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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How to Write a Research Proposal as an Undergrad

As I just passed the deadline for my junior independent work (JIW), I wanted to explore strategies that could be helpful in composing a research proposal. In the chemistry department, JIW usually involves lab work and collecting raw data. However, this year, because of the pandemic, there is limited benchwork involved and most of the emphasis has shifted to designing a research proposal that would segue into one’s senior thesis. So far, I have only had one prior experience composing a research proposal, and it was from a virtual summer research program in my department. For this program, I was able to write a proposal on modifying a certain chemical inhibitor that could be used in reducing cancer cell proliferation. Using that experience as a guide, I will outline the steps I followed when I wrote my proposal. (Most of these steps are oriented towards research in the natural sciences, but there are many aspects common to research in other fields).

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

“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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A Quick Crash Course in Statistics: Part 2

Most people’s New Years Resolutions, I imagine, are not about improving their knowledge of statistics. But I would argue that a little bit of knowledge about statistics is both useful and interesting. As it turns out, our brains are constantly doing statistics – in reality, our conscious selves are the only ones out of the loop! Learning and using statistics can help with interpreting data, making formal conclusions about data, and understanding the limitations and qualifications of those conclusions.

In my last post, I explained a project in my PSY/NEU 338 course that lent itself well to statistical analysis. I walked through the process of collecting the data, using a Google Spreadsheet for computing statistics, and making sense of what a ‘p-value’ is. In this post, however, I walk through how I went about visualizing these results. Interpretation of data is often not complete before getting a chance to see it. Plus, images are much more conducive than a wall of text when it comes to sharing results with other people.

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A Quick Crash Course in Statistics: Part 1

In PSY/NEU 338, From Animal Learning to Changing People’s Minds, my group recently presented our capstone project for the course: we researched irrationality, trying to understand when humans make irrational decisions, how that is implemented in the brain, and if certain things might actually be incorrectly labeled as ‘irrational’. Our emotions are a leading example: although some call them irrational, in practice, they play a key role in fine-tuning our decision-making and reasoning abilities. When you’re happy, for example, everything might be going more positively than expected. Your mood is thus encouraging you to continue the behaviors that led to those rewards, since that positive trend might continue (for a neuroscientific discussion of this topic, see this paper).

To demonstrate this phenomenon first-hand, we had students in the class play what is known as the Ultimatum Game:

You are the proposer. You have been given $100. You are tasked with splitting your money with a stranger, the responder. If the responder accepts the split that you propose, you both keep the money after the game ends. If the responder does not accept, no one keeps the money.

The question: how much money do you decide to offer the responder?

After reading this, students had five seconds to provide their answer. They were then asked to report their mood. The question we wanted to answer was simple:

Is the amount of money people offered statistically different between those who reported “positive” versus “negative” moods?

In this post, I’ll explain some of the basic statistics I used to formally answer this question, bolding some key terms in the field along the way. In my next post, I’ll walk through the programming aspect for visualizing those statistics. 

In Google Spreadsheet, I calculated the mean dollar amount for the “positive” and “negative” categories, equaling $32.2 and $66 respectively. The “equals” sign indicates a function, and D51:D55 corresponds to the cells containing the data for the “positive” category.
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Lost and Confused? Create a Map!

It’s said that a picture tells a thousand words; a map, however, can tell you a million.

To me, maps are not just tools for navigation. They have a variety of uses, enabling their creators to visualize a vast array of data efficiently and quickly. From questionable election forecasts to the location of monuments in a city, anything of your choosing can be mappable. Maps, in my experience, can be one of the most powerful tools in your research toolbox. Thus, I want to show you how you can use maps in your research, and the power they hold!

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How to Prepare for an In-Class Zoom Presentation

Presenting on Zoom can be difficult, as you must now learn how to keep a virtual audience engaged. Last spring semester, after returning home due to COVID-19, I had to quickly learn how to make this transition, as I was enrolled in CBE346: Chemical Engineering Laboratory (core lab). This course was laboratory based, and it consisted of 4 different lab rotations, after which all students had to complete a written report and a presentation. Due to the pandemic, 3 of those were completed over Zoom. 

In this post, I will give tips on how to prepare for a Zoom presentation, using the insights I gained from my core lab presentations.

Screenshot of the recorded video of my core lab presentation.
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A Freshman’s Guide to Writing a Research Policy Memo

The freshman seminars are one of the unique experiences at Princeton. While they may seem intimidating at first, they made me think of the process of research in my very first year in college. Not everyone might become a full-time researcher – I, for example, want to become a policy analyst – but many of our jobs will involve research, and the structure of the freshman seminar is very conducive to the research process. In the Economics of Immigration seminar that I took with Professor Leah Boustan during Fall 2019, we discussed aspects of the economic effects of immigration both on the receiving country and on the migrants themselves. Our final deliverable was a research policy memo – a document that describes a policy intervention by the government, by first arguing the need for it, then describing its advantages, and finally proposing a way by which it might be implemented. In order to write an effective memo, I had to research an issue that necessitated looking at it from diverse points of view. The process made me appreciate several principles of writing a policy memo.

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4 Tips to Organize Your Lost Folders and Misplaced Files

While I was working to finalize my research this summer, I realized something: I couldn’t find one of my sources central to my argument. Pouring through my various folders on my computer, I could not find this source. Between Excel sheets with undescriptive names and misplaced images, it wasn’t just that my source was missing; I lacked an entirely well-formulated, well-maintained organizational structure to keep track of my work.

If anything, organization should be easier in the digital space. Besides bytes, we’re not necessarily concerned with finding the space to store our papers, books, and other materials; in fact, we can create folders upon folders, meticulously grouping related works together to keep track of them.

But this is the trap. While I’ll see the mess before me on my desk, I don’t necessarily see that all of my folders are disorganized until I need to find something. I don’t see that I stored images for my essay on my Google Drive rather than in that class’s folder. In my experience, computer storage may facilitate organization, but it also hides potential messes from you until you need to find that one file for your assignment or research. And even if you’re the type of person where all of your work is spilled out onto your home screen, sifting through the documents at times is surely a nightmare.

So, I wanted to outline some of the steps that I’ve taken this school year to make sure that everything remains organized in this weird digital setting:

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