Visualizing COVID-19 Mutations Using PyMOL, a University Provided Resource

These days, it seems like every day we learn of a new variant of SARS-CoV-2 (the virus that causes COVID-19). However, it’s hard to understand what a variant is and how it changes the virus. In this post, I wanted to introduce PyMOL, a program that students have access to through the University. This program can be used to see what the spike protein and its mutations actually look like.

But first, here’s some background on SARS-CoV-2: COVID-19 is a disease caused by a strain of coronavirus called SARS-CoV-2. This virus gets inside the human cells by using something called a spike protein. This spike protein binds to a receptor on the human cell called the ACE2 receptor, and this allows the virus to infiltrate the cell. The variants of SARS-CoV-2 that we keep hearing about typically have different mutations on the spike protein. In the case of the B.1.1.7 variant, which is a variant that is thought to be 30-50 percent more infectious than other variants in circulation, the mutations are at a location that allow the spike protein to bind better to the ACE2 receptor. If you bind better to the receptor, you’re better at infiltrating the cell. The spike is also the target of the vaccine and our natural immune system.

Now, let’s try and look at where these mutations actually are.

This is an illustration of the SARS-CoV-2 virus published by the CDC. The spikes are in red, labeled with a white arrow.
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Doing Research in a Pandemic, An Interview with Molecular Biology Graduate Student Emily Mesev

For this Spring Seasonal Series, entitled Doing Research in a Pandemic, each correspondent has selected a researcher to interview about the impact of the pandemic on their research. We hope that these interviews document the nuanced ways the pandemic has affected research experiences, and serve as a resource for students and other researchers. Here, Nanako shares her interview.

For this seasonal series, I decided to interview Emily Mesev, a Ph.D. candidate in the Department of Molecular Biology. I was interested in how her experience as a graduate student differed from my experience as an undergrad. Because undergrads aren’t allowed to be in the laboratory (at least for Molecular Biology), I’ve had to change my thesis topic and redirect it to become computational. I was excited to find out whether the graduate student experience had changed in similar ways!

Emily at her laboratory bench this week.
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Professorship and Mentorship: An Interview with Molecular Biology Professor Zemer Gitai

This winter, for our seasonal series entitled “Professorship and Mentorship,” PCURs interview a professor from their home department. In these interviews, professors shed light on the role that mentorship has played in their academic trajectory, including their previous experiences as undergraduate and graduate students as well as their current involvement with mentorship as independent work advisers for current Princeton undergraduates. Here, Nanako shares her interview.

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As one can see from the many PCUR posts on Junior Papers

Professor Gitai wants students to be open minded about doing independent work. 

and Senior Theses, independent work is a huge part of the junior and senior experience here at Princeton. However, everyone has different views on why this process is important, and different departments have different requirements. For this Winter Seasonal Series, I decided to interview Professor Gitai, who I met when I took MOL214: Introduction to Molecular and Cellular Biology in the fall of my first year at Princeton. Read on to learn more about the thesis writing process for concentrators in molecular biology, and how to make sure you get the most out of this process!

 

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