“We Ball Outrageous”

Did you know that GSBS has a basketball team?

The Tufts Medical campus has had a long-standing basketball league that historically consisted of medical and dental student teams. It wasn’t until October 2019 that GSBS contributed its first team to the league. The Contaminators was founded by team captain Linus Williams (#6) and was made up of both PhD and MD/PhD students. With financial aid from the Graduate Student Council, The Contaminators bought green and gold jerseys.

The 2019 season started in October and ended in January with 9 Saturday games. The Contaminators started out their season strong, winning their first 3 games. The competition started to heat up later in the season, and The Contaminators entered the playoffs with a record of 4-5. This league’s playoffs were a double elimination tournament running through mid-February. The Contaminators won their first playoff game, but lost the following game, sending them to the loser’s bracket. They were eliminated in their very next game by the eventual champions, Nothing but Netters. Overall, The Contaminators ended their 2019-2020 campaign with a respectable 5-7 record.

Williams, who is known for scoring with his signature one-handed floater, said he was happy with how the season went: “We learned how to defend with man-to-man and with zones, and were able to adapt to whatever the situation called for.” One of the team’s weaknesses was dealing with defensive pressure, especially when Liam Power (#2), Point Guard and MVP, was not on the court. This resulted in more turnovers due to the restricted court vision of the ballhandler.

Team member Daniel Fritz (#11) said “The league was a perfect balance between fun and competition.” He wants to encourage other students to join who may be wary of a team sport that they’ve never played before.

The team recruited students with a wide range of experience in the sport, from first-timers who wanted to learn the fundamentals of the game to seasoned veterans who were lifelong basketball players. Regardless of skill, each teammate was a valued asset in a sport that requires cardiovascular fitness. Lack of female substitutes was especially felt with only 3 women on the team. The co-ed league required that one female player be on the court at all times. That meant one female player would have to play the entire game if the other two female teammates couldn’t make it (shout-out to Sasha Smolgovsky #12, Patriots fan). One of The Contaminators’ goals for future seasons is to increase the recruitment of players.

Although the season is over, there are upcoming opportunities to get involved. During the spring and summer, there will be pick-up games hosted by Williams and future team captain for 2020, Joshua Man (#24—Kobe). If you are interested in participating in pick-up games or the 2020 season, please contact Williams or Man via their Tufts email.

Other team members of The Contaminators:

#3, Zemplen Pataki—Valuable tall person who can shoot.

#4, Rachael Ryner—Author of this article.

#7, Zoie Magri—Played middle school b-ball and it shows.

#14, David Jetton—An owner of the Green Bay Packers who plays b-ball on the side.

#32, Mike Rist—Secret weapon when he’s not at a wedding in New Hampshire.

#33, Mike Thorsen—Team morale booster and team mascot.

2019 Nobel Prizes: Another Year Filled with Great Discoveries

This past December, the prestigious international Nobel prizes were awarded in recognition of academic, cultural and scientific advances. Before delving into this past year’s prizes, it seems only appropriate to take notice into how nominations to become a Nobel laureate occur. The process to select laureates begins in September when invitations are sent out to a select group to make nominations. The deadline for nominations is January 31 of the following year. Once nominations are in, there is a three-month process in which all nominations are being consulted on, with experts. After having consulted with experts, reports are written with recommendations during July and June. In September the Academy gets a report on final candidates and in October, after a majority vote, the Nobel Prize is announced. Bringing us full circle to this past December’s Nobel prize awards.

We begin with the Nobel Prize in Physics which this year was awarded for two separate discoveries, each of which I will comment on separately. The first, “the discovery of an exoplanet orbiting a solar-type star”, by Michel Mayor and Didler Queloz ushered in a new era for exoplanet astronomy. Before this, physicists wondered if there were other planets like ours in the solar system, and more deeply, wondered if there were planets just like our Earth that could sustain complex life. Since then, the interest in exoplanet astronomy has grown, and the tools at the disposal of scientists studying them have improved, with more exciting discoveries about exoplanets every year. The second, with equal value, “for theoretical discoveries in physical cosmology” by James Peebles is profound because his work attempts to understand the origins of the entire universe. A lot of active research in astrophysics depends on understanding what the initial conditions of the universe were like and wondering how the galaxies themselves came into existence. In building this article, it is worth mentioning many physicists felt the award for cosmology was bittersweet as it came a little too late for a certain well-known astronomer whose contributions to cosmology were also immense. Vera Rubin was an astronomer in the field of galaxy rotation rates that revealed the presence of dark matter. Dark matter is an essential component in the theories of cosmology, and many felt it sad to think her contributions did not get as much recognition from the Nobel committee when she was alive (She passed away in 2016).

