Category Archives: Humans of Tufts Boston

Humans of Tufts Boston: Ramesh Govindan, “Our ingenuity will pull us through”

Humans of Tufts Boston, 7 May 2020

Ramesh Govindan, CMDB, Fourth-year Ph.D. Student (Sixth-year M.D./Ph.D.): “Our ingenuity will pull us through

JH: How did you get started in science and what were you doing before medical/graduate school?

RG: I always had an interest in science, although I had a brief stint in college where I wanted to be a history major (my parents were terrified). I went to college thinking that I wanted to become a biomedical engineer, because my big interests at that time were in tissue engineering. Growing synthetic organs for transplantation seemed like the coolest thing on Earth (and it might be), and I wanted to be the guy to make it a reality. As I learned more biology and physiology as part of my major coursework, as well as a lot of the humanities courses I was required to take, I also became a lot more interested in the human elements of disease and medicine. So, on top of working in a biomedical engineering lab, I started volunteering at a local hospital in a Medical Specialties ward, through a program where we would visit patients who had been, or were anticipated to be, on the ward for a long time (weeks, months). I’d spend a few days a week there for a couple of hours at a time going on walks, playing board games, and chatting with the patients. I got to know a few people pretty well, including a particularly memorable guy who had poorly-controlled schizophrenia and type I diabetes, the combination of which prevented him from being discharged on his own. By the time I hit senior year, I was pretty confused as to what I wanted to do – science or medicine. I ended up taking a gap year at the NIH in a basic science cancer research lab, where we studied the mitotic kinetochore, a protein-chromatin-microtubule complex that forms during metaphase to regulate chromosome segregation. I had two projects there, first looking for substrates of Aurora B kinase, which orchestrates numerous processes in the kinetochore. The second was to study the role of a specific histone methylation (H3.3S31me) in mitosis. Our model system was Xenopus laevis frog eggs, which are highly mitotic and are great for immunoprecipitation. I applied to MD/PhD programs during that time.

The MD/PhD team at the 2018 Relays

JH: Why did you choose to do an MD/PhD?

RG: People ask this of MD/PhD students a lot, and I’m not sure if it’s out of a concern that we’re all secretly insane, or whether they actually think there’s some hidden driving motivation behind each person’s choice. I’ve come to realize over the years that I really don’t have a single reason why I chose this. There are a lot of small reasons, though. The first, probably, is that I was really torn between two professions. I enjoy science and the lab, but I also like helping people directly, with my own hands. To find out at the age of 20 that there was a career path that would allow me to do both of those things, even if it was only in theory, was something I had to jump at. The second reason I chose this is maybe more nebulous – I didn’t really see the downside. It was a challenge that only a relative few chose, and it opened up potential without closing any doors. In my mind, the regret of not having tried to do both would far outweigh the regret of having tried and failed. So I applied, then I got in, and, six years later, I’m still doing it. And yes, I still have two more years of medical school, five-ish years of residency, and then one or two more years of a fellowship, but I take it one step at a time and so far I’m really enjoying it!

The third reason was that medical school is free.

Waiting in line at the 2018 Extreme Beer Festival

JH: What drew you to microbiology for your thesis research?

RG: My interest in microbiology was not a deciding factor in any choice I’ve ever made. I’m not sure I even knew what a virus was before John Coffin and Katya Heldwein told me about them during lectures in my first year of medical school. And even then, I only wrote down enough information to pass whatever exam I had coming up. I didn’t realize that viruses would become such a big part of my life until I decided to join James Munro’s lab, and I only really joined because I liked his mentoring style and pew-pew lasers. But in the last four years, I’ve come to realize that viruses are maybe some of the coolest biological phenomena on the planet. They’re the only known replicating pathogen that is, by most definitions of “life”, dead. They’re nature’s freak killer robots. From a structural biology perspective, they are macromolecular machines perfected by evolution with only the goal of efficiency. They’re insanely amazing as research and therapeutic tools, and equally terrifying as agents of human disease. So I’m pleasantly surprised to have found virology as a PhD student, and I’m hoping to maintain a level of engagement with it as I move on my career.

Setting up a new hot pepper garden at Ramesh’s parents’ house in central MA

JH: Obviously COVID-19 has been getting a lot of press lately. As a future doctor, what do you think? Are there any questions that aren’t being asked that should be?

RG: These are truly terrifying times. The looming specter of COVID-19 has, I think, become a defining challenge for society. As a virologist-in-training, I hope that this pandemic helps us re-evaluate the ways in which we interact with the ecosystem and each other, and, as a doctor-in-training, I hope that we find new ways to organize ourselves to respond to emerging viral pandemics. The gut-wrenching part of this is that this entire pandemic, on nearly every level, is a product of human activity. From the encroachment of humans on untouched wilderness, to our inability to deal with global poverty, to our complacency in letting free market forces dictate the makeup of our healthcare systems, simultaneously all of us and none of us are to blame for this. For instance, while the lack of infectious disease (ID) doctors in this country isn’t specifically anybody’s fault, experts have been pointing out this shortage for decades. A root of the problem is that training in ID is financially devastating – you pay ~60k a year through medical school, then slog through a low-paying internal medicine residency, and then train for 2-3 years as a fellow in ID. As an ID doc, you make less than you would have if you had just stayed in internal medicine – you take a pay cut to get more training. Your salary as a doctor is tied to how much you can bill insurance, and if you don’t do any surgeries or procedures (like an ID doc), you bill less, and you make less. It’s ridiculous. We were able to fight HIV in the ’80s and ’90s because at that time, there were many more ID doctors in the country. Today, we’re out-gunned. 

