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basic principles of virology.




hi sir this the final exam i need your best answer;Attachment Preview;Final Exam Spring 2014.pdf Download Attachment;BIOL 513 Final Exam Part I (10 questions x 15 pts each);This final exam is designed to test your knowledge and ability to apply the concepts you have;attained this semester for the basic principles of virology. This exam includes questions that will;help you review topics that I feel every student taking this class should retain as well as the;types of questions you are likely to face on your comprehensive qualifying exam. You may use;your textbook or other written/internet sources of information to complete this exam, but;you may not collaborate with other students in the class. Note that the rules for;plagiarism for other written work in this class apply to this exam. Cut-and-paste from the;internet or other sources is unacceptable and will result in a zero for the exam. Write all;responses in your own words. Please abide by word limits to help you focus your responses.;Please do not include the question in your responses. When you complete the exam, make sure;you reread/proofread your responses to ensure they are well written, concise and answer all the;questions asked. I recommend that you research the questions and then start with a blank;screen and write your responses in your own words.;Submit to by 6:00 PM May 10.;Question 1;We started this class with each student providing a definition of a virus. Nearly 800 pages of text;reading and over 900 discussion board posts later, how has your personal definition of a virus;evolved? Write a paragraph (150 words or less) providing a comprehensive definition of a virus.;Comment on how your definition has changed from the beginning of the semester.;Question 2;Influenza A (H7N9) is one of a subgroup of influenza viruses that normally circulate among;birds. In late March of this year, a number of individuals in and around Shanghai, China were;stricken with severe influenza-like symptoms. These individuals were found to be infected with a;new H7N9 Influenza A virus, which had never before been observed to infect humans. To date;a total of 108 laboratory-confirmed cases of human infection with avian influenza A (H7N9);virus, including 22 deaths have been reported to WHO. Answer the following questions about;this virus. (Note: I am not expecting you to research the answer to these questions, but rather;use what you have learned this semester to provide plausible responses);a) Explain in laymens term what the term H7N9 influenza virus means (3-4 sentences;max).;b) The complete genome sequences of H7N9 virus from three patients have been;determined. The HA gene is most closely related to a 2011 duck H7N3 virus found in;Zhejiang China. The NA gene appears to be almost identical to a H7N9 virus found in;wild birds in Korea. The remaining genes appear to be closely related to a brambling;H9N2 virus found in 2012 near Beijing. Briefly describe likely mechanism(s) of how this;virus might have evolved.;c) Will the current seasonal vaccine influenza A vaccine likely be effective against the;H7N9 virus? How about antivirals such oseltamavir or zanamavir? Why or why not.;d) It is speculated that the new H7N9 virus is transmitted to humans directly from birds.;Unlike previous bird flu outbreaks (e.g. H5N1) this virus does not appear to make birds;sick. Briefly speculate how this virus could have no apparent effect on birds, but cause;such severe disease in humans.;Question 3;Influenza: Fact or Fiction. The book The Great Influenza by John Barry is a compelling story of;the 1918 influenza epidemic that killed millions worldwide. Although this is an excellent book, it;contains a number of factual errors concerning basic virology. Read the following quotes from;the book and explain why these statements are scientifically incorrect or misleading (Max 4;sentences/quote).;Quote 1;Soon the genes of the [influenza] virus spill into the cell, then penetrate to the cell nucleus;insert themselves into the cells genome, displace some of the cells own genes, and begin;issuing orders.;Quote 2;Each antibody carries thousands of receptors on their surface to recognize and bind to different;antigens.;Quote 3;But of all parts of the influenza virus that mutate, the hemagglutinin and neuraminidase mutate;the fastest.;Quote 4;Dendritic cells attack bacteria and viruses indiscriminately, engulf them, then process their;antigens and present those antigens in effect they chop up an invading