Leadership changes are exciting opportunities for the evolution of an institution. Our new Stony Brook University President, Dr. Maurie McInnis, has been hard at work for the last year guiding the University through a historically challenging time and laying the groundwork for campus-wide growth. President McInnis shared her vision for Stony Brook University and the MSTP’s role in that greater picture by answering questions from students. In the 8+ years we spend training at Stony Brook as medical and graduate students, MSTPs become integrally involved in the University and Suffolk County community. Individually and as a community, we leave our mark on Stony Brook and can effect lasting change in education and research. We are grateful for her thoughtful responses and look forward to developing our connections with President McInnis and working with her administration to increase equity and excellence across campus.

MSTP: What does “interdisciplinary research” mean to you? What are your views on MD/PhD training?

President McInnis: Training the next generation of physicians and physician scientists is the most important mission of the Renaissance School of Medicine. The Medical Science Training Program is of course a highly competitive, sought after placement, and I have a deep respect for the students who have worked so hard to reach this distinction. Their trajectory, securing significant positions and making promising “bench to bedside” contributions, is one way in which Stony Brook helps to advance the future of healthcare delivery.

But the future of healthcare will also involve a more integrated approach–one that culls research from across disciplines to provide the best care and, hopefully, build a better, more accountable and dynamic system. I believe Stony Brook is uniquely positioned for this evolution, as the work we do here is already so multi-faceted. We’re a state-of-the-art healthcare institution and simultaneously a cutting-edge research institution. I want to build on both of these strengths by bringing them closer together, blending our expertise across disciplines. And we are already seeing so many exciting examples of this unfold. The Institute for Engineering-Driven Medicine, for example, is drawing in faculty from all over campus—from the AI Institute to the Neurosciences Institute; from the Center of Excellence in Wireless Technology to the Center for Physical and Quantitative Biology—to collaborate on groundbreaking innovations in convergence science. With resources like our powerful partnerships with Brookhaven National Lab and Cold Spring Harbor Lab, our future physician scientists have access to collaborate with some of the most prolific scientists in the world.

The point is well-illustrated by this moment in time. Fighting the COVID-19 pandemic — one of the most complex challenges imaginable — has required researchers from many disciplines to come together. We have had to come at this situation from every angle–from immunology to public safety, mental health to economics. One example of many was highlighted in this week’s announcement that the Renaissance School of Medicine deployed a new in-house COVID Surveillance Screening platform to rapidly identify a positive case in a multi-person surveillance pool. This new technology was developed by Computer Science faculty and students who partnered with numerous divisions within Stony Brook Medicine, many areas on main campus, and an industry partner. It demonstrates how our multidisciplinary efforts, and our drive for collaboration across all areas of campus. The team will continue its work, and is now collaborating on the development of a COVID Mass Vaccination Project to be rolled out later this month for healthcare providers, employees, students and the community.

MSTP: We are proud that our University is being led by such a distinguished female president. You have a strong track record for promoting equity, diversity, and inclusion initiatives during your tenure as Executive Vice President and provost at UT Austin. What steps do you believe we must take and what steps are you taking to increase the numbers of female and BIPOC people serving in leadership positions at our University? What is your plan for making medical or graduate education more accessible for students representing historically marginalized groups?

President McInnis: I’m still relatively new — only six months in — but part of what drew me to Stony Brook was its unique set of priorities and demonstrated success in recruiting and educating a diverse group of students. Our infrastructure is very sound and strong, as demonstrated on the Provost’s Diversity Program Portal — there are descriptions of most of our initiatives, which focus on growth and access as early as K-12, to undergraduate STEM, to Postdoc and Graduate Student programs, to faculty programs. And of course, there are many support initiatives and resources offered by our faculty experts and program leaders, who I believe are similarly committed to promoting diversity, equity, and inclusion in leadership and in graduate and medical education.

It would be impossible to name all of these in a single interview, so for brevity’s sake I’ll highlight the Center for Inclusive Education as just one of our model programs. The CIE is a hallmark of the University’s ongoing commitment to advancing diversity in graduate education, academia, and the scientific workforce. It ensures that Stony Brook University is represented at several major national conferences for UR and URM STEM scholars each year including, among others, the Annual Biomedical Research Conference for Minority Students, the Society for the Advancement of Chicanos and Native Americans in the Sciences, and The Black Doctoral Network. In addition to national event recruitment each year, the Center coordinates close to 50 direct outreach and information events for underrepresented and underrepresented minority undergraduate scholars through institution-specific information sessions.

There is much more to the CIE, and to our diversity initiatives than I can articulate here; I encourage all of our students to look into the Center and connect with our Office of Equity, Diversity, and Inclusion and learn more about what Stony Brook University has to offer.

MSTP: What does a typical day look like for a University President?

President McInnis: Leading an institution as big and complex as Stony Brook University requires many different individuals working together as one cohesive unit. I have been focused on building a team made up of diverse talent and people who have varying viewpoints to share, and areas of expertise very different from mine. I like making data-informed decisions, but am also very relationship-driven when it comes to work and leadership. I see these approaches as working hand in hand for knowledgeable decision-making and accountable leadership.

Normally, I would be out and about meeting with everyone and getting to know this community–at department meetings, clubs, student and staff events. Even over coffee, during office hours and just walking around campus. What I hope our campus has come to know about me in this short time is that I believe in being open and inclusive. I want to listen, learn, engage, and collaborate. So, in my day-to-day, I am still trying to do that as much as possible in these more remote settings.