So, this has been a classic conversation with Ramesh where it gets really dark once he gets going. But it’s not all bad. I am, surprisingly, still an optimist, and I really do believe that our ingenuity will pull us through. Vaccine trials are already underway, and drugs like remdesivir are showing some promise. But we need to keep up our momentum once this pandemic is over, and rethink our preparedness for viral pandemics, because SARS-CoV-2 is just one of many pathogens to come.

Ramesh’s fish tank with Saruman, the betta fish

JH: What do you like to do outside of lab?

RG: Foremost, seeing my friends is my favorite thing to do. The friends I’ve made at Tufts have helped me in more ways than I can describe. Even if I somehow failed out of two doctorate programs, I know I’ll walk away with some of the best friendships I’ve ever had. If you’re asking after hobbies, then I think an easier question would be, ‘What doesn’t Ramesh like to do outside of lab?’ I think most people who know me know of my strange obsession with The Lord of the Rings, the greatest story ever told. More recently, I finished another fantasy series, the Wheel of Time, via audiobook on my drives out to UMass and my lonely nights in lab. I can’t recommend that series enough. During the final book (50-ish hours long) I had to periodically look up to the ceiling to let the tears drain back into my sinuses so that they wouldn’t splash into my ELISA plate. This was besides the tears I normally shed in lab. I also really enjoy gardening. I worked eighteen years a slave in my family’s yard, and then left home to realize that I actually enjoyed it the whole time, so besides heading home to work my parents’ garden I also have a small yard in Cambridge that I’ve been working on. Hand-in-hand with gardening, I’ve started keeping a freshwater fish tank with real plants that’s been pretty fun to maintain, especially in the winter when there’s no gardening to be done outside. I also enjoy cooking – I use the guides on Serious Eats and America’s Test Kitchen to try out new things when I can. It seems like during this pandemic there’s been a huge explosion of cooking on the internet, and I’m really enjoying that. I also can’t wait till summer rolls around so I can start smoking meats again. I generally think that people of our generation need more hobbies that are not Netflix, and I’m very grateful to have found hobbies that I enjoy and can share with my friends.

Humans of Tufts Boston: Logan Schwartz, “I am interested in helping an aging population”

Humans of Tufts Boston, 9 Apr 2020

Logan Schwartz, Genetics (JAX), Second-year Ph.D. “I am interested in helping an aging population”

JH: Thank you so much for agreeing to answer some questions! What were you doing before graduate school?

LS: I started my scientific career as a summer intern at Regeneron Pharmaceuticals for three summers right after high school and through college. I worked in the VelociGene Department aimed at developing genetically modified mammalian models of gene function and disease! I attended the University of Rochester and studied Molecular Genetics and Chemistry. After completing undergrad, I was working for Dana Farber Cancer Institute and MGH as a research technician studying the functional genetics and molecular mechanisms of chronic lymphocytic leukemia and cystic fibrosis.

The Trowbridge lab

JH: What drew you to the JAX program?

LS: I was drawn to the JAX program by the opportunity to work with Dr. Jennifer Trowbridge and the novel mouse models for studying clonal hematopoiesis (CH). The Genetics program at JAX is a unique graduate program with the freedom to take courses at The Jackson Laboratory in topics ranging from systems genetics to different computational languages. I really enjoy the close and collaborative community at JAX and I am happy to be a part of it!

Dr. Trowbridge is a leader in the field of hematopoietic stem cell (HSC) research and she is fearless with respect to developing and employing the new and best techniques to address scientific questions. She is an inspiring investigator to be mentored by, having navigated herself the challenges of achieving success as a woman in science.

The Trowbridge lab hikes in Acadia

I am particularly excited to work in this field of research because I am interested in helping an aging population. With the growing population of elderly individuals worldwide, preventative strategies to reduce aging-associated diseases are urgently needed. We acquire somatic mutations in our HSCs as we age, some of which can confer a competitive advantage and cause clonal HSC expansion, known as clonal hematopoiesis (CH). This is present in 10-15% of individuals aged 70 years or older. My thesis work in the Trowbridge lab strives to identify novel mechanisms that can be used as interventions to prevent aging-associated diseases and disorders of the hematopoietic system, with a specific focus on HSCs, which are responsible for the lifelong maintenance of a functional hematopoietic system.

Riding a camel with Rebecca Brown (Genetics program) in Israel

JH: Is there anything you think is under-appreciated in the field of genetics?

LS: Genetic Diversity! Many diseases are studied by using models on a single genetic background when no two humans with the same disease are genetically identical. My lab is using genetically diverse mice to determine if inherited genetic variants increase the likelihood of developing CH and that there are population differences in clonal advantages gained by specific mutations in particular genetic and environmental contexts. CH is most commonly driven by somatic mutations in the gene encoding DNA methyltransferase (DNMT3A), so we are testing the hypothesize that variation in genetic background dictates whether DNMT3A-mutant HSCs acquire a selective advantage. The work is still in progress so we will have to wait and see!

Logan’s cat, Eugene!

JH: What do you like to do outside of lab?

LS: Outside of the lab, I enjoy hiking/exploring Acadia national park, running, painting and trivia nights, and taking care of my fifty house plants! A couple of years ago, my friend gave me my first house plant, a snake plant. He told me they were impossible to kill, and somehow I still managed to kill it. I decided to try again, and somehow I was able to keep it alive. After that, it has become a sort of obsession, although I still kill succulents from time to time. The thing I love most about having plants is how much life they can bring into your home. I also love watching them grow and change over time!

