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.
For better or worse, the university is internally cloistered as an academic institution. Walls literal and metaphorical separate the departments. This is perhaps most apparent to students on an administrative level; each department has its own academic guidelines, grading policies, and research expectations. Deeper differences, though, may present in modes and content of knowledge production. Disciplines often preclude interdisciplinarity. Divergent methodologies might be applied to the same subject matter to produce different results; within a department, the range of expertise might end up applying similar methods to wildly different subjects.
I, for one, think that these disciplinary divisions often do more to stifle than to encourage intellectual growth or humanistic inquiry (on the problems and politics of the academic disciplines, see my interview with Daniela Gandorfer here). But, as things are, attempting to explain research across disciplines can be quite difficult– like speaking to someone in a different language without a translator. Seniors writing their theses are certainly familiar with this issue when trying to explain their work to people outside their department, or in some cases, anyone other than their adviser. When it comes to feedback on thesis work, then, it makes immediate sense to gravitate towards people with background in whatever you are writing about. They indeed might be able to give very pointed advice.
That said, there is still great value to turning towards those beyond the official borders of your discipline. A lack of familiarity with the subject matter can indeed be an asset– especially in terms of providing feedback on your writing and your writing/research process.
“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.
At Princeton, we are fortunate to have pretty much unrestricted access to a huge variety of research resources through our libraries– access which is free (or, at least, “free” after tuition…). However, as I have written before on this blog (see here and here), there may be situations where Princeton’s library system does not have the information you need for your research, and you have to venture outward to other libraries and archives, or, in some cases, engage in field work of some kind. Now, access to these resources, unfortunately may not be free. Usually the biggest expense here would be travel, but even given our current no-travel circumstances, research expenses remain in the form of document scans, books, photocopies, and human subject payment (all of which are acceptable uses of funding from the Office of Undergraduate Research (OUR) as of now).
When I first applied for departmental senior thesis funding early this spring, everyone was still uncertain about how long the effects of the COVID-19 pandemic would last. It seemed departmental administrators were optimistic: funding requests could still be made for summer travel. In my application, I detailed my intent to travel to university and state archives throughout the U.S. south for a thesis examining how antebellum Mississippi Valley planters conceptualized the idea of labor. But before I even heard back about whether I was to receive support, the department updated its funding parameters to prohibit summer travel and I had to redo my application in turn. My summer plans, of course, were not the first academic casualty of the strange 2020 world; nor would they be the last. Fortunately, though, there were ways to work around my newfound limitations: all of the archives that I wanted to visit offered services for resident librarians to scan and send materials from their collection, so I updated my application to ask for funds to pay for associated fees. Here, I’ll be sharing some tips for requesting archival materials to be scanned, which I hope will be helpful to any researcher unable to travel (pandemic or not).
This year, as we prepare to write our final papers in quarantine, it will be extra tough to locate the sources we need for our research. Without in-person access to campus libraries, this Dean’s Date will require some new strategies for accessing research materials. To help with this process, I’ve collected a few virtual research resources from my weeks of quarantine thesis work, as well as the beginnings of my Dean’s Date research (also check out Alec’s recent post for more tips):
Do not underestimate the library catalog. A lot of sources are available online, especially with the University’s new partnership with the HathiTrust Digital Library. Through this partnership, millions of scanned books have been made temporarily available to students—in addition to Princeton’s many existing online holdings. To see if a book is available online, just search for it in the Princeton library catalog. If you don’t see a digital edition listed, try clicking on a print edition and seeing if a scanned version is available through HathiTrust (if it is, there will be a link just below the book’s title and general information). You can also click the “Request” button under “Copies in the Library,” then “Help Me Get It” and a librarian will do their best to send you a digital copy—if it’s available—within a few days.
As a prospective English major, I’ve written a handful of English papers and have tried to learn what makes some stronger than the others. While the best way to write an English paper may differ based on whether you are writing about a poem, novel, play, or essay, and whether you plan to take a purely textual, historical, theoretical, or comparative approach, some fundamentals are applicable to many English assignments. Here are just some tips you can keep in mind while crafting your next paper:
It’s been almost four years, and the generosity of Princeton faculty continues to surprise me. So many professors here are not just accessible to students, but deeply invested in supporting us in and outside of the classroom. It typically isn’t too hard to find at least one research mentor among our 950 full-time faculty.
Nevertheless, one institution’s faculty cannot possibly cover every sub-field or research topic. This has become especially apparent as I’ve moved towards the specificity required of a thesis project. In my case, no professor on campus studies Vilna, the Eastern European city at the center of my thesis.
Of course, there are ways around this. For one, there is probably a professor on campus whose area of expertise has something in common with your project. My thesis adviser does not work on Eastern Europe, for example, but she is an expert in writing urban histories. So even though Vilna is new to her, she has been invaluable in guiding my methodology and argumentation.
She has also encouraged me to reach out to faculty and graduate students in other departments and at other institutions who might be more familiar with Vilna itself. Connecting with these scholars has turned out to be one of the most valuable aspects of my thesis process thus far. I’ve compiled some tips for accessing the rich academic network beyond your particular department or university.
Choosing a topic for independent work can be a challenging task. It can be difficult to narrow down the seemingly infinite research topics to one that you find compelling (see my post here with tips on how to do that), and on top of that, you have to juggle your research with coursework that may be unrelated. It isn’t always easy to switch gears between, say, literary criticism and your STL. That said, your coursework need not be totally separate from your independent work, and need not even parallel your independent work at the exact time you are conducting it. With courses for the spring semester just released, I want to suggest ways that you can structure your selections to complement (and even supplement!) your own research. This way, next semester, your own independent work may not actually be so “independent” after all.Continue reading Coursework and Independent Work: Using One to Guide the Other
Since coming to Princeton, I’ve become involved in diverse publishing and editing opportunities. One of the first undergraduate publications I joined was PURJ, the Princeton Undergraduate Research Journal. As a member of the Peer Review Board for PURJ, I learned more about the peer review process in academic research publications and had the opportunity to review manuscript pieces spanning incredibly diverse disciplines from the undergraduate body. In contrast to some other more specialized journals I’m involved in, such as Unfound, Princeton’s Journal of Asian American Studies, PURJ is a truly multidisciplinary publication that showcases work from the humanities, social sciences, natural sciences, engineering, and arts.
To learn more about the perks of being involved in a research journal, I interviewed Jasper Lee ’21, the current Co-Editor in Chief of PURJ. A molecular biology major, he first joined PURJ as a member of the Peer Review Board and then took on the role of Managing Editor of Peer Review. Here’s what Jasper shared about his experience with PURJ: