTGACAATTAGAGTTTGGTCAGAATTAAATATTGGGACAGGAACTTCAGCTTAT ACTTCACTCAATGTTTTAGCTAGATTTACAGATTTGGAGTTGCATGGATTAACTCCTCTTTCTACACAAA TGATGAGAAATGAATTTAGGGTCAGTACTACTGAGAATGTGGTGAATCTGTCAAATTATGAAGATGCAAG AGCAAAGATGTCTTTTGCTTTGGATCAGGAAGATTGGAAATCTGATCCGTCCCAGGGTGGTGGGATCAAA ATTACTCATTTTACTACTTGGACATCTATTCCAACTTTGGCTGCTCAGTTTCCATTTAATGCTTCAGACT CAGTTGGTCAACAAATTAAAGTTATTCCAGTTGACCCATATTTTTTCCAAATGACAAATACGAATCCTGA CCAAAAATGTATAACTGCTTTGGCTTCTATTTGTCAGATGTTTTGTTTTTGGAGAGGAGATCTTGTCTTT GATTTTCAAGTTTTTCCCACCAAATATCATTCAGGTAGATTACTGTTTTGTTTTGTTCCTGGCAATGAGC]] (if: _seq is 3)[(font:"Courier New")[TGACAAACACAAACCCTGACCAAAAATGTATAACTGCTTTGGCTTCTATTTGTCAGATGTTTTGTTTTTG GAGAGGAGATCTTGTCTTTGATTTTCAGGTTTTCCCGACCAAATATCATTCAGGTAGATTATTATTTTGT TTTGTTCCTGGTAATGAGCTAATAGATGTTTCTGGAATCACATTAAAACAGGCAACTACTGCTCCTTGTG CAGTGATGGACATTACAGGAGTGCAGTCAACTTTGAGATTTCGTGTTCCCTGGATTTCTGATACACCCTA TCGGGTAAACAGATATACAAAGTCAGCACATCAGAAAGGTGAGTACACTGCCATTGGGAAGCTTATTGTG TACTGTTATAACAGATTGACTTCTCCTTCTAACGTTGCTTCCCATGTTAGAGTGAATGTTTATCTTTCAG CAATTAATTTGGAATGCTTTGCTCCTCTTTATCATGCCATGGATGTTACCACACAGGTTGGAGATGATTC TGGGGGTTTTTCAACAACAGTTTCTACAGAGCAGAATGTTCCAGATCCCCAAGTTGGTATAACAACCATG AAGGATTTAAAAGGTAAAGCTAATAGGGGAAAAATGGATGTTTCAGGAGTGCAAGCACCTGTGGGAGCTA TTACAACAATTGAGGATCCTGTTTTAGCAAAGAAAGTACCTGAGACATTCCCTGAATTGAAACCTGGAGA GTCCAGGCATACATCAGATCATATGTCTATTTACAAGTTTATGGGAAGGTCTCATTTTTTGTGCACTTTT]] (if: _seq is 4)[(font:"Courier New")[CCAACCAAATATCATTCAGGTAGATTGTTGTTTTGTTTTGTTCCTGGGAATGAGTTAATAGATGTCACTG GAATTACATTAAAACAGGCAACTACTGCTCCCTGTGCAGTGATGGACATTACAGGAGTGCAGTCAACCTT GAGATTTCGTGTTCCTTGGATTTCTGATACACCCTATCGAGTGAATAGGTACACGAAGTCAGCACATCAA AAAGGTGAGTATACTGCCATTGGGAAGCTTATTGTGTATTGTTATAACAGACTGACTTCTCCTTCTAATG TTGCTTCTCATGTTAGAGTTAATGTTTATCTTTCAGCAATTAATTTGGAATGTTTTGCTCCTCTTTACCA TGCTATGGATGTTACCACACAGGTTGGAGATGATTCAGGAGGTTTCTCAACAACGGTTTCTACAGAGCAG AATGTTCCTGATCCCCAAGTTGGCATAACAACCATGAGGGACTTAAAAGGGAAAGCCAATAGGGGAAAGA TGGATGTTTCAGGAGTTCAAGCACCTGTGGGAGCTATTACAACAATTGAGGATCCAGTTTTAGCAAAGAA AGTACCTGAGACATTTCCTGAGTTGAAGCCCGGAGAGTCCAGACATACATCAGATCACATGTCCATTTAT AAATTCATGGGAAGGTCTCACTTTTTGTGTACTTTTACTTTTAATTCAAATAACAAAGAGTACACATTTC CAATAACCCTGTCTTCGACTTCAAATCCTCCTCATGGTTTACCATCAACATTAAGGTGGTTTTTCAATTT GTTCCAGCTGTATAGAGGACCATTGGATTTGACAATTATAATTACAGGAGCCACTGATGTGGATGGTATG]] (if: _seq is 5)[(font:"Courier New")[AATCAGCAAAAAATAGAAAAAGCCATTGAAGAAGCAGACAATTTTTGCATTTTGCAAATTCAAGATGTAG AGAAATTTGATCAGTATCAGAAAGGGGTTGATTTAATACAAAAGCTGAGAACTGTCCATTCAATGGCTCA AATTGACCCCAACTTGGGGGTTCATTTATCACCTCTCAGAGATTGCATAGCAAGAGTCCACCAAAAGCTC AAGAATCTTGGATCTATAAATCAAGCCATGGTAACAAGATGTGAGCCAGTTGTGTGCTATTTGTATGGTA AAAGAGGGGGAGGGAAAAGTTTGACTTCAATTGCATTGGCAACTAAAATTTGTAAACACTATGGTGTTGA ACCTGAGAAAAATATTTATACCAAACCTGTGGCTTCAGATTATTGGGATGGATATAGTGGACAATTAGTT TGCATTATTGATGATATTGGCCAAAATACAACAGATGAAGATTGGTCAGATTTTTGTCAATTGGTGTCAG GATGTCCAATGAGATTGAATATGGCTTCTCTTGAGGAGAAGGGCAGACATTTTTCTTCTCCTTTTATAAT AGCAACTTCAAATTGGTCAAATCCAAGTCCAAAAACAGTTTATGTTAAGGAAGCAATTGATCGTAGACTT CATTTTAAAGTTGAAGTTAAACCTGCTTCATTTTTTAAAAATCCTCACAACGATATGTTGAATGTTAATT TGGCCAAAACAAATGATGCAATTAAGGACATGTCTTGTGTTGATTTAATAATGGATGGACATAATATTTC ATTAATGGATTTACTTAGTTCTTTGGTGATGACAGTTGAAATTAGGAAACAGAATATGAGTGAGTTCATG GAGTTGTGGTCTCAGGGAATTTCAGATGATGACAATGATAGTGCAGTAGCTGAGTTTTTCCAGTCTTTTC]] (link-reveal-goto: "Identify unknown $F", "Final-id")[(set:$t to it + time)] , (link-reveal-goto: "Look at the sequence of another contig from this sequencing run", "Final-ResultsC")[(set:$t to it + time)], or (link-reveal-goto: "Prepare a new library and repeat the sequencing experiment?", "Final")[(set:$t to it + time)]?

"Hmmm," says your colleague, who has been helping you look at your sequencing results. "That doesn't look very much like a viral sequence to me. "I'm not sure you have identified a pathogen here ... would you like to either: (link-reveal-goto: "look at the sequence of another contig from this sequencing run", "dna-sequencing2")[(set:$t to it + time)], or (link-reveal-goto: "prepare a new library and repeat the sequencing experiment", "Final")[(set:$t to it + time)]?"

"So you're having trouble identifying a viral pathogen in unknown sample $F," your colleague says. "What seems to be the problem?" Which explanation do you give to your colleague? (link-reveal-goto: "My sequencing reactions just aren't working", "dna-seq-reason1a")[(set:$t to it + time)] or (link-reveal-goto: "I can't find any pathogen sequences", "dna-seq-reason1b")[(set:$t to it + time)] or (link-reveal-goto: "The sequences I get don't match any records in the database", "dna-seq-reason1c")[(set:$t to it + time)]

(set: $mistakes to it + 1) "What do you mean when you say that your DNA sequencing isn't working?" your colleague asks. "Don't you get any reads that you can assemble into contigs and then analyse?" "Ah," you say. "Well, I do get reads that I can assemble into contigs... the sequences that I get don't help me identify the pathogen, though." "Well, it sounds like the problem isn't with the DNA sequencing not working, then. If you're getting reads back and they're assembling into contigs and passing quality control, it sounds like the sequencing is working just fine." Maybe there's a better way to explain the problem? (link-reveal-goto: "Chat with a colleague more about why you're struggling to identify any pathogens present in unknown $F", "troubleshoot")[(set:$t to it + time)]

"So, you've looked through your data from the sequencing run and you aren't getting any pathogen sequences," your colleague says. "That's right," you say. "All of the sequences that I've looked at come from sample $F itself - they're from the $Ffood." "Hmmm," your colleague says. "What sort of pathogen were you expecting to find in sample $F?" "We weren't able to culture any bacterial pathogens from the sample, so we wanted to look for viruses." "Interesting," your colleague says. "What type of viruses might be in your sample?" (link-reveal-goto: "Viruses with DNA genomes", "dna-1b-dna")[(set:$t to it + time)], or (link-reveal-goto: "Viruses with RNA genomes", "dna-1b-rna")[(set:$t to it + time)]?

(set: $mistakes to it + 1) "What do you mean when you say that your DNA sequences don't match any sequences in the database?" your colleague asks. "What database are you using?" "Ah," you say. "Well, I do get reads that I can assemble into contigs... the sequences that I get don't help me identify the pathogen, though." "Well, it sounds like the problem isn't with the DNA sequencing not working, then. If you're getting reads back and they're assembling into contigs and passing quality control, it sounds like the sequencing is working just fine." Maybe there's a better way to explain the problem? (link-reveal-goto: "Chat with a colleague more about why you're struggling to identify any pathogens present in unknown $F", "troubleshoot")[(set:$t to it + time)]

"Viruses with DNA genomes, I see," your colleague says. "Are those commonly found in cases like this?" "I'm not sure," you say. "If I remember correctly, most enteroviruses are (link-reveal-goto: "viruses with RNA genomes", "dna-1b-rna")[(set:$t to it + time)]?," your colleague says.

"Viruses with RNA genomes, I see," your colleague says. "That's probably right - most of the enteroviruses have RNA genomes, if I remember correctly." "That's right," you say. "It sounds like you wouldn't be able to detect them using your current strategy, though. You were sequencing the DNA from sample $F, so you'll have missed out on sequencing any RNA viruses." "I guess that must be it," you say. "I'd better (link-reveal-goto: "go back and prepare a new library for sequencing", "Final")[(set:$t to it + time)] - this time I'll need to make a cDNA library instead.