microorganism into;pieces and display the antigens like a trophy flag.;Quote 5;During entry inside the endosomal vesicle, shape and form shift and create new possibilities as;the hemagglutinin faces a more acidic environment. This acidity makes it cleave in two and;refold itself into an entirely different shape.;Question 4;A clinical pathologist has sent you a cell line infected with an unknown virus. You are able to;expand the cell line and isolate the viral particles free of contaminating host cells. Structural;studies indicate that the virus is an enveloped virus. Answer the following questions.;A. To develop a routine assay for the virus, you attempt to set up a plaque assay. Although;you know that the cell line you are using is susceptible and permissive for the virus and;you follow the standard procedures for a plaque assay, you are unable to get plaques;when plating the infected cells in agar. Provide a plausible explanation for why you are;unable to get plaques (Can be answered in a few sentences).;B. To identify the genome type of the virus, you use the purified virus from human cells;lyse the cells and measure total nucleic acid polymerase activities. In addition, you also;are able to isolate the viral particles free of contaminating cells and measure polymerase;activity of the particles using the same assay. The data from these experiments are;depicted below. (Axis Legend Abbreviations: Dep is dependent and Pol is polymerase).;Given this data, what are the possibilities for the genome structure (DNA or RNA, singlestranded or double-stranded, linear or circular) of this virus? Explain why?;Polymerase Activity;Pol Activity (Arbitrary Units);16000;14000;12000;Infected-Lysate;10000;8000;Purified Viral Particles;6000;4000;2000;RNA-Dep DNA Pol;RNA-Dep RNA Pol;DNA-Dep RNA Pol;DNA-Dep DNA Pol;No Lysate Control;0;C. Based on your answer from Part B, briefly describe the likely mechanism of replication of;this virus from the point the genome enters the cell to assembly of new viral particles.;Where in the cell does replication occur and what is the source of polymerase used to;replicate viral genome?;D. Based on all the information above, which routes of entry and transmission (fecal/oral;respiratory, sexual transmission etc) can you rule out and which are most likely? Why?;Question 5;You are working in a virology lab in which a new graduate student who (has not had BIOL 513);is trying to work with a new virus. The student wants to establish a cell line in which the virus;can replicate to study the molecular biology of the virus. The HeLa cell line does not express the;receptor for this new virus, called Protein X, and therefore cannot support entry by this virus. To;make the cell line susceptible, the graduate student attempts to create a new cell line useful for;study of the virus by transfecting the gene for Protein X into the HeLa cell line. Although;immunohistochemistry studies clearly demonstrate that Protein X is being expressed on the;surface of the transfected HeLa cells, the graduate student can still not get the new virus to;replicate in HeLa cells. Explain potential mechanisms for why this might be the case. What other;types of proteins might need to be introduced to develop a useful cell line (200 words max).;Question 6;Describe the key molecular/cellular events in the HIV lifecycle from entry to assembly and exit;from the host cell. Indicate the most important enzymatic activities required for the HIV lifecycle;and whether these activities come from the host or virus. Suggestion: Draw a diagram of the;HIV lifecycle and then describe the diagram in word/paragraph format.;Question 7;There has been a (fictional) outbreak of tumors in blue jays on the USJ campus. Deep;sequencing studies of fecal samples from the birds reveals the presence of two previously;unknown viruses. The organization of the genomes of two viruses is depicted below;Virus A above has the structure above and includes the A gene which has the same exact;sequence as a normal blue jay gene. Virus B has no genes beyond the standard GAG-PROENV shown above. Given the information above, answer the following questions;a) What type of viruses are Viruses A and B (include Baltimore Classification)?;b) Virus A can be grown in culture. When the virus is injected in healthy blue jays, 100% of;the birds develop tumors. What type of tumor virus is Virus A? Suggest possible;functions of the A gene and how it could contribute to tumor formation.;c) When virus B is injected in health blue jays, ~5% develop tumors. What kind of