Blog Posts

The Solidified Path – Protein Engineering

By: Chengliang Liu

In high school I was known to be a student who really enjoyed STEM classes. As the acting president of the Math Club of my high school, I developed a deep interest in applying mathematical modeling to predict ways in which the world would evolve. I feel grateful that math has opened a new door for me to explore and enjoy the beauty of other sciences. I discovered chemistry and biology were where my true passion lay. Science has always attracted me because it is a method of problem-solving, though every subject of science has helped me to understand the world we live in better, and ultimately I choose this path for my degree.

Having this opportunity to work in the lab over this past summer has strengthened my passion for science. Experimenting with just a single plasmid that was coded for a specific targeted protein, until the pure protein is ready to be tested, is really an incredible experience. During class lectures, professors tried to teach the technical theories of science, but because of time limitations, the lecture is usually broken into fragments. In the grand scheme of things, students are not able to fully understand the reasoning behind the techniques. In lectures we always anticipate successful experiment results, however, this is not the case at all. In a research lab, more often than not this will take multiple trials until desired data can be collected. We discuss the problem we face and try to improve on the protocol, and bit by bit we figure out the issue and eventually solve it. This is what I viewed as the most rewarding part about science, and this is what motivated me to come [...]

December 9th, 2021|

My Journey to the Lab

By Aparajita Bhattacharya    

 

Growing up, I was utterly fascinated with the inner workings of the living world. This fascination as well as curiosity led me to major in molecular biology during college. However, my senior year, I found that I lacked work experience in the field and didn’t know how my knowledge from class would apply in the real world. Intending to fill this gap, I landed a credit-based volunteering opportunity in a genetics lab that used Drosophila as a model organism to understand aging and Alzheimer’s disease. This lab experience not only gave me a taste of the world of science, but also helped me to get my first job as a research assistant studying the molecular mechanism of Alzheimer’s disease. We sought to map the molecular causes of protein dysregulation, which lead to amyloid accumulation in the brain, and  eventually result in dementia. Since I am interested in more readily applied research, this project caught my attention. In my own small way, I was addressing a challenge facing human health by advancing the understanding of the origin of Alzheimer’s disease. Feeling fired up from my stint in the research lab, I entered a Master of Research in Molecular and Cellular Biology (MRes), which was like a mini-Ph.D. The program allowed me to assess whether I’d be interested in the commitment of a Ph.D. program.

Aparajita Bhattacharya, PhD Candidate 

 

As a part of the MRes, I worked in two labs executing two Master’s thesis projects. In the first, I investigated the unorthodox idea of translation in the nucleus using a yeast model in the School of Biosciences. In the second, [...]

October 11th, 2021|

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 [...]

August 12th, 2021|

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 [...]

June 3rd, 2021|

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 [...]

May 12th, 2021|

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 [...]

April 7th, 2021|

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.

March 23rd, 2021|

What I Want to be When I Grow Up

By Jacob Kronenberg

 

When I was little, I wanted to be an inventor. At the age of five, my grandmother told me that I descended from Thomas Edison. I did some investigating and it turns out that my grandmother’s grandfather was friends with Thomas Edison’s father, Samuel Edison. It’s a tenuous connection, but when you’re five, that’s more than enough. When I wasn’t building structures from Tinkertoys, Lincoln Logs, or Legos, I was sprawled out on my floor drawing solutions to the problems in my life with crayons. I remember dreaming up an automatic sorter to organize my messy room and a device to let me insert straws into Capri-Sun juice pouches without poking through the back side. You see, childhood’s most pressing problems. I was drawn to stories where the brilliant and solitary engineer devises thousand patents. If anyone asked me what I wanted to be when I grew up, I knew what to tell them.

 

In school, I focused on science extracurriculars. I joined the Science Olympiad team in middle school because I loved the competition and the excitement of a new problem. Plus, it was the hot thing to do in middle school. Believe me. Science is cool. All of those competitions prepared me for the height of my middle school science career, the epic eighth grade sludge test. Our science teacher mixed up a sludge and we had to use our knowledge of chemistry to separate and identify components from the glumpy sludge. While many other kids were frustrated by this impossible task, I reveled in the scientific problem solving challenge.

 

Outside of school, I was trying to invent too. I’d go over to my best friend’s house and build [...]

March 11th, 2021|

A day in the life of a scientist….

By Alara Tuncer

 

../Desktop/Screen%20Shot%202021-01-03%20at%206.05.11%20PM.png

https://pl.pinterest.com/pin/36451078205754885/

Beep Beep Beep. I woke up punching my alarm from a vivid dream of me in the fifth-grade science fair—sheepishly presenting about tungsten lamps. This is when I should’ve known that I was going to become a scientist. What kind of 10-year-old tries to build a light bulb with tungsten filaments?

 

It’s 9:20 am. I rub my eyes and pull the curtain reluctantly—yet—firmly and the light begins to illuminate my room. Hoping the sun does a better job at waking me than my alarm, I yawn. I feel sleepier than usual. It’s unavoidable for me really, to go about my day without dividing the total amount of sleep I’ve got the previous night with a single sleep cycle (roughly one and a half hours) to evaluate if I’ve gotten enough sleep.

 

I walk into the bathroom and turn on the tap to wash my face. I hear the faucet dripping, while I’m keen on avoiding scientific explanations for this, when I turn to observe the water sneakily escaping between my fingers from the hand I’ve been holding out—I’m caught in the flow of my thoughts just like the water, liquidious. I wonder why? Still, I carry on about my day, walking around on my tippy-toes so that my roommate doesn’t wake up to my creaking footsteps. Still, I hear noises caused by the unwilling force I’m exerting on the floor that is defiantly causing a surge of vibrations to travel along the floor, sharply cutting through the silence of the air.

 

I brush my hair and my teeth. You would’ve thought that my mind wandering into nothingness—thoughtless and lacking [...]

February 23rd, 2021|

Starting a Postdoc in a Pandemic

By Stanley Chu, PhD

Academia is a nomadic path for many of us who are in the early stages of our career. You spend a few years in one place to get your bachelor’s degree, pick up your life and move to go to grad school, move again for your postdoc (and again for your second postdoc), and then move again for your first job. And each time you move you have to start over, from finding housing to finding new friends. Each time is arguably more difficult as the size of your cohort and colleagues (your natural friends) shrink and you become more specialized and unique in your field.

I began my Postdoc tenure at the Montclare Lab in October of 2019. I had moved to New York City from my home in Atlanta. In the first few months, I did my best to find and furnish an apartment, make friends and explore New York City all on a postdoc budget. I spent my first Christmas in New York City alone, deciding that I could not afford to fly back home for the holidays. Instead, I kept myself busy writing a review paper.

Stanley

In March 2020, the World Health Organization declared that the COVID-19 outbreak was a pandemic. On that same day, the Montclare Labs shutdown it’s operations and we began to work from home for the next four months. Since we are mainly a wet lab, we had trouble finding any productivity at home, not to mention that most of us are in tiny New York City apartments that don’t have suitable [...]

February 2nd, 2021|