MSTP: What do you expect will be the most important, lasting impact the pandemic will have on higher education, particularly for graduate schools?

President McInnis: COVID-19 has presented us with an opportunity to analyze the advantages of different models of education while developing new teaching tools and methods along the way. We’ve been hearing from both faculty and students that some video conferencing and remote interactions have actually empowered students to speak more in the pedagogical setting. It’s allowed students who might have otherwise felt alienated or intimidated to participate! Similarly, remote models of the university experience have totally reimagined many extracurricular activities. Students who might often be busy commuting or working can still connect with their peers and classmates online for activities and social clubs. A student whose commute prohibits them from making it to a career fair on time now has the opportunity to attend. While I believe that in many–or even most–situations there is no better remote substitute for in-person and hands-on learning, especially in healthcare, I know that COVID-19 and the transition to remote and hybrid learning revealed that previous models of university life haven’t always served all students equally. Now we have the opportunity to fill those gaps.

It’s clear that if higher education is going to meet the changing needs of students in 2020 and beyond, while driving the social and economic mobility of our community, our academics need to do it all—they need to be accessible, rigorous and just as intellectually engaging as they always have been. My hope is that we can use our experience during this pandemic to spark positive change for future generations of Stony Brook students, faculty and community members.

MSTP: Are you enjoying living on Long Island?

President McInnis: I’ve spent so much of my life on the East Coast, and while I liked living in Austin with its huge cacti and Texan heat…I absolutely love being back in a lush, green environment. I’m actually originally from Florida, so upon taking this role I was very excited to be back in a place where there is water everywhere. This summer, my family and I regularly went kayaking, and took drives to Suffolk County parks and beaches with our dog. Now, I think entering an East Coast winter has given me the renewed ability to appreciate the changes of the season, and the distinct passing of time: to stop and reflect on all that we did this fall and look toward the New Year with resolve and hope. I love it when the snow is falling. There is a quiet and stillness that naturally leads to contemplation.  There’s nothing like a blanket of snow to make you slow your plans.

Of course, my experience living on Long Island has been necessarily narrowed due to COVID-19, and so what I’m really most excited for is to really get to know everyone in the community better, when that’s possible—to slowly, gradually, eventually be able to meet our students, staff, faculty, and alumni in person and shake their hands.

By Allen Chen

“You’ve trained to become physician-scientist’s and I salute you. Use the tools of science to prevent the next pandemic, and to cure all of the other diseases that afflict humanity.”

• Michael S. Brown, MD Physician-Scientist Nobel Laureate speaking via Zoom at Renaissance School of Medicine Class of 2020 Graduation Ceremony

Physician-scientist Michael Brown gave an inspiring and reassuring zoom graduation speech, amidst the COVID-19 pandemic. Mirroring his speech, many of our MSTP cohort across all classes have quickly joined the fight against COVID, becoming “COVID Warriors”, volunteering their scientific and medical knowledge to quell the pandemic, one that particularly afflicts those in NY and the Stony Brook area.

In this time, MSTP trainees have been in a call to arms in the form of RNA sequencing, plasma clinical trial research, guiding geriatric services, and using 3D printing to generate PPE for the hospital. MSTP students across the student body dedicated nearly 1000 hours total to help in these efforts. We highlight just some of the amazing way’s that SB’s MSTP members (even those who recently graduated) have given back to the Stony Brook’s Hospital and the Renaissance School of Medicine.

“COVID Warrior” PCR Diagnostic Testing

Nuri Kim (GS4) led the MSTP effort to secure and expand COVID-19 diagnostic testing at Stony Brook University Hospital under Pathology Department Chair Dr. Kenneth Shroyer, MD/PhD. Nuri described her experience there as fast-paced and demanding. Nationwide shortages of CDC-approved SARS-CoV-2 testing reagents meant the COVID-19 diagnostic volunteers had to find flexible and creative solutions on a day-to-day basis. Relying on prior experience with RNA extraction and PCR, Nuri and other MSTPs served as an important component of the hospital’s COVID-19 response. The student volunteer team provided results within 24-hour turnaround for over 800 patients and healthcare providers through the peak of the pandemic surge, during a period when New York State Health Department testing facilities were overwhelmed.

When asked how she got involved, Nuri responded, “I felt pretty helpless watching the pandemic arrive in New York. When the email came around from Dr. Kaushansky and Dr. Shroyer seeking volunteers with RNA experience, I registered immediately. It was a no-brainer.” From the beginning, Nuri worked alongside John Yuen (GS2) and under the supervision of pathology resident Dr. Karen Bai. She credits the team’s early success in establishing an in-house testing protocol to the team’s dedication, resourcefulness, and rapport. “Through the first weeks of volunteering, the hours were long. I feel extremely fortunate to have spent those early weeks with John and Karen.” Nuri also acknowledged RNA experts among their fellow MSTPs, Allen Yu (MS4) and Lilly Talbot (GS2), for their help in troubleshooting and soliciting scarce reagents from RNA labs across campus.