Tryptose Sulphite Cycloserine (TSC) medium is a selective and differential medium commonly used for the growth and identification of Clostridium perfringens. It contains indicators for sulphite reduction (ferric iron and sodium disulfite): if bacteria on the plate reduce the sodium disulphite, it will form a black precipitate with the ferric ions and the colonies on the plate will be black. TSC also contains an indicator for lecithinase activity (lecithin): if bacteria grown on the plate produce lecithinase, an opaque halo will form around the colonies. (link: "Click to see the TSC medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Tryptose</td> <td>15.0</td> </tr> <tr> <td>Soya peptone</td> <td>5.0</td> </tr> <tr> <td>Yeast extract</td> <td>5.0</td> </tr> <tr> <td>Sodium metabisulphite</td> <td>1.0</td> </tr> <tr> <td>Ferric ammonium citrate</td> <td>1.0</td> </tr> <tr> <td>Agar</td> <td>19.0</td> </tr> </table> pH 7.6 ± 0.2 @ 25°C; 25 ml of egg yolk emulsion and 400 mg D-cycloserine added after autoclaving.] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0587&c=UK&lang=EN" target="_blank">Read more about TSC medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on TSC")[You should consider whether streaking unknown $C1 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not grow unknown $C1 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on TSC")[You should consider whether streaking unknown $C2 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on TSC")[You should consider whether streaking unknown $C3 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not grow unknown $C3 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on TSC")[You should consider whether streaking unknown $C4 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on TSC")[You should consider whether streaking unknown $C5 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on TSC")[You should consider whether streaking unknown $C6 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 on TSC")[You should consider whether streaking unknown $C7 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on TSC")[You should consider whether streaking unknown $C8 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not grow unknown $C8 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on TSC agar")[Unknown $C9 grows on TSC agar plates incubated in an anaerobic jar; the colonies are black, surrounded by opaque halos. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "Unknown $C9 grows on TSC agar plates incubated in an anaerobic jar; the colonies are black, surrounded by opaque halos.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on TSC")[You should consider whether streaking unknown $C10 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 in/on (medium name)")[Unknown $C9 grows on TSC agar plates incubated in an anaerobic jar; colonies appear after 48h incubation, and are black, with no halos. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "Unknown $C9 grows on TSC agar plates incubated in an anaerobic jar; colonies appear after 48h incubation, and are black, with no halos.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on TSC")[You should consider whether streaking unknown $C12 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not grow unknown $C12 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on TSC")[You should consider whether streaking unknown $C13 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on TSC")[You should consider whether streaking unknown $C14 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on TSC")[You should consider whether streaking unknown $C15 on TSC is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not grow unknown $C15 on Tryptose Sulphite Cycloserine (TSC) medium")) (set: $clicks to it + 1)]]

(set: $clicks to it + 1) A starch hydrolysis test measures whether an organism has the ability to cleave the complex polysaccharide, starch. Organisms are grown on a starch agar plate, which is then flooded with an iodine solution after the organisms have grown. Iodine and starch interact to produce a dark blue/black colour. If the bacteria are starch+, a clear zone will appear around the bacterial colonies If the bacteria are test-, no clear zone will appear <img alt="(insert image alt text)" src="insert image location"> Figure 1. (Add figure legend and image credit). <a href="link" target="_blank">Read more about the (name) test</a> {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to see the starch hydrolysis test results for unknown $C1")[Unknown $C1 is test ''positive/negative''.OR You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to see the starch hydrolysis test results for unknown $C2")[Unknown $C2 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem3")[(link: "Click to see the starch hydrolysis test results for unknown $C3")[Unknown $C3 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C3 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to see the starch hydrolysis test results for unknown $C4")[Unknown $C4 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to see the starch hydrolysis test results for unknown $C5")[Unknown $C5 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to see the starch hydrolysis test results for unknown $C6")[Unknown $C6 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C6 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to see the starch hydrolysis test results for unknown $C7")[Unknown $C7 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to see the starch hydrolysis test results for unknown $C8")[Unknown $C8 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C8 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to see the starch hydrolysis test results for unknown $C9")[Unknown $C9 is starch ''positive''.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to see the starch hydrolysis test results for unknown $C10")[Unknown $C10 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C10 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to see the starch hydrolysis test results for unknown $C11")[Unknown $C11 is starch ''negative''.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to see the starch hydrolysis test results for unknown $C12")[Unknown $C12 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to see the starch hydrolysis test results for unknown $C13")[Unknown $C13 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to see the starch hydrolysis test results for unknown $C14")[Unknown $C14 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C14 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to see the starch hydrolysis test results for unknown $C15")[Unknown $C15 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C15 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)]]

Lowenstein Jensen (LJ) medium is an egg-based medium selective for growth of mycobacterial species (it contains malachite green, penicillin, and nalidixic acid to inhibit the growth of most Gram negative and most other Gram positive organisms). It can be supplemented with either glycerol or pyruvate. (link: "Click to see the LJ medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>L-Asparagine</td> <td>3.600 </td> </tr> <tr> <td>Potassium dihydrogen phosphate</td> <td>2.400</td> </tr> <tr> <td>Magnesium sulphate</td> <td>0.240</td> </tr> <tr> <td>Magnesium citrate</td> <td>0.600</td> </tr> <tr> <td>Potato starch, soluble</td> <td>30.000</td> </tr> <tr> <td>Malachite green</td> <td>0.400</td> </tr> </table> After autoclaving, aseptically add egg emulsion base and (optitonal) Gruft Mycobacterial Supplement (containing penicillin and nalidixic acid)] <a href="https://assets.thermofisher.com/TFS-Assets/LSG/manuals/IFU8500.pdf" target="_blank">Read more about LJ medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on LJ")[You should consider whether streaking unknown $C1 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not grow unknown $C1 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on LJ")[You should consider whether streaking unknown $C2 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on LJ")[You should consider whether streaking unknown $C3 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not grow unknown $C3 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on LJ")[You should consider whether streaking unknown $C4 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on LJ")[You should consider whether streaking unknown $C5 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on LJ")[You should consider whether streaking unknown $C6 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 on LJ")[You should consider whether streaking unknown $C7 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on LJ")[You should consider whether streaking unknown $C8 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not grow unknown $C8 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on LJ")[You should consider whether streaking unknown $C9 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on LJ")[You should consider whether streaking unknown $C10 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 on LJ")[You should consider whether streaking unknown $C11 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on LJ")[Unknown $C12 grows very poorly on LJ medium supplemented with glycerol. Unknown $C12 grows on LJ medium supplemented with pyruvate: the colonies are small and white, with irregular edges and a granular surface. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 grows very poorly on LJ medium supplemented with glycerol. Unknown $C12 grows on LJ medium supplemented with pyruvate: the colonies are small and white, with irregular edges and a granular surface")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on LJ")[You should consider whether streaking unknown $C13 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on LJ")[You should consider whether streaking unknown $C14 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on LJ agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on LJ")[You should consider whether streaking unknown $C15 on LJ is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not grow unknown $C15 on LJ agar")) (set: $clicks to it + 1)]]

Farrell's medium (FM) is a selective growth medium containing anti-fungal agents as well as antibiotics that suppress the growth of Gram-positive and most Gram-negative bacteria. A serum-dextrose agar (without the antibiotics) can be prepared to test the resistance of Brucella spp. to dyes such as thionin and basic fuchsin. (link: "Click to see the Farrell's medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Peptone</td> <td>10.0</td> </tr> <tr> <td>Lab-Lemco powder</td> <td>5.0</td> </tr> <tr> <td>Glucose</td> <td>10.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Agar</td> <td>15.0</td> </tr> </table> pH 7.5 ± 0.2 @ 25°C; after autoclaving, 5% horse serum and polymyxin B sulfate, bacitracin, natamycin, nalidixic acid, nystatin, and vancomycin are added.] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0169&c=UK&lang=EN" target="_blank">Read more about Farrell's medium</a> (link will oopen in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on FM agar")[You should consider whether streaking unknown $C1 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not try growing unknown $C1 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on FM agar")[You should consider whether streaking unknown $C2 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not try growing unknown $C2 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on FM agar")[You should consider whether streaking unknown $C3 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not try growing unknown $C3 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on FM agar")[You should consider whether streaking unknown $C4 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not try growing unknown $C4 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on FM agar")[You should consider whether streaking unknown $C5 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C55 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not try growing unknown $C5 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on FM agar")[You should consider whether streaking unknown $C6 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not try growing unknown $C6 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 on FM agar")[You should consider whether streaking unknown $C7 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not try growing unknown $C7 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on FM agar")[You should consider whether streaking unknown $C8 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not try growing unknown $C8 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on FM agar")[You should consider whether streaking unknown $C9 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not try growing unknown $C9 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on FM")[ (link: "Click to see the results from growing unknown $C10 on FM agar")[You should consider whether streaking unknown $C10 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not try growing unknown $C10 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 on FM agar")[You should consider whether streaking unknown $C11 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not try growing unknown $C11 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on FM agar")[You should consider whether streaking unknown $C12 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not try growing unknown $C12 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on FM agar")[Unknown $C13 only grows on Farrell's medium when in a 5–10% CO2 atmosphere. Unknown $C13 grows on serum-dextrose agar containing basic fuchsin; unknown $C13 does not grow on serum-dextrose agar containing thionin. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "Unknown $C13 grows on Farrell's medium when in a 5–10% CO2 atmosphere. Unknown $C13 grows on serum-dextrose agar containing basic fuchsin; unknown $C13 does not grow on serum-dextrose agar containing thionin.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on FM agar")[You should consider whether streaking unknown $C14 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not try growing unknown $C14 on FM agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on FM agar")[You should consider whether streaking unknown $C15 on FM agar is the best experiment in light of what you know about this growth medium and the other data available about this organism Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not try growing unknown $C15 on FM agar")) (set: $clicks to it + 1)]]

Trypticase soy agar or tryptic soy agar (TSA) is a general purpose, non-selective medium suitable for the growth of a wide variety of microbes. Some ''fastidious'' organisms do not grow on TSA. (link: "Click to see the TSA medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Tryptone (pancreatic digest of casein)</td> <td>15.0</td> </tr> <tr> <td>Papaic digest of soybean meal</td> <td>5.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Agar</td> <td>15.0</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C] <a href="https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/122/065/22091dat.pdf" target="_blank">Read more about TSA medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on TSA agar")[Unknown $C15 forms pale yellow colonies on TSA when the plate is incubated at 37 °C; it forms bright yellow colonies on TSA when the plate is incubated at 25 °C. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 forms pale yellow colonies on TSA when the plate is incubated at 37 °C; it forms bright yellow colonies on TSA when the plate is incubated at 25 °C.")) (set: $clicks to it + 1)]]

A niacin test can be used to measure the accumulation of excess niacin in bacterial culture medium (for example, most species of Mycobacterium tuberculosis are strongly niacin-positive.) The test uses paper strips containing indicator compounds which in the presence of niacin will produce a yellow colour. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are niacin+, a yellow colour will be produced. If the bacteria are niacin-, no colour will be produced.] <a href="https://tools.thermofisher.com/content/sfs/manuals/IFU21090.pdf" target="_blank">Read more about the niacin test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform the niacin test on unknown $C1")[You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not perform a niacin test on unknown $C1")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform the niacin test on unknown $C2")[You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not perform a niacin test on unknown $C2")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform the niacin test on unknown $C3")[You should consider whether this is the best experiment to identify unknown $C3 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not perform a niacin test on unknown $C3")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform the niacin test on unknown $C4")[You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not perform a niacin test on unknown $C4")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform the niacin test on unknown $C5")[You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not perform a niacin test on unknown $C5")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform the niacin test on unknown $C6")[You should consider whether this is the best experiment to identify unknown $C6 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not perform a niacin test on unknown $C6")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform the niacin test on unknown $C7")[You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not perform a niacin test on unknown $C7")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform the niacin test on unknown $C8")[You should consider whether this is the best experiment to identify unknown $C8 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not perform a niacin test on unknown $C8")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform the niacin test on unknown $C9")[You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not perform a niacin test on unknown $C9")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform the niacin test on unknown $C10")[You should consider whether this is the best experiment to identify unknown $C10 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not perform a niacin test on unknown $C10")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform the niacin test on unknown $C11")[You should consider whether this is the best experiment to identify unknown $C11 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not perform a niacin test on unknown $C11")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform the niacin test on unknown $C12")[Unknown $C12 is niacin ''negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 is niacin negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform the niacin test on unknown $C13")[You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not perform a niacin test on unknown $C13")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform the niacin test on unknown $C14")[You should consider whether this is the best experiment to identify unknown $C14 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not perform a niacin test on unknown $C14")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform the niacin test on unknown $C15")[You should consider whether this is the best experiment to identify unknown $C15 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not perform a niacin test on unknown $C15")) (set: $clicks to it + 1)]]

