Infection Revision PP - Weeks 2 (Second Half) - Week 3 (Full) FINAL.pptx

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1. MCQ – Weeks 2 (2 nd part) & 3 Welcome back. Please wait for the session to start. As usual, rules, so this session works for everyone  : Mics off. No long questions/explanations in the first hour, MCQ section. After the first hour, you can leave or stay for some general revision.

2. There are 20 questions total. In question sets of 4– 5 sets -, you ‘fight’ Pokemon gym leaders to try and get as many Pokemon as you can. If you get 2/3 of the first 3, you’ve won the battle. If you get 1 , you get one redemption question (but everyone’s going to try this question either way). Are you ready to see your first opponent & Pokemon ? You will be collecting Pokemon today! You will try to get 5 in total by ‘fighting’ 5 different gym leaders. PS – I know basically nothing about Pokemon … CBL Case 2. L2.5/2.6 – Stats. L2.7 – Clinical microbiology. L2.8 – GI pathogens. TEL2.10 – Sequencing. L3.1/3.2 – Pandemics. L3.3 – Virology. L3.6 – Emerging bacterial pathogens. L3.9/3.10 – Immunology. L3.11 – Flu & viral potentials. NOT 3.4/3.5 – key PH organisms. 3.8 – PCR. Tragic lectures.

3. No chance you’re getting past my minion memes. This gym leader. For this pokemon . This gym (arena).

4. You are challenged by Leader Farhan (L3.11) It’s your move. Your question is: What is true about avian influenzas? Typically H1 or H5 antigens . Bind α2, 6- linked sialic acid in bird cells. They can undergo reassortment with human influenzas H5N1 loses its polybasic site upon human infection 1 of 3 for: Pikachu.

5. You are challenged by Leader Farhan (L3.11) The answer to the question… What is true about avian influenzas? Typically, H1 or H5 antigens . Bind α2, 6- linked sialic acids in bird cells. They can undergo reassortment with human influenzas H5N1 loses its polybasic site upon human infection 1 of 3 for: Pikachu. A- No, most typically H5 or H7. B- No, it’s α2, 3 - linked sialic acids. C- Correct – this makes them more likely to infect humans & not be recognised by the immune system . D- No, it keep its polybasic site – means it can still be cleaved by many different types of protease-> more widespread disease.

6. You are challenged by Leader Farhan (L3.9) It’s your move. Your question is: What is not true about T or B cells? B cells activate T cells in adaptive immunity . T-cell receptors are not released from T cells. B-cell receptors can undergo antibody functions. 2 of 3 for: Pikachu. B and T cells can turn into memory cells.

7. You are challenged by Leader Farhan (L3.9) The answer to the question… What is not true about T or B cells? B cells activate T cells in adaptive immunity . T-cell receptors are not released from T cells. B-cell receptors can undergo antibody functions. 2 of 3 for: Pikachu. B and T cells can turn into memory cells. A- Correct, T (helper or CD4+) cells activated by APCs. T helper cells can activate B cells. B- Yes. C- Yes , unlike B-cell receptors. D- Yes, these functions include neytralisation and opsonisation.

8. You are challenged by Leader Farhan (L3.6) It’s your move. Your question is: What is true about anthrax-causing bacteria? Anthrax is caused by Bacillus cereus . The capsule in anthrax is eaten by phagocytes. The axtA gene on pXO1 regulates anthrax toxins and the capsule genes. The anthrax toxin is encoded on pX02 with the capsule. 3 of 3 for: Pikachu.

9. You are challenged by Leader Farhan (L3.6) The answer to the question… What is true about anthrax-causing bacteria? Anthrax is caused by Bacillus cereus . The capsule in anthrax is eaten by phagocytes. The axtA gene on pXO1 regulates anthrax toxins and the capsule genes. The anthrax toxin is encoded on pX02, as is the capsule. 3 of 3 for: Pikachu. A- Wtong , T (helper or CD4+) cells activated by APCs. T helper cells can activate B cells. B- Wrong, it is an anti-phagocytic capsule-> virulence. C- Yes , unlike B-cell receptors, useful in mammals unlike plCR (insects) . D- Mo, anthrax toxin encoded on pX01 with axtA . Only capsule on px02.

