Tufts Undergraduate Science Magazine Fall 2014 by Tufts Breakthrough Undergraduate Science Magazine

BREAKTHR Fall 2014

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Tufts Undergraduate Science Magazine

Volume V, Issue I

Civil engineering professor describes the origin of earthquakes and landslides Page 8

BROWN & BLEU

Biology professor uses cheese to study microbial diversity Page 10

uncovered Page 6

FROM THE EDITORS

OUR STAFF

Dear Readers,

Chief Content Editor

Welcome to our Fall 2014 issue of Breakthrough Magazine! We are elated to share this culmination of a semester’s worth of hard work from all of our wonderful group members and the ways in which we are expanding! In fact, we had more excellent articles than we could publish; we’ll be publishing a Breakthrough micro-issue in Spring 2015 in addition to our regular issue to accommodate the increased volume of submissions. In this issue we focused on research as well as undergraduate science groups at Tufts. We highlighted faculty research in Professor Catherine Freudenreich’s Lab on DNA repair mechanisms, Tufts Professor Robert Viesca’s work on earthquakes and plate tectonics, and new professor Ben Wolfe’s investigation of the microbiology of food. Additionally, we feature the interdisciplinary research initiative of the Tufts Institute for Innovation. We have made connections and served as a platform for undergraduate groups such as the Biomedical Engineering Society and Tufts Synthetic Biology. As a group we are making an effort to embody the spirit of innovation at Tufts by changing our publication process and encouraging online submissions from a broader base of writers. As you read this issue we hope that you enjoy learning about exciting science as much as we enjoyed writing about it. We aim to increase scientific dialogue on campus and we encourage you to get involved. Enjoy! Jen Hammelman, Chinami Michaels, and Isabel Yannatos Chief Editors

Jen Hammelman

Chief Creative Editor Chinami Michaels

Chief Managing Editor Isabel Yannatos

Lead Copy Editor Jeremy Marcus

Layout Director Amy Bu

Public Relations Directors Rebecca Lachs Maddi D’Aquila

Copy Editors

Jaclyn Foisy Maddi D’Aquila Nick Dorian Denali Rao David Hua Ashley Hedberg Rebecca Lachs Logan Garbarini

Assistant Layout Designers Sabrina McMillin Logan Garbarini Nick Dorian Allison Pine Yusi Gong

Webmaster

Ashley Hedberg

Photographers

Cover image: Original artwork by Chinami Michaels Background image: A collection of Saccharomycotina yeasts that grow in foods. Courtesy of Ben Wolfe

The opinions expressed in each article are those of the author and do not necessarily reflect the opinions of the magazine or its staff.

Nick Dorian Allison Pine Sabrina McMillin

Treasurer Yusi Gong

Breakthrough is a publication of the Tufts Undergraduate Research Journal, recognized by the Tufts Community Union (TCU) Judiciary and funded by the TCU Senate 2 | BREAKTHROUGH | Vol V Issue I Fall 2014

NTENTS

Tufts’ Undergraduate Science Magazine

Fall 2014 / Volume V / Issue 1

2 From the Editors 4 For the Painted Turtle, Never Aging Wins the Race By Nicholas Dorian

5 Engineering Living Materials The Omenetto lab reinvents technology with silk

By Logan Garbarini

6 A Classical Genetics Story

The Freudenerich lab elucidates the pathway for DNA post-replication gap repair

By Jennifer Hammelman & Tierra Ouellette

8 Faults, Friction, and Fractures Dr. Viesca models geological physics and mechanics to determine the origin of earthquakes and landslides

By Yusi Gong

10 Brown and Bleu

Dr. Wolfe uses cheese to study patterns of microbial diversity

By Sabrina McMillin & Jeremy Marcus

12 Re-Programming Life

Tufts Synthetic Biology’s conference and iGEM emphasize undergraduate research

By Christopher Ghadban & Petar Todorov

14 Research with Impact

Tufts Institute for Innovation supports collaboration across campuses

By Isabel Yannatos

16 Doping without Consequences

hGH testing allows athletes to avoid repercussions By Arlene Rosenberg

17 New Particle to Advance Research in the Cosmos

A powerful technique was used to discover a new meson

By Richa Parande

18 The BioMedical Engineering Society

Members of the BME society describe their research

By Rebecca Lachs

19 Size Matters

For bumblebee workers, why does size matter? By Nicholas Dorian

19 Citations

Join Us!

Want to submit an article or join our staff? Email us at tuftsresearch@gmail.com! Visit our website to learn how you can submit articles online: ase.tufts.edu/breakthrough Like our Facebook page and check out our blog at tuftsresearch.wordpress.com! Vol V Issue I Fall 2014 | BREAKTHROUGH | 3

For the Painted Turtle, Never Aging Wins the Race

he next time you’re thinking about getting a pet, consider how long you actually want to care for it. In most cases, fish are perfect for a 1-2 year responsibility, while dogs will have you playing fetch for 10-12 years. On the other hand, a painted turtle could keep you busy for upwards of 60 years! Painted turtles are endemic to North America’s wetlands and are named for their eye-pleasing yellow and red skin patterning (1). Since they are cold blooded, you can often see them basking on fallen logs or rocky outcrops to maintain their core temperature. Their diet consists of aquatic vegetation and the occasional unsuspecting invertebrate (a dragonfly nymph, for example). Painted turtles emerge from underwater hibernation in the spring and set out to reproduce—adult females reach sexual maturity after seven years. At a maximum longevity of 61 years, it is clear that painted turtles live longer than other animals of similar size. In fact, painted turtles don’t seem to age as they get older. Current research proposes that painted turtles exhibit a phenomenon known as negligible senescence. This means they meet three criteria: 1) failure to physically age, 2) decreased late life mortality, and 3) ability to continue reproducing without consequence. 1) Failure to physically age Physical aging is often described as a decline in functionality and a lack of growth. One proposed cause of aging is the rateof-living theory—if you have a higher metabolic rate, you’ll die younger. Painted turtles hibernate underwater for five months out of the year, and largely use anaerobic respiration to produce energy during this time., Therefore, they will accumulate less damage from harmful aerobic respiration by-products over the course of their lifetime. Although no consistent correlation has been shown between lower oxidative damage and increased longevity in mammals, it’s worth hypothesizing that this correlation exists for painted turtles.

2) Decreased late-life mortality Painted turtles meet the second criterion of negligible senescence: older adults are more likely to survive than younger adults. Turtle hatchlings have the highest mortality rate, since they are the most vulnerable to environmental stressors, whether it’s a particularly frigid evening or a hungry raccoon. Adults, on the other hand, have a lower mortality rate and are able to resist predation since they have a hard shell. On a species level, this lower mortality for all adult Painted turtles correlates with longer life: those species that can better escape predation will live longer (think porcupine vs. flightless chicken). This observation supports the theory thats, on a species level, if you can escape predation, you will live longer (2). Increased longevity gives an individual more opportunities to reproduce and pass on the traits which contributed to its prolonged survival. Over time, this can influence the average lifespan of the greater population. 3) Ability to continue reproducing without consequence From sexual maturity until death, female painted turtles show no decrease in reproductive ability. Around 97% of females will reproduce in a given year, and research suggests that older females may actually reproduce more often in a single season than younger females. In a study of the health of the painted turtle’s immune system, researchers observed that older turtles invested more energy into reproduction than growth (3). Interestingly, there are a handful of organisms like the naked mole rat and the red sea urchin that, like the painted turtle, fail to age. However, you will likely have to look further than the aisle next to the cat toys to find them. To learn more about negligible senescence and other theories at the forefront of the aging literature, consider enrolling in Bio 61 with Professor Mitch McVey next fall.

