Epidemics-throughout-history

Welcome to the virtual escape room, "Epidemics throughout history", Created by Josh Fleming for a 4th year Dissertation. You are a time travelling Doctor, you will be sent back in time, to take a test and understand the symptoms of someone with a particular disease, then travel back to present day in order to look at specific lab tests to understand the organism causing the disease. The purpose of this escape room is look at different periods of history affected by a prominant epidemic. At these different time periods its your job to understand what organism is causing the Disease. You will get a brief description of when and where you are, a rundown of the general symptoms experience by those with the illness, and have different tests in order to identify the pathogen. To start at the first time period please click begin. [[begin]]

(text-colour:black)+(bg:#cba02a)[You wake up, Its a very hot summers day, you are within the massive walls of a large city. The city is full of bright white buildings made of limestone, there are lots of theatres and arts centres. You look up and notice a tall Rocky hill, built on top of this hill a large recognisable building, the parthenon. You realise you are in Athens. It looks like it should be a calm cultural centre, however, the gates to the city are firmly closed, theres lots of shouting and it appears the city is under attack. The locals all look skinny, malnourished even. It appears as if the city has been under siege for some time. Then you notice the Ill, it appears as if those responable for treating the infected are activley avoiding them, great halls of people all suffering together. There are huge mass graves, and everyone is in a state of panic. [[Where am I?]] ]

(text-colour:black)+(bg:#cba02a)[It turns out you are in Athens- the year is 430 BC and it is right in the middle of the polyplesian war, Athens has been surronded for weeks by troops from the city state of Sparta. The already dense city had become overpopulated by refugees around athens hiding within the walls, with the overcramped conditions and poor hygiene, the locked in inhibitants. You notice a man writing, and talking to some of those infected, he appears to be taking nots of those who are ill to try and keep a record for his book. [[Speak to him]] [[Avoid him, try to speak to someone else who is ill]]]

(text-colour:black)+(bg:#cba02a)[He Introduces himself as Thucydides, He says he has been Keeping a record of those infected as he is a philosopher writing about the polyplesian war. [[Ask him about the symptoms of the disease]]]

(text-colour:black)+(bg:#cba02a)[ [[The man runs over to you anyway, annoyed your interfering with his patients|Speak to him]]]

(text-colour:black)+(bg:#cba02a)[He hands over his book, you read the description he has about those infected. It Reads; People were attacked without exciting cause, and without warning, in perfect health. It began with violent sensations of heat in the head, and redness and burning in the eyes; internally, the throat and tongue were blood-red from the start, emitting an abnormal and malodorous breath. These symptoms developed into sneezing and hoarseness, and before long the trouble descended into the chest, attended by violent coughing. Whenever it settled in the heart, it upset it, and evacuations of bile ensued, of every kind for which the doctors have a name; these also together with great distress. Most patients suffered an attack of empty retching, inducing violent convulsions, in some cases soon after the abatement of the previous symptoms, in others much later. The body was neither unduly hot externally to the touch, nor yellowish in colour, but flushed and livid, with an efflorescence of small blisters and sores. The majority succumbed to the internal heat before their strength was entirely exhausted, on the seventh or ninth day. It was deemed as death by exhaustion. [[You decide you want to take a Sample]] ]

(text-colour:black)+(bg:#cba02a)[You ask a person with the illness if you can take a sample with the swab you have, they agree, Where in the body do you take the sample from? The reason we need to take a swab is so we can have a sample of infected cells from the person that we can then go on to identify. [[You take a Throat swab|You take a Skin Swab]] [[You take a Skin Swab]] [[You take a Hair Swab]]]

(text-colour:black)+(bg:#cba02a)[As the disease was not presenting in the hair, the hair swab would turn up no findings, Try again. [[You decide you want to take a Sample]]]

(text-colour:black)+(bg:#cba02a)[Correct, well done. As the Disease is presenting in both the skin and the throat, we will get pathogenic cell with a swab in these areas. After taking the Swab you thank the patient and Thuciydes and decide its time to figure out what the pathogen is thats causing this epidemic. [[You close your eyes thinking of the lab]]]

(text-colour:black)+(bg:white)[(text-colour:black)[You open your eyes, back in the present day in the lab still holding your swab sample, now its time to figure out what the pathogen is. You remeber you still have a photo of Thucydides explanation of the symptoms. [[Thucydides description]] For this pathogen you will be using a nucleotide blast sequence in order to see the genome of the pathogen and hopefully figure out what it is. [[What is a genome?]] In order to separate the pathogen from the rest of the cells what must be done to the swab? [[hint|Centrifuge hint]] [[Answer Here]]]]

