Blog Posts

A (Not so Typical) Year of an Undergraduate Student

By: Bonnie Lin

 

March 11 th , 2020: NYU announced that all classes and non-essential research will be conducted
remotely as a precautionary measure for the COVID-19 issue that is getting worse. The sudden
transition into remote instruction was and still is, met with several challenges. However, classes
still managed to move forward with a combination of Zoom and online exams.
Research on the other hand is even more difficult, or even impossible, to fully transition to
remote operation. Ongoing efforts of research through remote settings increased to avoid
delay in research. Despite increased focus on literature research and computational
simulations, findings ultimately required experimental confirmation traditionally conducted
through wet bench research in a laboratory setting.

June 1 st , 2020: Remote research in computational design starts. As a Thompson Bartlett Fellow,
I worked on computationally designing phosphotriesterase (PTE) variants through incorporation
of non-canonical amino acid, p-fluorophenylalanine, to detoxify organophosphates. For ten
weeks, I was able to familiarize with the computational modeling software, Rosetta, and was
able to identify PTE candidates with increased catalytic efficiency and binding affinity with the
help of my mentor Farbod Mahmoudinobar and Dr. Montclare.

The idea of approaching protein engineering from a different perspective was full of challenge
and excitement. Both computational design through remote operation and wet bench research
are similar in two ways: that lasting feeling of accomplishment to participate and contribute to
the world of scientific discoveries and findings.

 

Covid

https://www.ehstoday.com/covid19/article/21150185/cdc-cuts-covid19-quarantine-time-for-exposure-to-others

Fall 2020: Classes are being held through a wide range of flexibility to accommodate students in
the midst of a pandemic. Undergraduates are offered a choice of taking in-person classes, fully
remote or blended (hybrid version). Laboratory courses are offered in-person only and for
those that cannot attend in-person have the option of taking these courses the following
semester. Research can now be conducted in-person but under certain restrictions and safety
precautions.

Although I enjoyed research from a different approach (computational design), I was ready and
eager to go back on campus. I was always a hands-on type of learner. I missed pipetting. I
missed protein expression and purification and struggling with making a dialysis bag. I missed
performing protein characterization studies. I missed being able to conduct an experiment with
my own hands and seeing results with my own eyes. However, what I missed the most is that
feeling, that feeling of anticipation while waiting for your analysis results, that feeling of
excitement to see results that agree with your previous studies, that feeling of observing
something different that might open the doors to unexpected discoveries fueled by our very
own curiosity. Despite the restrictions and precautions that needed to be taken, I was very
eager to go back to lab.

September 2 nd , 2020- My alarm rang earlier than usual as now I need to take commute into
account. After getting ready and completing the daily screener, I headed off to Tandon at
7:30AM. Due to safety concerns, instead of taking the subway (my usual form of commute
before the pandemic), I decided to drive to school which usually takes 1 hour with the traffic in
the morning. At around 8:30AM, I arrived at Tandon, tapped my ID and showed my completed
daily screener to the security officer.

11:00AM: After attending my first class, I made my way up to my research lab on the 8 th floor.
Although some remained the same, many changes have been made: 6 feet social distancing
where each research personnel are located at every other bench, laboratory shifts being
implemented to avoid everyone coming in all at once, limited capacity in the office space,
contact tracing and etc. Despite the changes being made, as soon as I held my first pipette of
the day to conduct my experiment, that feeling soon surged back into me. With added safety
precaution, I submerged myself into that feeling I missed for six months and got right to work.

Even with the midst of the pandemic, research is still ongoing. Even with the added boundaries
created by the pandemic, scientific discoveries are still being made every second every minute
every day. Why? Because science has no boundaries.

Unexpected Computational Research

By: Jason Chen

When I joined the Montclare lab for protein engineering and molecular design in the summer of 2020 (amidst a pandemic), I was eagerly expecting to be thrown into the wet lab world involving the prolific use of SDS-PAGE and the omnipresence of micropipette tips. Instead, I would find myself navigating a Unix shell often in the comfort of my bed (which was not great on my back, in retrospect). Scientific research is not all about wet lab work, as one might presume. In fact, computational work is one of the core driving forces of breakthroughs and advancements, especially in the field of protein engineering.