The pyrazinamidase test measures the activity of pyrazinamidase (PZase), an enzyme which converts pyrazinamide (PZA) to ammonia and pyrazinoic acid. Ferrous iron is added to detect the PZase activity, as pyrazinoic acid forms a pink complex with the ferrous iron. (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[If the bacteria are PZase +, a pink band will form at the surface of the agar. If the bacteria are PZase -, no colour will develop.] <a href="https://tools.thermofisher.com/content/sfs/manuals/IFU7136.pdf" target="_blank">Read more about the PZase test</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to perform the pyrazinamidase test on unknown $C1")[You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "You did not perform a pyrazinamidase test on unknown $C1")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to perform the pyrazinamidase test on unknown $C2")[You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not perform a pyrazinamidase test on unknown $C2")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem3")[(link: "Click to perform the pyrazinamidase test on unknown $C3")[You should consider whether this is the best experiment to identify unknown $C3 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not perform a pyrazinamidase test on unknown $C3")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to perform the pyrazinamidase test on unknown $C4")[You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not perform a pyrazinamidase test on unknown $C4")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to perform the pyrazinamidase test on unknown $C5")[You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not perform a pyrazinamidase test on unknown $C5")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to perform the pyrazinamidase test on unknown $C6")[You should consider whether this is the best experiment to identify unknown $C6 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not perform a pyrazinamidase test on unknown $C6")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to perform the pyrazinamidase test on unknown $C7")[You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not perform a pyrazinamidase test on unknown $C7")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to perform the pyrazinamidase test on unknown $C8")[You should consider whether this is the best experiment to identify unknown $C8 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "You did not perform a pyrazinamidase test on unknown $C8")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to perform the pyrazinamidase test on unknown $C9")[You should consider whether this is the best experiment to identify unknown $C9 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not perform a pyrazinamidase test on unknown $C9")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to perform the pyrazinamidase test on unknown $C10")[You should consider whether this is the best experiment to identify unknown $C10 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not perform a pyrazinamidase test on unknown $C10")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to perform the pyrazinamidase test on unknown $C11")[You should consider whether this is the best experiment to identify unknown $C11 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not perform a pyrazinamidase test on unknown $C11")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to perform the pyrazinamidase test on unknown $C12")[Unknown $C12 is pyrazinamidase ''negative''. Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 is pyrazinamidase negative")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to perform the pyrazinamidase test on unknown $C13")[You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not perform a pyrazinamidase test on unknown $C13")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to perform the pyrazinamidase test on unknown $C14")[You should consider whether this is the best experiment to identify unknown $C14 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not perform a pyrazinamidase test on unknown $C14")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to perform the pyrazinamidase test on unknown $C15")[You should consider whether this is the best experiment to identify unknown $C15 in light of what you know about this test and the other data available about this organism. Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "You did not perform a pyrazinamidase test on unknown $C15")) (set: $clicks to it + 1)]]

Middlebrook 7H9 medium is commonly used for the growth of mycobacteria, and can be used to test for oxygen preferences when made semi-solid by the addition of 0.1% agar. (link: "Click to see the Middlebrook 7H9 medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Ammonium sulphate</td> <td>0.500</td> </tr> <tr> <td>Disodium hydrogen phosphate</td> <td>2.500</td> </tr> <tr> <td>Potassium dihydrogen phosphate</td> <td>1.000</td> </tr> <tr> <td>Sodium citrate</td> <td>0.100</td> </tr> <tr> <td>Magnesium sulphate</td> <td>0.050</td> </tr> <tr> <td>Calcium chloride anhydrous</td> <td>0.0005</td> </tr> <tr> <td>Zinc sulphate</td> <td>0.001</td> </tr> <tr> <td>Copper sulphate</td> <td>0.001</td> </tr> <tr> <td>Ferric ammonium citrate</td> <td>0.040</td> </tr> <tr> <td>L-Glutamic acid</td> <td>0.500</td> </tr> <tr> <td>Pyridoxine hydrochloride</td> <td>0.001</td> </tr> <tr> <td>Biotin</td> <td>0.0005</td> </tr> </table> pH 6.6 ± 0.2 @ 25°C] (link: "Click to see the results from growing unknown $C12 in thioglycollate medium")[Unknown $C12 grows just below the surface, but not on the surface, of the growth medium. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "Unknown $C12 did not grow in thioglycollate medium.")) (set: $clicks to it + 1)]

1. Rename this passage to the name of the growth medium 2. ADD this code to each of the plates1, plates2, etc. passages: (link-reveal-goto: "Grow organism $C4 on/in (medium name)", "(name of THIS passage")[(set:$t to it + time)] 3. Edit the code for this passage as appropriate: (set: $clicks to it + 1) Insert brief description of medium here <img alt="insert alt text here" src="insert image link here"> Figure 1. Add figure legend and image credit (link: "Click to see the (insert name here) medium recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>insert name of component here </td> <td>insert amount in grams </td> </tr> <tr> <td>add as many/td> <td>rows as necessary</td> </tr> </table> pH (specify) ± (value) @ 25°C, or add any additional instructions here] <a href="link" target="_blank">Read more about X medium (Oxoid)</a> https://assets.fishersci.com/TFS-Assets/MBD/Instructions/IFU61274.pdf {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 in/on (medium name)")[Unknown $C1 (phenotype)] Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 in/on (medium name)")[Unknown $C2 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 in/on (medium name)")[Unknown $C3 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 in/on (medium name)")[Unknown $C4 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 in/on (medium name)")[Unknown $C5 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 in/on (medium name)")[Unknown $C6 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 in/on (medium name)")[Unknown $C7 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 in/on (medium name)")[Unknown $C8 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 in/on (medium name)")[Unknown $C9 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 in/on (medium name)")[Unknown $C10 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 in/on (medium name)")[Unknown $C11 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 in/on (medium name)")[Unknown $C12 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 in/on (medium name)")[Unknown $C13 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 in/on (medium name)")[Unknown $C14 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 in/on (medium name)")[Unknown $C15 (phenotype).] Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)]]

(set: $clicks to it + 1) An aesculin hydrolysis test measures the ability of an organism to hydrolyse the glucoside aesculin, producing glucose and aesculetin (which forms a black precipitate in the presence of ferric iron). Aesculin hydrolysis can also be detected by loss of fluorescence (aesculin fluoresces under UV light, while aesculetin does not). Your laboratory commonly performs an aesculin hydrolysis test as a spot test, but it can also be done by growing the organisms on agar containing aesculin and ferric iron (the medium can be made selective by adding bile salts). If the bacteria are aesculin+, fluorescence will be lost / a black precipitate will form If the bacteria are aesculin-, the sample will still fluoresce / no precipitate will form <img alt="(insert image alt text)" src="insert image location"> Figure 1. (Add figure legend and image credit). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC274422/pdf/jcm00217-0086.pdf" target="_blank">Read more about the aesculin hydrolysis test</a> {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "biochem1")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C1")[Unknown $C1 is test ''positive/negative''.OR You should consider whether this is the best experiment to identify unknown $C1 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem2")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C2")[Unknown $C2 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C2 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem3")[(link: "Click to see the aesculin hydrolysis test results for unknown $C3")[Unknown $C3 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C3 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem4")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C4")[Unknown $C4 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C4 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem5")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C5")[Unknown $C5 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C5 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem6")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C6")[Unknown $C6 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C6 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem7")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C7")[Unknown $C7 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C7 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem8")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C8")[Unknown $C8 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C8 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem9")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C9")[Unknown $C9 is aesculin ''positive''] Back to (link-reveal-goto: "perform another biochemical test?", "biochem9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem10")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C10")[Unknown $C10 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C10 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem11")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C11")[Unknown $C11 is aesculin ''positive''.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem12")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C12")[Unknown $C12 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C12 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem13")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C13")[Unknown $C13 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C13 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem14")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C14")[Unknown $C14 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C14 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)]] (else-if: _lastPassage is "biochem15")[ (link: "Click to see the aesculin hydrolysis test results for unknown $C15")[Unknown $C15 is test ''positive/negative''. OR You should consider whether this is the best experiment to identify unknown $C15 in light of what you know about this test and the other data available about this organism.] Back to (link-reveal-goto: "perform another biochemical test?", "biochem15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)]]

Double-click this passage to edit it.

1. medium - calculate number of grams needed, or medium - calculate %s -blood agar, thioglycollate, TSA, motility agar (all vol1) 2. specific medium 1 - SMAC 2 - PALCAM 3 - Hektoen 4 - mCCD 5 - MYP 6 - TCBS 7 - MSA 8 - XLD 9 - TSC 10 - CIN 11 - RCM 12 - LJ 13 - SDA 14 - TCBS 15 - ESIA 3. task (e.g. PCR calculation, biochemical test) nitrate - 3, 4, 5, 6, 7, 8, 9, 13 VP MR(?) 4 - hippurate 9 - aesculin starch/Gram's stain (iodine) - 5, 9 or 11 imvic - 1, 3, 8, 15 NaCl tolerance? - 6, 14 4. molarity?

