Genetics Question
Biology 312 – Virology Journal Club 4 paper summary Name:____________________________________ Date:_____________________ Paper:____________________________________ JC#:______________________ Why are we doing this? Professional scientists are part of an on-going conversation that stretches back for several centuries. The medium for that conversation is scientific articles, where new data is presented, put into historical context, and used to generate new models. The process of peer review serves as a check on the validity of the data and logic of the conclusions. Peer review happens both before and after a paper is published, in order to keep the conversation going. As developing scientists, critical evaluation of the literature is an important skill. Here, you will serve as post-publication reviewers, evaluating papers for validity and put the conclusions into context. This will give you new models of virology, a better understanding of the methods of this field, and opportunities to develop the skills needed for professional scientists. What should I do? Answer all of the following questions. Please type your answers in the space below each question If two papers were assigned, you only need to answer the questions for the primary literature article. Ask DHL if you’re not sure. JC4: Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain | PLOS Pathogens You can also look through the “story” of this paper here: https://nextstrain.org/narratives/twenty-yearsof-WNV Before you start, look at the difference between a clade and a lineage in phylogenetic terms. Q1: According to the authors, what is cool about this paper (2-3 sentences)? In other words, why did they do these experiments and write about them? Q2: Do a small amount of research on West Nile Virus. What does its life cycle look like as it passes between organismal vectors? What does its life cycle look like in the cell? Q3: The paper explains the evolution and spread of WNV by connecting genomic data to other types of data. Give an example of other information they draw on that helps inform and support their conclusions and reflect on how our understanding of infectious disease benefits (or not) from an interdisciplinary approach (discipline here could mean genomics/physiology/ecology or Biology/History/Geography). Q4: Now that we’ve seen how this data was used, let’s apply these lessons to the Mpox virus: https://nextstrain.org/mpox/clade-IIb Spend about 15 minutes looking at this data. What data did you look at and what conclusions can you draw? For example, can you tell where this virus arose in human populations? When was the first major international spread? When did the virus reach the US? How many different variants are present as of the most recent sampling data? Q5: What other applications do you see for NextStrain and viral sequencing data? How might you use it to study the other viruses in the database, like Influenza, Sars-CoV2 or Ebola?
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