More MSTP students and Stony Brook graduate students soon joined the fight, demonstrating the generosity of our student body. Of the MSTPs’ response, Nuri said: “The most remarkable aspect of this experience was the immediate and ruthlessly capable response from fellow students. Other MSTPs were raring to go as soon as we had a protocol and workflow in place.” Trainees spanning all phases of the program formed a highly-trained ensemble cast: Rachel Kéry (MS3), Allen Lee (GS3), Kelvin Chan (MS3), Kevin Murgas (GS1), Lucia Yang (MS2), Allen Yu (MS4), Camelia Zhang (GS1), Steven Lewis (MS2), Joshua Kogan (GS2), Soma Kobayashi (GS2), Michael Martinez (GS3), Craig Marshall (GS2) collectively volunteered over 500 hours.

By late April, the team had a deep enough roster to run RNA testing 90 hours per week to sustain COVID-19 testing through the month of April. A picture emerges (literal ones below) of the PCR team, fiercely pipetting, loading samples, and determining diagnoses while dedicating long hours. With such a great team of students involved in the PCR testing, it is was a great demonstration of how powerful joined efforts from the MSTP could be.

Dr. Ken Shroyer, a physician-scientist mentor at Stony Brook recognizes the efforts of our student body (Stony Brook Medicine website): “We are now about a month out since we began to ramp up efforts to provide in-house testing for SARS-Cov-2… I know that Karen Bai, Nuri Kim, John Yuen, and many others have been putting in long hours, even 7 days a week and late into the night to generate clinical data that has been invaluable to guide the clinical management of our patients.” The Department of Pathology and their facilities guided the diagnostic testing and procurement of resources for it. Dr. Ken Shroyer has mentored SB MSTP students and has been a great contributor to our education. We hope that such effective interdepartmental interactions may arise in the future.

3D Printing of PPE for hospital

While the PCR team had been busy at work in the midst of uncertain reagent supplies, there was even less certainty regarding hospital supplies of personal protective equipment (PPE). Given that people had been under duress, it is not surprising that hospitals across the country developed a need for such supplies, critical for standard of care. Without factories in the MSTP’s backyard, creativity and craftiness was required. Working in this regard students such as Agatha Lyczek (MS3) and Mikhail Gurevich (MS3). We interviewed Agatha and she described how it started: “Mikhail Gurevich and I wanted to help combat COVID with a creative approach. We first asked ourselves, where do we think the need will be? Our original plan was to create mechanical actuator for a bag valve mask that will act as a “helping hand” to help ventilate patients that would otherwise be without one. We assembled a team with other stony brook students and alumni to help with design.”

How does one go about generating PPE or ventilators? Agatha and Mikhail used Auto-Desk 3D modeling and printing to create adaptors that would serve to join readily available parts such as HEPA filters and scuba masks. A picture of such an adaptor is shown below. “Dr. Mikhail Guzman offered his laboratory to us to design and test the “helping hands” and also invited Mikhail Gurevich and me to join his other efforts of designing PPE to help protect healthcare workers.”

On an average day Agatha and Mikhail would engage in zoom meetings to discuss design and programming issues regarding the ventilator (Well, also upon their recent return to Medical School they announced their engagement! CONGRATULATIONS!!!). For the PPE, the team would monitor 3D printers and assemble parts as they were produced. Agatha led the modeling adaptor parts in order to repurpose scuba diving masks to be used as hospital PPE. It was a great learning experience for those involved, practicing aspects of teamwork, material design, and project completion. Raja Pillai (graduated April), Eric Roth (GS4) and Johansen Amin (MS3) also volunteered for separate efforts for PPE assembly. Well done!

2020 MSTP graduate’s hit the hospital floors as Assistant Physician’s

Brinda Alagesan, Greg Kirschen, and Bryce Shroeder, recent MSTP graduates, joined the fight in early April as freshly graduated medical students were asked to join the hospital staff as Assistant physicians. Jump starting their careers as interns they used their recently donned medical degree’s in order to crucially help manage patients in the hospital. When interviewed, Greg noted how he and other assistant physicians were involved in managing COVID patients across multiple floors, while leaving the most critically ill patients to intensivists and other attendings. Each assistant physician generally worked with two other residents and an attending physician. Greg commented about how at first, he was nervous but that he was overall well-prepared for the experience. When asked how it impacted his view on the physician-scientist career, he said “Inspired me further, if anything! It shows the strength of our basic science training, important for determining what is a reproducible or valid finding.” To sum up his experience, Greg lamented “An interesting note to leave on, a social worker who I worked with told me he was a part of the AIDS crisis. He told me that like the AIDS crisis, the COVID19 Pandemic is something that will shape how you will handle your career as a physician and scientist.” Greg and other assistant physician’s learned from this experience while contributing to management of the pandemic. We will miss them as they go on to become residents across the country.

COVID Plasma Study

Amidst the efforts in helping patients at the front lines, one MSTP student wondered how COVID-19 may impact those very people, the hospital staff. Using their sharp research acumen, a team of Stony Brook clinical researchers including MSTP’s Lillian Talbot (GS3) asked “what percentage of our Stony Brook University hospital staff have serum antibodies to COVID-19? And “are staff members who care directly for COVID-19 patients more likely to have serum antibodies than those without direct patient contact?” Lillian Talbot, working under the direction of Department of Anesthesiology’s Dr. Elliott Bennett-Guerrero, alongside a group of research coordinators, conducted antibody testing on 500 Stony Brook health care workers using a point-of-care assay developed by a local Long Island company. In their efforts, the COVID-19 Health Care Worker study team found that surprisingly, there were not significant differences in plasma COVID-19 antibody levels when comparing high risk departments (critical care, emergency medicine) to those at less risk. Lillian and colleagues thus provided evidence that hospital PPE may be sufficient to protect even the most high-risk hospital staff from COVID infection.

