All posts by Judith M. Hollander

Racist Science: Books on How We Got Here

When I originally began writing this – my next article for the Insight – it was going to be about things to read during a pandemic. George Floyd hadn’t been murdered yet. Protests hadn’t begun. And originally, I was going to put an extra section at the beginning of my article on racism in science and medicine.

That’s not enough; this topic really needs its own article and more. Speaking here as a white person, I can’t stress enough how critical it is for people like me to self-educate and do some thorough self-examination, and this article meant to be a point from which people can start.

Racism is endemic in our society, and it’s endemic in our sciences. It’s something that the scientific community has passively accepted and ignored for years, and it’s high past time to end that. If you’re new to this, welcome! Reading about racism is a great way to open your mind and determine where your own biases lie. It’s also a great way to keep yourself moving and thinking if you feel you’ve hit a standstill in your progress on this important and evolving topic. Identifying and uprooting biases and racism is a continuous learning process, one that I’m committed to being better at.

The title of each book on this list is linked to The Frugal Bookstore, Boston’s only Black-owned independent bookstore, where possible. Please join me in picking one (or more!) to read, and let’s start educating ourselves and doing better!

The Immortal Life of Henrietta Lacks (Rebecca Skloot)

The scientist that obtained Henrietta’s cells did so without her consent. More than 20 years after her death in 1951, her family finally learned the truth: that scientists had been using her cells for years, that people had made a lot of money from discoveries using those cells, and that they themselves never saw any of the profits.

Most students in the biological sciences are familiar with HeLa cells. Here, Skloot presents the reader with the story of Henrietta Lacks herself, as well as the results of race exploitation in scientific discovery. If you have a few hours to spare, check out the 2017 movie adaptation, featuring Renée Elise Goldsberry (of Hamilton fame) as Henrietta Lacks and Oprah Winfrey as Deborah Lacks.

Medical Apartheid: The Dark History of Medical Experimentation on Black Americans from Colonial Times to the Present (Harriet A. Washington)

The story of Henrietta Lacks is the tip of the iceberg when it comes to the history of exploiting African Americans for medical and scientific progress. It starts long before that, at least as far back as the 17th century. Medical Apartheid presents the first comprehensive history of medical experimentation on African Americans.

This is going to be an uncomfortable book to read. What we now think of as racism in the medical system – racial disparities in access to health care, morbidity, and mortality rates – began with horrific and nonconsensual experiments (a quick Google search on James Marion Sims, the so-called “father of modern gynecology” should do the trick, for anyone curious). And while we have made much progress in that regard, there is so much more left to be done.

Already read this one? Check out one of Washington’s other books on the intersection of race and medicine: A Terrible Thing to Waste details environmental racism and its contribution to racial disparities in disease.

Superior: The Return of Race Science (Angela Saini)

For many white people, the story of overt racism in science may end with the end of World War II and the Holocaust, when people realized the consequences (putting it quite lightly) of the mass implementation of eugenics. But science did not truly let go of racism. Society hadn’t (and still hasn’t) abandoned the idea. It just took on an even more insidious nature.

Superior covers racism throughout known history. It is a book exposing the way scientists cling to an idea of race as a biological truth, as something that is encoded in our genes. This is a book that reveals the propensity of science to look for genetic differences in races as a convenient way of explaining away a difference in disease risk, poverty, and other things, when so much more goes into an individual than genetics.

The Mismeasure of Man (Stephen Jay Gould)

And there is much more to an individual than genetics. Published in 1981, The Mismeasure of Man systematically dismantles the idea that differences between groups of people (such as races) comes from genetics, a malpractice often referred to as biological determinism.

While Gould received great reviews in the popular press, the scientific community gave him the cold shoulder with claims of historical inaccuracy and political bias.

We all have a lot of work ahead of us to successfully strip our communities of racism. The above works touch only on the highly visible aspects of racism in science; microaggressions and other vastly overlooked racist practices are yet another area in which the sciences need to get a whole lot smarter.  It’s not going to happen overnight, but it does need to happen. If you’re looking for more resources, please consult this #STEMforBLM Resource List. It contains more books on racism in science, as well as links to general resource lists (which contain titles like How to Be an Antiracist by Ibram X. Kendi, White Fragility by Robin J. Diangelo, and Between the World and Me by Ta-Nehisi Coates).

Books may not be everyone’s speed, but there are plenty of podcasts to check out if that’s more your style. There are two episodes of NPR’s Short Wave, a podcast on the science behind various news headlines, that might be particularly interesting. “Coronavirus and Racism are Dual Public Health Emergencies” details how systemic racism causes health disparities, such as during the Coronavirus pandemic. In “Science Is for Everyone – Until It’s Not” Brandon Taylor tells his heartbreaking story of why he had to leave science – because of how his fellow scientists treated him, as a Black person.