Written by Nick Dorian, a junior majoring in biology and environmental studies 4 | BREAKTHROUGH | Vol V Issue I Fall 2014

Engineering Living Materials Reinventing technology with silk

ne might not expect to find “Go lab focus on stabilizing the silk into novel Celtics” signs scrawled on the structures with useful properties. One rewhiteboard walls above a foosball searcher is currently trying to use silk in an table in the sterile halls of 200 Boston Ave. aerogel, an ultra light but highly structured Likewise, one might not expect cutting substance. These new structures would edge science to be using an ancient mate- open up a whole new field of potential aprial like silk. Yet in this refreshing environ- plications. The lab also creates hydrogels ment, Professor Fiorenzo Omenetto and that could eventually act as replacement for Dr. Benedetto Marelli are “using nature’s damaged eyes. materials to adapt to technology today” Others in the lab focus more on the through the technological reinvention of electronics side of silk applications. The lab silk. This reinvention is taking shape in the is able to integrate electronics and circuits form of all sorts of biocompatible sensors, into different silk materials that allow them from edible devices that communicate with to perform a host of biomedical tasks. Dr. your phone to implantable light sources. Marelli mentions the utility of silk as a tool By carrying out research on the ma- to “[sense] a part of your body difficult to terial in both basic and applied ways, the sensor.” Silk is biocompatible, meaning it silk labs at Tufts have does not elicit an imgarnered widespread mune response when Commercialization of recognition. Such recimplanted, so it can be science is going to be used to monitor the ognition can be attributed to the lab’s diverse surface of bones. Ala crucial engine staff. Dr. Omenetto ternatively, due to silk’s for the future. is formally trained as ability to transfer bea physicist and holds tween substrates easily, a degree in electrical engineering at the Omenetto says the silk “can easily make all Universita’ di Pavia in Italy. He has previ- sorts of surfaces technological because you ously researched ultra-fast and nonlinear can control the way silk adapts to complex optics at Los Alamos National Laboratory topologies so you can put very sophisticatin New Mexico. Among the other scientific ed electronics on a piece of paper.” staff there are physicists, material scientists, Thanks to the incredible research staff, mechanical engineers, and biomedical en- the lab is able to focus on a host of realgineers. world applications. Omenetto and Marelli This diverse team enables the lab to stress the importance of technology trans“solve the different fundamental issues that fer: “We try to be entrepreneurial as well appear in each discipline.” Dr. Marelli likes and I think that the pragmatics of developto describe the lab as “cross-disciplinary, ing technologies based on invention is very because we’re not merging different fields important. Commercialization of science is in one application, but we’re using one ma- going to be a crucial engine for the future.” terial in different areas.” As Omenetto mentions, their drive is “Not Some researchers in Dr. Omenetto’s blue sky for the sake of blue sky, but blue

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Top: Raw silk cocoons in the lab ready for processing. Middle: Proccessed silk material undergoing dialysis to exchange process chemicals with water so it can be used safely. Bottom: A cheerful looking silkworm sketched by a researcher on one of the walls. Photos courtesy of Nick Dorian.

sky for the sake of wanting to do something that has very high impact.” The silk lab researchers’ focus on impact has led and will continue to lead to innovative solutions to large-scale problems. That is if they can drag themselves away from the foosball table.

Written by Logan Garbarini, a freshman studying electrical engineering Full disclosure: The author currently conducts research under the guidance of Dr. Omenetto.

Vol V Issue I Fall 2014 | BREAKTHROUGH | 5

Classical Genetics Story:

Elucidating the pathway for DNA Post-Replication Gap Repair

he Prologue

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In this paper, House and colleagues elucidated pathways of chromatin modifications that contribute to the fidelity of DNA gap repair. More specifically, they looked at repair factors recruited to sites of endogenous lesions, (an example of naturally occurring DNA damage), that occur during DNA synthesis. Dr. House explained that naturally occurring DNA lesions can be barriers to replication. In order to continue DNA synthesis and cell division in the face of such barriers, the cell has evolved damage tolerance pathways, including post-replication repair.These pathways are important to cells as improper repair may cause DNA mutations, like the expansion of CAG repeats which are linked to neurodegenerative diseases, such as Huntington’s disease (1). Dr. House and her colleagues have made a significant contribution to the field of DNA repair pathways by showing how histone modifications are implicated in gap repair.

The untold story behind a classical genetic research paper is the journey that begins with a large genetic screen, and results in a small but significant contribution to the wide pool of scientific knowledge. In Tufts Professor Catherine Freudenreich’s lab, one of the longest journeys has been the work on the discovery of a new pathway related to gap repair after DNA replication. Historically, much research has been conducted to elucidate the mechanisms for double-strand break repair, where various forms of damage cause nicks occur in both strands of DNA, caused by various forms of damage. Particularly, it is known that specific proteins associated with DNA, known as histones, are modified as an important step in recruitment of repair proteins. The system of gap repair, where only one strand of the DNA is nicked, and the role of his- Schematic of DNA histone acetylation as a Setting the Scene: The Background mechanism of gap repair. tone modification is less understood. Spanning two graduate and many under- Image courtesy of Dr. Nealia House. This discovery came about in what was degraduate students, including Breakthrough scribed by Professor Freudenreich as a “clasalumnus Stephen Walsh, all of the Freudenreich lab’s hard work has sical genetics story” – a Tufts undergraduate performed a screen culminated in the discovery of a novel pathway for post-replication analysis on yeast in which genes are knocked out, or functionally gap repair. Like most, this discovery is the beginning of a new jour- mutated, and measured for some fitness based on the area of interney as an inceptive contribution to the important field of how cells est. In this case, the screen was searching for novel genes involved repair damaged DNA. with expansion of CAG repeats during DNA repair. Several of the genes selected for study from this screen were so-called histone The Main Character: First Author Nealia House deacetlyases, which remove acetyl groups from histone proteins, and which when deleted in mutant yeast strains significantly inA recent Ph.D. graduate of Tufts University in the Freudenreich creased the expansion of CAG repeats. Since these genes had not Lab, Dr. Nealia House has always had a curiosity for the natural yet been related to expansion repeats, it became the dissertation world around her that drew her to the field of biology. As an under- topic of Dr. Jiahui H. Yang, who managed to confirm that histone graduate at Smith College, she did research on splice variants of a acetylation and deacetylation was important to homologous repotential vaccine target for parasites that cause elephantiasis para- combination. However, the details of the repair pathway remained sites in the lab of Dr. Steven Williams. She also worked as a labora- unclear. Once Dr. House made the decision to pursue her Ph.D., tory assistant at New England Biolabs Summer Molecular Biology she linked this histone modification to the fidelity of gap repair. Workshops, hosted at Smith College. Dr. House then went on to attend Tufts for her master’s degree and worked as a lab manager for The Story the Freudenreich Lab before deciding to get her PhD. Her graduate and post-doctoral career has culminated in the publication of Working with various strains of yeast, Dr. House demonstratNuA4 Initiates Dynamic Histone H4 Acetylation to Promote High- ed a role for both histone acetyltransferases (HATs) and histone Fidelity Sister Chromatid Recombination at Postreplication Gaps. deacetlyases (HDACs) in gap repair. The dynamic acetylation6 | BREAKTHROUGH | Vol V Issue I Fall 2014