Some of Logan’s many house plants!

Humans of Tufts Boston: Noell Cho, “Representation Can Have a Broader Impact”

Humans of Tufts Boston, 12 Mar 2020

Noell Cho, Neuroscience, Second-year Ph.D. “Representation Can Have a Broader Impact”

JH: Thank you so much for taking the time to answer some questions! How did you get your start in science?

NC: My start in science harkens back to my high school on the island of Guam, when I volunteered to work at its endangered species lab under the direction of our AP Bio teacher Dr. Hauhouot Diambra-Odi. For decades, invasive species have completely destroyed Guam’s ecosystems. Of particular interest to our group was the introduced Philippine collard dove, which is threatened by the invasive Brown tree snakes. In the lab we designed experiments to learn more about existing bird migration patterns and behaviors. We delved into “field work,” which involved several camping trips on an uninhabited islet called Alupat island (approximately 200 meters off the western coast of Guam). We eventually presented the data at the International Student Science Fair in Kyoto, Japan. Unfortunately, some of Guam’s endemic bird populations, such as the Guam rail are deemed extinct in the wild and extirpated from the island. I was surprised to find that the New England Aquarium had these birds, a little piece of home right in Boston!

Cetti Bay in the southern region of Guam

JH: What drew you to neuroscience?

NC: I worked as a tech in several different labs and research areas, including cancer biology, immunology, and translational neuroscience. I worked in Clive Svendsen’s lab at Cedars-Sinai in Los Angeles, where I became involved in stem-cell transplantation studies in animal models of neurodegeneration, specifically the SOD1G93A rat model of ALS. I was fascinated that a neurodegenerative disease phenotype was able to be recapitulated in rodents harboring a mutated human ALS gene. Through these studies, I joined Gretchen Thomsen’s lab, whose particular focus was studying the link between repetitive TBI and ALS. My previous experience in immunology research motivated my investigation of selective inflammatory responses related to TBI-induced neurodegeneration. I fully credit working in the Thomsen lab as where I discovered my passion for neuroscience research.

The Thomsen lab at Cedars-Sinai. From left to right: Gretchen Thomsen (PI), Mor Alkaslasi, Patricia Haro-Lopez, Noell Cho

JH: What is your favorite technique that you use in lab?

NC: I’ve become an apprentice of electrophysiology since I joined the Moss laboratory here at Tufts. Tarek Deeb has been profound in imparting his knowledge of ephys and its many applications for neuroscience research. It’s intriguing to use the patch-clamp technique to measure the electrical properties and functional activity of neurons. My research experience has been primarily focused on looking at biochemical changes in neurological disease, so it has been refreshing to learn a new technique and observe electrophysiological changes in the brain. I remember that first moment, not too long ago actually, when I patched onto hippocampal neurons in mouse slices and observing action potential firing patterns. Seeing those spikes is so satisfying!

Members of the Moss lab representing at Relays

JH: Have you been following any fascinating new scientific developments or controversies?

NC: More recently, I’m trying to stay updated on new ephys systems in vivo and ex vivo. There are so many cool videos and photos that pop up on my feed of some of the most insane multipatch ephys rigs. Ed Boyden’s group has made tremendous advances in automated in vivo multipatch recordings. Automated multipatch rigs not only allow for ease of recording multiple neurons simultaneously, but also provide large-scale mapping of brain circuits. Multipatch clamp recordings also reveal more about connectivity between specific cell types in the brain, and automation provides a huge advantage in terms of time and feasibility. It’s always exciting to see the latest innovations that come out from the Boyden lab, but also it seems that robots are an inevitable part of scientific developments.

Noell presenting her repetitive TBI model at her first SFN!

JH: What do you do outside of lab?

NC: Because I’m a Boston transplant from Los Angeles, it was important to me to foster an environment at school that would feel like home. Thankfully, student organizations such as GWiSE and SPINES provided just that. Currently, I am the GWiSE secretary and operate media and communications for our group. As a first-year, I enjoyed the GWiSE coffee & conversations events that feature a woman in STEM and learning of their school and career experiences. I am so thankful for my former PI, mentor and friend, Gretchen Thomsen, who believed in me and is one of the reasons why I am in grad school today. I definitely benefit from the efforts of GWiSE and SPINES that provide programming surrounding diversity and inclusion, because ultimately representation can have a broader impact. You can follow GWiSE and SPINES on Twitter (@TuftsGwise and @TuftsSPINES)!

Checking out the East Coast surf in Montauk, NY

Humans of Tufts Boston: Uri Bulow, “Archaea Don’t Get Enough Love”

Humans of Tufts Boston, 13 February 2020

Uri Bulow, Microbiology, Third-year Ph.D. Student (Fifth-year M.D./Ph.D.): “Archaea Don’t Get Enough Love”

JH: Thank you so much for taking the time to answer some questions! So what were you doing before graduate school?

UB: I worked as a tech in a lab in Boulder for two years after finishing my degree in molecular biology. I was in a molecular cardiology lab, but I ended up working on a transduction system and found out that I enjoyed thinking about viruses more than myosin. I also loved the microbiology classes I took (thank you, Norman Pace and Shelley Copley), so when I came to Tufts I decided to join the microbiology department. Now I work on Lassa virus, which is a hemorrhagic fever virus. Hemorrhagic fever viruses (like Lassa or Ebola) are characterized by high fevers, multi-system organ failure, and hemorrhaging from mucous membranes (though this is less common than the name would suggest). I really enjoy being able to study such a simple and elegant system. Lassa only has 4 genes, any organism with more than that is just showing off!