(text-colour:black)+(bg:white)[You look at the photo. People were attacked without exciting cause, and without warning, in perfect health. It began with violent sensations of heat in the head, and redness and burning in the eyes; internally, the throat and tongue were blood-red from the start, emitting an abnormal and malodorous breath. These symptoms developed into sneezing and hoarseness, and before long the trouble descended into the chest, attended by violent coughing. Whenever it settled in the heart, it upset it, and evacuations of bile ensued, of every kind for which the doctors have a name; these also together with great distress. Most patients suffered an attack of empty retching, inducing violent convulsions, in some cases soon after the abatement of the previous symptoms, in others much later. The body was neither unduly hot externally to the touch, nor yellowish in colour, but flushed and livid, with an efflorescence of small blisters and sores. The majority succumbed to the internal heat before their strength was entirely exhausted, on the seventh or ninth day. It was deemed as death by exhaustion. [[Back to the lab|You close your eyes thinking of the lab]]]

(text-colour:black)+(bg:white)[After Centrifuging the cells, you load them into a Illumina MiSeq system in order to resd the genome of the pathogen. It must be noted that there are a few more steps needed between centrifuging and Genome sequencing, these steps are: RNA extraction, Reverse Transcription, PCR priming and PCR. After loading the sample, you let the machine run, after about 90 miuntes, there is an output of the genome. Its written in its nucleotide form. You need to copy and paste the following sequence into the large box in the program of BLAST. BLAST is the Basic Local Alignment Search Tool, it finds regions of similarity between biological sequences. With the following sequence it will match it up agaisnt the 1000's of known pathogens to understand what it is. Once you have been to blast and know what the pathogen is, answer on the next slide. [[Answer here]] (text-colour:red)+(bg:white)[When clicking the link below, right click and open the page in a new tab. Paste the FASTA sequence into the big box, scroll down and click BLAST. ] (link: "click here" [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome]] Copy the sequence below. The sequence produced by Illumina is as follows: ] (text-colour:black)+(bg:white)[ 1 accaaacaaa gttgggtaag gatagatcaa tcaatgatca tattctagta cacttaggat 61 tcaagatcct attatcaggg acaagagcag gattagggat atccgagatg gccacacttt 121 tgaggagctt agcattgttc aaaagaaaca aggacaaacc acccattaca tcaggatccg 181 gtggagccat cagaggaatc aaacacatta ttatagtacc aattcctgga gattcctcaa 241 ttaccactcg atccagacta ctggaccggt tggtcaggtt aattggaaac ccggatgtga ]]

(text-colour:black)+(bg:white)[Genomes are made of DNA. Each of your cells has a copy of your genome packed inside of it. You can think of it like an instruction manual or recipe book. The genome has all the instructions or “recipes” your body needs to work and look the ways it does. Viruses have genomes, too. A virus genome can be made of DNA or a similar molecule called RNA. Compared to your genome, a virus genome is tiny. [[Back|You close your eyes thinking of the lab]]]

(text-colour:black)+(bg:#4c524a)[You open your eyes, You are in the middle of a square on a very sunny day, you look around, the square and surrouding buildings have pathways of water between, you recognise this almost instantly as venice. What would normally be a bustling city is almost dead silent, there are massive painted crosses on most of the doors, there are boats on the canal with boats carrying out infected people, as well as boats filled with the bodies of those who have already died. Its quite the scene, you decide to go look for someone infected to try and get a sample [[You find someone]]]

(text-colour:black)+(bg:#4c524a)[You find someone lying on the floor, They have loads of purple swellings all over there body, some of these swellings were the size of eggs, some the size of apples. Blood and pus seeped out the swellings, however, these werent the only symptoms. You ask the person affected what else is wrong, they say how it has been getting worse over the course of a week. They have a high fever, but experience chills during the night, they struggle to do anything due to the painful nature of the swellings. They have been throwing up, and experiencing diarrohea. You cant help but feel sorry for the person, you ask to take a swab and they agree. Where do you take the swab from? [[Throat]] [[Skin]] [[Nose]]]

(text-colour:black)+(bg:#4c524a)[Incorrect the disease isn't presenting here Try again. [[Back|You find someone]]]

(text-colour:black)+(bg:#4c524a)[Correct, [[With the swab taken you close your eyes and think back to the Lab|Lab 1]] ]

(text-colour:black)+(bg:#4c524a)[Incorrect the disease isnt presenting here Try again. [[Back|You find someone]] ]

(text-colour:black)+(bg:white)[There are a number of different tests that can be performed on Bacterial species in order to find out what it is. With the sample, you streak for isolation so that its only the unkown pathogen being tested further. Look through each of the different tests in order to find out what the pathogen is. [[Gram Stain]]- Usually first step in the identification of a bacterium, Splits the number of possible candidates in 2, Either Gram negative or Positive. [[Microscope]]- Can see the shape of the bacteria. [[Thioglycolate broth]]- Tests between Aerobes (bacteria that require oxygen) and Anaerobes (bacteria which dont require oxygen). [[Spore count test]]- Tests if the bacteria is spore producing. [[Soft agar Assay]]- Used to study the motility of Bacteria. You can also view the [[symptoms]] of the pathogen again. Once reviewing the symptoms and the different tests [[Click here]] to answer what pathogen you think it is. [[Main Menu|Main Menu 2]]]