The Nobel prize in Physiology or Medicine “for their discoveries of how cells sense and adapt to oxygen availability” was awarded to William G. Kaelin Jr, Sir Peter J. Ratcliffe and Gregg L. Semenza. Every cell in our body requires oxygen for basic metabolic and physiological functions. Several animals utilize oxidation reactions to power the conversion of nutrients from food into energy, making oxygen essential for supporting life. This discovery completed the full picture of oxygen sensing in cells that began back in 1931 with Otto Warburg’s discovery concerning the enzymatic basis for cellular respiration, and Corneille Heymans in 1938 for his findings on the role of the nervous systems respiratory response to oxygen. The question that loomed over many scientists in the current century, that this year’s Nobel finally addressed, was cellular adaptation to oxygen availability through gene expression. The ability to alter gene expression patterns to oxygen availability is essential during normal physiological events from embryonic development to even exercise. This variation also extends to pathological states such as cancer and infection. William Kaelin, Peter Ratcliffe and Gregg Semenza found that during normoxia a transcription factor that alters normal physiological processes is degraded via the ubiquitin proteasome system. However, during hypoxic states such as cancer or infection this transcription factor is not ubiquitin tagged and thus not sent to the proteasome for degradation leading to alterations in gene expression. The question these scientists helped to answer is a textbook question that we will likely see being taught in early biology classes. It is also something we will likely see being applied to new therapeutics as it paves the way for promising new strategies to fight anemia, cancer and many other diseases.

Lithium ion batteries are everywhere from your smartphones to devices used on the International Space Station. The Nobel prize in Chemistry “for the development of lithium-ion batteries” was awarded to John B. Goodenough, M. Stanley Whittingham, and Akira Yoshino. The concept of lithium batteries has been around since 1991 and since their introduction to the field they have been revolutionary. The working principle of a battery is simple; it consists of two electrodes (metals like lithium) each connected to an electric circuit which itself is separated by an electrolyte that can accommodate charged species. Before we had lithium ion batteries, batteries relied on other metals such as copper, lead, and nickel. The main issue with the previous battery designs was that they were not rechargeable. Lithium on the other hand was rechargeable but prior to perfecting the design of the lithium battery, many worried it was too explosive. The current design of lithium batteries is not based on a chemical reaction as the designs preceding it were. Rather the new design relies on ions flowing back and forth between anode and cathode. This design is advantageous as it allows users to charge their batteries hundreds of times before the performance of the battery deteriorates. The work of these scientists is exciting as it introduces new power resources that other scientist can expand on in an era that seeks to lean away from fossil fuels. 

The last Nobel prize I will comment on is in Economics which was awarded to Abhijit Banerjee, Esther Duflo and Michael Kremer “for their experimental approach to alleviating global poverty”. According to the UN though, the global poverty rate has declined by half since the beginning of the twenty-first century, one in ten people in developing regions still live on less then two U.S. dollars. Many have attempted to help address the problem but have come short, describing the problem as too big. This year’s laureates went about addressing the crisis using a more strategic approach. The economists utilized a method familiar to many clinicians; they utilized Randomized Controlled Trials or RCTs. Instead of tackling poverty as a whole, they set up randomized trials in different locations in developing countries, in which they compared different groups with the same average character analyzing different things that contribute to poverty: education, health access, job availability, etc. By breaking down the problem, the economists were able to better define the needs of these developing countries in terms of resources they need, or have but aren’t utilizing. Today the field of developmental economics relies on field experiments as the gold standard for experiments done in order to give more valuable data.

