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News Archives: 2014-2015

Tufts University named 3rd in country for undergraduate degree in Biology
College Factual (USA Today) names Tufts University Biology Department in the top 10 colleges for an undergraduate degree. Read more >

Faculty News

The Department of Biology support staff won the "Extraordinary Colleague Award, For Surpassing Expectations" this year at the eighth annual Tufts Distinction Awards ceremony. The group consists of: Michael Doire, Michael Grossi, Eileen Magnant, Karin Murphy and Elizabeth Palmer. Congratulations staff!

Erik Dopman received tenure and has been promoted to Associate Professor. Congratulations Erik!

Science magazine features research by Professor Colin Orians on links between climate change, tea quality, and farmer livelihoods. Read more >

Assistant Professor Ben Wolfe's research was featured in a podcast from Gastropod about the science and history of cheese. Watch the podcast and read the article here.

Barry Trimmer, Professor of Biology, received a major NSF grant to study neuromechanics of soft-bodied locomotion totaling $610,000. Congratulations Barry!

Catherine Freudenreich, her graduate student Allen Su, and their collaborators in Basel, Switzerland, published a paper in Genes and Development entitled “Regulation of Recombination at Yeast Nuclear Pores Controls Repair and Triplet Repeat Stability”. Follow the coverage of this story at Tufts Now.

Benjamin Wolfe, Assistant Professor of Biology, has published a cutting-edge review in Cell, the highest impact factor journal in Biochemistry & Molecular Biology, entitled "Fermented Foods as Experimentally Tractable Microbial Ecosystems". (Benjamin & Dutton (2015) Cell 161: 49–55).

Sergei Mirkin, Biology Department Chair, was an organizer of the FASEB Summer Research Conference "Dynamic DNA Structures in Biology".

Mathers Foundation renewed its support for Michael Levin's Center for Regenerative & Developmental Biology with a continuation grant of $987K.

Eric Tytell, Assistant Professor of Biology received two grants this summer: Army Research Office W911NF-14-1-0268, "Coupling mechanical and neural properties for effective and adaptable locomotion", 6/1/14 - 5/31/17, $350,366. Army Research Office W911NF-14-1-0494, "Neuromuscular control of rapid linear accelerations in fish", 6/1/14 - 2/28/15, $48,157.

2014. Sass, E. (former undergraduate), J. L. Mortensen, and J. M. Reed. Habitat suitability model for the White-breasted Thrasher in Saint Lucia. Presented at the 2nd North American Congress for Conservation Biology (NAACB), Missoula, MT and the Joint meeting of the Association of Field Ornithologists & Wilson Ornithological Society, Newport, RI.

Elizabeth Crone received a grant to study "Pulsed floral resources and pollinator population dynamics". This is a four-year grant from the National Science Foundation to study how resources affect colony dynamics of bumble bees, in collaboration with Neal Williams (University of California, Davis).

J. Michael Reed, Professor of Biology, was mentioned in Nature regarding the Devil's Hole pupfish.

In Spring 2014, Catherine Freudenreich, started a new research direction and gave seminars at several French Institutes during her sabbatical stay at the Curie Institute, Orsay France.

Colin Orians, Professor of Biology, was mentioned in a New York Times article, On the Cusp of Climate Change, regarding Tea.

Jan A. Pechenik has carefully edited Charles Darwin’s Origin of Species (6th edition) for modern readers. The Origin of Species is one of the most influential books ever written, and yet it is rarely read today. Jan hopes that this version of the book will change that. He has shortened paragraphs, strengthened and reorganized sentences, clarified ideas, defined terminology, identified the various people referred to by Darwin, and included numerous photographs and drawings. The Readable Darwin has just been published by Sinauer Associates: www.sinauer.com