(set: $password to (prompt: "What is the Pathogen that you found in Athens", "Answer Here") ) (if: $password is "Measles" or "measles")[You are correct. This is the correct pathogen, well done! Now that you have completed a story, you go back to the main menu to choose the next story. [[Main Menu]]] (else:)[You entered the wrong Pathogen.[[Try Again?|correct]]]

(set: $password to (prompt: "How do we Seperate the Cells in the Swab?", "Answer Here") ) (if: $password is "Centrifuge" or "centrifuge")[You are correct. This is the right way to seperate the sample, well done![[Next step|correct]]] (else:)[You entered the wrong technique.[[Try Again?|You close your eyes thinking of the lab]]]

(text-colour:black)+(bg:white)[During a Gram stain the Unkown bacteria will be stained and washed a number of times in order to differentiate between Gram Negative and Gram positive bacteria. The unknown sample is first stained with Crystal violet and then with iodine to hold the stain within the bacterial cell. Then a decolorizer is added, gram negative cells do not retain the stain, while Gram positive cells will still be coloured. Then a counterstain is added in order to visualise Gram Negative cells. The results of the Gram Stain have the bacteria a Pink Colour [[If you need a hint]] [[Back to main lab page|With the swab taken you close your eyes and think back to the Lab]]]

(text-colour:black)+(bg:white)[A typical spore count test involves heating of a reconstituted powder sample to 80°C for 12 minutes before cooling culturing and enumerating colonies. The sample that you took, after the heating and cooling process did not grow on agar. [[If you need a hint|Hint 2]] [[Back to main lab page|With the swab taken you close your eyes and think back to the Lab]]]

(text-colour:black)+(bg:white)[1 microlitre of the unknown pathogen is inoculated onto soft agar, The agar was left for 24 hours. After 24 hours, the agar looked the similar to before, showing little blurring. [[If you need a hint|Hint 3]] [[Back to main lab page|With the swab taken you close your eyes and think back to the Lab]]]

(text-colour:black)+(bg:white)[When looking through a microscope the bacteria is mixed between small circular shaped and small rod shaped bacteria. [[Back to main lab page|With the swab taken you close your eyes and think back to the Lab]]] <style> img {max-width:100%;max-height:100%;} </style> <img src=https://upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Coxiella_burnetii_01.JPG/1920px-Coxiella_burnetii_01.JPG> </div>

(text-colour:black)+(bg:white)[Thioglycolate Broth is used to determine the oxygen requirements of different Bacteria. At the top of the tube where there is access to Oxygen, Obligate aerobes will be found. At the bottom of the tube Obligate anaerobes will be found, as there is no oxygen. The sample you took showed growth throughout the tube with a larger concentration towards the top. Such that it looked like number 3 from the diagram. [[Back to main lab page|With the swab taken you close your eyes and think back to the Lab]]] <style> img {max-width:100%;max-height:100%;} </style> <img src=https://upload.wikimedia.org/wikipedia/commons/9/90/Anaerobic.png> </div>

(text-colour:black)+(bg:white)[Gram Positive bacteria have thicker cell walls with more peptidoglycan, this means they retain the original stain. Gram Negative cells have a thinner layer and so are decoulorised. Crystal violet stain gives a Purple stain, whereas the counter stain is Pink [[Back to Gram Stain|Gram Stain]]]

(text-colour:black)+(bg:white)[If a bacteria produces spores then once cooled and cultured it will have survived the heating and will grow like normal on Agar. [[Back to Spore count test|Spore count test]]]

(text-colour:black)+(bg:white)[Motile bacteria will spread and blur the media. [[Back to Soft agar Assay|Soft agar Assay]]]

(text-colour:black)+(bg:white)[Symptoms include many purple swellings all over the body, some of these swellings were the size of eggs, some the size of apples. Blood and pus seeped out the swellings, however, these werent the only symptoms. Been getting worse over the course of a week. High fever, but experience chills during the night, struggle to do anything due to the painful nature of the swellings. Throwing up as well as diarrohea. [[Back|With the swab taken you close your eyes and think back to the Lab]]]

(set: $password to (prompt: "What is the Pathogen that you found in Venice", "Answer Here") ) (if: $password is "Yerisnia Pestis" or "yerisnia pestis")[You are correct. This is the correct pathogen, well done! Now that you have completed a story, you go back to the main menu to get your next story. [[Main Menu|Main Menu 2]]] (else-if: $password is "Black Death" or "The Black Death" or "black death" or "the black death" or "Bubonic Plague" or "bubonic plague" )[You have the name of the disease correct, the name of the pathogen that causes the black death is //Yerisnia Pestis//, however, The Black Death is still an exceptable answer is this instance. Now that you have completed a story, you go back to the main menu to access the next story. [[Main Menu|Main Menu 3]]] (else:)[You entered the wrong Pathogen.[[Try Again?|With the swab taken you close your eyes and think back to the Lab]]]