While the Health Care Worker Antibody Study was progressing, Principal Investigator, Dr. Bennett-Guerrero initiated an even more ambitious multi-departmental COVID-19 clinical study, a randomized controlled trial examining the efficacy of fresh frozen plasma donated from recovered or “convalescent” COVID-19 patients as a therapy for severe COVID-19 infection.  Lillian in collaboration with two other MSTP students Jason Carter (MS4) and Margaret Shevik (GS3) were instrumental team members on the convalescent plasma clinical trial, helping on the donor recruitment and plasma recipient sides of the trial.

Beginning in April, Lillian, Jason and Margaret have (with their thesis advisors’ approval) collectively worked hundreds of hours on the COVID clinical trial and have collaboratively authored two manuscripts detailing their work and findings. As Margaret and Lillian return to graduate school and Jason to the clinic, these experiences will certainly help them as they move on to their future physician-scientist careers. Learning how to establish clinical studies and communicate effectively to faculty across departments are valuable skills these MSTP students will continue to cultivate.

Geriatric Outreach Services

So much of the above great work was done to help those facing COVID within the hospital, but what about outside of the hospital facility? Locked indoors, many geriatric patients and others particularly at risk for the severe respiratory sequelae of the infection find it difficult to carry out daily tasks and stay upbeat. Thankfully, in order to help with this, Steven Lewis (MS2) led and helped organize efforts to help bring daily functionality and care to the homes of geriatric patients. When asked how he got into this service, he said “Social distancing had just recently begun and I was keeping in regular contact with my grandma, who is still isolating at home in New Jersey by herself. From talking to her, it became clear that a great burden of social distancing would fall on older patients, people like my grandma who told me she was crying each morning (luckily not anymore!) and scared to go outside for groceries.” Steven knew that there was great interest and motivation to help out from students around him, inspiring him to take action.

Steven contacted geriatrician specialist Dr. Strano-Paul, Assistant Dean for Clinical Education and a familiar mentor to the MSTP to see what could be done. They were able to set up two teams of students (including MSTP student Rachel Kéry (MS3) ) that were assigned to geriatric patients. They would act in reassurance, answering questions, providing emotional support, and initiating communication with their physicians if necessary. This organized effort allowed many phase II and III students to provide support calls to patients. Medical students in phase 1 helped in delivering medications and groceries that patients needed. The SB community is thankful that services like these were put in place for those vulnerable and stuck indoors.

Conclusion

The physician-scientist training is a long-term pursuit, with many roadblocks and hurdles that may arise, making the career both challenging and interesting. The COVID-19 pandemic has not been an easy time period for any Stony Brook MSTP trainee. Yet, during these times students from each year have been creative and generous, using their knowledge and skills gained thus far to help those affected. Here we have covered the highlights of these efforts that we hope represents the best of SB MSTP, but of course by no means have covered in detail all efforts from every student. We are thankful for all such efforts and for the fact that we have such a strong and talented student body that gives back to the community.

Allen Chen (GS4) studies neural circuit mechanisms and cognitive behaviors that underlie neuropsychiatric disease in Shaoyu Ge’s and Qiaojie Xiong’s labs.

By Nuri Kim.

Tyler Guinn (MS3) is a modern-day Renaissance man. Since starting the MSTP at Stony Brook in 2015, Dr. Guinn has juggled medical training, marathon running, reading the longest novels he can find, picking up an instrument (guitar) and foreign language (Ukrainian), and all the while completing his PhD in bioengineering in just three years. This year, he was also one of five recipients of the President’s Award to Distinguished Doctoral Student which is awarded to students for excellence in their research and contributions to Stony Brook University.  

In April, a month into the COVID-19 lockdown, Tyler defended his dissertation built around a cutting-edge tool, the Light-Inducible Tuner (LITer). His graduate research centered around designing an optogenetic system for tightly regulating gene expression in mammalian cells. Tyler received the National Defense Science and Engineering Graduate Fellowship (NDSEG), a highly prestigious award from the Department of Defense, for his visionary work on the application of LITers in cancer biology and toward tissue engineering.

I had the pleasure of chatting with Tyler over an hours-long interview – which was hardly enough time to scratch the surface! In addition to talking about his rich and diverse extracurricular life, we discussed his high-tech thesis, the life lessons that carried him through graduate school, and what it was like to be among the first PhDs defended on Zoom.

Name: Tyler Guinn

Hometown: Rowlett, Texas

Dissertation Lab: Gábor Balázsi Lab, Stony Brook University

Clinical Interests: Transplant surgery

Tips for resilience: Let curiosity pull you through adversity.

Remind yourself monthly, weekly, daily, even hourly (if you have to) what your goals are, why you are pursuing them, and how they are relevant to your life. It takes time to do this, but if you can articulate these goals, it becomes a matter of how, not if, you will accomplish them.

Find a hobby that you are not good at and practice it every day. See what happens with persistence.

Did you always know you wanted to be a physician and bioengineer?

Nooooo. No! In high school, I wanted to be a professional poker player, actually. I played poker every weekend. We had Native American casinos nearby in Oklahoma, so we would drive – this isn’t too good, but I did sneak in a few times under aged to play. But I think that’s like any aspiring professional poker player.