For more information on past and current Nobel laureates visit: https://www.nobelprize.org/all-2019-nobel-prizes/

References:

“All 2019 Nobel Prizes.” NobelPrize.org, www.nobelprize.org/all-2019-nobel-prizes/.

Kabisch, Maria, et al. “Randomized Controlled Trials: Part 17 of a Series on Evaluation of Scientific Publications.” Deutsches Arzteblatt International, Deutscher Arzte Verlag, Sept. 2011, www.ncbi.nlm.nih.gov/pmc/articles/PMC3196997/.

“Lithium Ion Battery.” Lithium Ion Battery – an Overview | ScienceDirect Topics, www.sciencedirect.com/topics/chemistry/lithium-ion-battery.

“Power System.” How Do Batteries Work?, www.qrg.northwestern.edu/projects/vss/docs/Power/2-how-do-batteries-work.html.

“Areas of Research.” Areas of Research | Max Planck Institute for Astrophysics, www.mpa-garching.mpg.de/27882/Areas_of_Research.

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.

2019 novel Coronavirus: The latest zoonosis

A new coronavirus has made the jump from its animal host into the human population from what is believed to be an animal market in Wuhan, China. Reminiscent of the coronavirus responsible for the SARS (Severe Acute Respiratory Syndrome) outbreak during 2002-3, this virus is making headlines around the world. As of this writing, it has already infected and killed more people in China in the past three months than the entire SARS outbreak. The current infected count is over 28,000 people with over 560 deaths, all but two of which are in China. While the risk to people outside of China is minimal at this time, the outbreak must be monitored carefully as reports of human-to-human transmission are being confirmed. Because this is a new outbreak, very little is known about this virus and rumors and unsubstantiated claims are running rampant in online communities. We must remember not to panic and rely on factual information from the Chinese and US CDC (Centers for Disease Control and Prevention) and WHO (World Health Organization).

Coronaviruses are a large family of viruses which circulate among animals such as camels, cats, and bats. The 2019- novel coronavirus (nCoV) is most similar to SARS, but is a different virus to that which causes SARS or MERS (Middle East Respiratory Syndrome). The 2019-nCoV causes respiratory illness in people with the potential to spread from person-to-person, although it is unclear on how easily this happens. Based on how other coronaviruses behave, 2019-nCoV transmission is most likely through respiratory droplets from infected individuals, as well as surface transfer to mucosal membranes. Reports of symptoms include fever, cough, shortness of breath, and in severe cases pneumonia in both lungs. Onset of symptoms can occur anywhere between 2-14 days after exposure.

An international response is mounting to contain the spread of this virus, and the WHO has declared this outbreak a public health emergency of international concern (PHEIC), the sixth time they have done so. There have been confirmed cases in 24 countries around the world. Airlines are restricting flights to and from China, and the United States is barring individuals who recently visited China from entering the country. There are similar travel restrictions in Australia, Japan, and Taiwan. Vaccine development is already underway in several countries with testing reported to begin as soon as this summer. A group at the National Institutes of Health (NIH) is targeting the spike proteins that the virus uses to attach to its host cell receptor, ACE2. Although, any vaccine is still a year away at minimum, so we must rely on a swift response from the global community in identifying new cases and blocking routes of transmission if we are to stop this from becoming the next pandemic.

This situation is evolving rapidly, and infection counts and deaths may increase each day. Travel restrictions and policy are likely to change rapidly as well.

For the most up to date information please see the CDC website here: https://www.cdc.gov/coronavirus/2019-ncov/index.html

And at the WHO here: https://www.who.int/emergencies/diseases/novel-coronavirus-2019

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

The Red Meat Article Controversy: HAMBURGLER STRIKES AGAIN

Pepperoni pizza. Pulled-pork sandwiches. Burgers. Bacon. These are some of the foods that I miss the most since deciding to reduce my meat consumption to virtually zero servings a week. My decision was environmentally and eco-consciously driven, but many Americans cut back meat consumption due to health concerns. The risk of red meat and processed meat consumption in cardiac disease, cancer, and overall quality of life has thoroughly pervaded the public conscience. But at the beginning of October 2019, a review was released in the Annals of Internal Medicine that recommended not changing current red or processed meat consumption. The authors concluded there is poor evidence linking red/processed meat consumption to adverse health risks, which directly contradicts years of nutrition research.