(text-colour:black)+(bg:white)[With your swab you are unsure whether the pathogen is a Virus or a Bacteria, you decide to do a culture test. [[what is a culture test]] After adding the sample to the culture, and leaving it for 24 hours, you see that there has been a large amount of growth by the pathogen. Do you think the pathogen is a Virus or a Bacteria? [[Virus]] [[Bacteria]] ]

(text-colour:black)+(bg:white)[A culture test allows us to distinguish between bacteria and viruses, the culture is set up to provide nutrients suitable for bacterial gorwth. Viruses require host cells in order to replicate, bacteria do not and can comfortable grow on culture. [[Back|Lab 1]]]

(text-colour:black)+(bg:white)[A virus cannot replicate and grow without host cells, so its not a virus in this instance. [[Back|Lab 1]]]

(text-colour:black)+(bg:white)[Correct, as the pathogen grew in the culture we can conclude that its a Bacteria. We must now perform [[further tests|With the swab taken you close your eyes and think back to the Lab]]. ]

(text-colour:black)+(bg:#fcaa5a)[You open your eyes, you are almost blinded by the sheer brightness of the sun bearing down on you. It takes you a few seconds to adjust to the brightness, the heat is also tremendous. As you look around you notice a few small bulidings that look recently deserted. As you look further around, you see a vast empty desert with the only population being that of cacti. You walk towards the buildings noticing little life whatso ever, there are a few bodies stricken about but most have been buried by the harsh dry sand. Due to the prescence of cacti and the dry hot desert you believe you are in mexico. You do eventually find someone, they seem quite upset and dont understand how you are here. You [[Start talking]] to them. ]

(text-colour:black)+(bg:#fcaa5a)[He explains how this village had been absolutley decemated by a disease. There had already been hard times due to severe drought, but the rains came back a moth ago, and so did the rats. He said everyone in the village died from this disease and he was the only one to survive. [[You ask about the symptoms]]]

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(text-colour:black)+(bg:#fcaa5a)[He says people were complaining of a high fever and a severe headache. They were extremely dizzy with vertigo, they all ahd black tongues. There Urine was dark and they had dissentery, as well as abdominsl pain. Large nodules first appeared behind the ears but then inveaded the face and down to the neck. The final stage was profuse bleedinmg from the nose, eyes and mouth with death occuring within 3-4 days. He said he had just recovered from the disease. [[You take a sample]]]

(text-colour:black)+(bg:white)[Once you have taken the sample, you close your eyes, and upon re opening you are back in the lab. You decide once again to do a culture test, once again the results show growth within the culture so you know the pathogen is? [[Bacteria|Bacteria 1]] [[Virus|Virus1]]]

(text-colour:black)+(bg:white)[Well Remembered! Once again we have the same set of tests as used in the previous test to help us narrow down what the pathogen is. [[Gram Stain|Gram Stain1]] - Splits the number of possible candidates in 2, Either Gram negative or Positive. [[Microscope|Microscope1]]- Can see the shape of the bacteria. [[Thioglycate Broth]] - Tests between Aerobes (bacteria that require oxygen) and Anaerobes (bacteria which dont require oxygen). [[Spore Count test]] - Tests if the bacteria is spore producing. [[Soft Agar assay]] - Used to study the motility of Bacteria. If you need, you can re view the [[Symptoms|Symptoms1]]. Once you think you know the answer, Click [[here]]. This is a hard question so if you need it, we can also sequnce bacterial pathogens just like viral ones. I would only reccomend this once youve had a guess just using the bacterial tests. [[sequence the bacteria]] [[Main Menu|Main Menu 3]]]

(text-colour:black)+(bg:white)[Incorrect, remember from the last passage, a culture test promotes the growth of bacteria not viruses. [[Try again|You take a sample]]]

(text-colour:black)+(bg:white)[ As before the unknown sample is first stained with Crystal violet and then with iodine to hold the stain within the bacterial cell. Then a decolorizer is added, gram negative cells do not retain the stain, while Gram positive cells will still be coloured. Then a counterstain is added in order to visualise Gram Negative cells. The results of the Gram Stain have the bacteria a Pink Colour [[Back to main lab page|Bacteria 1]] ]

(text-colour:black)+(bg:white)[When looking through a microscope the bacteria are rod shaped. [[Back to main lab page|Bacteria 1]] ]