While I was still in high school, I got a job as a clerk at Walgreens. I worked at the front – selling cigarettes, that sort of thing, which is kind of ironic.… But then a job opened up in the pharmacy, which is the opposite of cigarettes. The reason I took it was not that I was [motivated to] go into medicine. It was because there was a $3-4 increase in the pay rate, so I was like, “I’m going for that job! That’s going to help me with poker!”

And that’s where I first started thinking about medicine. What I realized from working in the pharmacy was that the same people came in every week and every month. I’m not always the best with names, but I remember faces very well. So I would remember them, and for the first time I started interacting with patients – not as much from the medical side but from the pharmacy side.

From there, I kind of fast-forwarded a few years to upper level courses. I didn’t do research the first two years at all, but I was taking those pre-med courses. In one of the first weeks of the class, there was a movie of ATPase in the membrane. The professor showed it, turned it on, and it started utilizing hydrogen atoms to produce energy. I thought, “This is insane.” This is a molecular machine. That was the idea that got me into research. [I had taken some] engineering classes earlier and that made me think, “I want to build those things. I want to build little machines just like that.”

So that’s when the research started. I started thinking: “I don’t even know if this exists… are there labs that do engineering and biology?” At the time, our school didn’t have an undergraduate degree in biomedical engineering. They had a PhD program, but the undergraduate degree until the tail end of my undergrad or shortly thereafter so I tried to focus on finding a bioengineering lab instead.

I found a bioengineering lab that was only taking graduate students. I emailed Dr. Leonidas Bleris. I think back to that often. I know I have that email somewhere. It was just kind of funny to re-read those early emails. I basically said, “Hey, I’m thinking about pursuing medicine and research. I have no experience. Can I come in? I can clean some dishes if you want me to. I don’t really have any talents with this, but I’m interested.”

He got back to me pretty quickly and invited me to come over to his office for a meeting. Early on, I was so scared going up to meet him, thinking I had this great opportunity in the nicest building on campus that I hoped I didn’t blow. If you ever have the chance to visit UT Dallas, I’d love to show you around because some of the older buildings were from the 60’s. It actually started as an engineering school out of a company called Texas Instruments – you probably recognize their calculators? A lot of the campus was not pretty when I started. But by the end they had built it up, and I mention all this because there was this one research building on campus that was really nice: the Natural Science and Engineering Research Laboratory. And that’s where Dr. Bleris worked.

I remember going up the elevator and feeling so intense like, “I don’t know how to interact with a professor. I’m always sitting at the back, or quiet, not raising my hand…” But he was like, “Come on in.”

He invited me to join the International Genetically Engineered Machine (iGEM) Team for the school that he advised. We tried a lot of things in that lab while working on iGEM projects… and in the end, most everything failed. But there was something about that that was so important to me. Even if you fail at something you scrape off your knees, get back up, and keep going because there’s something about the curiosity that keeps pulling you. I stayed in his lab for basically the whole time until I came to Stony Brook, about four and a half years. And I actually had a picture of him in the last slide of my defense because I had this collage of family and friends and old lab and new lab – everyone that had made a big difference in my life.

You were among the first handful of MSTP Zoom defenses. Can you tell us what that was like? Any surprises?

The internet at my house went out the day of my defense. It went out an hour before my defense, and I ended up going to the Laufer Center on campus and doing the defense there, haha.

Earlier in the day I thought I would relieve some stress, go for a nice walk with my fiancée. When we got back, I was like, “I’ll check the PowerPoint one more time, let me check my email…. Email’s not working. Internet’s not working. Oh my god!” I was panicking.

My dissertation was at 1:00pm, and by then it was 12:15pm. So, I was grabbed my laptop, a monitor, a laptop stand, a charger, and my N95 mask and went to school to school as fast as I could. I thought about making a joke about it at the beginning of the dissertation, but I got so focused on what my advisor Dr. Gábor Balázsi and committee were saying at the beginning of the dissertation that I forgot to do it.

It’s a funny little story. Always have a plan B.

I think whether we go back to physical defenses, having the Zoom component was really cool because my 82-year-old grandma came and watched. That would probably have never happened – one because she doesn’t fly, two because she’s across the country. Some of my old lab mates also got to join, which was cool seeing them. It gave me a boost of confidence.

For your dissertation, you built a tool that allows you to manipulate stem cells. How did you become interested in stem cell research?

I had been working on light-based gene regulation, or tools that turn gene expression in a cell on or off only when exposed to light. I was interested in exploring the question: What can light do that chemical signals can’t? At the end of the day, if you build the same tool with light-responsive versus chemical, what is the advantage?

Spatial development kept coming up as a potential answer to the first question. Organisms have spatial development: They have areas that develop first or differently from their neighbors. A question I had was: How do human cells develop? They come from some precursor state. Could a light tool direct a population of these precursor cells and control a single, small step toward development? Then, instead of a population, could we control just one stem cell going from one step to the next, while all the neighbors remain stem cells? The spatiotemporal control was something light could accomplish that chemicals could not.

I came at this project from that angle, first asking how do I apply the tool, then back-tracking to learn about the biology behind it. I don’t know if that’s controversial. People have different opinions on what comes first: the tool building and there’s the science. To me, these always went together. And what’s exciting to me about doing both is if you build the tool, you’re often going to be the first one to apply it.

So you took a technical question, married it to the biological problem of coordinating the development of populations of cells. This led to your designing the Light Inducible Tuner (LITer) system. What does it do, exactly?