10. You are challenged by Leader Farhan If you got 2 right, Pikachu is yours. If you got 1 right, I’ll let you try and get Pikachu if you get this next one right.

11. You are challenged by Leader Farhan (TEL 2.10) It’s your move. Your question is: What is not true about longer-read HTS. *HTS = high-throughput sequencing. Oxford nano-pore & Pacbio are examples. Higher accuracy per read vs short-read HTS. Full length transcripts are generated without gene fragmentation. Handles complex genomic regions like repetitive regions better vs short-read HTS. Redemption question for: Pikachu.

12. You are challenged by Leader Farhan (TEL 2.10) The answer to the question… What is not true about longer-read HTS. *HTS = high-throughput sequencing. Oxford nano-pore & Pacbio are examples. Higher accuracy per read vs short-read HTS. Full length transcripts are generated without gene fragmentation. Handles complex genomic regions like repetitive regions better vs short-read HTS. Redemption questionfor : Pikachu. B- Yes, and Ion Torrent/Illumina are short-read HTS technologies. B- Correct, this is called higher sequence fidelity (more accuracy). C- Yes , unlike short-read HTS, relying on overlapping shorter sequences to get the whole genetic sequence. D- Yes, you don’t need a gene assembler which can sometimes miss out regions like regions with regions/flanking regions.

13. You are challenged by Leader Farhan If you got this one wrong and haven’t got Pikachu yet, you’re outta luck…

14. I’m baaaaaack . This gym leader. For this pokemon . This gym (arena).

15. You are challenged by Leader Leda (L3.3) It’s your move. Your question is: What is correct in terms of viruses being able to enter/reproduce in cells? Permissive cells – cells have a functional receptor, viruses can enter. Persistent infections – occur when viruses remain in cells and cause no harm. Resistant cells – cells have no functional receptor, viruses can’t enter. Latent infection – viruses slowly release from cells & cause harm. 1 of 3 for: Charizard.

16. You are challenged by Leader Leda (L3.3) The answer to the question… What is correct in terms of viruses being able to enter/reproduce in cells? Permissive cells – cells have a functional receptor, viruses can enter. Persistent infections – occur when viruses remain in cells and cause no harm. Resistant cells – cells have no functional receptor, viruses can’t enter. Latent infection – viruses slowly release from cells & cause harm. 1 of 3 for: Charizard. B- No, this describes susceptible cells. Permissive cells let viruses replicate inside of them, regardless of whether they can enter. B- No, viruses are slow released from cells. C- Correct . D- No, viruses remain within cells, causing no harm.

17. You are challenged by Leader Leda (L3.2) It’s your move. Your question is: What is not a population-based intervention for COVID? Vaccination programmes. Using face masks to reduce spread. Closing hospitality, schools, workplaces/ Medical treatment inc. antivirals. 2 of 3 for: Charizard.

18. You are challenged by Leader Leda (L3.2) The answer to the question… What is not a population-based intervention for COVID? Vaccination programmes. Using face masks to reduce spread. Closing hospitality, schools, workplaces. Medical treatment inc. antivirals. 2 of 3 for: Charizard. B- Yes , reduces transmission, protects public. B- Yes , reduces transmission, protects public. C- Yes , reduces transmission, protects public. D- Correct. C are-based intervention like O2 therapy, antibody therapy.

19. You are challenged by Leader Leda (L3.2) It’s your move. Your question is: Which is the most likely to be statistically significant? Odds ratio = 1.5 (95% CI = 0.9-2.3) Odds ratio = 2.0 (95% CI = 1.3-3.1) Odds ratio = 27 (95% CI = 1-29) Odds ratio = 1.1 (95% CI = 0.8-1.1) 3 of 3 for: Charizard.

20. You are challenged by Leader Leda (L3.2) The answer to the question… Which is the most likely to be statistically significant? Odds ratio = 1.5 (95% CI = 0.9-2.3) Odds ratio = 2.0 (95% CI = 1.3-2.1) Odds ratio = 27 (95% CI = 1-29) Odds ratio = 1.1 (95% CI = 0.8-1.1) 3 of 3 for: Charizard. A- No , CI includes 1. B- Correct. CI doesn’t include 1 and has a narrow range . C- No , CI includes 1 and is massive. D- No, CI includes 1, despite CI being in a narrow range.