(text-colour:black)+(bg:white)[Thioglycolate Broth is used to determine the oxygen requirements of different Bacteria. The bacteria in this pathogen were found at the top of the broth. [[Back to main lab page|Bacteria 1]]]

(text-colour:black)+(bg:white)[1 microlitre of the unknown pathogen is inoculated onto soft agar, The agar was left for 24 hours. After 24 hours, the agar looked blurry. [[If you need a hint| Hint 4]] [[Back to main lab page|Bacteria 1]]]

(text-colour:black)+(bg:white)[The symptoms included high fever, severe headache, vertigo, black tongue, dark urine, dysentery, severe abdominal and thoracic pain, large nodules behind the ears that often invaded the neck and face, acute neurologic disorders, and profuse bleeding from the nose, eyes, and mouth with death frequently occurring in 3 to 4 days. [[Back to main lab page|Bacteria 1]]]

(text-colour:black)+(bg:white)[Non motile bacteria such as the Yerisnia perisis will not spread out so there would not be much blurring. [[Back|Soft Agar assay]]]

(set: $password to (prompt: "What is the Pathogen that you found in Mexico", "Answer Here") ) (if: $password is "Salmonella Enterica" or "salmonella enterica" or "Salmonella enterica")[You are correct. This is the correct pathogen, well done! Now that you have completed a story, you go back to the main menu to go to the next story. [[Main Menu|Main Menu 4]]] (else:)[You entered the wrong Pathogen.[[Try Again?|Bacteria 1]]]

(text-colour:black)+(bg:#706a5b)[You open your eyes, its a cold day yet the sky is clear, you are surronded by tall building that you recognise as victorian. In the far distance you notice a tall, well decorated bridge. Tower bridge, you then realise you're in london. There are large banners spread up between the houses that look like they're celebrating. Although it looks like there was a great celebration, some time has passed and everyone is back to work. You pick yourself up a newspaper off a bench and start to have a read. [[Read the newspaper]]]

(text-colour:black)+(bg:#7f6c64)[You open your eyes, its a pleasantly warm day, and you are surprised to hear people celebrating. You are within a beautiful city made of a white marbelled stone. You look around and recognise a massive circular building, you are looking at the colloseum and are standing within the city of ancient Rome. The city is very busy filled with people, everyone seems to be in a great mood. Most of those celebrating look to be soldiers covered in bright silver armour gleaming in the sunlight. Not all is as it seems, when you get closer, some of the people are beggining to show the first signs of illness. A group of these celebrating soldiers bump into you, in a freindly way ask you to join the celebrations. [[You start chatting to them]]]

(text-colour:black)+(bg:#7f6c64)[They tell tales of the recent journey they had faced. They say of how for the last 5 years they have been hundreds of miles from home fighting the parthian empire in the deserts to the far eastern border of the Roman empire. Having been victorious and capturing lots of parthias land. They tell how they arrived back to the city last week and have been out on the streets since having a huge party. You notice one man towards the back of the group with lots of spots over his face and ask him whats wrong? [[Whats Wrong?]]]

(text-colour:black)+(bg:#7f6c64)[He says how he noticed a rash forming on the tongue a couple of days ago however these sores have gotten worse and spread to the throat. He believes its just due to the alcohol thats been consumed during the celebrations. He does however say most of his soldier friends have also been experiencing the same problem so hes not so sure. You ask if he has anymore symptoms. He tells how hes had body aches and a fever, hes also experience vommiting but again decided that was due to alcohol. You decide to take a swab and head back to the lab. [[You close your eyes]]]

(text-colour:black)+(bg:white)[You Open your eyes back in the lab, with your sample. You are unsure whether your sample is a Viral or a bacterial pathogen so you first need to do a culture test. A culture test allows us to distinguish between bacteria and viruses, the culture is set up to provide nutrients suitable for bacterial gorwth. Viruses require host cells in order to replicate, bacteria do not and can comfortably grow on culture. After adding our sample to the culture and leaving it for 24 hours, no growth is exhibited. This means that our sample is a? [[Virus|Virus 1]] [[Bacteria|Bacteria1]] ]

(text-colour:black)+(bg:white)[With this Virus you once again want to sequence the genome in order to find out what it is. You decide this time to use the Sanger Sequencing method. In order to use this method, we first need to understand whether the Genome of the pathogen is RNA or DNA based. [[Difference between a RNA and a DNA Genome in a virus]] The way we will figue this out is by first performing a PCR reaction in order to amplify our sample in preperation for sequencinging. If this PCR reaction works then we know we have a DNA genome based pathogen. This is because PCR amplifies by that of DNA polymearase which as the name suggests only amplifys DNA. If the PCR reaction didnt work, we know its an RNA genome pathogen We would then have to amplify our RNA genome based pathogen. This can be done through reverese transcription PCR (rtPCR). Which uses reverse transcriptases instead of to convert the RNA to DNA, then amplifies as above. [[Go to PCR]] ]