{ (set: _ans to 15 * $vol13) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of tryptic soy agar (TSA) medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Tryptone (pancreatic digest of casein)</td> <td>15.0</td> </tr> <tr> <td>Papaic digest of soybean meal</td> <td>5.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Agar</td> <td>15.0</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C] How many grams of tryptone do you need to make $vol13 mL of TSA medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to see the hint: (set: _password to "")\ (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 3 * $vol19) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of motility agar is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>amount/litre</th> </tr> <tr> <td>Beef extract</td> <td>3.0 g</td> </tr> <tr> <td>Pancreatic digest of casein</td> <td>10.0 g</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0 g</td> </tr> <tr> <td>Agar</td> <td>4.0 g</td> </tr> <tr> <td>1% triphenyltetrazolium chloride solution </td> <td>5 mL</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C] How many grams of beef extract do you need to make $vol19 mL of motility agar? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5 * $vol18) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of motility agar is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>amount/litre</th> </tr> <tr> <td>Beef extract</td> <td>3.0 g</td> </tr> <tr> <td>Pancreatic digest of casein</td> <td>10.0 g</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0 g</td> </tr> <tr> <td>Agar</td> <td>4.0 g</td> </tr> <tr> <td>1% triphenyltetrazolium chloride solution </td> <td>5 mL</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C How many grams of sodium chloride do you need to make $vol18 mL of motility agar? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 25/10 * $vol5) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of thioglycollate medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>5.0</td> </tr> <tr> <td>Tryptone</td> <td>15.0</td> </tr> <tr> <td>Glucose</td> <td>5.5</td> </tr> <tr> <td>Sodium thioglycollate</td> <td>0.5</td> </tr> <tr> <td>Sodium chloride</td> <td>2.5</td> </tr> <tr> <td>Resazurin</td> <td>0.001</td> </tr> <tr> <td>Agar</td> <td>0.75</td> </tr> </table> pH 7.1 ± 0.2 @ 25°C How many grams of sodium chloride do you need to make $vol5 mL of thioglycollate medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5 * $vol4) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of blood agar is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Peptone</td> <td>23.0</td> </tr> <tr> <td>Starch</td> <td>1.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Agar</td> <td>10.0</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C 5% sterile defibrinated blood added after autoclaving. How many grams of sodium chloride do you need to make $vol4 mL of blood agar? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 15 * $vol24) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of tryptic soy agar (TSA) medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Tryptone (pancreatic digest of casein)</td> <td>15.0</td> </tr> <tr> <td>Papaic digest of soybean meal</td> <td>5.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Agar</td> <td>15.0</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C] How many grams of agar do you need to make $vol24 mL of TSA medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 15 * $vol8) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of thioglycollate medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>5.0</td> </tr> <tr> <td>Tryptone</td> <td>15.0</td> </tr> <tr> <td>Glucose</td> <td>5.5</td> </tr> <tr> <td>Sodium thioglycollate</td> <td>0.5</td> </tr> <tr> <td>Sodium chloride</td> <td>2.5</td> </tr> <tr> <td>Resazurin</td> <td>0.001</td> </tr> <tr> <td>Agar</td> <td>0.75</td> </tr> </table> pH 7.1 ± 0.2 @ 25°C How many grams of tryptone do you need to make $vol8 mL of thioglycollate medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 3/4 * $vol9) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of thioglycollate medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>5.0</td> </tr> <tr> <td>Tryptone</td> <td>15.0</td> </tr> <tr> <td>Glucose</td> <td>5.5</td> </tr> <tr> <td>Sodium thioglycollate</td> <td>0.5</td> </tr> <tr> <td>Sodium chloride</td> <td>2.5</td> </tr> <tr> <td>Resazurin</td> <td>0.001</td> </tr> <tr> <td>Agar</td> <td>0.75</td> </tr> </table> pH 7.1 ± 0.2 @ 25°C How many grams of agar do you need to make $vol9 mL of thioglycollate medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 55/10 * $vol10) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of thioglycollate medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>5.0</td> </tr> <tr> <td>Tryptone</td> <td>15.0</td> </tr> <tr> <td>Glucose</td> <td>5.5</td> </tr> <tr> <td>Sodium thioglycollate</td> <td>0.5</td> </tr> <tr> <td>Sodium chloride</td> <td>2.5</td> </tr> <tr> <td>Resazurin</td> <td>0.001</td> </tr> <tr> <td>Agar</td> <td>0.75</td> </tr> </table> pH 7.1 ± 0.2 @ 25°C How many grams of glucose do you need to make $vol10 mL of thioglycollate medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5 * $vol15) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of thioglycollate medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>5.0</td> </tr> <tr> <td>Tryptone</td> <td>15.0</td> </tr> <tr> <td>Glucose</td> <td>5.5</td> </tr> <tr> <td>Sodium thioglycollate</td> <td>0.5</td> </tr> <tr> <td>Sodium chloride</td> <td>2.5</td> </tr> <tr> <td>Resazurin</td> <td>0.001</td> </tr> <tr> <td>Agar</td> <td>0.75</td> </tr> </table> pH 7.1 ± 0.2 @ 25°C How many grams of yeast extract do you need to make $vol15 mL of thioglycollate medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to see the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 4 * $vol14) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of motility agar is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>amount/litre</th> </tr> <tr> <td>Beef extract</td> <td>3.0 g</td> </tr> <tr> <td>Pancreatic digest of casein</td> <td>10.0 g</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0 g</td> </tr> <tr> <td>Agar</td> <td>4.0 g</td> </tr> <tr> <td>1% triphenyltetrazolium chloride solution </td> <td>5 mL</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C How many grams of agar do you need to make $vol14 mL of motility agar? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5 * $vol20) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of tryptic soy agar (TSA) medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Tryptone (pancreatic digest of casein)</td> <td>15.0</td> </tr> <tr> <td>Papaic digest of soybean meal</td> <td>5.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Agar</td> <td>15.0</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C] How many grams of papaic digest of soybean meal do you need to make $vol20 mL of TSA medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) • (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5 * $vol25) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of tryptic soy agar (TSA) medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Tryptone (pancreatic digest of casein)</td> <td>15.0</td> </tr> <tr> <td>Papaic digest of soybean meal</td> <td>5.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Agar</td> <td>15.0</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C] How many grams of sodium chloride do you need to make $vol25 mL of TSA medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) • (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 23 * $vol1) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of blood agar is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Peptone</td> <td>23.0</td> </tr> <tr> <td>Starch</td> <td>1.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Agar</td> <td>10.0</td> </tr> </table> pH 7.3 ± 0.2 @ 25°C 5% sterile defibrinated blood added after autoclaving. How many grams of peptone do you need to make $vol1 mL of blood agar? Enter the number of grams in the box below and click "Answer" to earn the hint: (set: _password to "")\ (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5/100 * $vol2) (set: _ans2 to (string: _ans * 1000)) } Solve a problem to earn a hint to help you identify an unknown. To perform a Voges-Proskauer test, you require the following reagents (prepared fresh): Barritt’s reagent A: 5% (wt/vol) alpha-naphthol in absolute ethanol Barritt’s reagent B: 40% (wt/vol) KOH in deionized water (this might be replaced by a 40% (wt/vol) NaOH solution) How many milligrams (mg) of alpha-napthol do you need to make $vol2 mL of Barrit's reagent A? (set: _password to "")\ Enter the number of milligrams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 12 * $vol3) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of Hektoen Enteric Agar medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Proteose peptone</td> <td>12.0</td> </tr> <tr> <td>Yeast extract</td> <td>3.0</td> </tr> <tr> <td>Lactose</td> <td>12.0</td> </tr> <tr> <td>Sucrose</td> <td>12.0</td> </tr> <tr> <td>Salicin</td> <td>2.0</td> </tr> <tr> <td>Bile salts No. 3</td> <td>9.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Sodium thiosulphate</td> <td>5.0</td> </tr> <tr> <td>Ammonium ferric citrate</td> <td>1.5</td> </tr> <tr> <td>Acid fuchsin</td> <td>0.1</td> </tr> <tr> <td>Bromothymol blue</td> <td>0.065</td> </tr> <tr> <td>Agar</td> <td>14.0</td> </tr> </table> pH 7.5 ± (value) @ 25°C How many grams of sucrose do you need to make $vol3 mL of this medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5/100 * $vol31) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to test the ability of some of your unknown organisms to ferment certain carbohydrates. To do so, you will grow these organisms in medium containing a pH indicator and the carbohydrate (for example, the sugar mannitol). You have a 20% (w/v) stock solution of manniitol; the desired final concentration of mannitol in the growth medium is 1%. How many mL of your mannitol stock solution do you need to add to make up $vol31 mL of your growth medium? (set: _password to "")\ Enter the number of millilitres in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5/100 * $vol29) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to test the ability of some of your unknown organisms to ferment certain carbohydrates. To do so, you will grow these organisms in medium containing a pH indicator and the carbohydrate (for example, the sugar sorbitol). You have a 20% (w/v) stock solution of sorbitol; the desired final concentration of sorbitol in the growth medium is 1%. How many mL of your sorbitol stock solution do you need to add to make up $vol29 mL of your growth medium? (set: _password to "")\ Enter the number of millilitres in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 10 * $vol36) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of MYP medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Meat extract</td> <td>1.0</td> </tr> <tr> <td>Peptone</td> <td>10.0</td> </tr> <tr> <td>Mannitol</td> <td>10.0</td> </tr> <tr> <td>Sodium chloride</td> <td>10.0</td> </tr> <tr> <td>Phenol Red</td> <td>0.025</td> </tr> <tr> <td>Agar</td> <td>12.0</td> </tr> </table> pH 7.2 ± 0.2 @ 25°C, polymyxin added after autoclaving. How many grams of peptone do you need to make $vol36 mL of MYP medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 10 * $vol37) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of MYP medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Meat extract</td> <td>1.0</td> </tr> <tr> <td>Peptone</td> <td>10.0</td> </tr> <tr> <td>Mannitol</td> <td>10.0</td> </tr> <tr> <td>Sodium chloride</td> <td>10.0</td> </tr> <tr> <td>Phenol Red</td> <td>0.025</td> </tr> <tr> <td>Agar</td> <td>12.0</td> </tr> </table> pH 7.2 ± 0.2 @ 25°C, polymyxin added after autoclaving. How many grams of mannitol do you need to make $vol37 mL of MYP medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 1/10 * $vol33) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to test the ability of some of your unknown organisms to ferment certain carbohydrates. To do so, you will grow these organisms in medium containing a pH indicator and the carbohydrate (for example, the sugar mannose). You have a 10% (w/v) stock solution of mannose; the desired final concentration of mannose in the growth medium is 1%. How many mL of your mannose stock solution do you need to add to make up $vol33 mL of your growth medium? (set: _password to "")\ Enter the number of millilitres in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 12 * $vol38) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of Hektoen Enteric Agar medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Proteose peptone</td> <td>12.0</td> </tr> <tr> <td>Yeast extract</td> <td>3.0</td> </tr> <tr> <td>Lactose</td> <td>12.0</td> </tr> <tr> <td>Sucrose</td> <td>12.0</td> </tr> <tr> <td>Salicin</td> <td>2.0</td> </tr> <tr> <td>Bile salts No. 3</td> <td>9.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Sodium thiosulphate</td> <td>5.0</td> </tr> <tr> <td>Ammonium ferric citrate</td> <td>1.5</td> </tr> <tr> <td>Acid fuchsin</td> <td>0.1</td> </tr> <tr> <td>Bromothymol blue</td> <td>0.065</td> </tr> <tr> <td>Agar</td> <td>14.0</td> </tr> </table> pH 7.5 ± (value) @ 25°C pH 7.2 ± 0.2 @ 25°C, polymyxin added after autoclaving. How many grams of proteose peptone do you need to make $vol38 mL of MYP medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 1/10 * $vol34) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to test the ability of some of your unknown organisms to ferment certain carbohydrates. To do so, you will grow these organisms in medium containing a pH indicator and the carbohydrate (for example, the sugar arabinose). You have a 10% (w/v) stock solution of arabinose; the desired final concentration of arabinose in the growth medium is 1%. How many mL of your arabinose stock solution do you need to add to make up $vol34 mL of your growth medium? (set: _password to "")\ Enter the number of millilitres in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 12 * $vol39) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of Hektoen Enteric Agar medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Proteose peptone</td> <td>12.0</td> </tr> <tr> <td>Yeast extract</td> <td>3.0</td> </tr> <tr> <td>Lactose</td> <td>12.0</td> </tr> <tr> <td>Sucrose</td> <td>12.0</td> </tr> <tr> <td>Salicin</td> <td>2.0</td> </tr> <tr> <td>Bile salts No. 3</td> <td>9.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Sodium thiosulphate</td> <td>5.0</td> </tr> <tr> <td>Ammonium ferric citrate</td> <td>1.5</td> </tr> <tr> <td>Acid fuchsin</td> <td>0.1</td> </tr> <tr> <td>Bromothymol blue</td> <td>0.065</td> </tr> <tr> <td>Agar</td> <td>14.0</td> </tr> </table> pH 7.5 ± (value) @ 25°C pH 7.2 ± 0.2 @ 25°C, polymyxin added after autoclaving. How many grams of lactose do you need to make $vol39 mL of MYP medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 1/10 * $vol35) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to test the ability of some of your unknown organisms to ferment certain carbohydrates. To do so, you will grow these organisms in medium containing a pH indicator and the carbohydrate (for example, the sugar melibiose). You have a 10% (w/v) stock solution of melibiose; the desired final concentration of melibiose in the growth medium is 1%. How many mL of your melibiose stock solution do you need to add to make up $vol35 mL of your growth medium? (set: _password to "")\ Enter the number of millilitres in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 50 * $vol41) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You wish to test the sensitivity of a particular clinical isolate to antibiotics. Unfortunately, a selfish colleague has used up the last of the lab's antibiotic stocks without replenishing them. You need to make $vol41 mL of a 50 mg/mL stock of ampicillin. How many mg of ampicillin do you need? (set: _password to "")\ Enter the number of milligrams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 125/1000*$rxn6) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. While working in the lab, you wish to set up some diagnostic PCRs. The recipe for a single reaction is shown below: <table> <table border="1"> <tr> <th>Component</th> <th>Amount (50 µL reaction)</th> </tr> <tr> <td>10X Standard Taq Reaction Buffer</td> <td>2.5 μL</td> </tr> <tr> <td>10 mM dNTPs</td> <td>0.5 µL</td> </tr> <tr> <td>10 µM Forward Primer</td> <td>0.5 µl</td> </tr> <tr> <td>10 µM Reverse Primer</td> <td>0.5 µl</td> </tr> <tr> <td>Template DNA</td> <td>variable volume (1 ng–1 μg genomic DNA)</td> </tr> <tr> <td>Taq DNA Polymerase</td> <td>0.125 µL</td> </tr> <tr> <td>Nuclease-free water</td> <td>to 25 µL</td> </tr> </table> You wish to set up a mastermix for $rxn6 reactions. How many µL of Taq polymerase do you need to make up this mastermix? (set: _password to "")\ Enter the number of µL in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 40/100 * $vol7) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. To perform a Voges-Proskauer test, you require the following reagents (prepared fresh): Barritt’s reagent A: 5% (wt/vol) alpha-naphthol in absolute ethanol Barritt’s reagent B: 40% (wt/vol) KOH in deionized water (this might be replaced by a 40% (wt/vol) NaOH solution) How many grams of potassium hydroxide do you need to make $vol7 mL of Barrit's reagent B? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 12/100 * $vol11) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You normally perform the hippurate hydrolysis test using a <a href="https://assets.thermofisher.com/TFS-Assets/LSG/manuals/IFU61150.pdf" target="_blank">kit purchased from Remel</a> , but you have run out of one of the reagents - Hippurate Hydrolysis Reagent, 12% (w/v) ferric cloride. How many grams of ferric chloride do you need to make $vol11 mL of this reagent? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5 * $vol17) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. To stain endospores using malachite green, you need to prepare a solution of malachite green stain (0.5% (wt/vol) aqueous solution) How many milligrams of malachite green do you need to make $vol17 mL of this reagent? (set: _password to "")\ Enter the number of milligrams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 8/10 * $vol16 / 100) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. To perform a nitrate reduction test, you require the following reagents: Reagent A 0.6 mL N,N-Dimethyl-α-naphthylamine 100 mL 5N Acetic acid Reagent B 0.8 g Sulfanilic acid 100 mL 5N Acetic acid How many grams of sulfanilic acid do you need to make $vol16 mL of reagent B? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to $vol23/10) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. While working in the lab, you wish to set up some diagnostic PCRs. The recipe for a single reaction is shown below: <table> <table border="1"> <tr> <th>Component</th> <th>Amount (50 µL reaction)</th> </tr> <tr> <td>10X Standard Taq Reaction Buffer</td> <td>2.5 μL</td> </tr> <tr> <td>10 mM dNTPs</td> <td>0.5 µL</td> </tr> <tr> <td>10 µM Forward Primer</td> <td>0.5 µl</td> </tr> <tr> <td>10 µM Reverse Primer</td> <td>0.5 µl</td> </tr> <tr> <td>Template DNA</td> <td>variable volume (1 ng–1 μg genomic DNA)</td> </tr> <tr> <td>Taq DNA Polymerase</td> <td>0.125 µL</td> </tr> <tr> <td>Nuclease-free water</td> <td>to 25 µL</td> </tr> </table> You need to prepare a 10 mM dNTPs solution so that you can set up your PCR reaction. You have 0.1 M stock solutions of each of the dNTPs. How many µl of each dNTP stock solution should you use to make $vol23 µl of your 10 mM dNTPs solution? (set: _password to "")\ Enter the number of µL in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5/100 * $vol22) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to test the ability of some of your unknown organisms to ferment certain carbohydrates. To do so, you will grow these organisms in medium containing a pH indicator and the carbohydrate (for example, the sugar lactose). You have a 20% (w/v) stock solution of lactose; the desired final concentration of lactose in the growth medium is 1%. How many mL of your lactose stock solution do you need to add to make up $vol22 mL of your growth medium? (set: _password to "")\ Enter the number of millilitres in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 2/10 * $vol21) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to test the ability of some of your unknown organisms to hydrolyse aesculin. To do this, you must prepare a 0.02% (w/v) aesculin solution. How many milligrams of aesculin do you need to add to make up $vol21 mL of this solution? (set: _password to "")\ Enter the number of milligrams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5/100 * $vol26) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to prepare Kovac's reagent (for the indole test) according to the recipe below: <table> <table border="1"> <tr> <th>Component</th> <th>Amount</th> </tr> <tr> <td>//p//-dimethylaminobenzaldehyde</td> <td>5 g</td> <tr> <td>Amyl alcohol</td> <td>75 ml</td> </tr> <tr> <td>HCl (concentrated)</td> <td>25 ml</td> </tr> </table> Dissolve// p//-dimethylaminobenzaldehyde in normal amyl alcohol. Slowly add HCl. How many grams of //p//-dimethylaminobenzaldehyde do you need to add to make up $vol26 mL of this reagent? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans2 to (string: 0.1)) } Solve a problem to earn a hint to help you identify an unknown. While working in the lab, you wish to set up some diagnostic PCRs. The recipe for a single reaction is shown below: <table> <table border="1"> <tr> <th>Component</th> <th>Amount (50 µL reaction)</th> </tr> <tr> <td>10X Standard Taq Reaction Buffer</td> <td>2.5 μL</td> </tr> <tr> <td>10 mM dNTPs</td> <td>0.5 µL</td> </tr> <tr> <td>10 µM Forward Primer</td> <td>0.5 µl</td> </tr> <tr> <td>10 µM Reverse Primer</td> <td>0.5 µl</td> </tr> <tr> <td>Template DNA</td> <td>variable volume (1 ng–1 μg genomic DNA)</td> </tr> <tr> <td>Taq DNA Polymerase</td> <td>0.125 µL</td> </tr> <tr> <td>Nuclease-free water</td> <td>to 25 µL</td> </tr> </table> You set up a $rxn27 PCRs (50 µL reaction) as described. What is the final concentration of your reverse primer (in µM) in your reaction mixture? (set: _password to "")\ Enter the concentration in µM in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 10 * $vol28) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of MYP medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Meat extract</td> <td>1.0</td> </tr> <tr> <td>Peptone</td> <td>10.0</td> </tr> <tr> <td>Mannitol</td> <td>10.0</td> </tr> <tr> <td>Sodium chloride</td> <td>10.0</td> </tr> <tr> <td>Phenol Red</td> <td>0.025</td> </tr> <tr> <td>Agar</td> <td>12.0</td> </tr> </table> pH 7.2 ± 0.2 @ 25°C, polymyxin added after autoclaving. How many grams of sodium chloride do you need to make $vol28 mL of MYP medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 5/100 * $vol30) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to test the ability of some of your unknown organisms to ferment certain carbohydrates. To do so, you will grow these organisms in medium containing a pH indicator and the carbohydrate (for example, the sugar glucose). You have a 20% (w/v) stock solution of glucose; the desired final concentration of glucose in the growth medium is 1%. How many mL of your glucose stock solution do you need to add to make up $vol30 mL of your growth medium? (set: _password to "")\ Enter the number of millilitres in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 10 * $vol40) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of MacConkey/lactose Agar medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Peptone</td> <td>20.0</td> </tr> <tr> <td>Lactose</td> <td>10.0</td> </tr> <tr> <td>Bile salts</td> <td>5.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Neutral red</td> <td>0.075</td> </tr> <tr> <td>Agar</td> <td>12.0</td> </tr> </table> pH 7.4 ± 0.2 @ 25°C pH 7.2 ± 0.2 @ 25°C, polymyxin added after autoclaving. How many grams of lactose do you need to make $vol40 mL of MacConkey/lactose medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 25 * $vol42) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You wish to test the sensitivity of a particular clinical isolate to antibiotics. Unfortunately, a selfish colleague has used up the last of the lab's antibiotic stocks without replenishing them. You need to make $vol42 mL of a 25 mg/mL stock of chloramphenicol. How many mg of chloramphenicol do you need? (set: _password to "")\ Enter the number of milligrams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

