Undergraduate Researcher of the Week: Ridhi Chaudhary

Mon, 10 Aug 2020 09:48:39 -0400

Ridhi Chaudhary is a junior, majoring in Biological Sciences. She is a Meyerhoff and HHMI scholar, and also a member of the Honors College. Outside of undergraduate research, she has served as a learning assistant for general chemistry courses for the past year and a half, and she plans to start tutoring at the Chemistry Tutorial Center (CTC) in the fall. She is also a member of the Meyerhoff Student Council and the Secretary of the UMBC Medical Journal Club. Additionally, she has been volunteering with the Multiple Sclerosis (MS) Aquatics Program through the Shriver Center since her freshman year.

Title of your research project:

Identification of the Initial Nucleocapsid Recognition Element in the HIV-1 RNA Packaging Signal

Description of the Research:

Selective packaging of the HIV-1 genome during virus assembly is mediated by interactions between the dimeric 5ʹ-leader of the unspliced viral RNA and the nucleocapsid (NC) domains of a small number of assembling viral Gag polyproteins. We found that the dimeric 5′-leader contains more than two dozen NC binding sites with affinities that reside within a ∼150-nt region of the leader sufficient to promote RNA packaging (core encapsidation signal, ΨCES). The four initial binding sites with highest affinity reside near two symmetrically equivalent three-way junction structures. Unlike the other high-affinity sites, which bind NC with exothermic energetics, binding to these sites occurs endothermically due to concomitant unwinding of a weakly base-paired [UUUU]:[GGAG] helical element. Mutations that stabilize base pairing within this element eliminate NC binding to this site and severely impair RNA packaging into virus-like particles. NMR studies reveal that a recently discovered small-molecule inhibitor of HIV-1 RNA packaging that appears to function by stabilizing the structure of the leader binds directly to the [UUUU]:[GGAG] helix. Our findings suggest a sequential NC binding mechanism for Gag-genome assembly and identify a potential RNA Achilles’ heel to which HIV therapeutics may be targeted.

The full work can be found in the Proceedings of the National Academy of Sciences (PNAS):

https://www.pnas.org/content/early/2020/07/08/2008519117.abstract

Who is your mentor for your project?

My PI is Dr. Michael F. Summers in the Chemistry and Biochemistry department. I work under the guidance of Dr. Pengfei Ding who is a post-doc in the lab.

What research experiences have you had?

I am an undergraduate research assistant in Dr. Michael Summers lab. I have been working here as a Howard Hughes Medical Institute (HHMI) Scholar for the past 1 year and 3 months. I work under the guidance of Dr. Pengfei Ding and our research focuses on understanding the selective packaging mechanism of the HIV-1 genome, and the specific interactions between the Gag polyprotein and the viral RNA that facilitate packaging.

Prior to starting undergraduate research at UMBC, I was a Werner H. Kirsten student research intern at the National Cancer Institute (NCI) during my senior year of high school. At NCI, I was part of the RAS structural biology group that was focused on understanding the structure and function of various RAS proteins using X-Ray crystallography techniques.

How did you find the research opportunity?

I found this research opportunity through the Meyerhoff Scholars program as well as the Howard Hughes Medical Institute (HHMI) scholarship.

What academic background did you have before you started?

When I started my undergraduate research journey in Dr. Summers lab, I was just completing my first year at UMBC. As such, I had introductory knowledge to the biology concepts used in his lab and very little knowledge of the biochemistry principles. By spending time in the lab performing experiments, reading papers, attending seminars, and having meaningful discussions about the research with my lab peers, I have developed a stronger understanding of the broader disciplines including biochemistry and NMR structural biology that are integral to the research conducted in Dr. Summers lab.

How did you learn what you needed to know to be successful in this project?

Dedication and a willingness to learn are perhaps the most important components of being successful in a research lab. In Dr. Summers lab, I acquired the skills that are needed to be successful in the research i.e. RNA preparation, protein purification, and DNA recombinant technologies by training with more experienced undergraduates and graduate students. Reading and analyzing scientific papers is another useful skill that I have improved upon by working more closely with my mentor, Dr. Pengfei Ding and by participating in various journal clubs.

What was the hardest part about your research?

The hardest part about the research was the beginning phase when I was trying to wrap my head around the scientific world that governs the research. A lot of the techniques such as in-vitro RNA transcription were completely new to me and it took some time to understand not only how to perform a protocol correctly but also the scientific reasoning of why each step was done in a specific way. Becoming accustomed to the style of thinking that is needed to understand the intricacies of the research takes time, but the process certainly becomes much smoother by engaging with the research consistently.

What was the most unexpected thing?

The most unexpected thing was switching from wet-lab work to remote research due to COVID-19. I really enjoy actively working in the lab by performing experiments and visualizing the results. Thus, the abrupt switch to all remote research took some getting used to as remote research for wet-labs tends to be more passive.

How does this research experience relate to your work in other classes?

A lot of HIV-1 structural biology research is founded on basic biology and biochemistry principles. As such, a lot of the knowledge that I have gained through this research can directly be applied to courses like organic chemistry and biochemistry, and vice versa.

What is your advice to other students about getting involved in research?

If you are in any way interested in research, I suggest that you reach out to the various undergraduate research offices and programs on campus so someone can help you get connected with a lab that matches your interests. For instance, the Meyerhoff office is a really great resource that can help you get access to research opportunities on campus. If you are not a Meyerhoff scholar, you can apply to be an affiliate and receive the same advising as other Meyerhoff scholars.

Once you are in a lab, be willing to learn the ideas and techniques that are important for your research. Also, be open to interacting with the people in your lab and don’t be afraid to ask questions and get advice when you need it. In the beginning, you may feel like your questions are ‘dumb’ but just remember that everyone goes through the process of understanding the basics of the research which more often than not includes asking for clarification on seemingly ‘easy’ concepts. Lastly, try to read papers from your field on a regular basis as this will significantly improve not only your knowledge of your research but also your confidence while engaging with the research.

What are your career goals?

After graduating from UMBC, I aspire to earn an MD/PhD and pursue a career as a physician- scientist. I enjoy teaching and mentoring younger students, so I hope to incorporate those aspects into my future career as well.