Professors Sergei Mirkin, Catherine Freudenreich, and Mitch McVey, together with their colleagues from Brandeis James Haber and Susan Lovett, were awarded a 5 year Program Project Grant from NIH entitled "Mutations Arising during DNA Repair", which totals $8.6 million. Many human diseases are associated with alleles that can be as simple as single-nucleotide changes to copy-number variants, gene fusions and translocations. The wealth of recent whole-genome sequencing has led to the realization that recent mutation plays important a role as variations that arose in distant ancestors. These disease-associated alleles can arise from mutational events that are provoked by errors arising in a number of ways during DNA replication, including (a) ionizing radiation, (b) the excision of mobile genetic elements, (c) the formation of double strand breaks (DSBs) at stalled replication forks, (d) replication slippage in DNA sequences that form alternative secondary structures, (e) conflicts between replication forks and the transcription machinery, and (f) the filling-in of single-stranded DNA. This Program Project focuses on these different sources of mutation in a highly interactive set of projects that link researchers at Brandeis University and Tufts University studying three powerful model organisms: the bacterium E. coli, the single cell eukaryote, the budding yeast S. cerevisiae, and the metazoan, fruit fly D. melanogaster. Its goal is to understand in great detail the way various types of mutations arise as well as to identify transcription, replication and DNA repair factors whose defects elevate their appearance.

Jan Pechenik received a 3 year NSF grant entitled "Ocean Acidification/Collaborative Research/RUI: Effects of Ocean Acidification on Larval Competence, Metamorphosis, and Juvenile Performance in a Planktotrophic Gastropod" totaling $315,000. Levels of CO2 in the air are now about 40% higher than they were at the start of the Industrial Revolution about 200 years ago. At least 1/3 of our excess CO2 production has been absorbed by the ocean, making it substantially more acidic as the CO2 forms carbonic acid. Understanding the likely impact of this increasing ocean acidification (OA) on marine animals and ecosystems is complicated by the fact that other features of the environment are also expected to change appreciably (e.g., seawater temperatures will increase and food availability and nutritional value may decline), by the fact that stresses experienced in early development can have lasting effects even after metamorphosis, and because the molecular mechanisms lying behind the responses measured to date are poorly understood. Our study will help us to understand how ocean acidification under different environmental conditions will impact the development, dispersal, and metamorphosis of the marine snail Crepidula fornicata, a common species native to the eastern U.S. that has become established in the coastal waters of the Pacific Northwest, Europe, and elsewhere. Our study should also help to predict future changes in the range of this invasive species. In addition, our work on the molecular basis for its responses to environmental change will extend the usefulness of this species as a model for future studies of development in molluscs and related species.

Michael Levin has received a 3-year, $493,649 award from the Templeton World Charity Foundation to study how the information stored and processed by an electrical network in non-neural tissues provides control for their regeneration.

Elizabeth Crone's paper, "Desynchronization and re-synchronization of reproduction by Astragalus scaphoides, a plant that flowers in alternate years" Ecological Research, Volume 28 (2013), pp. 133-142, has been selected as one of three outstanding papers whose authors are awarded the Ecological Research Paper Award. The award ceremony will be held in the Annual General Meeting of ESJ in Hiroshima, Japan.

Sara Lewis was invited to talk about Lewis Lab research on firefly evolution at the TED2014 Conference in Vancouver, BC.

Catherine Freudenreich has been awarded a fellowship from the Institut Curie for senior researchers on sabbatical. Support from the Edmond de Rothschild and Yvette Mayent Foundations enables Institut Curie to award fellowships each year, allowing internationally-renowned scientists to spend time working at one of the Research Centre's laboratories. Catherine will be collaborating with scientists at the Orsay Research Center, giving talks, and interacting with researchers at both the Orsay and Paris Curie Institute locations for three months, March-May 2014.

Catherine Freudenreich was awarded a 3 year-long NSF grant entitled "Role of ISWI Chromatin Remodeler in Transcription-coupled Repair and Genome Stability" totaling $570,000.

Congratulations to Michael Levin, who together with David Kaplan, have just received a $1M award from the W. M. Keck foundation to fund their project titled "Harness Natural Bioelectricity for Limb Regeneration".

Michael Romero received a grant from NSF to hold a workshop entitled "Stress in the Healthy Animal." It was a joint workshop between researchers typically funded by NSF (i.e. non-medical research) and researchers funded by NASA. Wild animals and astronauts are similar in that they are generally healthy yet have to cope with stressors from the environment. The workshop explored what theoretical and technical advances are needed to make progress in understanding stress under these conditions.