During my first few weeks, the learning curve was very steep. Although I was armed with three semesters of coding experience from my computer science courses, I was still mystified by the Unix interface and the modeling software called Rosetta. I perused through countless random Github and Stack Overflow web pages trying to figure out how to execute basic commands. I read and reread past papers about our protein construct (phosphotriesterase or PTE) to understand the meaning behind the work.

Most importantly, I received guidance and encouragement from my mentor, the patient and wise post-doctoral associate Farbod Mahmoudinobar. It also didn’t hurt to have worked with other undergrads on the project, Bonnie and Jakub, who sympathized with the struggles of undertaking computational work for the first time. We often connected through Zoom to troubleshoot difficulties and work together throughout the learning process.

Eventually, I grew more comfortable with the project. I gained a better understanding of the background of PTE as well as the overarching goals of our project. I was finally equipped with the necessary mental tools to computationally enhance the properties of PTE by altering its amino acids. Just as I was beginning to think that I had learned all I needed to know, I was faced with a whole new set of questions to answer. That’s the beauty of science.

Sure, I was now able to use the modeling software to modify our target protein, but this was just the tip of the iceberg. How should I interpret the output information from the new models? How could I use the knowledge from past design iterations to improve future designs? And the one that nagged at my brain most of all: why is a phenylalanine in this particular position and orientation more favorable than a histidine in that particular position? Finding the answers to these questions would require the convergence of these newly learned computational skills and my undergraduate chemistry background.

Learning to use a protein modeling software is like learning a new language. You first master the vocabulary, syntax, and how to put together sentences that can be understood by others. However, being able to functionalize and make meaning of tens of thousands of simulated results is akin to sifting for gold nuggets in a sandy riverbed. It’s a daunting task, but someone must do it to find the hidden treasures. And once the gold is found, it’s possible that the gold was actually just a shiny rock, a piece of fool’s gold, and you must start the sifting process all over again. Maybe you even need to look in a new riverbed.

275b6a8d-a01f-4a3b-b5f4-3081a4832936 4164034c-6cf2-41aa-b5c7-9af89ec8afd5

Distilling the results of a modeling software such as Rosetta necessitates patience, an ability to recognize patterns, and a level of competence in the building blocks of proteins called amino acids. The multidisciplinary nature of the work requires both understanding of the software as well as the science behind the results. Similar to wet lab work, successful computational work is as much a testament to proficiency of technique as it is to the ingenuity and breadth of knowledge held by the researcher.

In my time here at the lab, I feel that I’ve only turned over one leaf in the forest that constitutes computational research. There is still so much to learn, and I am in awe of the broad scope of design applications that are possible through the Rosetta software and in powerful interactive interfaces such as the Unix shell. Although I’ve since started performing wet lab work with another mentor (the brilliant and wholesome PhD candidate, Jacob), I’m grateful to have been afforded the chance to step out of my comfort zone and explore an area of research I would not have been exposed to otherwise. Although computational work was often frustrating, like the many times I’d queue a Rosetta job for hours only for it to fail upon starting, the collaboration and the learning experience made it all worthwhile.

 

From the Frontlines of COVID-19

By Joseph Thomas

I still felt incredibly groggy in the morning when I rolled over to check my email inbox on my phone. I usually joke that my brain isn’t fully “on” until I have my morning coffee and this cold April Saturday was no exception. I was staying in a Philadelphia suburb with my partner, their roommate, and their roommate’s parents. My partner was immunocompromised, and when the virus began to rapidly spread in New York City we made the decision to leave for a safer, more spread out environment. When we left there was fear that New York City would be quarantined, that the rich had been tipped off early to flee in helicopters, and that being trapped inside could be a death sentence for anyone vulnerable. Luckily those all turned out to be rumors, but the situation in the city was still dire. Only a few days prior I had sipped my therapeutic morning coffee and watched a livestream of the USNS Comfort docking in Manhattan, in anticipation of the human suffering that was soon to overflow from emergency rooms citywide.