JH: Getting an MD/PhD requires a great deal of dedication and time. Why did you go for an MD/PhD, and did you decide you wanted to go into medicine or science first?

UB: I always knew I wanted to be a scientist, and I figured that if a PhD takes 6 years and an MD/PhD takes 8, I might as well throw in the free MD since it would be interesting and it’s only an additional 2 years. At the time I didn’t really know what residency was, or that MD training doesn’t end when you graduate. Oops. Since starting this program I’ve discovered that I actually enjoy medicine, and making a career of both science and medicine sounds pretty ideal to me.

JH: Are there any major controversies in your field right now? What are they, and what are your thoughts?

UB: I know that this doesn’t need to be said to any GSBS students, but people need to get over this antivaxxer nonsense that’s threatening the health of our country. Vaccines are arguably the single greatest healthcare achievement we have ever made as a species, and watching them get dismissed by parents who would rather use essential oils and spells to ward off evil spirits is incredibly frustrating. The CDC actually estimates that 2.5 million lives are saved every year due to vaccination.*

JH: Is there anything you think is under-appreciated in microbiology (or medicine, if you prefer) as a whole?

UB: I think that archaea don’t get enough love. They’re a whole separate domain of life, comparable to bacteria or eukaryotes, and we know so little about those adorable little weirdos. Did you know that their plasma membranes aren’t bilayers, and that they use ether-linked lipids instead of ester-linked lipids? They live in every known biome on Earth, even inside our own GI tract, yet we know so little about them. What are they up to?

JH: What do you like to do outside of lab?

UB: Lately I’ve been really enjoying the Berklee student concerts. They’re super cheap and those kids are super talented. Shout-out to Mike Thorsen for introducing me to them. My favorite thing to do is to experiment in the kitchen. I recently dry-aged a beef striploin for 90 days, made my own lox, smoked some cheese, and I’m currently making pineapple vinegar. I also really enjoy marathoning the Lord of the Rings with friends, photoshopping my PI’s face into funny pictures, growing super-hot peppers, and canceling plans so I can stay home and read.

The famous lox

*Uri kindly provided this further evidence for the benefits of vaccines from an economic standpoint: “A recent economic analysis of 10 vaccines for 94 low- and middle-income countries estimated that an investment of $34 billion for the immunization programs resulted in savings of $586 billion in reducing costs of illness and $1.53 trillion when broader economic benefits were included.” Orenstein and Ahmed. Proc Natl Acad Sci U S A. 2017 Apr 18. 114(16):4031-4033.

Humans of Tufts Boston: Léa Gaucherand, “I Fell in love with research”

Humans of Tufts Boston, 22 October 2019

Léa Gaucherand, Microbiology, Third-year Ph.D. Student: “I Fell in Love with Research”

JH: Thank you so much for taking the time to do this! To begin with, where did you grow up?

LG:I grew up in the North East of France, in a city called Nancy in the Lorraine region. There are many differences between life in France and here; university is very cheap, like 100 – 200 euros [110 – 220 USD] a year. Also, the Ph.D. system is different because it’s only 3 years (you do it after your Master’s). You don’t have rotations, you just apply to one project in one lab and for funding from the government or other agencies.

JH: What were you doing before graduate school?

LG: I actually have a Master’s degree in Health and Drug Engineering and a multidisciplinary Engineering degree (equivalent to a Master’s but it is a weird concept that only exists in France where you do a little bit of everything). As part of my studies I did an internship in bioengineering research at the Infectious Disease Research Institute in Seattle and I fell in love with research (and with someone in Seattle). I went back to Seattle after graduating and started as a volunteer in Dr. Tom Wight’s lab at the Benaroya Research Institute. I then got a technician position in the same institute in Dr. Adam Lacy-Hulbert’s lab, and after two years there I moved to Boston for grad school!

JH: When you first moved to Seattle, did you encounter any culture shock?

LG: I had actually already lived in San Francisco for 6 months for another internship one year before I moved to Seattle, and I had a pen pal from Pennsylvania that I visited for a week in high school. I don’t think I really had any culture shock, it was more the excitement of being somewhere new and fully independent.

JH: How did you first become interested in pursuing science as a career? Was there anything in particular that steered you towards microbiology?

LG: My interest actually came pretty late. I was always good at maths and just liked thinking about science in general, but I had no idea whatsoever what I wanted to do. That’s why I went to the French engineering school I mentioned earlier, to still have a broad science background without deciding yet what I wanted to do. It was only there that I realized I missed learning about chemistry, and the only class I really enjoyed was about human physiology and bioengineering. I took extra classes during my last year to have a more specialized degree, and did the internship [in Seattle] that really opened my eyes about what research was and how much I enjoyed it. It’s only once I was a technician that I worked on viruses. I thought they were the coolest thing so I wanted to learn more about them, and about how they interact and evolve with the host. I applied to a bunch of programs, most of them more virology-focused than Tufts, but I really enjoyed my interview at Tufts Micro. It just felt right.

The Gaglia Lab

JH: What do you like to do outside of lab?

LG: Outside the lab I like to play volleyball (we have a great team at Tufts Micro!). I say it’s a Micro volleyball team but it’s not official at all. Another Micro student, Allison (in the Camilli lab), has a net so we go play with a few people from Micro (and other programs) at the Boston Common in the summer. Everyone is welcome and it would actually be great if we had more players! I also like to watch intellectual movies and travel. My husband showed me two intellectual movies in the past few weeks that I really enjoyed: Burning by director Chang-dong Lee and Shoplifters by director Hirokazu Koreeda. Unfortunately, I don’t have time to travel that much (apart from going back to France twice a year). The last big trip I took was right before moving to Boston, to Panama and Hawaii.