(set: $test to (a: "Gram stain is positive", "Malachite green is negative", "catalase is positive")) (set: _lactose to 0) (set: $test to it + (a: "lactose fermentation is positive")) (set: $test to it + (a: "lactose fermentation is positive")) (for: each _item where it contains "lactose", ...$test)[(set: _lactose to it + 1)] (if: _lactose > 0)[You should test for aerobic growth] (else:)[You should test for lactose fermentation!]

If you would like a hint to help you identify any of your unknowns, you must earn the hint by solving a calculation--based problem (similar to the types of problems that you might have to solve in a clinical microbiology lab.) If you answer incorrectly, you will be provided with a different question. (If you are struggling to enter the right answer, please check that you are answering the Points that you earn here can be applied towards a hint that will help you identify any of your unknowns. (You can redeem these points in the unknown's notebook page.) You currently have earned $earnedclues hints. Would you like to (link-reveal-goto: "solve a problem to earn a hint", "Problem")[(set:$t to it + time)]?

{ (set: _ans to 1/1000 * $vol12) (set: _ans2 to (string: _ans/1000)) } Solve a problem to earn a hint to help you identify an unknown. The recipe for making up 1 L of thioglycollate medium is shown below. <table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>5.0</td> </tr> <tr> <td>Tryptone</td> <td>15.0</td> </tr> <tr> <td>Glucose</td> <td>5.5</td> </tr> <tr> <td>Sodium thioglycollate</td> <td>0.5</td> </tr> <tr> <td>Sodium chloride</td> <td>2.5</td> </tr> <tr> <td>Resazurin</td> <td>0.001</td> </tr> <tr> <td>Agar</td> <td>0.75</td> </tr> </table> pH 7.1 ± 0.2 @ 25°C How many grams of resazurin do you need to make $vol12 mL of thioglycollate medium? (set: _password to "")\ Enter the number of grams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1) (link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

There are a number of resources to help you linked in the "Library" at the top of the game pages; you can also use your course notes, textbook(s), and any other resources that you can find (remember, however, that not all information on the internet is trustworthy.) You can come back to these instructions at any point by clicking "About" at the top of the page. (b4r:"solid")+(b4r-size:4)+(b4r-color:red)[''Important note:'' Refreshing or reloading this page in your browser will result in a new set of unknown organisms being chosen for you to identify. Only refresh the page if you want to start the game over again!] You will receive a different number of randomly selected samples to analyse depending on the difficulty level you select. (link-goto: "Choose difficulty level", "LevelChoice")

{(if: $choice is 1)[(display: "Key1")] {(if: $choice is 4)[(display: "Key4")] (else-if: $choice is 6)[(display: "Key6")] (else-if: $choice is 8)[(display: "Key8")] (else-if: $choice is 12)[(display: "Key12")]}

{(set: $showFooter to true) (set: $t to time) (if: $choice is 1)[You have chosen to play this scenario in $mode mode. Note that demo mode works exactly like the other modes, except that your ability to sequence the 16S gene or whole genome sequence of the organism has been disabled - you need to work through the different tests and use logic to identify the unknown. Your task is to identify 1 bacterium isolated from a food produced in the factory. The case is linked at the bottom of this page: click to begin when you are ready. When you have identified the unknown, you will be able to escape the room by clicking the "Escape the room" link at the top of the page. Good luck!] (else-if: $choice is >1)[ You have chosen to play this scenario in $mode mode. Your task is to identify $choice bacteria isolated from different foods produced in the factory. The cases are linked at the bottom of this page: you can solve them in any order. When you have identified all $choice unknowns, you will be able to escape the room by clicking the "Escape the room" link at the top of the page. Good luck!] }