My eyes finally focused a bit more and I saw the email I had been waiting for. “How quickly can you get back to Brooklyn? I want you to start training on how to run Coronavirus tests on Monday.” A former colleague of mine was organizing graduate students and medical students to help the overwhelmed medical staff of University Hospital Brooklyn. In the previous weeks I had emailed everyone I could think of, from hospitals all the way to the National Guard, trying to find some way I could help. As a scientist I felt so helpless just sitting around as the world collapsed all around. In that process I had placed my name on a list of student volunteers that my colleague created, but in the back of my mind hoped I would never get called up. The hospital had just been declared an emergency COVID-only site by the New York state governor and needed extra hands to handle the tsunami of polymerase chain reaction (PCR) based tests that needed to be run. Low-income Black communities in New York disproportionately bore the brunt of COVID-19 in neighborhoods like East Flatbush where the hospital is located, and the numbers of people coming into the emergency room every day were staggering. New York City emerged as the disease epicenter for the entire country at that time and some of the news reports starting to come out were terrifying. Being selected meant that I would have to leave my partner behind in Philadelphia while I went back into the proverbial lion’s den for an undetermined length of time. Getting COVID-19 and ending up intubated in the emergency room was a non-zero chance. All of this sank in as I read the email over and over while my partner slept peacefully next to me.

Last photo taken after loading the car to drive New York City from Philadelphia.

I had self-taught myself PCR in the last months of 2019. It is a useful technique and crucial to my PhD thesis work. I never thought learning a specific technique would highlight me of all people,  to do anything special, but here I was in 2020 doing just that and it all seemed surreal. These were my thoughts as I loaded my small car with as much food as it would fit and left Philadelphia for Brooklyn. People still in New York City were saying it was becoming hard to get certain groceries, so I prepared for the worst and bought enough food to hold up for a month aiding the emergency response if needed. I drove up I-95 in eerie isolation, not seeing other cars for miles on the northbound side. I was scared but also excited. I kept thinking how silly it was that I just happened to be a biomedical engineering PhD student during a pandemic. Somehow uniquely qualified to make a difference yet drowning in imposter syndrome that I was about to be the frontline defense to a global crisis.

By a stroke of luck my partner had an apartment 4 blocks from University Hospital Brooklyn, so this was my new home since I could walk to and from the hospital and living alone would prohibit me from spreading the virus to anyone else at home. I spent my days running PCR tests on the Cepheid system that had recently won emergency use authorization. We were required to be decked-out in PPE since we were handling dozens of patient samples a day, some of which surely contained COVID-19. The hospital itself had been transformed into a viral response hotspot. Triage tents were set up outside the ambulance bay and the cafeteria had been converted into an emergency overflow ward. Refrigerated trucks had been sent over as well since the morgue had run out of space and the tide of patients was endless. When I came home from the hospital, the first thing I would do was spray my clothes with ethanol then immediately shower and change to ensure that I wouldn’t end up infecting myself by continued exposure to my hospital clothes. Evenings became time to work on my graduate studies, which almost seemed ridiculous in comparison with what I was seeing during the day. Self-care became a crucial activity because burnout was ever present, and I was living alone in a stressful environment.

Wearing an N95 mask and medical gown while running tests.

 

As time went on, the tide began to turn in the fight against the virus. Each day I worked at the hospital I would run more and more tests, but the ratio of positive tests to negatives was shrinking. The lockdowns had bought hospitals around the country invaluable time to experiment with treatments and statistics showed the number of patients dying every day was receding. The public support for frontline healthcare workers around the hospital was overwhelming. Every evening at 7 pm I would open the apartment window and hear people cheering, clapping, and banging pots. I had been feeling depressed and felt detached from this practice until one evening on the phone my partner said, “They are cheering for you, you should be so proud of everything you have done.” In June, the hospital lost its COVID-only designation and I ended my time there. My PhD lab was reopening, and I knew it was time to shift gears back to my own research. I saw firsthand how valuable my research and lab skills were and I was emboldened to finish my degree. I had developed a new confidence in my own abilities and a new interest in using my skillset to combat infectious disease. Working a frontline pandemic response gives you training you will not get elsewhere in a PhD program. It was a sobering reminder that science is a high stakes game and that our actions as scientists do have far reaching effects, but this also means that the work we do can positively impact people.