deacetylation of chromatin serves as a platform for protein com- patients with Huntington’s disease, and particular chromatin replexes involved in DNA repair. Acetylation of histone H4 lysine 16 modeling occurs that contributes to memory. In the Huntington’s (H4K16) has been shown to play a role in DNA repair and the loss model, regulation of histone acetylation can alleviate some of the of H4K16 is linked to human cancers (2, 3). In the paper, House memory deficit. Moreover, there is evidence that shows that the et al. suggests a model for repair that includes H4K16 acetylation lifetime CAG expansions are the cause of degeneration in this disby the HAT NuA4. The modified histone may function to recruit ease. If there is a way to decrease the expansions that occur during proteins with bromodomains, which bind to the acetylated (modi- a patient’s lifetime—perhaps utilizing the knowledge of the dynamfied) lysine, and are important for gap induced HR repair (4). Thus, ic H4 acetylation at DNA replication gaps—then the onset of the the histone acetylation provides a marker for DNA damage and diseased phenotypes can be delayed. For the Freudenreich Lab, the recruits proteins that move histones aside investigation of H4K16 in gap repair will be a (remodelers), which then facilitates repair procontinuing part of their research. When asked cesses. HDACs also play an important role in what steps will be taken in the future to further It’s a whole new ensuring specific targeting of chromatin remodthis research, Professor Freudenreich stated “At field in a way… we elers to the location of DNA damage. When Dr. the end of our paper we presented a model for House and colleagues knocked out the histone how we think this modification is recruiting annow have the first H4 HDACs, their results suggested “a global inother protein that we found was important… so handle on the types our next step is to test that model.” crease in H4 acetylation, leading to loss of the locus-specific signal of damage” (4). This reFor our very own Breakthrough alumnus of chromatin modisulted in compromised repair fidelity and CAG Stephen Walsh, the experience in the Freudfications needed to repeat instability. Thus, both HATs and HDACs enreich lab has been essential to his growth as play an important role not only in the historical a researcher. Walsh has moved on to a job as repair gaps.” sense of chromatin compaction and de-coma research technician in Robert Langer’s lab at paction but also as facilitators of gap repair prothe Koch Institute at MIT, where he is working cesses. The dynamic interaction allows for the to develop “new drug delivery systems using specific recruitment of remodeling complexes RNAi and CRISPR technologies, with theraat CAG repeat sites to promote repair. This discovery has greater peutic potential in treating cancer and other genetic diseases.” implications than simply the discovery of one of many repair path- When asked to comment on his experience, he said “Nealia and ways; as said by Professor Freudenreich, “It’s a whole new field in Catherine are two of the most intelligent people I’ve ever met, and a way… we now have the first handle on the types of chromatin being able to work with them in developing this histone acetylation modifications needed to repair gaps”. Unveiling the pathway to H4 story was one of the most rewarding experiences I had at Tufts. I modification in post-replication gap repair was not easy, says Tufts am enormously grateful to both of them for giving me the level of graduate and Breakthrough alumni Stephen Walsh, “There were challenges and responsibilities that they did.” With such as story as one or two times when a yeast strain construction or a certain as- this, the journey to post-replication gap repair has just begun, and say was abandoned after multiple technical difficulties. Although we are excited to see what next will come from the current memit was tough to give up on something you had worked on, we had bers and alumni of the Freudenreich lab. to recognize which of our data was most important, be confident with it, and move forward”. A New Chapter Begins It has been shown that acetylation patterns are changed in

By Jennifer Hammelman, a junior majoring in biology and computer science and Tierra Ouellette, a junior majoring in biopsychology

Yeast used as model system to study DNA repeats caused by mutations in repair mechanisms. Photo courtesy of Tierra Ouellette.

Vol V Issue I Fall 2014 | BREAKTHROUGH | 7

hen people think “earthquake”, many imagine the ground trembling beneath them, buildings and bridges collapsing before them, and children and sirens wailing around them. Earthquakes happen every day around fault lines, and most are so small that people don’t even notice. However, a large earthquake wreaks havoc on the lands it affects, often with years, if not decades, of consequences in the aftermath. What causes this intense devastation and disaster? Can we predict the onset of an earthquake? For geophysical investigators such as Robert Viesca, these are the questions that they devote their work to.

Faults, Friction, & Fractures:

Civil Engineering: “Where Society Meets the Earth”

Geological Physics and Mechanics

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Robert Viesca, a young and passionate Tufts undergraduate alumnus, is currently an assistant professor at Tufts studying the physics and mechanics of earthquakes and land deformation. After graduating from Tufts in 2005 with a Civil Engineering degree, he earned his PhD at Harvard and completed a post-doc fellowship at Dalhousie University in Nova Scotia, focusing on fracture physics, earthquakes, and landslides. His work contributes to both a physical understanding of geologic processes and the progressive field of geosystems engineering, which investigates how man-made structures interface with the natural structure of the earth in “earthinfrastructure interactions”. For example, landslides are geological events that deeply affect the engineering and building infrastruc-

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8 | BREAKTHROUGH | Vol V Issue I Fall 2014

Earthquake’s Origin Similarly, earthquakes occur when a body of rock starts to rupture at a previous break. As a rock breaks it weakens, and further deformation is localized to a sliding surface known as a fault. Many earthquakes, especially the most dangerous ones, are caused by the rapid failure of a fault. Two pieces of earth’s crust that were previously locked together due to high friction eventually slip past each other due to shear stress on the interface reaching a critical level. This sudden movement releases the stress, releasing energy which propagates outward as waves. Dr. Viesca is interested in these types of catastrophic failures and the physics of the initiation of the fault rupture—the moment when the plates go from being stable to the point where stress is released over large portions of the fault. By analyzing field and laboratory data and developing models, he strives to answer questions such as what determines the origin of an earthquake, whether or not we can predict the magnitude of an earthquake from its onset, and what factors drive changes in fault strength. Data Compilation Through History

... a fault line can be observed as a window to the past.