21. You are challenged by Leader Leda If you got 2 right, Charizard is yours. If you got 1 right, I’ll let you try and get Charizard if you get this next one right.

22. You are challenged by Leader Leda (L3.1) It’s your move. Your question is: Which is these terms is NOT part of the epidemiological triad: Environment. Agent . Time. Host. Redemption questionfor : Charizard.

23. You are challenged by Leader Leda (L3.1) The answer to the question… Which is these terms is NOT part of the epidemiological triad: Environment. Agent . Time. Host. Redemption questionfor : Charizard. A- Yes , ecological conditions favouring host-agent interactions. B – Yes, organism producing infection. C- Correct – not in the triad (but key part of descriptive epidemiology). D- Yes , organism affording subsistence/lodgement to infectious agent. ^NOTE: in the middle of the triad, there is the word disease.

24. You are challenged by Leader Leda If you got this one wrong and haven’t got Charizard yet, you’re outta luck…

25. This is going to be a long one but I know you can get through it. This gym leader. For this pokemon . HMS Student Hollie This gym (arena).

26. You are challenged by Leader Hollie (L2.7) It’s your move. Your question is: What is not true about microbial typing Typing is when a microbiologist aims to classify different species of bacteria from a source. Whole Genoming Sequencing has the best resolution and it allows you to type effectively. Used to track hospital outbreaks of anti-biotic resistant bacteria. Pulsed field electrophoresis separates an isolate’s DNA by size and compares it to a reference - use is declining. 1 of 3 for: Eevie .

27. You are challenged by Leader Hollie (L2.7) The answer to the question… What is not true about microbial typing Typing is when a microbiologist aims to classify different species of bacteria from a source. Whole Genoming Sequencing has the best resolution and it allows you to type effectively. Used to track hospital outbreaks of anti-biotic resistant bacteria. Pulsed field electrophoresis separates an isolate’s DNA by size and compares it to a reference - used is declining. 1 of 3 for: Eevie . A- Correct , Classify strains of the same bacteria from a strain/source. B- Yes, newest technology  C- Yes , it is crucial for this. D- Yes, being replaced by WGS etc.

28. You are challenged by Leader Hollie (L3.3) It’s your move. Your question is: What is true about the history of identifying viruses The Chamberlain filter allowed scientists to find out that viruses weren’t toxins. The Electron Microscope allowed us to see whether viruses has a nucleic acid genome. Hershey-Chase experiment proved that labelled proteins were found in new phages . The fact that some organisms infecting plants seemed smaller than bacteria began research on viruses. 2 of 3 for: Eevie .

29. You are challenged by Leader Hollie (L3.3) The answer to the question… What is true about the history of identifying viruses The Chamberlain filter allowed scientists to find out that viruses weren’t toxins. The Electron Microscope allowed us to see whether viruses has a nucleic acid genome. Hershey-Chase experiment proved that labelled proteins were found in new phages . The fact that whatever was infecting some plants seemed smaller than bacteria began research on viruses. 2 of 3 for: Eevie . A- No, proved that viruses were smaller than bacteria. B- No, it allowed for visualisation of structures but not inside nuclei. C- No, the radioactive DNA is what was found in new phages . D- Correct , whatever infecting tobacco passed through the Chamberlain filter, proving it wasn’t a bacterium.

30. You are challenged by Leader Hollie (L2.8) It’s your move. Your question is: Which of these GI pathogens is a parasite? Vibrio. Shigella. Cryptosporidiosis. Listeria. 3 of 3 for: Eevie .

31. You are challenged by Leader Hollie (L2.8) The answer to the question… Which of these GI pathogens is a parasite? Hepatitis. Shigella. Cryptosporidiosis. Listeria. 3 of 3 for: Eevie . A- No, virus. B- No, bacteria. C- Correct , a parasite – other GI parasites include amoebiasis, giardiasis. D - No, bacteria.

32. You are challenged by Leader Hollie If you got 2 right, Eevie is yours. If you got 1 right, I’ll let you try and get Eevie if you get this next one right.

33. You are challenged by Leader Hollie (L3.10) It’s your move. Your question is: Which is not a key part about autoimmunity. Chronic inflammation due to a sustained immune response. Immunosuppressants to stimulate inflammation to remove pathogenic trigger. Initiation by pathogen or cell damage. Cross-reactivity with self-antigens. Redemption question for: Eevie .