Sergei Mirkin was awarded a 4 year-long competitive renewal of his NIH grant on Replication of Simple DNA Repeats totaling $1,335,525

Sara Lewis gave an invited plenary lecture on the evolution of insect nuptial gifts at the Royal Entomological Society's annual meeting held in St. Andrew's Scotland in September

Barry Trimmer, Professor of Biology, has been named Editor-in-Chief of Soft Robotics (SoRo), a groundbreaking peer-reviewed journal. Soft Robotics is a journal for research into the development and application of soft materials in mobile machines. There is an urgent need for robots that can safely interact with living systems and function in complex natural, or human-built, environments. For these machines to be adaptable and sustainable we must have a better understanding of soft materials and know how to make new ones. It is also important to know how to build appropriate soft structures, actuators, and sensors; how to control movements in high deformation devices; and how to interface electronics, optics, and power solutions into such non-traditional materials. More information on Soft Robotics >

Michael Levin, Director of Tufts Center for Regenerative and Developmental Biology, was featured on Smithsonian.com in with an article, Surprising Science: These Decapitated Worms Regrow Old Memories Along with New Heads (Smithsonian, Jul. 11, 2013). Another article was published on Nature World News in July, Decapitated Worms Retain Old Memories after Regrowing Heads. Also, Dr. Levin is the winner of a High-Performance Computing Cluster Research Grant from Silicon Mechanics. This complete high-performance computing cluster, valued at $79,000, will be used as a key component of an exciting, multidisciplinary effort to transform the way biological pattern formation is investigated.

Colin Orians and his collaborators recently received two NSF grants to continue their research. First, as part of a collaborative research project with Evan Preisser and Carol Thornberg (University of Rhode Island), the Orians lab received a three-year grant ($300,000) to examine the interactions between eastern hemlock and two invasive insect herbivores. Many thanks go to Coco Gomez who was instrumental to the success of this proposal. Second, the Orians lab along with colleagues at Tufts, Montana State University, and University of Florida received a four year grant ($931,000) to examine the effects of climate and herbivory on tea quality, and tea quality in turn affects consumer responses and farmer livelihoods in China.

Student and Post Doc Highlights

Graduate students Emily Pitcairn, Kyle Jewhurst, and Kaylinnette Pinet were awarded SDB travel fellowships to present their research at the National Society for Developmental Biology (SDB) meeting in Snowbird, Utah July 2015.

This grant is awarded by SYNENERGENE, a four year project from the European Commission aimed at establishing an open and honest dialogue about the potential benefits and risks of synthetic biology. SYNENERGENE has partnered with the iGEM to provide grants to teams around the world. Last year, as the only North American recipient, the Tufts Synthetic Biology team investigated bacteriophage therapy. This year, the team will explore the intellectual property claims surrounding CRISPR-Cas9 genome editing.

Rebecca Levy, Thesis MS student, published a paper "Explaining the sawtooth: latitudinal periodicity in a circadian gene correlates with shifts in generation number" in the January 2015 issue of the Journal of Evolutionary Biology. A photo of our species, the European corn borer, also made it onto the journal cover! (Click on image to view journal cover.)

Simran Kaushal, PhD candidate from the Freudenreich lab, received a Graduate School Research Award and also participated in the GIFT Program.

Natalie Kerr, PhD candidate from the Crone lab, attended the BES Symposium: 2015 Demography beyond the population in Sheffield, UK.

Rachael Bonoan, PhD candidate from the Starks lab, has been awarded three grants (the Foundation for the Preservation of Honey Bees, Inc. Research Grant, the Essex County Beekeepers Association Grad Student Research Grant, and the Animal Behavior Society Student Research Grant). She also won 1st place in the research portion of the annual Graduate Student Photo Contest. Rachael also attended the Animal Behavior Society 2015 Conference in Anchorage, AK where she gave a presentation on the seasonality of mineral preferences in honey bees.

Anthony Scibelli, graduate student in the Trimmer lab, presented at the 2014 regional Society of Integrative and Comparative Biology conference.

From the McVey Lab: Kelly Beagan won the Best Poster Award at the Zing DNA Polymerases conference in Oxford, England in August of 2014. Varandt Khodaverdian won a Graduate Student Research Award from Tufts in the fall of 2014. Kasey Rodgers published a review titled "Error-prone repair of DNA double-strand breaks" in the Journal of Cellular Physiology in May of 2015.