Image of the San Andreas Fault

first moments of landslide formation. Combining Dr. Viesca’s work on pore pressure with an understanding of the geometry and composition of the land may aid in the assessment of slope stability in landslide-prone areas.

ture of certain locations, as geological environments susceptible to landslides are often risky places to build structures. In landslides, an entire column of soil can flow at a time—imagine soil flowing down an inclined surface like a high-viscosity fluid, collapsing, enveloping, and destroying everything in its path. These events are often caused by rainfall, which accumulates in the soil and rocks deep below the surface after a rainstorm, elevating a force called pore pressure. This pore pressure pushes particles apart, and the fluid accumulation weakens the interface between soil particles by reducing normal stress at the contacts, thus reducing the friction keeping the two interfaces together. A single intense rainfall event can lead to an extremely intense increase in pore pressure, which causes a sudden slip in the interface. Part of Dr. Viesca’s PhD work centered on how elevations of pore pressure translate to the

Because earthquakes are subterranean phenomena, the physical condition of the . fault that contained an earthquake-generating rupture is difficult to assess through drilling. Thus researchers generally infer how an earthquake propagated by looking at seismic activity. Additionally, the rock hosting a fault is occasionally uplifted to ground level. After a long period of weathering, the top of the rock is eroded off and a fault line can be observed, and can act as a window into the past. Another method of data collection especially useful for events predating the seismology era is the analysis of written historical records (for example, of church bells ringing and the ground shaking). Historians can use these records to map out where the effects of an earthquake were felt in order to estimate its epicenter, or origin, and use an intensity scale to plot its propagation: regions where people report highest intensity are closer to the earthquake’s origin, while cities further away feel only residual effects. For more recent earthquakes, established GPS and seismometer networks can be used to monitor earthquake propagation. These systems are placed at many locations throughout the world and

can measure displacement, allowing researchers to see surface movement over time. Seismometers have a high sampling rate and can be used to measuring surface velocity changes. This allows scientists to track wave propagation in all three dimensions during a seismic event. In contrast, GPS systems have the ability to track long-term motion of tectonic plates by measuring the horizontal displacement over periods long periods of time. They can also be used to visualize wave propagation over an area during the event of an earthquake. Mathematical Modeling of Movement Once field data has been collected, Dr. Viesca and his active community of researchers utilize mathematical analysis and modeling to interpret the sizeable amount of data collected. Shear and normal forces can be recreated to observe the transition from static to dynamic friction in the laboratory. Dr. Viesca uses this to create mathematical models for the movement and physics of the plates. Currently, one of his focuses is on determining and modeling the initial, pre-seismic events that occur at the site of a larger, earthquake-generating rupture. Understanding the physical processes active before and during a rapid fault failure is necessary to determine the sequence of events leading to an earthquake. However, rupture dynamics are difficult to model in the lab since it would be difficult to simultaneously recreate the high temperatures, pressures, and sliding rates occurring on a fault. Instead, he uses seismic data to constrain the physical processes acting on the fault, including feedback between sliding, frictional heating, and weakening mechanisms (such as thermal pressurization of pore fluid). Through this, he and others in the field can explore how all of these factors interplay to determine the strength and extent of the rupture propagation and gain insight into the movement and mechanics of the fault. Physics is truly key to figuring out the origins of ruptures that generate waves, which can carry enough energy to destroy entire cities, as these cracks will surely break your mother’s back.

Written by Yusi Gong, a junior majoring in biomedical engineering Vol V Issue I Fall 2014 | BREAKTHROUGH | 9

ou don’t see logs of cheese lying around in the forest.” While he may not be collecting samples in the wild, Dr. Benjamin Wolfe has traveled the world exploring microbial diversity in cheese and other fermented foods. The latest leg of Wolfe’s journey began when he joined the Tufts University Department of Biology as an Assistant Professor in September 2014. He is known not only within the scientific community for his extensive research in microbiology, but also to the “foodie” community for his frequent contributions to several popular publications including Boston magazine and food journals such as Lucky Peach. While Wolfe claims a lifelong general interest in food, how it’s made, and the people who create it, he attributes his academic interest in food production to his undergraduate experience at the College of Agriculture and Life Sciences at Cornell University. “I was exposed to people who were farmers and plant scientists, people who were doing rural sociology in farming communities, so it was a great place for me to begin...I also just loved eating. I think food is really interesting and can be a beautiful expression of raw materials and people’s efforts.” Although the professor has devoted his time to the study of microbial communities within a wide variety of products-from salami casings in delis to cigarette butts on the streets of Boston--his passion for artisan cheese predates his study of aged foods. “I found going into a cheese shop kind of like going into a natural history museum, where you could see all these different collections of microbes that reflected places and people and milk and cows and all these stories that come with cheese,” says Wolfe. While working towards his Ph.D. at Harvard University in 10 | BREAKTHROUGH | Vol V Issue I Fall 2014

Introducing Dr. Benjamin Wolfe 2005, Wolfe became interested in using the Amanita genus of mushrooms to investigate connections between genomics and the ecology of organisms. Many of the species in the genus live in symbiosis with tree roots, receiving sugars from the trees while providing them with fertilizing nutrients obtained from the soil. Wolfe strove to understand the evolutionary history of that relationship by investigating the expression and inheritance of genes across these symbiotic Amanita species. Towards the end of his work on this mushroom project, Wolfe began collaboration with Harvard microbiologist and cheese specialist Rachel Dutton. At the time, she was starting a project seeking to develop a cheese model system for studying microbial communities. Wolfe volunteered himself as both a fungal expert and a cheese aficionado, and the two spent the next four years developing and refining the system. “I think it was a marriage of [microbiology with] my really strong passion for food;” said Wolfe, “this amazing opportunity...to be able to merge the two together, and here I am now.” As it turns out, cheese makes an ideal model system for Wolfe’s research. In a laboratory context, this seemingly unassuming dairy product offers many advantages over comparable microbial environments. Unlike the ocean or soil, we know exactly what components make up the cheese environment. This means we know what the microbes need to survive, making it easy to generate and maintain cultures. Making this process even more convenient is the ubiquity and reproducibility of cheeses. People have been making the same cheeses for hundreds if not thousands of years in different places all over the globe. Wolfe and his fellow researchers can go to any cheese shop or cheese producer and

obtain samples of what amounts to a consistent and replicable ecosystem. What’s more, the communities present on cheese rinds are reasonably complex yet manageable. Any given cheese rind may have twenty to thirty different species of both bacteria and fungi from all different types of environments. Experiments performed on this hybrid ecosystem can thus be extended and applied easily to larger, more complicated systems. By breaking down and analyzing the component species of different cheese environments, the Wolfe lab has been able to get a big-picture understanding of the patterns of diversity in these microbial communities. Moving forward, they hope to be able to understand the molecular mechanisms that underlie those patterns. Additionally, the lab is seeking to understand just how those mechanisms and pathways come about in multi-species systems. Investigation into experimental evolution of individual organisms has been underway for some time, but as Wolfe points out, “...if you look at nature, we know that these microbes are living in communities where there are many interacting parts.” By using the cheese model he hopes to expand on our understanding of how inter-species interactions affect the rate and direction of evolution., which Wolfe believes could “…have interesting implications for thinking about how we design microbial communities.” Wolfe’s progress in food sciences attracted the attention of internationally re-