34. You are challenged by Leader Hollie (L3.10) The answer to the question… Which is not a key part about autoimmunity. Chronic inflammation due to a sustained immune response. Immunosuppressants to stimulate inflammation to remove pathogenic trigger. Initiation by pathogen or cell damage. Cross-reactivity with self-antigens. Redemption question for: Eevie . A- Yes, + ve feedback loop infact . B- Correct , they decreased inflammation as do monoclonal antibodies like anti-TNF(alpha), corticosteroids and anti IL-6/12. Other treatments like CTLA-4 inhibit T cell activation. C – Yes . D – Yes the self-antigen is mistaken for the insult/pathogen.

35. You are challenged by Leader Hollie If you got this one wrong and haven’t got Eevie yet, you’re outta luck…

36. Why are you out of CBL so early??? This gym leader. For this pokemon . HMS Student Dawn This gym (arena)

37. You are challenged by Leader Dawn (L2.6) It’s your move. Your question is: Which is true in terms of statistics. A low p-value value won’t help you state whether an association is statistically significant. P-value are independent of effect size & sample size. Multivariate analysis is when you look at a few variables in isolation and see their effect on the outcome. Multi-variate analysis helps you find which variables are associated with an outcome, considering confounders 1 of 3 for: Lucario

38. You are challenged by Leader Dawn (L2.6) The answer to the question… Which is true in terms of statistics. A low p-value value won’t help you state whether an association is statistically significant. P-value are independent of effect size & sample size. Multivariate analysis is when you look at a few variables in isolation and see their effect on the outcome. Multi-variate analysis helps you find which variables are associated with an outcome, considering confounders 1 of 3 for: Lucario A- No, this does help you, <p0.05 = association is likely to be real and you can reject null hypothesis. B – No , they are dependent on effect & sample size.. C – No, you look at the variables simultaneously-> adjusted odds ratio. D- Correct , it makes use of regression.

39. You are challenged by Leader Dawn (TEL2.10) It’s your move. Your question is: Which is true about sequencing. A large amount of ddNTPs are added to synthesise the complementary strand. Sanger sequencing helped a lot in the Human Genome Project. Sanger sequencing is a HTS (high-throughput sequencing) technique. Modern Sanger still widely uses autoradiograms & gel electrophoresis. 2 of 3 for: Lucario

40. You are challenged by Leader Dawn (TEL2.10) The answer to the question… Which is true about Sanger sequencing. A large amount of ddNTPs are added to synthesise the complementary strand. Sanger sequencing helped a lot in the Human Genome Project. Sanger sequencing is a HTS (high-throughput sequencing) technique. Modern Sanger still widely uses autoradiograms & gel electrophoresis. 2 of 3 for: Lucario A- No, large amount of d NTPs, ddNTP are chain terminating only (thus few). B- Correct , it was instrumental as other tech hadn’t been invented. C – No . D – No, uses fluorescence, capillary electrophoresis.

41. You are challenged by Leader Dawn (L3.1) It’s your move. Your question is: Which describes an outbreak spreading to a big geographical area, but isn’t considered global. Cluster. Outbreak. Epidemic. Pandemic . 3 of 3 for: Lucario

42. You are challenged by Leader Dawn (L3.1) The answer to the question… Which describes an outbreak spreading to a big geographical area, but isn’t considered global. Cluster. Outbreak. Epidemic . Pandemic. 3 of 3 for: Lucario A- No, not the right scale. B – No , 2+ cases linked in time & space. C - Correct , it was instrumental as other tech hadn’t been invented. D – No, global spread.

43. You are challenged by Leader Dawn If you got 2 right, Lucario is yours. If you got 1 right, I’ll let you try and get Lucario if you get this next one right.

44. You are challenged by Leader Dawn (L3.11) It’s your move. Your question is: Which is not a factor increasing the chance of a new pandemic. High level of biodiversity. Pathogens with high mutation rates. Deforestation. Sparse human populations . Redemption question for: Lucario

45. You are challenged by Leader Dawn (L3.11) The answer to the question… Which is not a factor increasing the chance of a new pandemic. High level of biodiversity. Pathogens with high mutation rates. Deforestation. Sparse human populations . Redemption question for: Lucario A- No, increases human-pathogenic wild life interaction. B – Yes , increased chance it will jump to humans. C – Yes, increases human-pathogenic wild life interaction. D - Correct , it was instrumental as other tech hadn’t been invented.