Which book will you be reading? Have you read any of these, and if so, what did you think?

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!

How Do You Figure?: Graphic Design Software For Scientists

As I sit at home writing what will (hopefully) be my very first first-author manuscript, I began to wonder how scientists go about making their figures for a paper. Like many things in academia, it was probably going to be lab-specific: someone would have started using a particular software, taught the next graduate student how to use it before they left, and that student would teach the next. And so on, and so forth.

With this in mind, I took to Twitter to ask students (and @AcademicChatter), how, exactly, were they figuring?

BioRender (@vanesque89, @Nicole_Paulk)

Price: Free for personal/educational (limited) use, various paid plans
Platform: Web-based

Think of BioRender as your scientific clip-art library. BioRender has a collection of over 20,000 different icons covering more than 30 fields of the life sciences. The colors of each icon can be customized, and the drag-and-drop functionality makes figure creation very quick. Even better, there’s nothing to download! It’s right there in your browser, ready whenever and wherever you are working.

CorelDraw (@AdemaRibic)

Price: $249/year or $499 (one-time purchase)*
Platform: Windows, Mac

Originating in Ottawa, Canada, CorelDRAW touts vector illustration, layout, photo editing, and typography tools. It works on both Windows and MacOS.

*Editor’s note: Corel Education Edition is a one-time payment of $109 (thanks to Adema Ribić for this correction!)

Adobe Photoshop and Illustrator (@Nicole_Paulk)

Price: $20/month for the first year, $30/month after that (student pricing, includes all Adobe apps)
Platform: Windows, Mac, some apps available for iOS and Android

Almost everyone is familiar, at this point, with Adobe Creative Cloud, Adobe’s suite of software for designing things (literally, any and all of the things). Photoshop is useful for raw images (such as overlaying fluorescent images and stitching together microscope images). Illustrator, in contrast, is for creating vector art and illustrations, but it’s also useful for aligning the different panels for a cohesive figure. The most updated version of Illustrator seems to have kept this in mind: the Adobe website specifically mentions its use in making infographics, including the ability to edit data through a charts function.

GraphPad Prism
Price: $108/year (student pricing)
Platform: Windows, Mac

Prism is less for making figures and more for making graphs, but it’s worth mentioning here since many of us include graphs in our figures. In Prism 8, you can draw lines or brackets on graphs to indicate significance. A centered text box is automatically included for your asterisks! These graphs can be exported as images and then arranged easily in another application as panels of a figure.

Affinity Photo and Designer (@SimonWad)
Price: $50 per app, one-time purchase
Platform: Windows, Mac, iPad

These are popular alternatives to Adobe Photoshop and Illustrator. One of the major complaints about Adobe was its movement to a cloud-based subscription model. Affinity uses a one-time purchase model, and is also considerably more affordable. The company also has an alternative to Adobe InDesign (called Publisher).

This is by no means an exhaustive list of all the possible software you could use to make a figure. Many people swear by PowerPoint as their favorite way of assembling figures. Here are a few other pieces of software to check out that are free to all:

Gimp
Price: Free!
Platform: Windows, Mac, Linux

Gimp is a high-quality raster image editor. Think of this as the free version of Photoshop. It can do a lot of the same things, but it’s missing some of the advanced tools, such as using adjustment layers to non-destructively edit images.

Inkscape
Price: Free!
Platform: Windows, Mac, Linux

Inkscape is a vector graphics editor with shapes, layers, text on paths, and the ability to align and distribute objects. If you’re looking for something like Illustrator to handle vector graphics but don’t want to shell out the money, this is a great option!

Scribus
Price: Free!
Platform: Windows, Mac, Linux

Scribus is an open-source alternative to Adobe InDesign. It has many of the same features as InDesign, but unfortunately can’t open InDesign files.

Thank you to everyone who responded, and happy figuring!

Cover image by Mudassar Iqbal from Pixabay

Sources:
biorender.com
coreldraw.com
adobe.com/products/photoshop.html
adobe.com/products/illustrator.html
graphpad.com
affinity.serif.com
products.office.com
gimp.org
digitaltrends.com/photography/gimp-vs-photoshop/
inkscape.org
scribus.net

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.

New Year, New You: A Guide to Making Your Goals S.M.A.R.T.

Happy New Year, everyone!

There’s a lot of motivation flowing at the beginning of a new year (and, in this case, a new decade!) to set goals — and subsequently crush them. Most often, I quickly find that my dedication to stick with whatever harebrained New Year’s resolution I may or may not have come up with is waning (exponentially decaying with a half-life of about 4.5 days, resulting in only 1% of my original motivation still present and accounted for at the end of January). And while my resolutions have typically focused on personal development, this year I’m turning my attention to the lab.