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ing layperson foodies. He decided to expand his reach by collaborating with his husband Scott Jones, chef de cuisine at Menton. Together, they are the authors of Chefology, a popular column on the Boston magazine website. Although Wolfe spends most of his time in the lab, he plans to continue writing for a less scientific audience as long as there is demonstrated interest. “You can put a piece of camembert on a table and people become drawn into that and then you can start layering in more technical scientific information that normally would immediately turn them off, by having this food in front of them. And so it becomes this sort of calming more accessible interesting engaging thing that it’s not just a petri dish or a table full of information or something more sort of sterile in many ways.” Wolfe sees Tufts as a perfect fit for his interests. The Biology department appeals to him because of its diversity. Nowadays, he says, departments across the country are being split up into specialized sections. He appreciates that here at Tufts he works alongside investigators working on everything from genetics to evolution to ecology. “It’s a great place for... people in my lab to be able to do a lot of the molecular work but think about it in the context of ecology and evolution in a broader sense,” said Wolfe. Furthermore, Wolfe has been hearing from many different departments about how food is being integrated into the undergraduate and graduate experiences. Faculty are being hired around “food clusters” designed to span departments on the theme of food. For

Food is important for people who study people or people who study animals or people who study microbes or people who study ethics. You know, food is everything.

nowned Chef David Chang, founder of the Momofuku restaurant group. Thus began a series of successful collaborations in microbial education. Chang asked Wolfe and Dutton to contribute an article about miso to his quarterly food journal, Lucky Peach. After this collaboration, Wolfe began writing individual pieces, starting with a view on fermentation entitled “American Microbial Terroir,” featured in the publication’s American Food Issue. “[The article] was really fun and the response [it received] was amazing. I saw people who wouldn’t think about yeast versus mold versus bacteria using this technical language to understand food. I went to a salami shop in London and I saw they had actually cut it out and put it on the wall, and I think to myself, ‘That’s my article!’ ” While continuing his position as Lucky Peach’s expert microbiologist, Wolfe began to view his articles as a tool for educat-

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Wolfe, this is simply an extension of a fundamental truth that has guided him in the lab and at the dinner table. “Food is important for people who study people or people who study animals or people who study microbes or people who study ethics. You know, food is everything.”

Written by Sabrina McMillin, a senior majoring in political science, and Jeremy Marcus, a junior majoring in computer science and biology Images by Sabrina McMillin Vol V V Issue Issue II Fall Fall 2014 2014 || BREAKTHROUGH BREAKTHROUGH || 11 11 Vol

RE-PROGRAMMING LIFE:

Tufts Synthetic Biology

iology and the life sciences have experienced major innovations over the last half century. Today, the genome of any organism can be affordably sequenced. We have the ability to write in the code of life, for about 20 cents per A, T, C, or G. The genetic engineering toolbox is becoming much larger and significantly cheaper, sparking interest in the standardization and streamlining of genetic engineering as these tools become increasingly accessible. Investigators have dubbed this nascent field “synthetic biology.” The field has incredible breadth, from creating new technologies to detecting landmines to synthesizing cost-effective antimalarials for the developing world. Tufts’ Synthetic Biology (Syn.Bio.) was founded in order to foster interest in this emerging discipline by engaging undergraduate investigators. Tufts Synthetic Biology The goal of Tufts Syn.Bio. is to bring together a group of students who have a passion for scientific inquiry and a diverse set of backgrounds, including biology, chemistry, computer science, and engineering. The interdisciplinary nature of their work allows the team to foster creativity while developing ideas from concepts into actualizations with real-world implications. They challenge the undergraduate community to consider the implications – ethical, social, socioeconomic and political – of synthetic biology, while challenging themselves to become leaders in the field. They push their members to explore the broad applications of synthetic biology, while empowering them to develop their own skills by pursuing original research. After careful review and editing, original proposals written by team members become the focus of their research and their findings are entered in the annual International Genetically Engineered Machine (iGEM) Competition. This premier undergraduate synthetic biology competition has attracted over 240 teams from 36 countries. Tufts’ Synthetic Biology has already experienced a number of notable successes. Last fall, Founding Directors Petar Todorov (A’14) and Christopher Ghadban (E’14) taught an Experimental College course at Tufts University to familiarize interested students with molecular biology techniques. Participants were guided through the process of drafting project proposals, which were later vetted by the Tufts Syn.Bio faculty advisor, Professor Nikhil Nair from the Department of Chemical and Biological Engineering. Guest lectures provided introductions to fields such as biophysics and metabolic engineering, as well as a thorough overview of small, large, and start-up companies. The team has enjoyed excellent networking opportunities with student peers, 12 | BREAKTHROUGH | Vol V Issue I Fall 2014

From the left: Dr. Nikhil Nair, Mark Mimee, Dr. Andrew Camilli, Dr. Sebastien Lemire, Christopher Ghadban, Anna Kuchment, Robert Citorik, Dr. Robin Pierce – The Future of Phage and Synthetic Biology, October 2014.

faculty, and industry professionals alike, including J. Craig Venter and President Monaco. Ribosponge and Bacteriophage This year, the team is entering the iGEM Competition with a project that investigates bacteriophage-mediated enhancement of biofilm formation. Biofilms consist of adherent cells often embedded within a self-produced extracellular matrix. The cells within biofilms enter a stationary state and are resistant to many forms of treatment, including antibiotics. Biofilms are ubiquitous in nature and are often implicated in harmful processes, including infections, tooth decay, biofouling, and chronic wounds. However, they have also been utilized constructively in sewage treatment plants and petroleum-contaminated aquatic environments. Bacteriophages are viruses that only infect a specific strain or species of bacteria. They are composed of proteins encapsulating a DNA or RNA genome, and replicate within a bacterium following the injection of their genome into its cytoplasm. They have widespread applications and are perhaps the most diverse and abundant entities on the planet. We devised a method to infect pathogenic bacteria with a phage, which spreads an RNA element through the bacterial population that can effectively double biofilm production. This element, dubbed the “ribosponge,” acts to bind a bacterial messenger molecule which affects bacterial motility and biofilm formation. Because the signal is universal among many different bacteria, it should theoretically serve to enhance biofilm formation in many different microorganisms. The Future of Phage and Synthetic Biology The members of Tufts Syn.Bio. have given considerable thought to the ways in which their project affects policy and

(EPA), and United States Department of Agriculture (USDA) for food, environment, and agricultural applications respectively. However, they have yet to be approved in the western world for human therapeutics. Different classifications of phages face different challenges in the regulation and approval processes. Naturally occurring phages have greater potential for more rapid approval, but face greater difficulty in terms of intellectual property (IP) and industrial integration. Engineered phages have the potential for greater efficacy and clearer IP rights, but face additional challenges in regulatory approval. Furthermore, phage-related techniques must overcome the considerable challenge of integration into the health care industry. Given the specificity of phage, experts in the requisite, rapid diagnostics for accurate treatment will be required. The co-evolution of the phage and the bacteria must be observed, and delivery mechanisms must be developed and improved. The difficulty extends beyond the realm of science as well; can this treatment be made readily available for individuals of all socioeconomic backgrounds? As antibiotic resistance becomes a more pressing issue, these challenges inherent to the search for alternative therapies must be met head on. The conference write-up will cover these points and be used to expand the conversation. See their website at www. TuftsSyntheticBiology.com to learn more and follow these developments.