Weathered mural in Downtown Brooklyn, photographed in Summer 2020. As of writing, the death toll in the US stands at 500,000 and rises every day.

 

This pandemic has caused trauma at all levels, from institutions to individuals. It has laid bare healthcare inequities by disproportionately targeting poor communities and communities of color. I have reflected much on what life was like from March to June and I am still processing everything that happened. My reflection has also given me a new perspective on my identity. Before the pandemic I would describe myself as a scientist, as if it was the defining feature of my existence on this Earth. My experience has made me revise this though, and to view myself as a human being who just happens to do science for a living. I was in no way insulated from the human effects of the pandemic just because I could mix a buffer solution or because I have a graduate degree. Mental health is just as important as experiments and data, and to not recognize this is to dehumanize myself. This is true for everyone across the board. We have been through hell and we owe it to ourselves to be kind to ourselves and to each other because we are not out of the woods yet. I check the news daily and I see cases rising in the USA and around the world. As scientists we may find ourselves back on the frontlines, but I know we still have a lot of fight left in us and we will rise to meet the challenge. COVID-19 felt like a sucker punch out of nowhere but being up close and personal with all the amazing people mounting the response makes me confident that if/when another pandemic arises, we will be ready.

 

Rolling with the Punches

 

It was December of 2019. The ground was full of snow, my student home looked like a
holiday store exploded in it, and peculiar news was circulating after a mystery disease infected a
Wuhan, China local who ate a bat; we thought it was probably fake news…
The year was coming to a close, and so was the second last semester of my undergraduate
career. Of course, my mind was tossing and turning between excitement and denial. My four
years at Queen’s University in Kingston, Ontario, shaped me into the person I have become. The
thought of starting a new journey at a new school had already crossed my mind but moving on so
soon felt as if I was cheating on the very place that I was lucky to call home. Not to mention that
my brain was fried after so many early mornings and late nights at the library, drowning myself
in coffee.

Taking a break from academics was a foreign concept that required a great deal of
consideration. I researched all the schools in Canada looking for the perfect program until one
day, my curiosity led me to the Biotechnology and Entrepreneurship master’s program webpage
at NYU. Needless to say, I fell in love with the program in an instant. I started imagining the
possibility of this new life; however, the idea did not go further. While my family was extremely
supportive of my goals, they were not quick to send me off to another country without first
applying to Canadian programs. With my lack of excitement towards what other schools had to
offer, I had decided to hold off on applying to a master’s program and take time away from
academics.

In a search for a new plan, I started talking with friends about travelling the following
year. We stayed up late talking about all the places we will get to tour as school became more
distant in my mind. At the age of 21, travelling with my best friends across the globe was a
pretty easy fix to overcoming my fear of taking a break from studying. In Thailand, tanning on
the beach, volunteering in elephant sanctuaries, hiking through wild forests – sounds good to me!
After months of debates and contemplations, everything was finally falling into place, and I
could not be happier. Until…

March 13th, 2020 – the beginning of the unpredictable.

My undergraduate university decided to shut down in preparation for remote learning. At
the time, I had decided to stay in my student home to celebrate what I thought was an extra
reading week with my friends. However, all the fun and games transposed into a red light in my
future plans. I was jobless, travelling was no longer a reliable option, and I had no idea what to
do at the end of my fourth year – which, might I add, was a month and a half away. The anxiety
slowly crept in. I started researching the virus more each day, wishing I could fight against it.
But how?

It was that moment when I realized I had to go back to school. I am a scientist – THIS is
the time for me to contribute to the world. Sadly, it took a global crisis and lack of plans to shake
me, but at that point, it was too late. I had not applied to a master’s program, and I lacked the
skills and qualifications for any job I found in the biotechnology field.