tumor;virus is virus B? Contrast how its mechanism of carcinogenesis is different from Virus A.;Question 8;A graduate student is tasked by his thesis advisor to design various simple synthetic viruses.;Unfortunately, this student has not taken BIOL 513 and he fails to include essential gene(s);required for successful production of infectious progeny. Listed below are the virus types and a;list of the genes the student includes in the viral genome. Explain what gene(s) are missing;such that the viruses below would not be able to replicate and produce infectious progeny. Each;part can be answered in 3-4 sentences.;Part A;Virus A is a simple retrovirus that contains the following genes;NC is the nucleocapsid protein, Pro is viral protease, RT is reverse transcriptase and VR is the;viral receptor/envelope protein. What additional gene would be required for this virus to replicate;and produce progeny? Justify your answer.;Part B;Virus B is a non-enveloped circular ssDNA virus that is designed to replicate in the cytoplasm.;VP1-4 are capsid proteins, vTF is a transcription factor that initiates production of viral RNA and;ori is a DNA binding protein that binds viral origin of replication. Explain what additional genes;would be needed for this virus to replicate in the cytoplasm.;Part C;An enveloped segmented dsRNA virus that contains two segments which express only 4 viral;proteins: A matrix protein that binds to envelope membrane, NS1 a protein that interferes with;Major Histocompatiblity Complex (MHC) expression on cell surface, VR the viral receptor for;host and a RNA-dependent RNA Polymerase (RdRP). What additional genes are required for;this virus to make infectious progeny? Justify you answer.;Viral RNA Polymerase;Capsid proteins;Viral Protease;Virus D;A single-stranded (+) strand RNA virus with the following genome;VP1, VP2, VP3 and VP4 are capsid proteins, Pro is a viral protease and Poly A is a protein that;binds the poly A tail of the genome to facilitate replication. What additional gene would be;required for this virus to replicate and produce progeny? Justify your answer.;Part E;Given the viral proteins for virus D, suggest a mechanism for how this virus could ensure that;viral proteins are made selectively over host proteins.;Question 9;Part A.;Describe the journey of a hypothetical enveloped (-)RNA virus (diagram below) through the;three basic host barriers to infection: Physical barriers, Innate Immune Response and Adaptive;Immune Response. After overcoming physical barriers, how are viruses recognized at each;step, what cells are involved, what soluble factors are involved, which adaptive immune effector;cells recognize the F an N viral proteins and how is the virus eliminated at each step? For;simplicity, lets assume that only the Fusion Protein (F) and Nucleoprotein (N) are recognized by;the adaptive immune response. (500 words max.)? (Suggestion: Draw a diagram outlining the;key steps and then convert your diagram to words. Your response should not be an exhaustive;description, but rather a summary of the most important steps)..Part B Evasion of Immune Response;Almost all viruses have to produce viral proteins that aid evasion of the host immune response.;For each of the viral proteins listed below, explain why the activity described would enable the;virus to avoid immune response. What aspect of the immune response does the protein inhibit;(i.e. intrinsic, innate or adaptive)? Limit response to 4-5 sentences/ protein.;a) In addition, to facilitating transcription of viral genes, the P protein also inhibits the TAP1;transporter located in the membrane of the endoplasmic reticulum membrane.;b) In addition to coating the viral RNA, the N protein inhibits the host enzyme PKR.;c) Matrix Protein M binds to the host Myd88 protein and inhibits its ability to transduce;signals in the cell.;Question 10;Global pandemics caused by viruses have occurred throughout recorded history. Briefly;speculate how the new H7N9 Influenza A could become a global pandemic. Include in your;description answers to the following questions (400 word limit).;a. What aspects of modern society increase the opportunities for a global pandemic with;H7N9?;b. What are the factors that could make the H7N9 virus more dangerous and increase the;severity of disease and epidemics? Think of both viral factors, host factors and;environmental factors. (Suggestion: Re-read the sections on emerging viruses in our;text: Vol II Chapter 10.


Paper#16436 | Written in 18-Jul-2015

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