practices in synthetic biology. The use of phage beyond the laboratory raises poignant bioethical questions. Can we safely deploy genetically engineered phages that have the ability to replicate, spread, and evolve? Could phages be used for harm instead of good by nefarious actors? Are there more appropriate ways to regulate and approve the deployment of phages clinically and commercially? In Moving Forward addition, members of the general public know very Tufts Synthetic Biology little about these useful will present the results from the viruses and tend to treat SYNENERGENE grant and the them with apprehension. ribosponge project at the annual Tufts Synthetic Biology iGEM competition in November received a grant from the 2014. Through participation in the European Commission’s iGEM competition, undergraduate SYNENERGENE Project researchers have an excellent which aims to initiate and opportunity to foster intellectual foster public dialogue connections and network with on synthetic biology and world-class leaders from science mutual learning processes and industry while increasing the among a wide variety of visibility of Tufts engineering and From the left: Dr. Sebastien Lemire, Dr. Andrew Camilli, Anna Kuchstakeholders. They are one science in the broader synthetic of eight teams to have been ment, Christopher Ghadban, Mark Mimee, Robert Citorik, Dr. Robin Pierce – The Future of Phage and Synthetic Biology, October 3, 2014 biology community. Through awarded the grant and the the course and lecture series, only team in the United Tufts Synthetic Biology expands undergraduate education and States. In addition to the required written application and moral mentors underclassmen at the intersection of science, ethics, and scenarios on phage utilization, Tufts Synthetic Biology hosted a regulation to promote their involvement in life sciences research. conference which brought together leaders of industry, regulation, They have begun to pave the way for increasingly interdisciplinary and research to discuss the intersection of bacteriophage and independent undergraduate research at Tufts. therapy, synthetic biology, and society. The conference, entitled ‘The Future of Phage and Synthetic Biology’, consisted of two main events. The first was a professional workshop between our participating experts, held under Chatham House rules, to discuss and advance a pre-written framework for bacteriophage applications and associated safety and regulatory considerations. This was followed by a public forum to present the results and implications before shifting to guided, informal discussion. Phage applications are amazingly varied and hold incredible promise. To date, they have been approved by the Food and Drug Administration (FDA), Environmental Protection Agency

Tufts Sythetic Biology would like to thank its sponsors: TCU Senate, Tufts Institute of Global Leadership (IGL), GSL Biotech LLC, Lucigen, AddGene, VWR International, ThermoFischer, New Englad Biolabs (NEB), and Integrated DNA Technologies (IDT).

Written by Christopher Ghadban (E14) and Petar Todorov (A14) Vol V Issue I Fall 2014 | BREAKTHROUGH | 13

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Research with Impact

Tufts Institute for Innovation Supports Collaboration across Campuses

his summer the Tufts Institute for Innovation (TII), an exciting new venture in collaborative and leading-edge research, was officially launched. The TII is a new initiative at Tufts that is bringing together researchers across multiple campuses and disciplines in order to address important global problems. By shaking up the way academia traditionally works, the TII hopes to deliver the most global impact possible. The TII plans to address limitations in the way academic research is conducted in order to expand the scope of problems that can be addressed and to implement solutions with greater impact. As Deputy Director Lauren Linton explains, “It’s just the nature of the beast in academia. You have faculty, they’re in departments, they have a tenure process they adhere to, they have ways in which they apply for their grants and funding, that all support the existing concept that you work within your

“

To really be successful in working outside your discipline and creating multi-disciplinary teams, something has to change.

”

discipline. To really be successful in working outside your discipline and creating multi-disciplinary teams, something has to change.” The TII is taking the first step by requiring that projects involve researchers from at least two campuses and disciplines. This allows researchers to consider multiple aspects of a problem and to build a team that includes different viewpoints and draws on Tufts’ expertise in addressing societal and global needs. Founding Director and Professor of Chemistry David Walt states, “at TII we are focused squarely on

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finding the best solutions to pressing global challenges… We aim to deliver solutions to these problems by comprehensively tackling them from the lab bench all the way through to implementation.” This focus on implementation will be expanded in the future to incorporate public policy and social science arenas. Many health and environmental challenges involve aspects of politics, culture, and socioeconomics; having members on a team that represent those issues will deliver greater impact by changing policy, delivering a vaccine, or commercializing a product, for example. President Anthony Monaco, whose office initiated the TII as part of the T10 Strategic Plan, has first-hand experience directing the Wellcome Trust Centre for Human Genetics at Oxford where he “saw the power of bringing the different perspectives of multiple disciplines into one building to work on a set of diseases which have complex causes and therefore

needs for diagnosis and therapy. The TII is using a similar approach but is going one step further in trying to bring teams together to consider not only the scientific challenges but also the implementation and policy obstacles that must be overcome in order for the research to have impact in a real world setting.” The Institute had its official launch ceremony on August 28, 2014. It is currently based on the Boston Health Sciences campus, although it involves faculty and research on all three of Tufts’ Boston, Medford, and Grafton campuses. The TII is funding four projects that began this year after their first request for proposals; the second request went out in September and proposals are due in January. The next round of funding will begin in May 2015 with initial budgets of $50,000 to $100,000 per project, but the Institute will also offer continued support to help write grants and raise funds beyond the first year. The inaugural focus area for TII is “Microbes: Improving the Environment and the Human Condition.” The first four projects are addressing issues in public health, disease detection and vaccination. Professor Gillian Beamer’s team will generate a platform to develop a simple, handheld, temperature stable, quick diagnostic test for tuberculosis. No currently available test is specific, sensitive, direct, and rapid at the same time. Professor Elena Naumova is leading a team that will have field sites in Ghana and India. It will integrate informa-

tion from environmental water sampling, health care reporting, remote sensing imagery, and meteorological records to build a surveillance system for water-associated infectious diseases such as cryptosporidium, schistosomiasis, and cholera. Professor Xingmin Sun’s team aims to develop a Clostridium difficile vaccine and to clinically evaluate the best vaccine candidate to manage C. difficile infections, which commonly arise from long hospital stays. The final team, led by Professor Sam Telford, aims to fight Lyme disease in humans by developing a Lyme disease vaccine for mice in order to limit their effectiveness as a car-

rier for the causative microbe. The institute is also committed to involving undergraduates in its projects. “TII will provide a spark for undergraduates to engage deeply in active citizenship and service learning,” says Professor Jonathan Garlick, a member of the executive committee. An undergraduate symposium is planned for spring 2015 that will continue as a seminar series. Applications are expected to be available in December for a program to offer paid summer research opportunities. Students will have until March to apply for funding and the program will begin in June 2015. Director David Walt has high hopes for the future of the TII. He says, “We hope that Tufts Institute for Innovation will make an impact on how research is conducted by demonstrating that our integrated, comprehensive approach to problem solving will make a real difference in the world… We hope the ‘TII way’ becomes woven into the fabric of the institution. Tufts has so much expertise in a broad array of fields. We want to take advantage of this expertise and forge collaboration.”