(b4r:"solid")+(b4r-size:4)+(b4r-color:red)[''Important note:'' Refreshing or reloading this page in your browser may result in a new set of unknown organisms being chosen for you to identify. Only refresh the page if you want to start the game over again!] (link-reveal-goto: "Play the game: demo mode (1 scenario)", "Main")[ (set: $list to $demo))'s 1st) (set: $cases to $demo) (set: $choice to 1) (set: $mode to "demo") (set: $showFooter to true) (set: $finalorganism to "none") (set: $16S to 0) (set: $WGS to 0) ] (link-reveal-goto: "Play the game: easy mode (4 scenarios)", "Main")[ (set: $list to (shuffled: ...(datanames: $easy))'s 1stto4th) (set: $cases to $easy) (set: $choice to 4) (set: $mode to "easy") (set: $showFooter to true) (set: $finalorganism to "fungus") ] (link-reveal-goto: "Play the game: medium mode (6 scenarios)", "Main")[ (set: $list to (shuffled: ...(datanames: $medium))'s 1stto6th) (set: $cases to $medium) (set: $choice to 6) (set: $mode to "medium") (set: $showFooter to true) (set: $finalorganism to "virus") ] (link-reveal-goto: "Play the game: challenging mode (8 scenarios)", "Main")[ (set: $list to (shuffled: ...(datanames: $challenging))'s 1stto8th) (set: $cases to $challenging) (set: $choice to 8) (set: $mode to "challenging") (set: $showFooter to true) (set: $finalorganism to "virus") ] (link-reveal-goto: "Play the game: very challenging mode (12 scenarios)", "Main")[ (set: $list to (shuffled: ...(datanames: $very))'s 1stto12th) (set: $cases to $very) (set: $choice to 12) (set: $mode to "very challenging") (set: $showFooter to true) (set: $finalorganism to "virus") ]

{ (set: _ans to 50 * $vol45) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You wish to test the sensitivity of a particular clinical isolate to antibiotics. Unfortunately, a selfish colleague has used up the last of the lab's antibiotic stocks without replenishing them. You need to make $vol45 mL of a 50 mg/mL stock of gentamycin. How many mg of gentamycin do you need? (set: _password to "")\ Enter the number of milligrams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 10 * $vol43) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You wish to test the sensitivity of a particular clinical isolate to antibiotics. Unfortunately, a selfish colleague has used up the last of the lab's antibiotic stocks without replenishing them. You need to make $vol43 mL of a 10 mg/mL stock of tetracycline. How many mg of tetracycline do you need? (set: _password to "")\ Enter the number of milligrams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: _ans to 50 * $vol44) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You wish to test the sensitivity of a particular clinical isolate to antibiotics. Unfortunately, a selfish colleague has used up the last of the lab's antibiotic stocks without replenishing them. You need to make $vol44 mL of a 50 mg/mL stock of kanamycin. How many mg of kanamycin do you need? (set: _password to "")\ Enter the number of milligrams in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

{ (set: $earnedclues to it -1) (if: visits is 1)[ Hint: Consider the results of the oxidase and catalase tests. (set: $hintsC1 to it + (a: "Consider the results of the oxidase and catalase tests. "))] (else-if: visits is 2)[ Hint: Consider the phenotype of this organism on MacConkey agar. (set: $hintsC1 to it + (a: "Consider the phenotype of this organism on MacConkey agar. "))] (else-if: visits is 3)[ Hint: The IMViC tests (indole, methyl red, Voges Proskauer, and citrate) are often helpful for identifying this type of unknown. (set: $hintsC1 to it + (a: "The IMViC tests (indole, methyl red, Voges Proskauer, and citrate) are often helpful for identifying this type of unknown. "))] (else-if: visits is 4)[ Hint: Consider the results of the motility test. (set: $hintsC1 to it + (a: "Consider the results of the motility test."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on Simmons Citrate agar. (set: $hintsC1 to it + (a: "Consider the phenotype of this organism on Simmons Citrate agar."))] (else-if: visits is 5)[ Hint: Consider the phenotype of this organism on MacConkey/sorbitol agar. (set: $hintsC1 to it + (a: "Consider the phenotype of this organism on MacConkey/sorbitol agar."))] (else:)[There are no more hints left, sorry!] } Would you like to: (link-reveal-goto: "earn another hint to help solve your unknown?", "EarnAClue")[(set:$t to it + time)], (link-reveal-goto: "go back to study the case overview for organism $C1", "Case 1")[(set:$t to it + time)], or (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

{ (if: $C1soln is >= 1)[Congratulations, you have identified your unknown organism! (link-reveal-goto: "Click to escape the room!", "DemoFinal")[(set:$t to it + time)]] (else:)[You can escape the room after you have identified the unknown organism. (link-reveal-goto: "Do you need some help?", "Hint0")[(set:$t to it + time)] ] }

If you are not sure how to identify your organism using its 16S sequence, you should try <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi" target="_blank">looking into NCBI BLAST</a>, and reading the extensive help documentation available there (link will open in a new window) (link-reveal-goto: "Do you need another hint to help you identify your unknown?", "Hint0")[(set:$t to it + time)] or would you like to (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

If you are not sure how to identify your organism using its whole genome sequence, you should try looking up the accession number at <a href="https://www.ncbi.nlm.nih.gov/genome/" target="_blank">NCBI genome</a>, and reading the extensive help documentation availabble there (link will open in a new window) (link-reveal-goto: "Do you need another hint to help you identify your unknown?", "Hint0")[(set:$t to it + time)] or would you like to (link-reveal-goto: "go back to the main menu", "Main")[(set:$t to it + time)]?

Xylose Lysine Deoxycholate (XLD) agar is a selective and differential medium based on xylose fermentation, lysine decarboxylation, and H2S production. It is commonly used for the isolation of salmonellae and shigellae. (link: "Click to see the XLD agar recipe") [<table> <table border="1"> <tr> <th>Component</th> <th>grams/litre</th> </tr> <tr> <td>Yeast extract</td> <td>3.0</td> </tr> <tr> <td>L-Lysine HCl</td> <td>5.0</td> </tr> <tr> <td>Xylose</td> <td>3.75</td> </tr> <tr> <td>Lactose</td> <td>7.5</td> </tr> <tr> <td>Sucrose</td> <td>7.5</td> </tr> <tr> <td>Sodium desoxycholate</td> <td>1.0</td> </tr> <tr> <td>Sodium chloride</td> <td>5.0</td> </tr> <tr> <td>Sodium thiosulphate</td> <td>6.8</td> </tr> <tr> <td>Ferric ammonium citrate</td> <td>0.8</td> </tr> <tr> <td>Phenol red</td> <td>0.08</td> </tr> <tr> <td>Agar</td> <td>12.5</td> </tr> </table> pH 7.4 ± 0.2 @ 25°C] <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM0469&c=UK&lang=EN" target="_blank">Read more about XLD medium</a> (link will open in a new window) {= (set: _lastPassage to (history:)'s last) (if: _lastPassage is "plates1")[ (link: "Click to see the results from growing unknown $C1 on XLD agar")[Unknown $C1 grows XLD agar, producing opaque yellow colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates1")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C1 overview?", "Case 1")[(set:$t to it + time)] (set: $notebookC1 to it + (a: "Unknown $C1 grows on Xylose Lysine Deoxycholate (XLD) agar, producing opaque yellow colonies.")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates2")[ (link: "Click to see the results from growing unknown $C2 on XLD agar")[You should consider whether streaking unknown $C2 on XLD agar is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates2")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C2 overview?", "Case 2")[(set:$t to it + time)] (set: $notebookC2 to it + (a: "You did not grow unknown $C2 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates3")[ (link: "Click to see the results from growing unknown $C3 on XLD agar")[Unknown $C3 grows on XLD agar, producing red colonies with black centres. Back to (link-reveal-goto: "choose another growth medium?", "plates3")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C3 overview?", "Case 3")[(set:$t to it + time)] (set: $notebookC3 to it + (a: "You did not grow unknown $C3 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates4")[ (link: "Click to see the results from growing unknown $C4 on XLD agar")[You should consider whether streaking unknown $C4 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates4")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C4 overview?", "Case 4")[(set:$t to it + time)] (set: $notebookC4 to it + (a: "You did not grow unknown $C4 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates5")[ (link: "Click to see the results from growing unknown $C5 on XLD agar")[You should consider whether streaking unknown $C5 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates5")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C5 overview?", "Case 5")[(set:$t to it + time)] (set: $notebookC5 to it + (a: "You did not grow unknown $C5 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates6")[ (link: "Click to see the results from growing unknown $C6 on XLD agar")[You should consider whether streaking unknown $C6 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates6")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C6 overview?", "Case 6")[(set:$t to it + time)] (set: $notebookC6 to it + (a: "You did not grow unknown $C6 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates7")[ (link: "Click to see the results from growing unknown $C7 on XLD agar")[You should consider whether streaking unknown $C7 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates7")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C7 overview?", "Case 7")[(set:$t to it + time)] (set: $notebookC7 to it + (a: "You did not grow unknown $C7 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates8")[ (link: "Click to see the results from growing unknown $C8 on XLD agar")[Unknown $C8 grows on XLD agar, producing red colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates8")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C8 overview?", "Case 8")[(set:$t to it + time)] (set: $notebookC8 to it + (a: "Unknown $C8 grows on Xylose Lysine Deoxycholate (XLD) agar, producing red colonies")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates9")[ (link: "Click to see the results from growing unknown $C9 on XLD agar")[You should consider whether streaking unknown $C9 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates9")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C9 overview?", "Case 9")[(set:$t to it + time)] (set: $notebookC9 to it + (a: "You did not grow unknown $C9 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates10")[ (link: "Click to see the results from growing unknown $C10 on XLD agar")[You should consider whether streaking unknown $C10 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates10")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C10 overview?", "Case 10")[(set:$t to it + time)] (set: $notebookC10 to it + (a: "You did not grow unknown $C10 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates11")[ (link: "Click to see the results from growing unknown $C11 on XLD agar")[You should consider whether streaking unknown $C11 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates11")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C11 overview?", "Case 11")[(set:$t to it + time)] (set: $notebookC11 to it + (a: "You did not grow unknown $C11 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates12")[ (link: "Click to see the results from growing unknown $C12 on XLD agar")[You should consider whether streaking unknown $C12 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates12")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C12 overview?", "Case 12")[(set:$t to it + time)] (set: $notebookC12 to it + (a: "You did not grow unknown $C12 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates13")[ (link: "Click to see the results from growing unknown $C13 on XLD agar")[You should consider whether streaking unknown $C13 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates13")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C13 overview?", "Case 13")[(set:$t to it + time)] (set: $notebookC13 to it + (a: "You did not grow unknown $C13 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates14")[ (link: "Click to see the results from growing unknown $C14 on XLD agar")[You should consider whether streaking unknown $C14 on XLD is the best experiment in light of what you know about this growth medium and the other data available about this organism. Back to (link-reveal-goto: "choose another growth medium?", "plates14")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C14 overview?", "Case 14")[(set:$t to it + time)] (set: $notebookC14 to it + (a: "You did not grow unknown $C14 on Xylose Lysine Deoxycholate (XLD) agar")) (set: $clicks to it + 1)]] (else-if: _lastPassage is "plates15")[ (link: "Click to see the results from growing unknown $C15 on XLD agar")[Unknown $C15 grows on XLD agar, producing mucoid yellow colonies. Back to (link-reveal-goto: "choose another growth medium?", "plates15")[(set:$t to it + time)] or to the (link-reveal-goto: "case $C15 overview?", "Case 15")[(set:$t to it + time)] (set: $notebookC15 to it + (a: "Unknown $C15 grows on Xylose Lysine Deoxycholate (XLD) agar, producing mucoid yellow colonies.")) (set: $clicks to it + 1)]]