As graduate students, we’re often spread thin, what with trying to get our experiments done, train new students, and meet with our advisors. Add to that taking classes (at least in your early years), keeping on top of the literature, creating your own literature, and networking, and it’s a wonder that any of us have time to focus on things other than our degrees. What are we to do when we want to set goals and make sure we achieve them?

I was musing over how to write this article over dinner with a friend one evening when she mentioned S.M.A.R.T. criteria. While I’d heard of this acronym before, I never knew exactly what it meant, or how I was supposed to apply it, until she explained it to me. It makes a whole lot of practical sense, so I’m going to pay it forward and share it all with you, in case you were similarly unaware of its meaning and potential.

S.M.A.R.T. criteria were first introduced by George Doran in 1981 (1). In the article he published, Doran states that objective should be [(quoted)]:

            Specific – target a specific area for improvement.

            Measurable – quantify or at least suggest an indicator of
            progress.

            Assignable – specify who will do it.

            Realistic – state what results can realistically be achieved,
            given available resources.

            Time-related – specify when the result(s) can be achieved.

Keep in mind that this article was originally meant for managers with a team. Other sources and articles on S.M.A.R.T criteria use other words (e.g. “achievable” in place of “assignable” and “relevant” instead of “realistic”) (2). For graduate students, using “achievable” might be more realistic than “assignable,” since, unless we’re managing another student, we’re going to “assign” the work to ourselves.

Let’s set an example goal, say, reading more of the literature in a particular field. How can we make this into a S.M.A.R.T. goal? For each letter in the acronym, there will be a list of things to consider and refinement of the goal to include the necessary information.

Specific
Consider the goal, who will be involved, and what your motivation is.

I want to read more papers to gain a better understanding of the role of Wnt signaling in cancer.”

Measurable
How can this goal be quantified? How will you know if you’ve made progress?

“I want to read 20 papers to gain a better understanding of the role of Wnt signaling in cancer.”

Assignable/Achievable
For graduate students, reading 20 scientific journal articles is certainly an achievable goal. So we get a checkmark here!

Realistic/Relevant
Consider what resources are available to help you achieve this goal. Is this goal relevant to your overall objectives (earning a graduate degree)?

Using journal access provided by the university library, I want to read 20 papers to gain a better understanding of the role of Wnt signaling in cancer.”

Time-related
Consider what your deadline is (perhaps you’re writing a review article on Wnt signaling and a section on cancer will be included) and whether it is realistic.

“Using journal access provided by the university library, I want to read 20 papers by June 15th to gain a better understanding of the role of Wnt signaling in cancer.”

Consider this article as a starting point when setting goals. The nice thing about S.M.A.R.T. is it gives you an achievable goal to go after, but the bad thing is it puts you in a structured box, which can prevent you from taking some bigger risks that could really pay off! It’s important to know when your goals need to be more flexible than S.M.A.R.T. criteria allows them to be, but if you, like me, find yourself getting frustrated for setting goals and not achieving them, this may be a good place to start.

References:
1. Doran GT. (1981) There’s a S.M.A.R.T way to write management’s goals and objectives. Management Review 70(11):35-36.
2. https://www.mindtools.com/pages/article/smart-goals.htm

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

CACHE Your Antibodies to Save Cash!

No antibody is perfect for every application, but if you’re on a budget and everything you’ve found looks about the same, here are a few things that you should consider before purchasing.

A simple way to remember this information is with the mnemonic CACHE: Citations, Application, Clonality, Host, Epitope. The more “yes” answers that can be applied to the questions below, the more likely the candidate antibody is to be successful for the experiment at hand.

1) Citations: Does the literature support the functionality of the antibody?

A good antibody will have numerous citations supporting its use. More often than not, the manufacturer will not have validated the antibody for exactly what you need. And if the goal is to do immunohistochemistry (IHC) on paraffin-embedded kidney tissue, but the manufacturer only validated the antibody for Western blotting, the literature is the best place to go to see if someone else has used a particular antibody for that purpose. Check out CiteAb for this; it is an excellent resource to compare antibodies!

2) Application: Has the antibody been validated for the desired application?

If so, make a little mental checkmark that this might be a good one! If not, consider the applications it is validated for, and compare them to your own. An antibody for Western blotting, for instance, which may recognize the target in a denatured form, might also work for immunoprecipitations. An antibody validated for flow cytometry and fluorescence-assisted cell sorting (FACS) could recognize the native form of the protein found in a tissue section.

3) Clonality: Is the clonality appropriate?