Students interested in getting involved should contact Special Projects Manager, Jessica Ketchen, at jessica.ketchen@tufts.edu. Written by Isabel Yannatos, a senior majoring in physics Vol V Issue I Fall 2014 | BREAKTHROUGH | 15

At present, there is no precise level for which an athlete is considered to be “positive” hGH; there is simply a level at which they are deemed questionable. In this case, the conservative testing threshold allows many athletes who take hGH supplements to

Want to

Dope

Without Consequences?

A look into the process of hGH testing and how athletes are avoiding repercussions

he World Anti-Doping Agency (WADA) is the leading agency in the fight against doping in sports today. Over the summer, I had the opportunity to work at the WADA laboratory in Montreal under the tutelage of Professor Christiane Ayotte, one of the leaders in the development of new drug testing methods. As an intern in the biological section of the lab, I spent my summer testing for levels of Erythropoiesis-Stimulating Agents such as Erythropoietin (EPO), and continuous erythropoietin receptor activators (CERA) that were over the legal limit. However, I spend the majority of my time in the lab testing blood samples for human growth hormone (hGH). HGH is a hormone secreted in the Pituitary gland, and is known to stimulate the growth and regeneration of cells that help sustain vigorous exercise. There are two isoforms of this molecule, one with a molecular weight of 20 kilodaltons, and one that’s 22 kilodaltons. While hGH is naturally secreted in the blood, athletes will often supplement their supply with a synthetic version of the 22 kpa molecule in an effort to enhance their athletic performance. Since hGH is anabolic, meaning it an accelerate protein synthesis and the breakdown of fat stores, it’s able to increase muscle mass and increase muscle recovery time [3] – two things that are invaluable when training for an athletic competitions. Every year, WADA receives hundreds of blood samples that must be checked for abnormal levels of growth hormones. The test that is currently being used by WADA to detect this hormone is the hGH Isoform Differential Immunoassay [4]. This test is used to detect fluctuations in the natural ratio between the aforementioned isoforms of hGH. However, catching an athlete doping with hGH is very difficult and, in fact, out of the more than 10,000 tests that were administered between 2004 and 2013, only 12 have come back as positive [1]. This is due to two major issues: the first being that hGH has a half life of 2.5 hours in blood, and the second being that, at the moment, WADA has a very conservative testing threshold.

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“

At present, there is no precise level for which an athlete is considered to be ‘positive’ hGH; there is simply a level at which they are deemed questionable.

”

slip through the system without any sort of repercussions. In fact, during clinical testing where subjects were given growth hormone supplements, subjects did not exceed the isoform cutoff for a positive test. Since testing for this drug is questionable at best, hGH has become one of the most used drugs in sports today. However, it can have serious adverse effects that are often overlooked. For instance,

one study showed that in 40% of the male athletes they observed who had taken steroids experienced elevated blood pressure, sleeplessness, increased irritability, decreased testosterone levels, depression and loss of hair [2]. However, even more concerning are the cardiovascular issues that can arise in healthy, young athletes from prolonged use of hGH. For instance, steroids are now being associated with diseases such as cardiomyopathy, acute heart failure, and cardiac sudden death [2]. In order to stop the increased amount of steroid use in athletics today, it is necessary to either create a more precise test for hGH supplements, or to take into consideration a stricter testing threshold in relation to the Isoform Differential Immunoassay. Otherwise, players like Alex Rodriguez, Sammy Sosa, Barry Bonds and many others who’ve been “suspected” of steroid use will continue to exploit the flaws in our system and will keep setting a bad example for young athletes today.

Written by Arlene Rosenberg, a junior majoring in biology

New particle to advance

new particle named Ds3* was recently discovered in the Large Hadron Collider (LHC) in Geneva. It is a type of meson, meaning it contains one quark and one antiquark. There are six known flavors of quarks: up, down, strange, charm, top, and bottom. The Ds3* is made up of a strange quark and a charm antiquark. Scientists from the University of Warwick found the Ds3* by using a technique called Dalitz plot analysis, which consists of waiting for a particle to decay into quarks, and then tracking their motion in the LHC. This is the first time Dalitz plot analysis has been used on data from the LHC. Scientists can now study the Ds3* to better understand the strong interaction – one of the four fundamental forces – between particles (1). The strong force holds quarks together and is carried by gluons, much

like the electromagnetic force is carried by photons. Professor Tim Gershon, the lead scientist, says the Ds3* “provides a benchmark for future theoretical calculations.”(2) Furthermore, research into this newly discovered particle could also help to explain one of the greatest challenges in cosmology. Though it is believed that equal amounts of matter and antimatter were produced after the Big Bang, our universe now predominantly contains matter. Investigation of the Ds3* may help explain this asymmetry. Gershon believes that “this same technique [Dalitz plot analysis] could be used to search for new particles and sources of asymmetry that are not included in the Standard Model [of particle physics].”(1) Written by Richa Parande, a freshman majoring in economics

strange quark

Large Hadron Collider (LHC)

charm antiquark

Ds3* meson Illustration by Chinami Michaels

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Does size matter? The

Bio Medical Engineering Society

Heather McSherry (2016) is a Biomedical Engineering major minoring in Studio Art. She has worked in the Kaplan Lab and Fantini Lab in the past. In the fall of 2013, Heather worked on the project, “Inhibition of Breast Cancer Cells due to Doxycycline, Ion Channel Shifting, and Change in Ion Concentration.” The objective of this experiment was to see how the addition of doxycycline or the modification of ion channels within cancerous cells would affect the metastasis, proliferation, and cytotoxicity of the cells. In the spring she worked on, “Proposed Device Design for the Delivery of a Silk-Based Gel to Repair Vocal-Folds and Prevent Preterm Birth.” A silk gel with cross-linking properties was discovered to help in several medical applications. Heather helped design a syringe device to mix the three liquid components of the gel and apply them to the affected tissue. Emily Eickhoff (2015) is a senior biomedical engineer. During her time at Tufts she has been involved in numerous labs, but her current Senior Design Project research is focused in the Georgakoudi Lab. Emily is working to design an optically-modified laparoscope to improve visualization of lesions in the peritoneal cavity. Yusi Gong (2016) is a Biomedical Engineering major who has worked in the Xu Lab on exosome isolation techniques. Exosomes are vesicles that are naturally secreted by cells and contain biomarkers such as proteins and microRNA. They can be found in many body fluids including urine, blood, and saliva. Previous work has indicated that they can be used in diagnostics of certain diseases, as many disease-state cells secrete exosomes containing high concentrations of specific microRNA sequences. Thus, the Xu Lab is trying to efficiently isolate exosomes from urine samples, so that their contents can be sequenced. Kathleen Li (2016) is a Biology and English double major who works in the Xu Lab. Over the summer, she transformed and cloned plasmids containing the PTEN gene to be used for lentiviral infection. PTEN is a tumor suppressor gene necessary in cell cycle regulation. Mutated PTEN is associated with various cancers. Lentivirus is a delivery vector that can infect producer cell lines, permanently changing exosome characteristics formed. Lentivirus by itself will stimulate an immune response, but exosomes are well tolerated in the body. In addition, exosomes can deliver to the cytoplasm, where PTEN performs its functions. Xu Lab’s work with exosome drug delivery attempts to find a more safe and efficient way of delivering genes. Written by Rebecca Lachs, a sophomore majoring in biology 18 | BREAKTHROUGH | Vol V Issue I Fall 2014

Robert Watson Gifford Yuki Ito (2015) (2016) work together on a Kaplan/Omenetto joint project. They culture comprehensive human skin models to use as an in vitro model to study accelerated wound healing. They are currently developing a device to stimulate these skin models with electricity to signal faster and more efficient wound healing. Both Yuki and Watson study biomedical engineering with a minor in engineering management.