(text-colour:black)+(bg:white)[Incorrect, As the culture provides the nutrients for microbial growth not viral growth, then as there is no growth exhibited by the sample we can determine its not a bacteria, so must be a virus. [[Back|You close your eyes]]]

(text-colour:black)+(bg:white)[RNA Viruses have there genetic material in a single stranded manner compared to DNA's double stranded. RNA mutates at a higher rate compared to DNA due to its Unstable nature as a single stranded molecule. In host cells, DNA replication of the virus occurs in the nucleus wheras in RNA virare it takes place in the cytoplasm. [[Back|Virus 1]]]

(text-colour:black)+(bg:white)[For our PCR reaction we need to create a mastermix to load into the machine. A mastermix is a batch mixture of PCR reagents all at optimal concentrations. The mix includes DNA polymerase, dNTPs, Magnesium Chloride and Buffer. As well as our sample. After adding all the reagents you are left with a total volume of the mixture 10 µL there are 25 moles of DNA polymerase. What is the concentration of DNA Polymerase in the mastermix? Once you have the answer go [[here|PCR Answer]] If you need a [[hint|Hint PCR]] [[Main Menu]]]

(set: $password to (prompt: "What is the Concentration of DNA polymerase in the mastermix (moles/L)", "Answer with just a number") ) (if: $password is "2.5")[You are correct. This is the correct concentration, well done! Now we must sequence the Pathogen as before. [[Sequencing]]] (else:)[You entered the wrong concentration.[[Try Again?|Go to PCR]]]

(text-colour:black)+(bg:white)[Good Job! After finishing the PCR and the other reactions required for sequencing, you are once again left with a FASTA sequence for the pathogen you swabbed in Rome. Once the sequence is copied paste it into the big box on the website below. Then Click BLAST to allign the sequence with all the known genome sequences to find our pathogen. (text-colour:red)+(bg:white)[When clicking the link below, right click and open the page in a new tab. Paste the FASTA sequence into the big box, scroll down and click BLAST. ] (link: "click here" [[https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome]] The FASTA sequence is as follows: (text-colour:navy)+(bg:white)[ 1 ctcgagagta tatgttgttg aacgttattg tttgagaaat agttgatgca tcagaatggt 61 ttgcatttat tgtagacgta ataatgcact acattgtttc ctcgtctatc tatatgtttt 121 gataagttat aacacgtttc aatctctagt tttatttttt tgtacgtcac atcttcatcc 181 agtagacgac atagaataca tgtgcaatct ttgccacaat ccatagctat tttggtgcta 241 attattccta tattatattt cacaaaaaat gatgaaggca atcattcctc ataagataat 301 aaaaagtgta ttgagagtga gtaagcatga aaaagattta gtatttagca gtgcggatat 361 gatccaagag ggtgaaatag tcgttctcgt tcagaatctt ttgcagcata agtagtatgt 421 cgatatactt atcgttgaag actcttccag agacgatagc taattgagta caaagtccaa 481 tgattgcaca aagttctttg gcggttttca tggagtcatt tctgatgaaa catttaatga 541 tctccacgca attgtctata ttgtcccacg gaagtgaatc cgagaactcc ttcaactcgc] Once you know the name of the pathogen answer [[here|Smallpox answer]] [[Main Menu]]]

(text-colour:black)+(bg:white)[For questions like this we must use the equation n=CV, where n stands for number of moles, C stands for Concentration and V stands for volume. If you can rearrange the equation, the question becomes more simple. [[Further hint]] [[Back|Go to PCR]]]

(text-colour:black)+(bg:white)[To solve the answer for concentration the equation must looke like this: C=n/V [[Back|Hint PCR]]]

(set: $password to (prompt: "What is the Pathogen that you found in Rome", "Answer Here") ) (if: $password is "Variola Virus" or "Variola" or "Variola virus" or "Smallpox" or "smallpox")[You are correct. This is the correct pathogen, well done! Now that you have completed a story, you go back to the main menu to choose the next story. [[Main Menu|Main Menu 2]]] (else:)[You entered the wrong Pathogen.[[Try Again?|Sequencing]]]

(text-colour:black)+(bg:#706a5b)[In the middle of the newspaper there are reports of an illness starting to affect people, they say it has come from the german trenches, but its named for the spanish. ] <style> img {max-width:100%;max-height:100%;} </style> <img src=https://www.artnews.com/wp-content/uploads/2020/05/web-0674.jpg> </div> (text-colour:black)+(bg:#706a5b)[You put [[down]] the newspaper and decided to try and get a sample.]