I’ve never read a lick of nutritional research in my life, but I have enough experience in reading scientific literature to attempt a summary of the review for you here. The authors integrated evidence from studies that included at least 6 months of red meat or processed meat consumption and at least 1,000 participants. They additionally took into consideration the feasibility of reducing meat consumption, the cost of meat consumption, and the personal preference of eating meat for the participants. However, they excluded environmental impact and humane animal practices into their consideration.

The evidence was evaluated with a set of guidelines the authors outlined, which included systematic review and GRADE (Grading of Recommendations, Assessment, Development, and Evaluation) methodology. GRADE is traditionally used in rating clinical drug trials, so that recommendations can be made regarding a drug’s efficacy and safety. GRADE was not designed nor has it been used before in nutritional research. After the evidence was rated in this manner, a “low conflict-of-interest” group of experts and some public members outside of the science community made their recommendations. Their findings weren’t very conclusive; evaluation of the evidence provided little certainty in the risks associated with red meat and processed meat consumption.

The use of the word “certainty” in the article highlights the bias that the authors’ methodology introduces; it is a subjective quality. Our faith in the authors’ discernment depends on our faith in the authors themselves.

How was the group of experts and public members making the recommendation determined to be “low conflict-of-interest”? The panel was asked to disclose any financial or intellectual conflicts from within the past 3 years. Only those with none were invited to participate in the panel. But is 3 years long enough? Dr. Bradley Johnston, the head researcher of the article, has industry ties that lie just outside the 3 year window. The New York Times and the Washington Post reported on this and another author, Dr. Patrick Stover, who has similar ties to the beef industry through the Agriculture and Life Sciences (AgriLife) program at Texas A&M.

In the wake of the red meat article, prominent leaders in the field of nutrition and public health have criticized its recommendation. Prior years of nutritional research have illuminated the risk of frequent red and processed meat consumption in contracting heart disease and cancer. Some experts point to the distrust that this direct contradiction instills in scientific research, whose relationship with the public is already challenged in areas like global warming.

Environmental impact and humane animal practices were among the evidence that the panel did not take into consideration while making their recommendation. How would their recommendation change if they had considered these conditions? The evidence is staggering. Red and processed meat consumption contribute to the accumulation of greenhouse gases through animal agriculture and deforestation. Additionally, while meat consumption is rising across the globe, the stress on water availability, biodiversity, natural ecosystems, and the animals themselves increases as well. Higher demand for red meat has resulted in the sub-ideal conditions for animals that documentaries like Food Inc. have made us familiar with. Cattle, pork, and poultry often have limited access to open pasture and are fed unnatural diets with antibiotics to save money. Confronting this information was enough for me to decide to reduce meat consumption.

For many, incorporating meat into their diet is easier and cheaper than eating a plant-based diet. For those looking to reduce their carbon footprint through what they eat, I suggest purchasing poultry (cheaper) and meat alternatives (increasingly more accessible) over red meat. However, people also care about the nutritional value in their food. The rise in popularity of plant-based meat alternatives can be seen in the fast food industry. Notably, Burger King has released their Impossible Whopper within the last year, which uses an Impossible Burger patty made from soy and potato protein with the crucial ingredient of heme (the molecule attributed with “meaty” flavor). Despite whether it comes from a fast food restaurant or the meat aisle, we should still be reading the nutritional facts before congratulating ourselves on choosing the “healthy option”.

Overall, while doing my research into the red meat article controversy, my take-aways were as follows:

-A panel of experts and members of the public made a recommendation to not change current red or processed meat consumption habits based on a review of evidence that weakly points to adverse health consequences.

-Like most recommendations, this one has sources of bias despite the authors’ efforts to minimize them.

-Human nutrition research also has its own caveats, confounding factors, and complexities. Since researchers can’t control everything that a person eats in a day, we can’t expect a study to be completely accurate.

-Some of the authors have ties to trade industries. Whether those ties influenced the recommendation of the article remains uncertain.