Livia Baer-Bositis received funding through the Tufts University Graduate Student Research Competition as well as the Tufts Water Diplomacy IGERT traineeship.

Rachael Bonoan has participated in various invited talks for beekeepers and the general public. She gave a talk to the Boston Area Beekeepers Association, the Barnstable County Beekeepers Association, the Portsmouth, RI Garden Club, Pint of Science, and was part of Catalyst Conversation's "The Buzz About Bees".

Allen Su, Freudenreich lab, received the following awards: (1) Best Thematic Poster Award in DNA replication and repair theme by American Society of Biochemistry and Molecular Biology (ASBMB) in Experimental Biology 2015 annual meeting in March 2015. (2) Yeast Genetics Meeting Travel Award from Genetics Society of America (GSA) in July 2014.

Michael Babokhov, Fuchs lab, received a graduate student research award from GSAS and he also received an EAPSI (East Asia Pacific Summer Institutes) award from NSF and conducted research in Japan.

Michael Babokhov and Ishtiaque Quasem presented their research at the 2015 American Society for Biochemistry and Molecular Biology meeting in Boston.

The following presented at scientific conferences:

Jewhurst, K., and McLaughlin, K.A. (2014) A novel model of oxidative heart disease in Xenopus laevis. 74th National Society for Developmental Biology Conference, Seattle, WA.

Pitcairn, E., and McLaughlin, K.A. (2014) Investigating the role of transmembrane voltage potential during embryogenesis. 74th National Society for Developmental Biology Conference, Seattle, WA.

Parker, C.E., Franco, L., Romero, L.M. 2015. Are novel objects stressful? The relationship between heart rate and neophobia in the European starling (Sturnus vulgaris). Soc. Integ. Comp. Biol.

Rao, R., Parker, C.E., Romero, L.M. 2015. Daytime vs. nighttime incorporation of exogenous corticosterone in feathers of European starlings. Soc. Integ. Comp. Biol.

Flower, J.E., Mark A. Mitchell, M.A., Norton, T.M., Andrews, K.M., Nelson, S.E., Parker, S.C., Romero, L.M. 2014. Baseline plasma corticosterone levels in rehabilitation and free-ranging nesting loggerhead sea turtles (Caretta caretta). Amer. Assoc. Zoo Vets.

The Department of Biology congratulates Crista Wadsworth for being selected the first recipient of the Lily Glidden Award. Crista will be using the award to backpack in the mountains near Crested Butte, CO for two weeks in June and July. She will use this opportunity to observe and collect butterflies to continue her research on dormancy in Lepidoptera. Crista is a 5th year Ph.D. candidate in the Dopman laboratory.

Congratulations to the Tufts Synthetic Biology Team for winning Gold at the iGEM competition! Read more about iGEM in the Tufts Daily.

Livia Baer-Bositis, Ph.D. candidate, BA, Biological Sciences, Northwestern University, 2013

Cassandra Donatelli, Ph.D. candidate, BA, University of Rochester, 2014

Rory Fuller, Ph.D. candidate, BS, Biology & Biotechnology, Worcester Polytechnic Institute, 2006

Prasong Mekdara, Ph.D. candidate, BA, Psychology & Biology, California State University Fresno, 2010; MA, Biology, California State University Fresno, 2014

Esther Miller, Ph.D. candidate, BA, Biological Sciences, University of Oxford, 2005

Ritwika Mukherjee, Ph.D. candidate, BS-MS, Biological Sciences, IISER-Thiruvananthapuram, India, 2014

B. Taylor Sands, Ph.D. candidate, BA, Biological Sciences, Cornell University, 2011

Anthony Scibelli, Ph.D. candidate, BS, Neuroscience, Western N.E. University, 2014

Eric Scott, Ph.D. candidate, BA, Biology, Whitman College, 2006; MS, Ecology, Evolution, Cons., U. of Illinois Urbana-Champaign, 2010

Ekaterina Spivakovsky-Gonzalez, MS, Biochemistry, University of Oxford, 2013

Allison Levine, Coursework MS, BA, Psychology, University of Michigan, 2008; MA, Science Education, 2010

James Schultz, Coursework MS, BA, Biology, Carthage College, 2014

Michaela Snead, Coursework MS, BA, Biology, Mt. Holyoke College, 2011

Elyse Bolterstein, a postdoctoral fellow in the McVey lab, took an assistant professor position at Northeastern Illinois University, starting September 1, 2014. Congratulations Elyse!