Summer volleyball on the Common

Humans of Sackler: Becca Silver, “Enthusiasm was contagious (no pun intended)”

 

I’m Ila Anand, a fifth-year student in the Microbiology program. I’ve recently taken over the “Humans of Sackler” portion of the Newsletter, which was originally pioneered by Andrew Hooper. In this issue I had the honor of getting to know our GSC president, Rebecca Silver, better known as “Becca.” It was a delight sitting down with this die-hard Bruins fan and discussing a variety of topics—from finding out she loves butter pecan ice cream and Figaro’s to discovering how she first broke into science. I hope you enjoy our conversation and are better acquainted with our GSC president!

IA: Hi Becca! Let’s start with what were you doing before you started graduate school?

RS: I was having a good time in college at the University of Maine in Orono! Besides the academics, my favorite part of college was having my friends nearby and being able to spend time with them whenever I wanted. I had a pretty diverse group of friends in college and I still keep in touch with them. I’m originally from Portland, Maine and spending time with close friends was also a big part of my childhood. My favorite memories are from Fourth of July when my friends and I would hang out at a lake house. The lifestyle in Maine is generally much more slow-paced. That is actually one of the biggest differences I noticed when I started grad school—there’s much more of a “rush” in Boston compared to Portland, where the people are more laid-back.

IA: Sounds like there are definitely some cultural differences between the cities. Where else have you traveled to in the past?

RS: I’ve mostly traveled on the East coast. I’ve visited the majority of the North East and I’ve also visited Georgia and Florida. I’ve actually never traveled to the West Coast but if I had the opportunity to attend a conference I would totally go. I also really want to ski in the mountains of Colorado at some point in the future. Outside of the U.S. I’ve traveled to Canada and Bermuda. I visited Bermuda when I was fairly young (ten years old) and I vividly remember that time period because two weeks before the vacation I had pneumonia. At the time it was awful because I missed school and was trying to recover (I had a lot of Pediasure!), but in the end, because I also went on vacation, I ultimately took a month off of school and my teachers didn’t assign me any extra homework. You could say that was my first introduction to the infectious disease field!

 

IA: That does sound awful! So when did you actually become interested in pursuing research and studying science?

RS: Well, I was a bioengineer back in college and honestly pursuing research was a decision I made on the whim. I took an immunology elective class my junior year of college and quickly realized I really like immunology. The class was much more interesting than any of my bioengineering classes- the lectures were awe-inspiring! The professor really emphasized infectious disease clinical examples like super gross rashes all over the body, etc. The professor was so excited and his enthusiasm was contagious (no pun intended). After taking the class, that summer I took the GRE and applied for grad school the fall of my senior year. It was literally a 6-month turnaround from being a bioengineer to wanting to be an immunologist!

 

IA: What was your first experience working in a lab?

RS: My first experience doing lab work was during a Co-Op internship at Idexx, which is a veterinary biotech in Portland, ME. I interned at Idexx during the summer going into my junior year of college. I was involved in developing a lateral flow assay that is similar to an ELISA and this rapid immunoassay detected digging worms in infested dog feces. It was a triple detection assay so it was able to detect whipworm, roundworm, and hookworm. My internship involved developing positive and negative controls for the assay. My boss at Idexx played on the same recreational hockey team that I did in Maine and she was a Tufts alumnus. Later, when I decided I wanted to go to grad school, I reached out to her for a reference and she’s the one who influenced me to apply to and attend Tufts Sackler.

IA: That’s really neat that you play rec-hockey. How did you get into that? What else do you like to do outside of bench research?

RS: I picked up hockey in high school when I was fourteen. My friend asked me to try out for the school team because they needed more people and now it’s one my favorite activities to do. I currently play on a Greater Boston rec-team called South Shore Women’s Hockey League. We have a lot of fun! In addition to hockey, I like to run. I run with a group in Jamaica Plains called the Forest Hill Runners and my favorite spot to run is in Peters Hill in the Harvard Arboretum. It has the best view of the whole city, in my opinion. I also like to cook and play video games—specifically strategy games, like Civilization 6. As GSC president, I’ve also been heavily involved in planning the Sackler relays. Our plans are kind of top secret but I can tell you that this year we’re going to have relays in June rather than July and we’re going to have an awesome raffle. Of course, my favorite part about relays is winning- go Immunogenetics!

Humans of Sackler: Patrick Davis, “I’ve been Accused of being a Science Robot”

Humans of Sackler, 23 March 2017

Patrick Davis, Neuroscience, Fifth-Year M.D./Ph.D. Student: “I’ve been Accused of being a Science Robot”

For this issue of Humans of Sackler, I had the opportunity to sit down with Patrick Davis, an M.D./Ph.D. student in the Neuroscience program. Although I see medical students coming and going around Sackler every day, I confess I haven’t gotten to know many of them – or much at all about the medical school curriculum. So it was a great pleasure to learn more about this from somebody who is as passionate about medicine as he is about science research; Patrick and I had a particularly engrossing conversation about the differences between these two kinds of higher education, and I hope you, dear reader, enjoy and benefit from it as much as I did!

 

Young Pat with the Chestnut Hill Academy Theoretical Physics Group

AH: How did you become interested in studying science?