(if: $showFooter)[ --- <center>(if: $choice is 1)[Unknown to identify: [(link-reveal-goto: "$C1", "Case 1")[(set: $t to it + time)] ]]</center> <center>(else-if: $choice is > 1)[Unknowns to identify: (for: each _case, ...$list)[(link-reveal-goto: $cases's (_case), _case)[(set: $t to it + time)] | ]]</center> --- ]

You will be able to carry out various tests to determine the identity of the unknown bacteria from the food samples - for example, you can look at the bacteria under the microscope, carry out some biochemical tests, or grow the bacteria on various selective or differential growth media. Try to think like a detective and use logical reasoning to identify each unknown. Choose your experiments wisely - only perform an experiment if it will help you identify the organism! (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[''[A note about budgets:]'' In the clinical lab, you have limited budgets and you do not want to use resources (reagents, agar, time, etc.) on experiments that will not help with the identification of your unknown. In the escape room, all the virtual experiments you perform will be counted - try to identify the bacteria with the smallest number of experiments possible. Your lab has a small budget for Sanger sequencing - enough for you to be able to sequence the 16S rRNA gene from one organism. You also have a small budget for next generation sequencing (Illumina) - enough for you to be able to sequence and assemble the genome of one organism. Make sure you spend your budgets wisely - when you have used up your budget, you will not be able to do any more sequencing!] The escape room will automatically track how many tests you perform, and how long you take to exit the room - try to be as quick and efficient as possible! Can you beat your friends out of the room? (link-goto: "Click for some tips and resources", "About3")

{ (set: _ans to 1/10 * $vol32) (set: _ans2 to (string: _ans)) } Solve a problem to earn a hint to help you identify an unknown. You want to test the ability of some of your unknown organisms to ferment certain carbohydrates. To do so, you will grow these organisms in medium containing a pH indicator and the carbohydrate (for example, the sugar rhamnose). You have a 10% (w/v) stock solution of rhamnose; the desired final concentration of rhamnose in the growth medium is 1%. How many mL of your rhamnose stock solution do you need to add to make up $vol32 mL of your growth medium? (set: _password to "")\ Enter the number of millilitres in the box below and click "Answer" to earn the hint: (input-box: bind _password, "X====", 1)(link: "Answer")[{ (if: (lowercase: _password) is _ans2)[ (go-to: "Answer") ] (else:)[ (go-to: "Incorrect") ] }]

You prepare a cDNA library for Illumina sequencing. While you are setting up the reverse transcriptase (RTase) reactions, one of your colleagues stops by your bench and asks what you are doing. You explain to your colleague that: (link-reveal-goto: "RTase transcribes ssRNA to DNA", "cdna-sequencing-reason1")[(set:$t to it + time)] (link-reveal-goto: "RTase transcribes ssDNA to RNA", "cdna-sequencing-reason2")[(set:$t to it + time)]

You have one final unknown to identify before you can escape the room. Sample $F4 is a portion of $F4food. No potential bacterial pathogens were isolated from this sample: however, HPLC analysis suggests that it may be contaminated with ''aflatoxins''. One of your colleagues suggests that the sample was probably contaminated by an Aspergillus species that produces aflatoxins. To determine if this is the case, you decide to: (link-reveal-goto: "try to amplify one of the genes involved in aflatoxin biosynthesis by PCR", "Final4-PCR")[(set:$t to it + time)]

You have one final case to solve before you can escape the room. Sample $F6 is a portion of $F6food. You suspected that it was contaminated with ''norovirus'', and you have obtained a set of sequencing reads derived from nucleic acids isolated from the sample. Some of the workers who handled this $F6food have had symptoms consistent with norovirus infection. To determine whether they are the source of the norovirus present in your sample $F6, you have also obtained sequence reads from samples taken from these individuals. (link-reveal-goto: "Click here to see the norovirus sequences", "Final6b")[(set:$t to it + time)]

You have one final unknown to identify before you can escape the room. Sample $F8 is a portion of $F8food. No potential bacterial pathogens were isolated from this sample: you suspect it may be contaminated by a virus instead - probably an ''enterovirus'' of some type. To identify this virus, do you want to: (link-reveal-goto: "Prepare a DNA library from sample $F and sequence it using Illumina technology", "Final-seq-DNA")[(set:$t to it + time)] or (link-reveal-goto: "Prepare a cDNA library from sample $F and sequence it using Illumina technology", "Final-seq-cDNA")[(set:$t to it + time)]? GIARDIA

The sequences you obtained from your samples are: (if: $final6 is "A")[(font:"Courier New")[ >sequence1 sample $F6 ATGAAGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAACAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence2 worker1 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence3 worker2 ATGAAGATGGCGTCGAATGACGCCGCTCCATCTACTGATGGTGCAGCCGGCCTCGTGCCAGAAAGTAACAATGAGGTCATGGCTCTTGAACCCGTGGCTGGTGCCGCCTTGGCAGCCCCGGTCACCGGTCAAACAAATATTATAGACCCTTGGATTAGAGCAAATTTTGTCCAGGCCCCCAATGGTGAATTTACAGTCTCTCCCCGAAATGCCCCTGGTGAAGTGCTACTGAATCTAGAGTTGGGTCCAGAATTAAATCCTTATCTGGCACATTTAGC >sequence4 worker3 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence5 worker4 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGTTCTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence6 worker5 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCAAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATCGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC ]] (if: $final6 is "B")[(font:"Courier New")[ >sequence1 sample $F6 ATGAAGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAACAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence2 worker1 ATGAAGATGGCGTCGAATGACGCCGCTCCATCTACTGATGGTGCAGCCGGCCTCGTGCCAGAAAGTAACAATGAGGTCATGGCTCTTGAACCCGTGGCTGGTGCCGCCTTGGCAGCCCCGGTCACCGGTCAAACAAATATTATAGACCCTTGGATTAGAGCAAATTTTGTCCAGGCCCCCAATGGTGAATTTACAGTCTCTCCCCGAAATGCCCCTGGTGAAGTGCTACTGAATCTAGAGTTGGGTCCAGAATTAAATCCTTATCTTGCACATTTAGC >sequence3 worker2 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence4 worker3 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence5 worker4 ATGAAGATGGCGTCGAATGACGCCGCTCCATCTACTGATGGTGCAGCCGGCCTCGTGCCAGAAAGTAACAATGAGGTCATGGCTCTTGAACCCGTGGCTGGTGCCGCCTTGGCAGCCCCGGTCACCGGTCAAACAAATATTATAGACCCTTGGATTAGAGCAAATTTTGTCCAGGCCCCCAATGGTGAATTTACAGTCTCTCCCCGAAATGCCCCTGGTGAAGTGCTACTGAATCTAGAGTTGGGTCCAGAATTAAATCCTTATCTGGCACATTTAGC >sequence6 worker5 AGATGGGGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGTAAGTAATAATGAGGCAATGGGTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCAAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATCGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC]] (if: $final6 is "C")[(font:"Courier New")[ >sequence1 sample $F6 ATGAAGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAACAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence2 worker1 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCAAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATCGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence3 worker2 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence4 worker3 ATGAAGATGGCGTCGAATGACGCCGCTCCATCTACTGATGGTGCAGCCGGCCTCGTGCCAGAAAGTAACAATGAGGTCATGGCTCTTGAACCCGTGGCTGGTGCCGCCTTGGCAGCCCCGGTCACCGGTCAAACAAATATTATAGACCCTTGGATTAGAGCAAATTTTGTCCAGGCCCCCAATGGTGAATTTACAGTCTCTCCCCGAAATGCCCCTGGTGAAGTGCTACTGAATCTAGAGTTGGGTCCAGAATTAAATCCTTATCTGGCACATTTAGC >sequence5 worker4 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGTTCTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC >sequence6 worker5 AGATGGCGTCGAATGACGCTACTCCATCAAATGATGGTGCTGCCGGCCTCGTGCCAGAAAGTAATAATGAGGCAATGGCTCTGGAACCCGTGGTGGGGGCGTCTTTAGCCGCCCCTGTCACTGGCCAAACTAATATAATAGACCCCTGGATTAGAACTAATTTTGTCCAAGCCCCTAATGGTGAATTCACAGTTTCCCCTAGAAATTCCCCTGGAGAGATATTGGTCAATTTGGAGTTGGGTCCAGAACTGAACCCTTATCTGGCACATTTAGC ]] (link-reveal-goto: "Click here when you are ready to tell your colleagues about your findings", "Final6c")[(set:$t to it + time)]

You obtained the sequence for an Aspergillus flavus gene infolved in aflatoxin biosynthesis from the NCBI databases so that you can design PCR primers. (font:"Courier New")[ATGGGATCTATTGGTAGGGAACAGGAGTTAATCCCCATCCAGGCTGCCCAGAGAGGCGCTGCCCGGATCT GCGCTACTTTTGGGGGTCAAGGGTCTAACAATCTGGACGTGTTAAAAAACCTACTAGAGTTATACAGGCG ATATGGCCCAGATCTGGATGAGCTACTAGATGTGGCATCCAACACGCTTTCGCAGCTGGCTTCTTCCCCT GAAGCAATAGACGTGCACGAGCCCTGGGGTTTCGACCTCCGACAATGGCTGGCTACACCGGAGCTTGCTC CTAGCAGGGAAGTTCTTGCCCTGTCGCCACGAAGCTTTCCCTTAAATACGCTGATTAGCCTGGCGCTTTA TTGTGCAACTTGTCAAGAGCTTGAACTTGATCCTGGCCAACTTCGATCCCTCCTTCATAGTTCCACGGGG CATTCCCAAGGCATATTGGCGGCGGTGGTCATCGCCCAAGCCGAGAGCTGGTCAAACTTTTATGACGCCT GCAGGACGGTGCTCCTGATATCTTTCTGGATTGGACTCGAGGCTTACCTCTCCACCCCATCCTCCGCCGT GTCGGATGCCATGATCCAAGATTGCATCGAACATGGCGAGGGTCTTCTTTCCTCGATGCTCAGTGTCTCG GGGCTCTCCCGCTCCCAAGTTGAGAAGGTAATTGAGCACGTCAACAACGCACTGGGAGAATGCACCCAAT GGGTGCATTTGGCGCTGGTTAACTCCCACGAAAAGTTTGTCTTGGCGGGACCACCTCAATCCCTATGGGC] Which pair of PCR primers do you want to order to try to amplify this sequence? (link-reveal-goto: "PCR primers option 1", "PCRprimers1")[(set:$t to it + time)]: (font:"Courier New")[ATGGGATCTATTGGTAGGGAAC] and (font:"Courier New")[GACCACCTCAATCCCTATGGGC] (link-reveal-goto: "PCR primers option 2", "PCRprimers2")[(set:$t to it + time)]: (font:"Courier New")[ATGGGATCTATTGGTAGGGAAC] and (font:"Courier New")[GCCCATAGGGATTGAGGTGGTC]

Having designed your PCR primers, you place an order to have them synthesized ... (after: 2s)[= (after: 2s)[= You have to wait a few days for the primers to be synthesized and delivered... (after: time + 2s)[= while you are waiting, you go ahead and extract some DNA from your sample ... (after: time + 2s)[= and make sure you have some Taq polymerase in stock (after: time + 2s)[= After your oligos are delivered, you prepare your PCR mastermix ... (after: time + 2s)[= Add some DNA extracted from your sample $F4 ... (after: time + 2s)[= pop the reaction into the thermocycler and wait ... (after: time + 2s)[= (link-reveal-goto: "Click to run your PCRs on an agarose gel", "PCR1result")[(set:$t to it + time)]