-There are good reasons for reducing meat consumption that pertain less to the health of an individual and more to the health of an entire planet.

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

NOTES FROM THE LIBRARY

RESEARCH GUIDES TO HELP YOU GET STARTED ON YOUR RESEARCH

Many people turn to Google when they are brainstorming a research topic. I am not here to shame anyone on that practice, especially because I am guilty myself! But as many librarians will say, you can always start with Google but NEVER end there.

There are better resources to help get you started on your research. The following are some research guides that have a curated list of resources based on topic/subject area.

As always, if you need help navigating any of these resources, please feel free to make an appointment with me or drop by Sackler Library Office Hours!

FINDING INFORMATION

SCHOOL OF BIOMEDICAL SCIENCES RESEARCH GUIDE. This will guide you through finding journal articles, chemical/drug information, protocols/methods, data, data analysis/visualization, and more!

PROBLEM-BASED LEARNING. For those of you working/researching in a clinical setting, this guide will help you with some resource that might be helpful in answering clinical questions. This guide includes a variety of resources that include, but is not limited to, point-of-care tools, e-book collections, clinical practice guidelines, drug information, etc.

BIOINFORMATIC RESOURCES. If you need bioinformatics resources, this is a guide that directs you to databases, tools, journals, books, and bioinformatics at Tufts.

STUDY DESIGNS IN THE HEALTH SCIENCES. This guide will help you gain an introductory understanding of the different types of study designs that are frequently used in the health sciences.

ADVANCED SEARCHING TECHNIQUES. If you have a handle on basic searching in databases like PubMed or Ovid, you might find this guide helpful. It will give you some tips and strategies for advanced searching on a variety of databases.

OTHER RESOURCES

APPROACHING THE LITERATURE REVIEW. This is a great place to start if you need help with your literature review. It walks you through the steps of approaching your literature review and links you to other resources that might be useful.

DOCTORAL RESOURCES. You should visit this guide if you need help with your dissertation, teaching, or locating career information!

FINDING FUNDING. This guide is specifically designed to help you find funding (both on and off campus), as well as write grant proposals. It will also give you tips on finding successfully awarded grants on PubMed and other databases.

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.

NOTES FROM THE LIBRARY

Introduction

Hello everyone! My name is Andrea Kang and I recently joined the Research & Instruction Librarians at the Hirsh Health Sciences Library (HHSL). One of my roles is to be the library liaison to the School of Biomedical Sciences. I am so excited to be a part of the Tufts community and hope I can make your lives a little bit easier, whether that is by helping you through your literature review for your thesis, or giving you tips on research data management, or connecting you with resources that HHSL has to offer you. Here are some things that I can help you do throughout your time at Tufts:

FIND JOURNAL ARTICLES & MORE. I can help you find articles, datasets, health statistics, chemical/drug information, etc. and equip you with the skills on how to do it yourself in the future! Even if you know the basics, I can help with troubleshooting or refining search strategies.

GET YOU STARTED ON A RESEARCH DATA MANAGEMENT. Government funders among others are requiring rigorous research data management (RDM) plans for your research, some requiring that you meet with a librarian. But beyond these requirements, RDM can make your life (and others’ lives) easier in the long run. I can provide tips on best practices and where to get started with your RDM plan.

HELP ORGANIZE YOUR CITATIONS. If you are still using Microsoft Excel/Word, Google Sheets, or going old school with pencil and paper to organize the bazillion articles you found for your research, STOP. There are other ways that you can manage your citations that will save you time in the long run! I can help you with tools like Zotero, Mendeley, and EndNote (which is FREE because Tufts pays for it), or connect you with the experts here at HHSL.

CONNECT YOU WITH OTHER RESOURCES. There are so many other resources available at HHSL. Whether you need to use test prep books, borrow a phone charger, just need advice on where to start your research, or learn skills like R/R studio, I can help connect you to the resources you need. Just reach out!

To make an appointment with me, you can go to my page and schedule an appointment through the scheduler. If there are problems with this, you are more than welcome to call me at (617)-636-0385 or email me at andrea.kang@tufts.edu.