PD: I had a physics teacher in 11th and 12th grade – Marty Baumberger – who was just the best teacher ever. He got me so into physics that I started a Theoretical Physics group at Chestnut Hill Academy… I went to Brown University as a physics major. I loved the open curriculum, but I was a terrible student. I didn’t do well my first year, so I switched to an economics major for about a year, and that was completely unfulfilling. Eventually I came to my senses and switched to biology… The thing about Brown: it’s chaos. There are no required classes, so you just mix and match and do whatever. There are requirements for your major, but you could theoretically never take a math class if you never wanted to. What happened to me was the best-case scenario: the first year and a half made me a more dedicated student. I learned that if I’m not doing something I really want to do then I’m going to be lazy, and if I don’t work hard then I’m not going to do well.

 

At a Macklis Lab get-together, chatting with friend and mentor Alex Poulopoulos (left)

AH: What was your first experience with neuroscience research?

PD: When I graduated from Brown, I didn’t know right away that I wanted to do med school or neuroscience. I ended up working at Jeff Macklis’s lab at Mass General Hospital for two years after college, and that was my first real exposure to neuroscience. Jeff made his name with a series of studies on induction of neurogenesis in the neocortex. I met Alex Poulopoulos there, who has been a mentor ever since, and a very good friend. I would credit Alex almost entirely with piquing my interest in neuroscience, but also with my development as a scientist. I love to come up with an idea, test it, go through the whole process myself, interpret my own data, talk to other people about their data – I like the actual scientific process. Alex just started his own lab at University of Maryland School of Medicine; anybody reading this, please apply to his lab! You could not ask for a better person to work for. He’s interested in how neural circuits self-organize, which is extremely interesting to me as well.

 

With pals from Brown University

AH: Why did you choose the M.D./Ph.D. path and how have your medical and scientific training differed?

PD: I could never be just an M.D. because I love science too much. The fundamental quality of a scientist is curiosity; medicine is more like service and helping people, curiosity about the people themselves, empathy. The preclinical years are a lot of memorization, but once you get into the hospital, it’s more like an apprenticeship. You’re learning how to do the day-to-day things that a doctor does: how to walk through clinical decision-making, interview a patient, present that information to other doctors, how to work with your hands if you’re doing a surgery rotation… Because medicine is an applied science, the goal there is all oriented around the health of the patient; I don’t think that’s really what science is about. For a long time, medicine has been done in a very parochial way: people in this hospital do it this way, people in another hospital do it another way. Evidence-based medicine still gets a lot of pushback. Take stenting for example: doing a coronary artery stent for someone with angina. About half of the stents in this country are done for stable angina – chest pain when you exercise, but not an acute threat to your health – and it’s now been shown over and over again that that is no better, and possibly worse, than just giving them statins and blood pressure reduction medication and telling them to eat their vegetables and exercise a little bit. It’s because doctors think in terms of, ‘I see it happen, it intuitively makes a lot more sense to me, so it must be this.’ Of course the lines are blurred in real life, but a true scientist would say, ‘We have to trust the evidence, why don’t we look at what’s causing the increased risk of doing the stent, or why do statins work?’ The curiosity that is absolutely necessary to be a good scientist is not necessary to be a good doctor… The types of mind that are selected for by these two professions are almost non-overlapping, they’re completely different.

 

Even science robots enjoy a night on the town every now and then

AH: What do you like to do when you’re not studying medicine or neuroscience, and how do you find the time and energy to do it all?

PD: I love to teach, I really like being in the didactic role and seeing people learn and discover things for themselves. I tutor for the MCAT, I used to tutor for the SAT, I’ve volunteered for things like middle school science fair mentoring and the Brain Bee. These kids in the Brain Bee were extremely impressive; they knew more facts for this test than I would have! Thomas Papouin and I also started a class trying to teach grad students the basics of the scientific method. There’s a whole rich history of how to think formally and scientifically; and the more aware you are of it and the more you practice it – like by applying these things to your own rotation project or qualifying exam – the better you get at it. The notion that, by just reading papers, this will happen – for some people, maybe it will, but the purpose of the program is to maximize the probability of this happening for everybody… I’ve been accused of being a science robot: the joke between Alex Jones and me is that when I get home, I have a scotch and read PubMed… The M.D./Ph.D.s that I’ve spoken to, the ones that succeed, are recharging one half of their brain while the other one works. Like a shark, like a science shark!

 

Relaxing by a picturesque mountain lake in the Cordillera Blanca, Peru

AH: Have you had many chances to travel outside of the U.S.?

PD: I’ve traveled through Europe a bit, I’ve been to Peru, Brazil… I was in Berlin at one point, and I decided to just hop on a train and go to Prague. I spent two full days and a night there, and it was awesome. Most of the people spoke English at tourist-type places, but it was fun to walk around, take pictures, be completely by myself… I had a Cormac McCarthy book called “All the Pretty Horses”, and it was nice just being on the train, reading or watching the sites, then walking around the city and going to a café for a coffee or beer. I don’t know much else about Prague, but aesthetically, I can’t imagine a prettier city. Part of why I enjoyed the city so much was because I didn’t expect it to be that way: of course when you go to Rome, you know that one of the greatest civilizations existed here and that every step you take is rich with history, but I didn’t expect this in Prague.

 

Enthusiastically sharing data at the Society for Neuroscience annual meeting

AH: What topic have you studied for your thesis work?