When you run your PCR products on a gel, stain it with Gel Red, and visualise it on a UV transilluminator, you observe a band of ~800 bp size (and no bands in your negative control). You think that: (link-reveal-goto: "Your PCR reactions just aren't working", "PCRres1")[(set:$t to it + time)] or (link-reveal-goto: "You have detected the presence of an aflatoxin-producing organism in the sample", "PCRres2")[(set:$t to it + time)] or (link-reveal-goto: "You want to double-check the sequence of the aflatoxin biosynthetic gene to confirm the size of the fragment you are amplifying", "PCRres3")[(set:$t to it + time)]

You decide to chat about your failed PCR results with your colleague who works in the lab next door. "So you're having trouble with your PCRs," your colleague says. "What seems to be the problem?" Which explanation do you give to your colleague? (link-reveal-goto: "My PCR product is the wrong size", "PCRfailure1")[(set:$t to it + time)] or (link-reveal-goto: "I don't get any PCR product at all", "PCRfailure2")[(set:$t to it + time)] or (link-reveal-goto: "Never mind - I think my PCR actually worked after all, let's look at the gel again", "PCRresults")[(set:$t to it + time)]

That's right - the fact that you detected a band of the correct size in your sample, and none in your negative control, suggests that your sample $F4 likely contained an organism capable of producing aflatoxins. Since these mycotoxins are carcinogenic, this is pretty bad news! The good news is, you've solved the final puzzle and can now (link-reveal-goto: "escape the room", "Final-summary")[(set:$t to it + time)]

The sequence for an Aspergillus flavus gene involved in aflatoxin biosynthesis that you used to design your PCR primers was: (font:"Courier New")[ATGGGATCTATTGGTAGGGAACAGGAGTTAATCCCCATCCAGGCTGCCCAGAGAGGCGCTGCCCGGATCT GCGCTACTTTTGGGGGTCAAGGGTCTAACAATCTGGACGTGTTAAAAAACCTACTAGAGTTATACAGGCG ATATGGCCCAGATCTGGATGAGCTACTAGATGTGGCATCCAACACGCTTTCGCAGCTGGCTTCTTCCCCT GAAGCAATAGACGTGCACGAGCCCTGGGGTTTCGACCTCCGACAATGGCTGGCTACACCGGAGCTTGCTC CTAGCAGGGAAGTTCTTGCCCTGTCGCCACGAAGCTTTCCCTTAAATACGCTGATTAGCCTGGCGCTTTA TTGTGCAACTTGTCAAGAGCTTGAACTTGATCCTGGCCAACTTCGATCCCTCCTTCATAGTTCCACGGGG CATTCCCAAGGCATATTGGCGGCGGTGGTCATCGCCCAAGCCGAGAGCTGGTCAAACTTTTATGACGCCT GCAGGACGGTGCTCCTGATATCTTTCTGGATTGGACTCGAGGCTTACCTCTCCACCCCATCCTCCGCCGT GTCGGATGCCATGATCCAAGATTGCATCGAACATGGCGAGGGTCTTCTTTCCTCGATGCTCAGTGTCTCG GGGCTCTCCCGCTCCCAAGTTGAGAAGGTAATTGAGCACGTCAACAACGCACTGGGAGAATGCACCCAAT GGGTGCATTTGGCGCTGGTTAACTCCCACGAAAAGTTTGTCTTGGCGGGACCACCTCAATCCCTATGGGC] (link-reveal-goto: "Go back to evaluate your PCR results?", "PCRresults")[(set:$t to it + time)]

(set: $PCRsize to 1) "My PCR product is the wrong size," you say to your colleague. "Oh?" they ask. "What were you expecting?" (link-reveal-goto: "I thought it would be larger than 800 bp", "PCRsize")[(set:$t to it + time)(set: $PCRsize to it +1)] or (link-reveal-goto: "I thought it would be smaller than 800 bp", "PCRsize")[(set:$t to it + time)(set: $PCRsize to it -1)]

"You don't observe any PCR product at all?" your colleague asks. "I thought you said there was an ~800 bp band in your gel?" You say, "Yes, but... (link-reveal-goto: "I think it is probably a nonspecific band", "PCRnon")[(set:$t to it + time)] or (link-reveal-goto: "Never mind - I think my PCR actually worked after all, let's look at the gel again", "PCRresults")[(set:$t to it + time)]

"Well," your colleague says. "Let's have (link-reveal-goto: "have another look at the DNA sequence", "PCRres3")[(set:$t to it + time)] you're amplifying, and see if we can figure out how large the fragment should be." (if: $PCRsize is 2)["I think you may have just made a mistake," your colleague says. If this amplifies correctly, you won't have a product larger than 800 bp... ] (else-if: $PCRsize is 0)["I see," your colleague says. "You were probably expecting a band of 770 bp ... but you must remember the limit of resolution on your agarose gel. You wouldn't likely notice a difference between 770 and 800 bp..."] (link-reveal-goto: "Go back to reevaluate the results obtained from running your PCRs on an agarose gel", "PCRresults")[(set:$t to it + time)]

"Well," your colleague says. "It isn't present in your negative control - and I know you'll have done the controls properly - so it seems quite unlikely that it's a nonspecific band." You say, (link-reveal-goto: "It must be a nonspecific band - it's the wrong size", "PCRfailure1")[(set:$t to it + time)] or (link-reveal-goto: "Never mind - I think my PCR actually worked after all, let's look at the gel again", "PCRresults")[(set:$t to it + time)]

When you run your PCR products on a gel, stain it with Gel Red, and visualise it on a UV transilluminator, you observe that there are no bands in your sample (and no bands in your positive control). You think that: (link-reveal-goto: "Your PCR reactions just aren't working", "PCR1res1")[(set:$t to it + time)] or (link-reveal-goto: "You have determined that your sample is NOT contaminated with an aflatoxin-producing fungus", "PCR1res2")[(set:$t to it + time)] or (link-reveal-goto: "You want to double-check the sequence of the PCR primers you designed to make sure they were correct", "Final4-PCR")[(set:$t to it + time)]

You decide to chat about your failed PCR results with your colleague who works in the lab next door. "So you're having trouble with your PCRs," your colleague says. "What have you tried so far?" (if: visits > 3)["Have you double-checked the sequence of your PCR primers?"] After a bit of a chat, you decide that you would like to troubleshoot your PCR by: (link-reveal-goto: "Repeat the PCR - using all new reagents", "PCR1result")[(set:$t to it + time)] or (link-reveal-goto: "Repeat the PCR - using different settings on the thermocycler", "PCR1result")[(set:$t to it + time)] or (link-reveal-goto: "You want to double-check the sequence of the PCR primers you designed to make sure they were correct", "Final4-PCR")[(set:$t to it + time)]

You go to tell the good news to your colleague in the lab next door. "I think I've finally found an uncontaminated sample!" you say. "Huh," your colleague says. "Are you sure? It looks like your positive control didn't work, so...." "Oh," you say. "(link-reveal-goto: "Maybe my PCR reactions just aren't working", "PCR1res1")[(set:$t to it + time)]"

"Wow," your colleague says. "It seems pretty unlucky that so many people would have norovirus all at the same time." "Well," you say, "it is pretty contagious, so it's not all that unlikely." "Well, what do you think likely happened in this case?" your colleague asks. Based on the results from your sequencing experiment, you think that the most likely source of the norovirus in the contaminated food is .... (if: visits > 3)[Your colleague says, "Hmm, looks like this is a tricky one to figure out. (link-reveal-goto: "Want some help", "6Help")[(set:$t to it + time)]?] (dropdown: bind $final6choice, "Select the source of the infection", "worker 1", "worker 2", "worker 3", "worker 4", "worker 5", "worker 1 or worker 2", "worker 1 or worker 3", "worker 4 or worker 5", "worker 2 or worker 3", "worker 2 or worker 5", "none of the workers") (if: $final6 is "A")[(link-reveal-goto: "Click to check your answer", "Final-answer6A")[(set:$t to it + time)]] (if: $final6 is "B")[(link-reveal-goto: "Click to check your answer", "Final-answer6B")[(set:$t to it + time)]] (if: $final6 is "C")[(link-reveal-goto: "Click to check your answer", "Final-answer6C")[(set:$t to it + time)]]

(if: $final6choice is "worker 1 or worker 3")[You have correctly identified the likely source of the norovirus, well done! (link-reveal-goto: "Click to see a summary of your results", "Final-summary")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have not correctly identified the source of the norovirus - do you want to look at the sequences again?", "Final6b")[(set:$t to it + time)]]

(if: $final6choice is "worker 2 or worker 3")[You have correctly identified the likely source of the norovirus,, well done! (link-reveal-goto: "Click to see a summary of your results", "Final-summary")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have not correctly identified the source of the norovirus - do you want to look at the sequences again?", "Final6b")[(set:$t to it + time)]]

(if: $final6choice is "worker 2 or worker 5")[You have correctly identified the likely source of the norovirus,, well done! (link-reveal-goto: "Click to see a summary of your results", "Final-summary")[(set:$t to it + time)]] (else:)[(link-reveal-goto: "You have not correctly identified the source of the norovirus - do you want to look at the sequences again?", "Final6b")[(set:$t to it + time)]]

Your colleague says, "So you've been trying to figure out the source of this norovirus contamination based on the nucleotide sequences obtained from your samples ... have you been doing pairwise sequence alignments?" "That's right," you say. "Well, what seems to be the trouble?" (link-reveal-goto: "I'm not quite sure how to interpret the results", "6Helpb")[(set:$t to it + time)] or (link-reveal-goto: "My top hit isn't matching the correct answer when I check it", "6Helpb")[(set:$t to it + time)]

"Well," your colleague says, "remember that you need to evaluate how well your sequences align - you should be taking into account the score, e-value, % identity, and so on when you analyse them by BLAST... and presumably, if two sequences are aligning very well, that indicates that they diverged very recently from a common ancestor." "Of course," you say. "I knew that." "And of course you know that you should look carefully at all of your hits - don't just choose the first one because it is a good match." "Right," you say, "I guess I'll (link-reveal-goto: "I'll go back and look at those sequences again", "Final6b")[(set:$t to it + time)]."

{(set: $seconds to $t/1000) (set: $minutes to $seconds/60) (set: $minutes to (round: $minutes)) (if: $C1hints is not 0)[(set: $hints to $hints + $C1hints's length)] } (print: (either: "Hooray! You nailed it!", "Way to go! You're a rock star!", "High-fives all around! You aced it!", "Cheers to your success! Well done!", "Fantastic job! You're a champion!", "Woo-hoo! You've reached the top!", "Bravo! You crushed it!", "Celebrate good times! You did it!", "Hip, hip, hooray! You're a winner!", "Amazing work! You're on fire!", "You're a star! Congratulations!", "Party time! You conquered it!", "Kudos! You've made it happen!", "Smiles and applause! You succeeded!", "To the moon and back! You've achieved greatness!")) It took you approximately $minutes minutes to escape the room. You played in $mode mode and identified $choice bacterium correctly: very well done! You used $clicks pieces of data, and needed $hints hints to escape the room. (b4r:"solid")+(b4r-size:4)+(b4r-color:red)[''As a reward for escaping the room:'' Here's a fun trivia fact about a foodborne pathogen! $funfact] {= (b4r:"solid")+(b4r-size:4)+(b4r-color:blue)[''Some things to reflect on:'' What were the most informative tests for identifying the unknown organism? Could you have identified the unknown with less data (performed fewer experiments)? What have you learned that will help you better identify unknown organisms next time?] (link: "Click here if you would like to play again")[(restart:)]