Jaclyn Foisy Ava Sanayei (2016) (2016) are both Biomedical Engineering majors who work together in the Kuo lab. Their research has been focused on supporting graduate students’ projects and improving devices in the lab. All projects in the Kuo lab are aimed towards understanding tendon properties (especially embryonic tendons, which heal without scarring) so that progress can be made towards improving techniques for tendon injury recovery. One device was developed to mechanically stretch embryonic tendons in a sterile environment with a known load applied. Another device used in the lab places a cyclic loading on tendons and is currently being improved by adding a component that will calculate the actual strain being placed on the tendon to ensure the accuracy of the programming of the system.

For bumblebee workers, yes.

t’s a beautiful day in the park. At your feet, a bee lands in a patch of white clover. She grabs hold of the nectar-rich snowball, sticking her tongue into the flower and vigorously buzzing her abdomen. In that moment, you decide take a closer look, and you notice that it’s a bumblebee—fuzzy and macaronisized with yellow and black coloration. Within the colony, this assiduous worker bee is responsible for leaving the nest to forage for nectar and pollen, and will travel great distances to do so. But other workers exist too, carrying out their existence from inside the colony, responsible for taking care of newly laid eggs with the collected resources. So, how are jobs assigned? Bumblebees exhibit a behavior known as alloethism, or division of labor based on size—in this case, the largest bees forage, while the smallest bees reside at home. To facilitate this separation, a 10-fold variation in body size can exist for bumblebee workers in a colony (1)—for scale, that’s the same as the difference in weight between a penny and a field mouse.

The million-dollar question then arises: why are some bumblebee workers larger han others? In search of an answer, researchers hypothesize that eggs laid on the periphery of the colony are neglected by workers and never fully develop (2). Others refute this, saying such great variation could not arise from nutrition alone, and rather suggest that this division evolutionarily maximizes colony growth—larger bees are inherently better foragers and smaller bees can better navigate the colony (3). A more recent hypothesis posits that since larger bees seem to be better at every task—in and out of the nest—it would seem intuitive that a limitation in resources would be dictating size variation; even with unlimited food, smaller bees are still produced (1). Regardless, it seems that future investigation is needed; finding the answer may not be as simple as a walk in the park.

Written by Nick Dorian, a junior studying biology, environmental studies, and bees Photo by Nick Dorian

Citations

Page 4: For the Painted Turtle, Never Aging Wins the Race [1] Van Dijk PP (2013) Chrysemys picta. The IUCN Red List of Threatened Species. Version 2014.2. http://www.iucnredlist.org/details/163467/0. Accessed 21 September 2014. [2] Congdon JD, Gibbons JW, Brooks RJ, Rollinson N, Tsaliagos RN (2013) Indeterminate growth in long-lived freshwater turtles as a component of individual fitness. Evol. Ecol. 27, 445-459. [3] Schwanz L, Warner DA, McGaugh S, DiTerlizzi RD, Bronikowski A (2011) State-dependent physiological maintenance in a long-lived ectotherm, the painted turtle (Chrysemys picta). Exp. Biol. 214, 88-97.

Page 14: Research with Impact Interviews by Isabel Yannatos

Page 16: Want to Dope Without Consequences? [1] (2012) Steroids (Anabolic). National Institute of Drug Abuse. Available: http:// www.drugabuse.gov/drugs-abuse/steroids-anabolic. Accessed 12 October 2014 [2] (2014) Human Growth Hormone (hGH) Testing. The World Anti-Doping Agency. Available: https://www.wada-ama.org/en/questions-answers/hghtesting#node-5456. Accessed 3 October 2014. [3] Epstein D (2013) A First Step Towards hGH Testing – In the Wrong Direction. Page 6: A Classical Genetic Story Sports Illustrated. Available: http://mmqb.si.com/2013/07/24/hgh-test/. Accessed [1] Mirkin, SM (2007) Expandable DNA repeats and human diseases. Nature 447: 2 October 2014. 932-940. [4] Hartgens F, Kuipers H (2004) Effects of Androgenic-Anabolic Steroids in Ath[2] Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, letes. The American Journal Of Sports Medicine. 34 (8): 513-554 Bonaldi T, Haydon C, Ropero S, Petrie K. et al. (2005) Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Page 17: New Exotic Particle Ds3* Nat. Genet. 37: 391-400. [1] Dickerson K (2014) New Exotic Particle Could Help Explain What Holds Mat[3] Pfister S, Rea S, Taipale M, Mendrzyk F, Straub B, Ittrich, C, Thuerigen O, Sinn ter Together. LiveScience. TechMedia Network. Available: http://www.livescience. HP, Akhtar A, Lichter P (2008) The histone acetyltransferase hMOF is frequently com/48271-new-particle-ds3-discovered.html. Accessed 19 October 2014. downregulated in primary breast carcinoma and medulloblastoma and constitutes a biomarker for clinical outcome in medulloblastoma. Int. J. Cancer. 122: 1207-1213. Page 19: Size Matters [4] House N, Yang J, Walsh S, Moy J, Freudenreich CH (2014) NuA4 initiates dy- [1] Couvillon MJ, Jandt JM, Duong N, Dornhaus A (2010) Ontogeny of worker namic histone H4 acetylation to promote high-fidelity sister chromatid recombi- body size distribution in bumblebee (Bombus impatiens) colonies. Ecol. Entom. nation at post-replication gaps. Mol. Cell. 55(6). doi: 10.1016/j.molcel.2014.07.007. 35: 424-435. PMID: 25132173. [2] Couvillon MH, Dornhaus A (2009) Location, location, location: larvae position inside the nest is correlated with adult body size in worker bumble-bees (Bombus Page 8: Faults Friction and Fractures impatiens). Proc. R. Soc. B. Published online. Interview by Yusi Gong [3] Goulson D, Peat J, Stout JC, Tucker J, Darvill B, Derwent LC, Hughes WOH (2002) Can alloethism in workers of the bumblebee, Bombus terrestris, be exPage 10: Brown and Bleu plained in terms of foraging efficiency? Anim. Behav. 64: 123-130. Interview by Sabrina McMillin and Jeremy Marcus

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