Kelly Beagan, a graduate student from the McVey lab, won the Best Poster prize at the Zing DNA Polymerases conference for her work on DNA polymerase theta.

Jen Mortensen, PhD candidate in the Reed laboratory, presented at the following conferences:
2014. Mortensen, J. L. and J. M. Reed. Population viability of an endangered avian cooperative breeder following habitat loss. Presented at the 2nd North American Congress for Conservation Biology (NAACB), Missoula, MT & the Joint meeting of the Association of Field Ornithologists & Wilson Ornithological Society, Newport, RI. Jen Mortensen also presented her research at a White-breasted Thrasher conservation planning workshop held in Saint Lucia in February of 2014, where I was invited as the species technical expert. The conservation action plan, which includes scientific research, education, and media components, and was assembled over the course of a few weeks based on outputs from a 2-day workshop attended by individuals from Saint Lucia government ministries, Saint Lucia media, and local and international NGOs. The citation for the action plan that she co-wrote: Felix, M. L., J. L. Mortensen, M. N. Morton, and J. Tschirky. 2014. The Gòj Blan Plan: an action plan for recovering the white-breasted thrasher on Saint Lucia. Report to the Trust for the Management of Rivers, Saint Lucia Forestry Department, Saint Lucia National Trust, Durrell Wildlife Conservation Trust, and the American Bird Conservancy. Jen also co-wrote the White-breasted Thrasher species account for the Cornell Lab of Ornithology Neotropical Birds online publication. Citation: Mortensen, J. L., K. F. Freeman, M. N. Morton. 2014. White-breasted Thrasher (Ramphocinclus brachyurus), Neotropical Birds Online (T. S. Schulenberg, Editor). Ithaca: Cornell Lab of Ornithology; retrieved from Neotropical Birds Online.

Leone Brown, currently a postdoctoral researcher in the Crone lab, was awarded a "Mathematical Biology" (Intersections of Biology and Mathematical and Physical Sciences and Engineering) postdoctoral fellowship from the National Science Foundation. Lee will be leaving Tufts at the end of February to start her project at the University of Georgia.

Kirsi Alahuhta, a Ph.D. student at the University of Oulu in Finland, arrived in September for a 6-month Fulbright fellowship in the Crone lab. She will be building empirically-based population models to study life histories of northern orchids.

Rachael Bonoan, graduate student in the Starks lab, had a publication this past spring in Naturwissenschaften (Bonoan, R. E., R. R. Goldman, P. Y. Wong and P. T. Starks (2014) Vasculature of the hive: heat dissipation in the honey bee (Apis mellifera) hive. Naturwissenschaften 101(6): 459-465.) and presented results from this study at the International Society of Behavioral Ecology this summer. The same study was also reviewed in The Economist, ScienceDaily and TuftsNow.

Kelsey Graham and Rachael Bonoan, PhD candidates in the Starks lab, had a featured story in Tufts Now, Keeping Bees Healthy. This research was done with the assistance of a summer REU student, Marlen Rodriguez from Fullerton College.

Emily Pitcairn and Kyle Jewhurst, doctoral students in the McLaughlin lab, were awarded Graduate Student Travel Awards to attend and have their work presented at the Society for Developmental Biology 73rd Annual Meeting to be held in Seattle, WA July 2014. Kyle was also awarded a travel fellowship from the SDB!

Brook Chernet, Levin Lab, successfully defended his Ph.D. thesis, "Bioelecteric Detection and Control of Tumor Growth in Xenopus laevis". Anne Madden from the Starks Lab also defended her Ph.D. thesis, "Vespid Microbiology: Characterizations and Implications of Paper Wasp Microorganisms Across Levels of Biological Organization". Congratulations Brook and Anne! Congratulations also go to Christine Lattin, Romero Lab, who successfully defended her Ph.D. thesis, "Beyond plasma hormones: Investigations upstream and downstream of circulating corticosterone".