The idea was to make a tool that allows you to tune your proteins of interest to very precise levels. Many biological tools could knock down or overexpress proteins, but these often had limited control, acting as ON or OFF switches. Also, unregulated gene regulatory systems often produce very high gene expression noise. Lastly, recent biological findings have suggested the gene dose or how much a gene is expressed can be as important as whether a gene is expressed at all. Systems attempting to address these above issues had been done in chemical systems, but hadn’t been worked out in optogenetic systems. Our light-responsive circuits are designed to minimally perturb what else is going on in the cell and control the single variable you’re interested in. This lets you control, for example, proteins that drive stem cell differentiation or migration or proliferation using a radio knob where you can turn up the volume, essentially.

While that’s similar to well-established chemical gene regulatory systems, a light responsive system also allows you to control the expression spatially. Chemical systems cannot do that because they rely on diffusion which globally activates a cell population, but you can control where to apply light, therefore only stimulating small groups or even single cells.

A third important improvement to existing systems if that LITers include a way to create stable cell lineages. Optogenetic systems were often transiently transfected. When you do transient transfection, you can get uneven distributions, where some cells may get one number of copies and another cell gets another – and that can dilute out from a cell over time. It is not a stable system. That in itself is a source of confounding factors. Our system can be stably integrated into a cell’s genome using CRISPR-Cas9. This ensures that every cell you analyze is truly identical, lineage-wise.

How do you predict or hope this technology will impact not just the landscape of gene engineering research but also your career going forward? How do you see this research project translating to the clinic – in the short term or in the long term?

One thing we’re doing now is using LITer to look at proliferation and migration and how these two cellular processes work during wound healing. For the original work, we did not knock out the endogenous genes. But we do have that capacity and our future directions involve looking at genes involved in epithelial-to-mesenchmal transition (e.g. BACH1 or ZEB1). We’re in the process of making cell lines that have the integrated gene circuit with the endogenous gene knocked out. We’ll be using these cell lines to test a range of gene expression completely under our control from underexpression to overexpression without any interference from the endogenous gene.

Now this is really far off in the future, but maybe in thirty years, this is a conceivable long-term goal for LITers and systems like it. These systems may get to the point where we can take certain cells from a person and utilizing different genetic approaches, develop tissues de novo and replicating them down to spatial architecture.

This could work by integrating LITer gene regulation with a technology similar to something in radiation oncology, where you can shoot X-rays from multiple angles to target cancer while reduce harm from any one angle. The idea would be, instead of killing cells with X-rays, to use light to induce gene expression spatially and specifically without affecting any one cell too much. Having this sort of system could direct cell populations to develop spatially to generate new tissues or organs. I think it is a little science-fiction right now, maybe it’ll happen in our lifetime. That’s what I’m hopeful for.

You completed your dissertation in just three years! What were some habits or perspectives that helped you achieve this?

A bullet journal! I used this to basically map out future tasks, daily things, weekly things, monthly things. I tried electronic calendars. It doesn’t work for me. It works for some people. What I realized for me that you get a little notification at the bottom, I just click “x” and ignore it because I’m in a middle of a task. But if I keep this in front of me before I go to bed, put it on my desk or wherever I look first, it’s facing me in the morning.

I don’t think bullet journals will work for everyone, and I think it’s fine. That’s the other thing. Try new things for a week. If you try it for only a day, you can get annoyed with it, and it’s hard to see if it’s making a difference. But try it for a week, and you can get a better sense if it’s your thing. The only reason why I stuck with this is because it kept working. I know some people on Google Calendar who are super organized, I think, but I guess I’m still in analog for now.

Also, I think it’s important not to count research as the sole metric of success for MD/PhD. When you interact with your peers, are you cordial? Are you respectful? Are you friendly? Are you actually friends with them? If you’re a professor, are your colleagues miserable when they see you? Are they trying to avoid you at the gatherings or the holiday parties? Those seem like subtle and small things, but I think I’ve realized the value of incubating those other aspects of life.

The idea that life starts “after med school” or “after residency” or “after fellowship” – but if you really follow that all the way through, you wake up in fifty years and realize, “I did not live.”

You have to integrate life because the training is important, the career is important – I’m not trying to encourage anyone not to focus on the career. It may be a cliché, but the idea of having well-rounded aspects of life: You need different aspects. Maybe you need family, friends, career, fitness, interests, hobbies, and relaxation. If you like certain things, have them in moderation.

As cohort-mates, you and I have talked a good deal over the years about these ideas – and in particular how we think about them in relation to our shared love of literature. And I’ve been so impressed each time we sit down to chat it seems you’ve read another handful of books for recreation, even while maintaining productivity. Can you share five titles that helped you through your training so far?

The first is Crime and Punishment. Dostoevsky integrated so much psychology and interpersonal dialogue and showed that if you think of yourself as an atom, you’re isolated. And maybe it’s easy to think about that when focused on the career mindset, but you are an atom in a molecule, which is a molecule in a cell which is a cell in a body, which is a person in a nation, which is in a world… It’s so complicated, it’s so connected. To assume that you’re nothing but the atom is to neglect all that complexity. You can’t neglect those other things of life, essentially.

The second was East of Eden by John Steinbeck. It was for me… and I don’t know how other people feel, but for me it was terribly emotional. Terribly emotionally gripping. The multigenerational sins of a family, and how that propagates, and how redemption does and does not relieve that guilt… yeah, that was a very important book to me.