PD: Under Leon Reijmers’ mentorship, I’m trying to figure out how ‘extinction learning’ happens in the brain: it’s a medically-relevant type of learning that underlies treatment for psychiatric disorders like PTSD. In extinction learning, the patient repeatedly gets exposed to the thing they’re afraid of, you gradually increase the ‘stimulus intensity’, and they learn that it’s safe. So for example, if they’re afraid of spiders, you would show them a picture of a spider at first, then maybe have them in a room where there’s a spider in a corner, then work your way up to having them handle a spider. What I’ve found is that there’s a particular cell type in the amygdala – the parvalbumin interneuron – which acts a critical hub for this kind of learning: if you silence these cells, then you shut down the process of extinction learning. Now I’m using that finding as a jumping-off point to really figure out what’s going on. I’m manipulating parvalbumin interneurons with different frequencies of stimulation and seeing how the amygdala – and the rest of the brain – responds to that. It looks like I can ‘toggle’ the fear state up or down just by controlling this specific type of neuron!

 

Contemplating the mysteries of the universe

AH: Where do you see the field of neuroscience heading in the near future?

PD: I think that we have tools in neuroscience that 15 years ago, you couldn’t have even fathomed. Not just optogenetics, but recording techniques, chemogenetics, optical electrophysiology, simultaneous local field potentials with single units, closed loop systems… The engineers like Ed Boyden have done us a great favor. But now it’s time for us to step up. I think that in the next 2, 5, 10, 15 years there are going to be many, many discoveries that are really going to blow things open. Once we fall out of love with the mere application of modern tools to hypotheses we already kind of assumed to be true, then we’re going to ask the question: how? You have to record neurons’ endogenous activity, then do experiments that are really informative about what’s going on. In neuroscience, because we have these techniques, we can start asking this kind of question.

Humans of Sackler: Nafis Hasan, “I Refused Determinism”

Humans of Sackler, 30 January 2017

Nafis Hasan, Cell, Molecular & Developmental Biology, Fourth-Year Student: “I Refused Determinism”

This month I present, for your reading pleasure, excerpts from my interview with Nafis Hasan from CMDB. Nafis and I had a remarkably wide-ranging conversation covering existential philosophy, cultural differences between Bangladesh and the US, the exquisite symmetry between ecology and cell biology, and current controversies in carcinogenesis research. I can only hope to capture in the space below a mere whisper of his deeply-considered intellectual convictions and passion for social justice. Fortunately, Nafis has also authored an editorial on Science Activism in this very issue, and I strongly urge you, dear reader, to check that out next!

 

Having a grand time in Dhaka
Having a grand time in Dhaka

AH: Where did you grow up?

NH: I grew up in the house that my father and his brothers built in Dhaka, Bangladesh, and moved to the U.S. when I was 18. Most of my dad’s siblings and their families lived with us in Dhaka. As kids, we didn’t really have the notion of “privacy” for the longest time: the elders would each get a room and the kids would sleep in the living room on a big mattress. My cousins and I would all get into trouble at the same time… it was fun!

 

On the road with college friends
On the road with college friends

AH: Have you had any opportunities to travel around the States?

NH: For F1 visa (student visa) holders, you have a 3-month window where you have to find a job or get into school. After graduating from Lafayette College [in Easton, Pennsylvania], I thought, “If I have to leave the country, I might as well see it.” So when one of my friends said, “Let’s do a road trip,” I said “Let’s do it!” We started from Pennsylvania, went down to Virginia, our first stop was Shenandoah – I had actually never been camping before that, it was all a very new experience. We had two American kids, a Colombian kid, and a kid from South Africa… It was very liberating, and I started to see the country as it really is. At the same time, on the road, I was interviewing for jobs. I remember doing a job interview [by video phone] at a McDonalds in Idaho. I borrowed a shirt from one of my friends who dresses nicer than I do, since the interviewer could only see the top half of me… Over the course of two months, I think I applied to 200 jobs. Finally, I ended up getting a research tech job at Thomas Jefferson University in Philly.

 

Basking in the beauty of nature at Yellowstone
Basking in the beauty of nature at Yellowstone

AH: What was it like adjusting to American culture?

NH: When I came to America, I had no idea what to expect, I had only heard things from my cousins who came here for college and what was on TV. One thing that I had in my mind was that I was going to try and meet as many people of different nationalities as I can. But there was a big cultural divide, how they grew up versus how I grew up. I think the road trip really helped me to understand the diversity of American people and especially during these times when people are so polarized, I reach out to that experience. We grew up seeing this version of America as the land of opportunity, the land of freedom, but America is not the government, is not their foreign policy, is not the consumerism that has taken over the world… America is more about the people that you meet here, and that’s how I see the country. America encapsulates the dichotomy of homogeneity versus heterogeneity, and I think that’s so beautiful.

 

The scholar/activist as a young man
The scholar/activist as a young man

AH: When did you begin to discover your interest in biology research?

NH: In Bangladesh I went to a private school that taught everything in English. The division of sciences starts in 7th grade, and biology was definitely the most interesting to me. At the same time, I was caught up in the process of deconstructing my religious identity, because I was reading biology which has hard facts about how your body works, which calls into question how life was created… I found that more fascinating than having a set answer imposed by some superior being.

 

Positive work environment!
Positive work environment!

AH: How did you choose your field of study for grad school, and why is it so interesting?

NH: I started reading a lot of scientific nonfiction, presenting cancer as a very complex biological phenomenon, which was fascinating to me. I also had a solid foundation in breast cancer by the time I applied for grad school and I wanted to pursue that… I had seen lots of tumors, but no mammary glands. The more I learn about the mammary gland, the more I am fascinated by it. It develops throughout life: initially it’s just a branched structure that looks like sticks; when you get pregnant, it almost flowers, with grape-like clusters that come up through alveologenesis and these alveoli then revert back to the branched structure after weaning. It’s comparable to how trees shed leaves in the Fall, except in reverse: this course of nature – the seasons that you see – the same dynamic is there in animal tissue. And all of this is happening through the lifetime, after the majority of the organs are already fully developed!