(text-colour:black)+(bg:#706a5b)[As you are walking around the town you see signs for London Hospital and so decide to head there. As you are walking you get some dirty looks from people, most of them are in masks, they all are distanced from one another. You get to the [[Hospital]]]

As you enter you are surprised by the sheer amount of people getting treated. There are lines of beds filled with the infected. <style> img {max-width:100%;max-height:100%;} </style> <img src=https://i.guim.co.uk/img/media/80cc28f99e794d7a49769f2ea8a95c72b0a3c5e6/1_324_2986_1792/master/2986.jpg?width=465&quality=85&dpr=1&s=none> </div>[The most surprising thing you see is the number of young adults that are infected, compared to the Flu we are used to affecting the very young and old.] You decide to [[talk to a nurse]].

The nurse tells of how quickly the Flu has spread, as soon as the soldiers returned they brought it with them. She says patients came in with a sudden very high fever, a strong dry cough with bad headaches and body aches. They have a sore throat and a runny nose, and are so tired they cant get out of bed. <style> img {max-width:100%;max-height:100%;} </style> <img src=https://i.guim.co.uk/img/media/80cc28f99e794d7a49769f2ea8a95c72b0a3c5e6/1_324_2986_1792/master/2986.jpg?width=465&quality=85&dpr=1&s=none> </div> You take a sample and [[close your eyes]].

(text-colour:black)+(bg:white)[Now that your back in the lab, you need to do some tests. Once again we need to do a culture test, after adding the sample to the culture and waiting for 24 hours there is no change. Is the sample a virus or a bacteria? [[Virus|Virus 2]] [[Bacteria|Bacteria 2]]]

(text-colour:black)+(bg:white)[Correct, so you know its a virus, what is the name of the illness? [[Newspaper article]] is here if you need reminding of the name. Answer [[here|Spanish Flu 1]] [[Main Menu|Main Menu 4]]]

(text-colour:black)+(bg:white)[Incorrect, a culture test promotes the growth of bacteria not viruses. [[Back|close your eyes]]]

(set: $password to (prompt: "What is the Illness affecting London", "Answer Here") ) (if: $password is "Spanish Flu" or "spanish flu" or "Spanish Influenza" or "spanish influenza")[You are correct. This is the illness affecting london[[Back to the Lab|Lab 3]]] (else:)[You entered the wrong illness.[[Try Again?|Virus 2]]]

(text-colour:black)+(bg:white)[Now we know the pathogen is a form of Influenza it makes it easier for us to narrowing it down the the correct type. There are 4 different types of Influenza, type A, B, C, and D. Type D is not known to cause illness in humans so we can rule that out. We can narrow this down by using a Rapid Influenza Diagnostic Test (RIDT), which is a type of antigen detection assay, that takes only 15 minutes. Measures the prescence of antibodys for Influenza type A. The results come back positive. This means we have what types of influenza? [[Type A]] [[Type B]] [[Type C]] [[Type D]]]

(text-colour:black)+(bg:white)[Correct, well done, now we know what type of Influenza it is, we need to determine the subtype in order to treat it. Influenza A Viruses are divided into further subtypes based on two surface proteins: hemagglutinin (H) and neuraminidase (N). There are 18 different H subtypes and 11 different N subtypes. We are going to need to sequence the sample in order to find out what it is. In order to sequence this Infuenza we are going to need a Primer in order to sequence. [[What is a primer?]] [[Design the primer]]]

(text-colour:black)+(bg:white)[Incorrect, as the test is positive for the antigens of Type A we can assume our sample is Type A. [[Back|Lab 3]]]

I(text-colour:black)+(bg:white)[ncorrect, as the test is positive for the antigens of Type A we can assume our sample is Type A. [[Back|Lab 3]]]

(text-colour:black)+(bg:white)[Incorrect, as the test is positive for the antigens of Type A we can assume our sample is Type A. [[Back|Lab 3]]]

(text-colour:black)+(bg:white)[A primer is a short nucleic acid sequence that provides a starting point for DNA synthesis. This allows for our sequence to read the genome of our pathogen. Its a complimentary set of nucleotides to that of the pathogen. [[back|Type A]]]

(text-colour:black)+(bg:white)[The First line of the genetic code of the pathogen is as follows: tcaattatat tcaatatgga aagaataaaa gaactaagga atctaatgtc gcaatctcgc what would be the correct Primer that created this sequence. [[Hint|Primer hint]] [[1]]- agttaataca acaaatacct [[2]]- agttaatata agttatacct [[3]]-agaatttctg agtaataccg [[4]]-agttaatata agttatagct]

(text-colour:black)+(bg:white)[Remember primers are complomentary, so it must be the opposite nucelotide to the one thats shown. Adenine binds to Thymine Cytosine binds to Guanine. [[Back|Design the primer]]]

(text-colour:black)+(bg:white)[Incorrect If you need some help with this question try the [[Hint|Primer hint]] You can try again [[here|Design the primer]]]