One book changed my career path, research and medicine-wise. That one is called When Death Becomes Life: Notes from a Transplant Surgeon by Joshua Mezrich. It’s by a transplant surgeon. I had played around with the idea of surgery before I came to Stony Brook, but I kind of dropped it when I thought of a research career. That book rekindled my interest in pursuing surgery, and at the moment, that’s what I’m leaning towards now.

That was a second book about surgery I could not put down,The Puzzle People: Memoirs of a Transplant Surgeon. It was written by Thomas Starzl who did the first liver transplant. He wrote that book in the style of an autobiography, but it is also about the development of transplant medicine. And I think from reading both Mezrich and Starzl…what it made me see was the overlap in engineering and surgery – and specifically in transplant surgery. After I read them it became so obvious. How did I not see that? But well, you know now.

I have to add this – The Master and Margarita. The Russians… That book… had some things. Like this parody of the Soviet Union and how terrible it was, punishing innocent people, and how Bulgakov uses Christ imagery – the innocent being put to death. I think the common theme in all of them goes back to the atom analogy. You’re not an isolated quark. You’re connected in different ways. I think that’s what so cool about these narratives.

Nuri Kim (GS4) studies codon usage bias in Mycobacteria in Jessica Seeliger’s lab.

By John Yuen, Andrea Arreguin, Luke Torre-Healy, Dillon Voss, and Isabel Sakarin

We first have to touch upon what it means to be a physician-scientist. Many people familiar with physician-scientist training will portray a story of self-sacrifice – forgoing your 20’s and 30’s to reach some sort of enlightenment as a medical professional who is trained to think critically like a scientist. As with most stories, the path is hardly linear as trainees try to balance aspects of clinical and research careers. Continuing to parse through what that may look like as graduates, we will typically undergo more training, perpetual grant writing, and a litany of administrative tasks, as we continue to juggle a wide range of responsibilities throughout our careers.

As banal and grueling as we make the training seem, why then, did we choose the path of becoming a physician-scientist? Although all MD/PhD students have their own unique reasons for choosing this career path, a unifying theme is that with this path we have the privilege of choosing a profession where we can not only think critically about problems, but also be empathetic to the challenges that people face daily. Simply, we get to have a job where we can choose to do things that can directly improve people’s lives and wellbeing. While this should no longer necessitate writing or saying: race impacts people’s lives and wellbeing.

We, as members of the Stony Brook Medical Scientist Training Program (MSTP), will no longer remain silent in combating injustice in our society. We mourn and condemn the murders of George Floyd, Breonna Taylor, Tony McDade, Ahmaud Arbery, and the innumerous Black and Brown lives lost to racial injustice every day.

As MD/PhD students we remain at an institution for around eight years, which affords us the opportunity to enact and see change at our institution. This national movement, brought up by the nation becoming acutely aware of racial injustice in the form of police brutality and systemic racism, grants us the opportunity to fight for change. We are frustrated by small, performative fixes that often serve to placate those of us with privilege instead of creating meaningful change.The time for incremental change is behind us.

As MD/PhD students and as a program that trains future medical professionals, we have a responsibility to look at the data and face the challenge of combating injustice and inequality every day. Looking inward at our MSTP cohort, we currently have very few students from communities underrepresented-in-medicine. We must do better.

Inequity and inequality is something that our program is focused on addressing. Students in our program have been advocating for the enactment of some short-term and long-term changes to our program, including the formation of an MSTP Diversity and Inclusion Committee. The committee is working towards the following goals:

• Building a more anti-racist environment that values the contributions and well-being of students from underrepresented groups in medicine.
• Advocating for the hiring of faculty from underrepresented groups in medicine.
• Inviting the Center for Inclusive Education on interview days.
• Pushing for additional implicit bias training for MSTP leadership, interviewers, and students.
• Adding a statement on our commitment to anti-racism to the MSTP website
• Updating our website to more prominently feature current students
• Providing a statement of anti-discrimination to invited candidates for interviews that states our full support of individual expression.
• Advocating for additional financial support to underrepresented students.
• Discussing health disparities and systemic racism in our MSTP journal club and clinician scientist dinners.

Similar to what the coronavirus epidemic is revealing every single day, our lives are inextricably intertwined. Poignantly, there are many social determinants of health that contribute to the disproportionate deaths of people of color, especially those who are Black. As Nelson Mandela put it, “to be free is not merely to cast off one’s chains, but to live in a way that respects and enhances the freedom of others.” We, especially those who choose to become physician-scientists, have a responsibility to continue to use data to be anti-racist and address other inequities in society, as healthcare is inextricably intertwined with the status of the people that it serves.

We the MSTP Diversity and Inclusion Committee take these issues seriously and will continue to work with our program directors to ensure that they are addressed. Creating lasting change requires engagement from the entire community. Please reach out to us if you would like to get involved in these efforts.

The SBU Diversity and Inclusion Committee can be reached at MSTP_diversityandinclusion@stonybrook.edu.

(Written by John Yuen, edited and signed by Andrea Arreguin, Luke Torre-Healy, Dillon Voss, and Isabel Sakarin)

John Yuen (GS2) is studying micro-RNA based interventions in oncology in Jingfang Ju’s lab.