 

100 miles?!
First Century – Repping Sackler at 2015 Tufts Century Ride

AH: What is one of the big challenges or controversies in your field at the moment?

NH: Traditionally, cell culture is done in two dimensions, on plates that are usually plastic – and plastic is not a natural substrate for cells to grow on, so you can’t recapitulate the same 3D environment where the cells are growing inside an organism. You can either try to mimic the natural environment as much as possible, or try to make a scaffold that is biocompatible… Cells need to be able to manipulate their environment, just as the environment should be able to provide them with physical or chemical cues to make them grow or organize in certain ways. Our lab has a very organic approach to it: we do 3D cultures in type 1 collagen, the predominant structural protein found in the mammary gland stroma. We believe that “organicism is greater than reductionism.” This is where we’re at odds with a lot of others in the cancer field, where reductionism is still the predominant philosophy. And we’re not saying it’s bad! It’s just insufficient to explain carcinogenesis.

Humans of Sackler: Stacie Clark, “Full of Surprises”

Humans of Sackler, 1 December 2016

Stacie Clark, Molecular Microbiology, Third-Year Student: “Full of Surprises”

For this issue of Humans of Sackler, I had the chance to chat with Stacie Clark from the Microbiology program. As someone who mostly socializes within Neuroscience, it’s a real privilege for me to meet students from other programs and learn about some of the incredible, borderline-science-fiction work that’s going on right under my nose here at Sackler! Equally striking, I’ve found, is the treasure trove of unique passions and fascinating life experiences that lie just below the surface of our fellow students when we really get to talking. I’m grateful to Stacie for sharing a few of hers, and hope that you, dear reader, enjoy our conversation!

 

001
Hiking through Glacier National Park, Montana

AH: When did you realize that you wanted to pursue a career in science?

SC: My parents told me they always knew I’d end up in science. From the moment I could walk, I was outside digging for beetles and worms and building terrariums. I was in the honors science program in high school, and I did a year-long project on hand sanitizer and bacterial survival. I was working in a lab as a high school student, and realized I really liked doing that. I think I was born for science, and my parents were super-supportive. When I was growing up, we went hiking all the time, they took us to the EcoTarium in Worcester, and we were members at the Museum of Science and Aquarium. So I was always exposed to all sorts of science.

 

002
Swimming at a waterfall in El Yunque rainforest, Puerto Rico

 AH: What places have you traveled to outside of Massachusetts?

SC: I studied abroad in Puerto Rico. Worcester Polytechnic Institute does this differently: they call it the IQP, Interactive Qualifying Project. The point of this project is to teach you how to work effectively in groups and communicate with people outside the university. I worked in the rainforest in Puerto Rico, and we did a project evaluating stream crossings. We wanted to look at how their bridges were affecting stream flow and water quality, so we got to hike all through the [El Yunque] rainforest and evaluate all these different stream crossings. We got to see parts of the rainforest that no one gets to see!

 

003
With Pablo the capuchin monkey in Costa Rica

 AH: What did you do between graduating from WPI and starting your Ph.D. at Sackler?

SC: Before I started grad school, I had always wanted to work with exotic animals. So I literally just Googled ‘volunteer experience in Costa Rica’ and this small remote place in Costa Rica popped up. I booked a two-week trip, went by myself back-packing in Costa Rica, and volunteered at an animal rehabilitation center. It was quite an adjustment: I was on a mountainside in southern Costa Rica, and it got pitch-black at 6 o’clock at night. I would go into the rehabilitation center, clean the cages, prep all the food, and then feed and play with the animals. The monkeys were my favorite, and there was also an anteater. His name was Gomer; if you went into his cage and just yelled out ‘Hey Gomer!’ he’d come crawling out, and he loved being held. We’d do enrichment activities for some of them too – so with the anteater, I would walk with him out in the jungle and let him go searching for termites and ants on his own, and then I’d go bring him back to his cage. I think everyone should go on at least one trip by themselves, because you learn a lot about yourself and it’s just a good experience!

 

004
At the beach with Kid Rock

AH: What do you like to do when you’re not working in the lab?

SC: I volunteer at the animal shelter in Quincy; I’ve been doing that every Monday for four years. I take the dogs out for walks, play with them, cuddle with them if they want to… They only get to go outside twice a day, that’s the only time they get to really play with people. I understand that work-life balance is really important to your mental health, so volunteering on Mondays is the one thing that I won’t let grad school take away from me. It’s something that I do for me that I enjoy – and I’m also a big dog person. 

 

005
Group photo with the Leong Lab (middle row, second from right)

 AH: There are so many disciplines within biology – what got you interested in studying bacteria specifically?

SC: I’ve always been fascinated that an organism so small can have such a large impact on humans – that still blows my mind! They’re incredible organisms that can mimic the proteins we have, which I find pretty amazing. We’re full of bacteria, they do a lot for us – and the microbiota is a huge field now. Everyone is fascinated in studying microbiota and the impact they have on our health in general. 

 

006
Out on the town with friends

 AH: What particular species of bacteria do you study, and what makes it so interesting?

SC: Yersinia pseudotuberculosis is a model pathogen that we use to study community behavior of bacteria within its host. Yersinia can establish a distinct niche within the spleen of a mouse, and once it forms a microcolony, it can replicate to high numbers despite the presence of the immune system. You get a recruitment of innate immune cells to the site of infection, triggering a response in the bacteria to create specialized populations within that distinct cluster; I always thought that was cool, the response between the bacteria and the host cells.