And what is the difference between monoclonal and polyclonal antibodies, anyway? Monoclonal antibodies (mAbs) are produced by a single population of B cells that is derived from a single cell, while polyclonal antibodies (pAbs) are produced by multiple B cell clones. Each has its own advantages and disadvantages. For example, monoclonal antibodies bind to a single epitope, resulting in high specificity and low background, but staining with them is easily lost if the antigen is degraded. Polyclonal antibodies, on the other hand, are resistant to this problem in that they bind to multiple epitopes. This promiscuity can also result in higher background staining, but also greater sensitivity. Choosing to use a monoclonal antibody versus a polyclonal antibody will largely depend on the target of interest and the application of the antibody.

4) Host: Is the host for the antibody different than the species of the target?

The best practice is to use an antibody raised in a host other than that of the sample species, to avoid any potential binding of the secondary antibody to endogenous immunoglobulins within the sample. Preventing cross-reactivity within the sample minimizes background staining and is a relatively simple way to ensure better results, but this is probably the least important question to consider. There are kits available to block cross-reactivity when the source of the sample is the same as the host of the antibody.

5) Epitope: Is the antigen used to raise the antibody present in your sample (or does it have significant homology)?

Multiple epitopes can be targeted within a single molecule, and antibodies can be raised against entire proteins, a protein fragment, or a particular sequence. If you are working with samples from an uncommon organism (plant biology, anyone?), you will be relying mainly on homology of your protein of interest with the epitope that the antibody targets. This is also a good place to consider your experimental conditions. As an example, FACS requires an antibody that targets an extracellular epitope so that it can bind to live cells.

These questions are not a substitute for optimizing an antibody in the lab, but they do make it much easier to choose antibodies that work, and work reasonably well, faster.

References

CiteAb – The Life Science Data Provider, 2019, www.citeab.com/. Accessed 13 September 2019.

Lipman et al. (2005) Monoclonal Versus Polyclonal Antibodies: Distinguishing Characteristics, Applications, and Information Resources. ILAR Journal 46(3):258-268.

“Polyclonal vs Monoclonal Antibodies.” Pacific Immunology, https://www.pacificimmunology.com/resources/antibody-introduction/polyclonal-vs-monoclonal-antibodies/. Accessed 13 September 2019.

“Antibody Basics.” Novus Biologicals, https://www.novusbio.com/support/general-support/antibody-basics.html. Accessed 13 September 2019.

Book Review: If I Understood You, Would I Have This Look on My Face?

From Goodreads.com

When I was getting ready for school in the morning as a tween-going-on-teen, I’d often have the TV on in the background, playing reruns of whatever television shows adults enjoyed in those days. So I’ve never actually seen a full episode of M*A*S*H, and really only know it by the sound of the helicopter blades in the opening segment, which was often playing as I walked out the door. But I’m definitely familiar with the actor who played Hawkeye in this show, Alan Alda. After Hawkeye’s tour was over, Alda hosted Scientific American Frontiers for 12 of its 15 seasons, and that show was most certainly not just background to my middle school mornings. For me, Scientific American Frontiers was a sit-down-stop-everything-else-and-only-watch-TV kind of show. Naturally, I decided I had to read Alda’s latest memoir, If I Understood You, Would I Have This Look on My Face?, which encompasses his experience with scientific communication in an amusing and relatable way. As Alda says in the introduction, “Developing empathy and learning to recognize what the other person is thinking are both essential to good communication, and are what this book is about.”

            Storytelling is an important aspect of science. When we’re giving a talk, we have to convince the people listening that the research is worth their time and attention. Alda argues that communicating isn’t just telling. It is simultaneously observing and determining whether the audience follows, and whether what you’re saying resonates with them. In many ways, it’s akin to a performance, which is perhaps why an actor with a prolific track record like Alda is so successful at it. Using small studies and anecdotes as evidence, Alda suggests in this book that things like improvisation or audience-synchronization exercises can improve presentation skills.

            His principle extends to written audiences as well. A writer cannot observe and react to a reader’s thoughts, confusions, or frustrations, but they can learn to think about a reader’s state of mind and anticipate the reader’s expectations. In essence, a writer can learn to be familiar with the experience level of their target reader and what questions they might ask if they were in the room, and adjust the narrative or delivery of the story accordingly.

            If I Understood You, Would I Have This Look on My Face? is a quick read, but that doesn’t hinder its capacity to home in on the important points above. This is not a how-to book; just reading it will not inherently improve your ability to communicate or your grant writing. But it may give you an idea of how to practice getting into your audience’s head and engaging with them in an easy and effective manner. Every audience will be different, and it is our responsibility – as researchers, as authors, as presenters – to be able communicate the intricate concepts of our research in a way that is readily comprehended by both scientists and non-scientists alike.