46. You are challenged by Leader Dawn. If you got this one wrong and haven’t got Lucario yet, you’re outta luck…

47. rrrright ? This elite, godly gym leader. For this pokemon . HMS Student surangi This gym (arena)

48. You are challenged by Leader surangi (L2.6) It’s your move. Your question is: Which is true in terms of the influenza life cycle. Viral polymerase is very accurate, beneficial as this reduces mutations. NA fuses viruses to siliac acid, allowing virus to infect other cells. RNA polymerase transcribes – ve vRNA into + ve mRNA. Increasing endosomal pH via M2 -> change to HA’s shape-> endosome-membrane fusion & release of viral DNA. 1 of 3 for: Mewtwo

49. You are challenged by Leader surangi (L2.6) The answer to the question… Which is true in terms of the influenza life cycle. Viral polymerase is very accurate, beneficial as this reduces mutations. NA fuses viruses to siliac acid, allowing virus to infect other cells. RNA polymerase transcribes – ve vRNA into + ve mRNA. Increasing endosomal pH via M2 -> change to HA’s shape-> endosome-membrane fusion & release of viral DNA. 1 of 3 for: Mewtwo A- No, it’s error prone-> mutations B – No , after replication, HA cleaves siliac acid to stop new virions sticking to cell. C - Correct . C – No, decreasing endosomal pH. Also M1 uncoating!

50. You are challenged by Leader surangi (L3.6) It’s your move. Your question is: Which is not a true way bacteria avoid phagocytic destruction They have anti-phagocytic capsules. Release toxins to kill immune cells. Secrete enzymes to break down phagocyte’s DNA. Using stealth and immune evasion. 3 of 3 for: Mewtwo

51. You are challenged by Leader surangi (L3.6) The answer to the question… Which is not a true way bacteria avoid phagocytic destruction They have anti-phagocytic capsules. Secrete enzymes to break down phagocyte’s DNA . Release toxins to kill immune cells. Using stealth & immune evasion. 2 of 3 for: Mewtwo A- Yes – reduce engulfment. B - Correct , there aren’t any ‘ DNAases ’ to break down intracellular phaagocyte DNA. C – Yes – destroys phagocytes before they themselves get destroyed . D – Yes – reduces recognition .

52. You are challenged by Leader surangi (L3.9) It’s your move. Your question is: Which is not a pattern recognition receptor (PRR). Toll-like recptors . NOD-like receptors. TCRs. C-type receptors. 3 of 3 for: Mewtwo

53. You are challenged by Leader surangi (L3.9) The answer to the question… Which is not a pattern recognition receptor (PRR). Toll-like recptors . NOD-like receptors. TCRs . C-type receptors. 3 of 3 for: Mewtwo A- Yes – membrane-bound PRR. B – Yes – cytoplasmic PRR. C - Correct , T-cell receptors are in adaptive immune response, not innate. D – Yes, membrane-bound PRR.

54. You are challenged by Leader surangi If you got 2 right, Mewtwo is yours. If you got 1 right, I’ll let you try and get Mewtwo if you get this next one right.

55. You are challenged by Leader sarangi (CBL Case 2) It’s your move. Your question is: Which is a defining virological feature oe coronaviruses. Single stranded RNA genome in an envelope. HA as surface proteins. Lock of protein coat. Circular DNA genome. Redemption question for: Mewtwo

56. You are challenged by Leader sarangi (CBL Case 2) The answer to the question… Which is a defining virological feature oe coronaviruses. Single stranded RNA genome in an envelope. HA as surface proteins. Lock of protein coat. Circular DNA genome. Redemption question for: Mewtwo A – Correct. B – No, influenza does. Coronviruses have spike proteins. C- No, they have an envelope; they’re not a naked virus. D – No , they have RNA.

57. You are challenged by Leader surangi . If you got this one wrong and haven’t got Mewtwo yet, you’re outta luck…

58. Hope you enjoyed yourself and hope you caught them all .

59. Tricky topic areas: Emerging bacteria pathogens. Surveillance (because it’s a picture lecture). PCR. Flu & viral potentials.