One afternoon, I received a call from my aunt, a professor at Rensselaer Polytechnic
Institute in Albany, New York. She had asked what my plans were for next year as a graduate,
and I was embarrassed when telling her that I had none. That call had changed everything. My
aunt informed me that her university accepted late applicants due to the effects of COVID-19
and urged me to inquire if NYU was doing the same. Within one week, I found myself back in
Toronto with my application to NYU well on its way, and one hell of a surprise for my parents,
who had no idea I even applied.

Fast forward two more weeks – the CDC had already declared the pandemic, the world
had gone virtual, social distancing was the new motto, and I was sitting on the floor of my
bedroom staring at an acceptance letter to NYU with my name on it. Before even having time to
process everything, my parents were already on the phone with my grandparents, running around
the house cheering for their “little scientist” with pride. With my family’s excitement and
support, including my great uncle, an NYU alumnus who praised the school, I was finally within
reach of my goals. All of a sudden, I possessed a beam of light in a world filled with so much
darkness. It was my first time feeling so proud of myself – I was ready to take on this new
chapter.

It is December again. The end to the longest, most challenging year. I am at home in
Toronto, surrounded by my incredible family, concluding my first semester as a graduate student
at NYU Tandon School of Engineering, and studying in a program that feels as if it was made for
me. I am working as a research assistant at the Montclare Lab that not only is partaking in the
fight against COVID-19 but many other health issues that society has been battling for years. I
have the pleasure of learning from brilliant scientists every day who continue to shape me
beyond what I thought was possible. If I was told last December where I would be right now, I
would have laughed and denied it. I did not believe I would find success this quickly, nor did I
see myself in New York City. Through enduring the sadness and frustrations this year’s events
have brought, I learned to close my eyes and jump – accept the unknown – and fight against the
obstacles that face before me. My journey to graduate school and my time in it have taught me
that it is up to me to control my dreams. Putting up walls when things get tough might help at the
moment but taking action will change the outcome. All I have to do is roll with the punches.

-Neta Benor

Walking my own path

By Andrew Wang

As the saying goes, “If you feel like you’re the smartest person in the room, you’re in the wrong room”. Throughout the years I’ve had the opportunity to enjoy the company of some very smart people, not just in STEM but also diverse fields like journalism, law, politics. As much as I have tried to abide by that quote, I would be lying if I didn’t admit that doing so is also a constant source of stress. I couldn’t help comparing myself to those more well-spoken, more analytical, more put-together than me, who could seemingly summon knowledge on any topic on demand and held an unshakeable image of confidence. When surrounded by such people, it’s easy for me to feel like we’re not cut from the same cloth, or that I lacked aptitude.

This was the case for me and biomedical engineering. Despite being interested in biomedical science and engineering since a formative event in my childhood (a topic for another time!), while an undergrad at Berkeley I pursued a biochemistry degree because I had doubts that I could match up to the more rigorous requirements of the bioengineering major. While there were many interesting aspects of biochemistry, there were also classes that I didn’t really care for.

As a result, I decided to step outside my comfort zone and joined a robotics club called Pioneers in Engineering (PiE) on campus despite knowing almost nothing about mechanical or electrical engineering. PiE is mostly an engineering club, but it’s one with a social mission – to help local underserved high school students become interested in STEM through robotics mentorship with low barriers to entry.

Some high school students working with their mentor (a college student) to build a robot!

I was amazed at how much working in a team to finish a larger project with wide ranging impact is different from completing a class assignment. I learned how to ask for help; to my surprise I found so many willing teachers among my peers. While not immediately useful for club work, my biological background allowed for a mutual exchange in ideas with my friends and often resulted in lively discussion on several topics on the intersection of technology and biology, such as human-robot interaction. These experiences have helped me develop my own path without comparing myself to others. I gained the confidence to pursue my interests further, leading me to take several bioengineering classes and go to grad school for biomedical engineering.

-Andrew Wang

@acuteWangle