By Lillian Talbot and Nuri Kim

Members of the MSTP have found ingenious ways, big and small, to contribute to the fight against the COVID-19 pandemic. Reflecting on the ways the MSTP mobilized as a community, we began to ask ourselves whether and how MSTP students are well-equipped to act during medical and scientific crises. Through reflection and discussion, we hope to further cultivate and encourage these positive attributes: a strong student network, resilience in the face of uncertainty, and an intimate understanding of the science underlying medicine. While weighing MSTP experiences in COVID-19 clinical practice and research, we also examine ways in which we fell short in our response to the pandemic and discuss innovative ideas to foster connection while practicing safe social distancing as we move into the future.

Early in medical school, MS1s form strong bonds with their medical classmates that often outlast even residency. In addition to these friendships, MSTPs participate in a second community: one among our MSTP as a whole. Building relationships with students across cohorts empowers students to find good labs, living arrangements, and emotional support. Meanwhile, it also provides us with a dynamic network for collaborations, as we quickly proved when asked to recruit additional student volunteers for our respective COVID service-learning projects. Whether in the clinic running trials for antibody tests or in the molecular pathology labs processing patient samples for COVID-19 RNA testing, we found reliable and hard-working team members who quickly committed to volunteering long hours on irregular timetables.

In these uncertain times, the proverb “the chain’s only as strong as its weakest link” feels particularly resonant. Teams have had to rely heavily on one another to safely engage in COVID-19 research and clinical testing. Our classmates not only joined COVID-19 efforts eagerly, they came with diverse and deep skill sets and remained committed even when the work was grueling and unglamorous. This camaraderie left a large impact not only on our perception of our classmates but concretely toward the timely and effective care of patients at Stony Brook Hospital. The worst of the pandemic proved that our MSTP student network is one of our most valuable assets, and we are grateful to all of our classmates for maintaining this inclusive and open community. When called to action by a fellow MSTP, our classmates responded not by asking, “What’s in it for me,” but rather “How can I help?”

The feeling of uncertainty is an inevitable component of graduate school we all wrestle with during our years at the lab bench. In medical school, a strict curriculum with little flexibility is laid out from day one. The agreement is that if you follow the roadmap for four years you will walk across the stage degree in hand. The path for attaining a PhD is far more variable, with some students finishing in two years and others taking closer to six to meet their committee’s requirements. The daily effort expended on a research project, while perhaps loosely correlated to success, does not guarantee a tangible result. We believe this degree of uncertainty — and commitment to values despite uncertainty — that MSTPs negotiate throughout graduate training strengthens us. Graduate school may have inoculated us somewhat against the sheer uncertainty produced by the global pandemic. Though the way forward is not perfectly clear, MSTP students have collectively mustered extraordinary flexibility, inventiveness, and dedication to seeing projects through to the end.

While it might seem obvious, we also believe our strong background in science technique and theory coupled with our medical training made MSTP students hugely valuable in the COVID-19 fight. The projects we joined demanded a high degree of organization and routine communication with faculty and staff throughout the hospital — skills honed by years at the bench, working with PIs and alongside labmates. We could draft and execute protocols for the University Hospital’s clinical diagnostic labs because we easily apprehended both the technical details and application of PCR testing thanks to our extensive wet lab experience. We could staff clinical trials and explain serology testing modalities to patients with confidence because we are trained in bedside manner, abreast on the most current literature on these topics, and even have hands-on experience applying them. Our MD/PhD background allows us to be medical and scientific translators, readily transitioning between two worlds that often don’t interface seamlessly.

Staying connected has been a challenge for us all over the last three months. We are often self-proclaimed introverts, and aspects of quarantine have suited many of us. However for those without roommates or partners, social isolation has also taken a toll. Throughout our time at Stony Brook our directors have developed programing that fosters cohesion from the top down. If we are to avoid erosion to our community it is up to us students to imagine and implement new ways to interact and learn together from a safe social distance. While the faculty deliberate how journal clubs, orientation BBQs, and retreats will look in the fall, students will need to work hard in unofficial capacities to ensure our community stays strong and vibrant and that those who are feeling lonely or sad have a place to turn.

One promising student-led initiative is the newly-established MSTP Diversity and Inclusion Committee (DIC). Committee member John Yuen’s (GS2) piece in this same issue describes the group’s goal to counteract the effects of systemic racial injustice in the program, and one of the major prongs of their action plan is to build a more unified MSTP student body. Student-driven efforts like the DIC’s will be vital toward conserving and strengthening a sense of community in present circumstances. The administration welcomes feedback and ideas from trainees on how we can best support each other despite the isolating and often troubling pandemic conditions.

COVID-19 is here to stay for our foreseeable future. While this is a strange time to be a student, we can find strength in our academic community of peers and faculty. We at the newsletter wish to thank all of our fellow trainees for their positive output and solidarity during this tragic and disruptive time. Congratulations to all those who have defended theses, returned to medical school, submitted grants, survived their first year of the program and learned new skills all during a global pandemic. Our incoming first year students face significant challenges, beginning medical school with an all-remote first semester. We are delighted they have joined our community and are committed to making extra effort to help our MS1s feel engaged. Keep on going, friends, and don’t hesitate to reach out to your community if you need anything.

Lilly Talbot (GS2) is the newly elected MSTP student representative in the medical school curriculum. She studies the mechanism of neurodegeneration in ALS through a process termed the Retrotransposon Storm in Josh Dubnau’s lab.

Nuri Kim (GS4) studies codon usage bias in Mycobacteria in Jessica Seeliger’s lab.