(text-colour:black)+(bg:white)[Well Done! After design lots of primers we can once again sequence the genome of the Influenza pathogen. The results of the sequencing are as follow: You need to copy and paste the following sequence into the large box in the program of BLAST. BLAST is the Basic Local Alignment Search Tool, it finds regions of similarity between biological sequences. With the following sequence it will match it up agaisnt the 1000's of known pathogens to understand what it is. You can find blast here: link: "click here" [[https://blast.ncbi.nlm.nih.gov/Blast.cgi]] Once you know what the H and N subtype of the Influenza A is answer [[here|Final answer]] ] (text-colour:cyan)[1 tcaattatat tcaatatgga aagaataaaa gaactaagga atctaatgtc gcaatctcgc 61 actcgcgaga tactcacaaa aaccaccgtg gaccatatgg ccataatcaa gaaatacaca 121 tcaggaagac aggaaaagaa cccgtcactt aggatgaaat ggatgatggc aatgaaatat 181 ccaattacag cagacaaaag gataacggaa atgattcctg agagaaatga ccaaggacaa 241 actttatgga gtaaaatgaa tgatgccgga tcagaccgag tgatggtatc acctctggct 301 gtgacatggt ggaatagaaa tggaccaatg acaagtacaa ttcattatcc aaaaatctac 361 aaaacttatt ttgaaaaagt cgaaaggtta aaacatggaa cctttggccc tgtccatttt] [[Main Menu|Main Menu 4]]

(text-colour:black)+(bg:white)[Incorrect If you need some help with this question try the [[Hint|Primer hint]] You can try again [[here|Design the primer]]]

(set: $password to (prompt: "What is the H and N number of the spanish Flu", "Answer Here") ) (if: $password is "H1N1" or "h1n1" or "11")[You are correct. This is the correct H and N subtype of Influenza, well done! You have completed the final story. Thank you very much for playing, please head back to the [[Main Menu|Main Menu 5]] to answer my short survey. (else:)[You entered the wrong Pathogen.[[Try Again?|2]]]

Well done! After completing the first story the main menu is now available. This page provides a place to have a break between the stories and gives a place to access the survey, i would reccomend trying all the different stories if you can. Now that you have completed a story, before you finish with this virtual escape room, it would be fantastic if you could answer the short survey at the foot of the page to help with my dissertation. [[Story 2|Smallpox start]] Open this link in a new tab if you wish to answer the survey. [[https://strathsci.qualtrics.com/jfe/form/SV_2rQHzo6IKga1CLA]]

Well done! After completing the first story the main menu is now available. This page provides a place to have a break between the stories and gives a place to access the survey, i would reccomend trying all the different stories if you can. Now that you have completed a story, before you finish with this virtual escape room, it would be fantastic if you could answer the short survey at the foot of the page to help with my dissertation. To continue with the story click on [[Story 3|Black Death Start]]. The survey is here: Open this link in a new tab if you wish to answer the survey. (link: "click here" [[https://strathsci.qualtrics.com/jfe/form/SV_2rQHzo6IKga1CLA]]

Well done! After completing the first story the main menu is now available. This page provides a place to have a break between the stories and gives a place to access the survey, i would reccomend trying all the different stories if you can. Now that you have completed a story, before you finish with this virtual escape room, it would be fantastic if you could answer the short survey at the foot of the page to help with my dissertation. To continue with the story click on [[Story 4|Cocoliztli Epidemic]] The survey is here: Open this link in a new tab if you wish to answer the survey. (link: "click here" [[https://strathsci.qualtrics.com/jfe/form/SV_b1TKFoGT2RZgl0O]]

Well done! After completing the first story the main menu is now available. This page provides a place to have a break between the stories and gives a place to access the survey, i would reccomend trying all the different stories if you can. Now that you have completed a story, before you finish with this virtual escape room, it would be fantastic if you could answer the short survey at the foot of the page to help with my dissertation. To continue with the story click on [[Story 5|Spanish Flu start]] The survey is here: Open this link in a new tab if you wish to answer the survey. (link: "click here" [[https://strathsci.qualtrics.com/jfe/form/SV_eDQgZpDNvzftsfY]]

Well done! You have completed the entire virtual escape room, i really hope you enjoyed it. Before you go it would be great if you could answer my short survey to help with my dissertation. The survey is here: (link: "click here" [[https://strathsci.qualtrics.com/jfe/form/SV_01WTgaGtTFBrTrU ]]

(text-colour:black)+(bg:white)[After sequencing the bacterial genome, and pasting the FASTA sequence into BLAST, the result you get is a 98% match of //Salmonella enterica//. [[Back|Bacteria 1]]]

(text-colour:black)+(bg:white)[In order to seperate the cells they need to be spun very quickly using a specific machine. [[Back|You close your eyes thinking of the lab]] [[Further hint|h1]]]

(text-colour:black)+(bg:white)[The specific machine is a centrifuge. [[Back|You close your eyes thinking of the lab]]]