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

Posted on by Nanako Shirai

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

Posted on by Nanako Shirai

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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How to Write An Email To Someone You Don’t Know

Posted on by Nanako Shirai

“What? Why would I ever need to read an article about how to write an email?” This is what my first thought would’ve been if I ever saw an article like this. While many Princeton students probably understand the basics of how to write an email (type, then hit send), today, I wanted to go over tips to use when “cold emailing” someone.

Before coming to Princeton, the emails that I wrote were sent to my friends and high school teachers. I’d only ever emailed people that I already knew. However, throughout the years, I’ve learned that email is wonderful ⎯ and useful for research ⎯ because you can contact people who you don’t already know! Although learning how to write emails is something that’s not taught formally, I think it’s increasingly important to know what to do and what not to do when you’re trying to catch the attention of someone you’ve never met or talked to.

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Kicking Off The New Academic Year

Posted on by Nanako Shirai

Welcome back to the 2020-2021 academic year, which will be unlike any school year that we’ve had before. While it has been and remains a tumultuous time, I personally hope that going to classes (even remotely) will help bring a sense of normalcy back into our lives. What will hopefully aid in the process is PCUR, which will be up and running as always! Our correspondents from across grade levels and academic disciplines will reflect on what it is like to be a remote college student, and share tips and advice that they learn throughout the year.

This year, we have three new correspondents: Abhimanyu, Austin, and Ryan! We are excited for them to join the current crew of correspondents, which include Kamron, Alex, and Saira.

Abhimanyu Banerjee ’23 – Social Sciences Correspondent

Concentration: Economics

Degree Program: A.B.

Research Interests: Monetary policy, fiscal policy, income inequality, financial bubbles, sustainability

Bio: I am a sophomore from Gainesville, Florida. I am interested in economic policy, particularly how it can be used to tackle such issues as alleviating recessions, reducing inequality, and promoting sustainability. I am also a researcher for the Policy Punchline podcast here on campus. In my free time, I am an avid chess player and have played competitively for over a decade.

Austin Davis ’23 – Humanities Correspondent

Concentration: Undecided

Degree Program: A.B.

Research Interests: History, historical memory, urban studies, post-1900 United States, social stratification and structures, and post-1400 Europe.

Bio: I am a sophomore from Pittsburgh, PA. Even though I am undecided, I plan on concentrating in History most likely. One of my interests that has especially emerged at Princeton is the intersection of urban studies and historical memory. Outside of school and research, I am the USG Historian, a Peer Academic Advisor for Forbes College, and a PAI Community Ambassador.

Ryan Champeau ’23 – Social Sciences Correspondent

Concentration: Princeton School of Public Policy and International Affairs

Degree Program: A.B.

Certificate Programs: Program in French Language and Culture, Cognitive Science, Creative Writing

Research Interests: Psychology, Social Media, Public Policy, History

Bio: I’m a sophomore from New Jersey who likes dogs, writing, and photography! I’m interested in exploring how I can use research to have a positive impact on the Princeton community and beyond. On campus, I’m a big sister for the Big Brothers Big Sisters program, player and social chair for the club ultimate frisbee team, member of the Whitman College Council, and Community Action leader. I’m also really enthusiastic and love to rap!

We’re looking forward to a great year, even with everything that is going on. Please stay safe, and if you have any specific questions or topics that you would like to see us write about, submit them here!

⎯ Nanako Shirai, Chief Correspondent

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Post-Princeton Life: An Interview with Bennett McIntosh ’16

Posted on by Nanako Shirai

For this year’s Spring Seasonal Series, entitled Post-Princeton Life: The Experiences of PCUR Alumni, each correspondent has selected a PCUR alum to interview about what they have been up to. We hope that these interviews will provide helpful insight into the many different paths Princeton students take after graduation. Here, Nanako shares her interview.

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In my last post, I wrote about how to get the most out of your short-term research internship. In this post, I provide some more insight I got about how to get the most out of my summer internship— this time from a more credible source: a Princeton alumnus. I interviewed Bennett McIntosh ’16, who used to write for PCUR, about his Princeton research experience.

Here’s a bit about Bennett:

Bennett McIntosh ’16 studied chemistry at Princeton and is currently a freelance science writer.

Bennett McIntosh is a freelance science writer and reporter living in Boston, covering the intersections of scientific research, technological change, and social welfare. He is currently helping to relaunch Science for the People, a magazine of science and politics whose first iteration grew out of the 1960s anti-war movement.  While studying chemistry at Princeton, he wrote opinion columns for the Daily Princetonian, science stories for Innovation, and lousy jokes for the Princeton University Band.

 

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Going on a Research-Intensive Study Abroad: Oxford-Princeton Biochemistry Exchange

Posted on by Nanako Shirai

As a sophomore, I’ve finally started to get better at navigating Princeton, and there are many perks that come with that. But at the same time, this is when things can start to feel monotonous. During the winter, I started to look for ways to rid myself of this feeling, and one of the ways that I thought of was to study abroad. This week, I decided to interview Leslie Chan, a junior in the molecular biology department, about her experience going abroad to Oxford University in her junior fall.

The Oxford-Princeton Biochemistry Exchange is a program where selected juniors from the molecular biology department exchange places with an Oxford student for a semester and do research in a laboratory setting — it’s distinctive in that the students don’t take classes at Oxford, but rather become full-time lab members at a Biochemistry laboratory at Oxford. You still get transfer credit though, so you get to graduate on time!

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Maybe Research Isn’t My Thing – A Few Questions to Ask Yourself Before You Give Up on Research

Posted on by Nanako Shirai

This computer and gel scanner were my best friends during my summer internship – I took many, many pictures of DNA samples and made many, many mistakes over the four week period.

As the weather gets warmer and summer gets closer, a lot of people’s minds are on their upcoming summer research internships. I know from my personal experience that doing research over the summer can be quite frustrating — it seems like you’ll never get any results and it’s so easy to say that “research just isn’t my thing.” In this post, I want to highlight a few things to think about before you decide that pursuing research as a profession isn’t for you.

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Things to Check for Before Submitting your Writing Seminar Paper

Posted on by Nanako Shirai

As a Writing Center fellow, I definitely have conferenced my share of writing seminar essays, and I know that there are a lot of common themes that first years worry about. In this post, I wanted to make a checklist of exercises to try before you submit your final draft!

I tried the first exercise with my R3 to make sure that there was a good balance between the primary sources and my own voice.

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Professorship and Mentorship: An Interview with Molecular Biology Professor Zemer Gitai

Posted on by Nanako Shirai

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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Learning from Summer Experiences – Redefining Research

Posted on by Nanako Shirai

Since many of you (including myself) have probably started thinking about your upcoming summer plans, in this post, I wanted to do a reflection on my past summer and how my perception of research changed through that experience.

At the Kyoto Symposium, scholars from the University of Tokyo and Kyoto University met up for a poster presentation. This is at the Nijo Castle.

This past summer, I spent 11 weeks in Japan, which was something that was only possible thanks to Princeton’s incredibly long summer. (For readers unfamiliar with Princeton’s schedule — this happens because Princeton starts the fall semester later than most schools.)

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