Anne A. Madden, doctoral candidate in the Starks Laboratory, along with Rob Dunn--a professor of biology at NC State University, presented an educational talk "You fermented my beer with what?!" at the World Beer Festival in Raleigh, NC, as part of a NC Science Festival initiative. She, along with her undergraduate students from the Fall 2013 class "Experiments in Ecology (Bio51)," isolated a wild yeast that was used by the head brewmaster of NC State's Food Science program, John Sheppard, to brew a number of beers showcased at the World Beer Festival.
More information on the collaboration and event can be found at: Your Wild Life and NC public radio.

Matt Kamm, 1st year graduate student in the Michael Reed laboratory, was quoted in a Boston Globe article, "Long-extinct heath hen comes to life in archival film". Read article >

Jen Mortensen, 4th year doctoral student in the Michael Reed laboratory, just came back from St. Lucia, where she participated in an international effort to develop a management plan for an endangered bird species – the white-breasted thrasher. Jen has been working on them for several years, and was invited to give a talk and to co-write the plan (which she is doing now).

Ailene Ettinger, Post Doc in the Crone Laboratory, was awarded a two-year NSF Postdoctoral Research Fellowship in Biology ("Intersections of Biology and Mathematical and Physical Sciences and Engineering").

Ryan McGinty's proposal won a competition for the MinION Access program (MAP); he was chosen to join the very first wave of MAP participants! MAP program was started by Oxford Nanopore to allow scientists in developing sensing applications, such as DNA sequencing, on their proprietary platform. In this platform, DNA is being continuously decoded while travelling through a tiny nanopore. This methodology has huge advantages over the existing sequencing methods, and it might drop the cost of sequencing a complete human genome below $1000. Ryan will receive free Nanopore machine and all necessary supplies to carry out whole genome sequencing for his studies. Congratulations to Ryan for bringing us all into the new era of genome sequencing. Ryan is a 3rd year graduate student in the Mirkin Laboratory.

Carolyn Bauer, a doctoral student in the Romero lab, won the "Aubrey Gorbman Best Student Presentation Award" for her talk in the Division of Comparative Endocrinology at the Society of Integrative and Comparative Biology meeting in Austin, TX. She also recently published a manuscript: Bauer, C.M., Hayes, L.D., Ebensperger, L.A. & Romero, L.M. (2014) Seasonal variation in the degu (Octodon degus) endocrine stress response. General and Comparative Endocrinology 197: 26-32.

Christine Lattin, graduate student in the Romero laboratory, presented her research at two different conferences: the Society for Environmental Toxicology and Chemistry meeting in Nashville, TN in November 2013 and the Society for Integrative and Comparative Biology meeting in Austin, TX in January 2014.

Christine also received travel grants from both the Tufts Institute for the Environment and the Society for Environmental Toxicology and Chemistry to attend the meeting in Nashville.

She was also a co-author on three new publications:

Lattin, C. R. and L. M. Romero (2013). "The size of a melanin-based plumage ornament correlates with glucocorticoid receptor concentrations in the skin of that ornament." Biology Letters.

Knapp, C. R., K. N. Hines, T. T. Zachariah, C. Perez-Heydrich, J. B. Iverson, S. D. Buckner, S. C. Halach, C. R. Lattin and L. M. Romero (2013). "Physiological effects of tourism and associated food provisioning in an endangered iguana." Conservation Physiology 1(1): cot032-cot032.

Kennedy, E. A., C. R. Lattin, L. M. Romero and D. C. Dearborn (2013). "Feather coloration in museum specimens is related to feather corticosterone." Behavioral Ecology and Sociobiology 67(2): 341-348.

Carolyn Bauer, a doctoral student in the Romero lab, won the "Aubrey Gorbman Best Student Presentation Award" for her talk in the Division of Comparative Endocrinology at the Society of Integrative and Comparative Biology meeting in Austin, TX. She also recently published a manuscript: Bauer, C.M., Hayes, L.D., Ebensperger, L.A. & Romero, L.M. (2014) Seasonal variation in the degu (Octodon degus) endocrine stress response. General and Comparative Endocrinology 197: 26-32.

Anne A. Madden, doctoral student in the Starks lab, was one of eight individuals awarded a two year Alfred P. Sloan Foundation Microbiology of the Built Environment Postdoctoral Fellowship. She will be pursuing research investigating the contribution of arthropods to the microbial communities of houses in association with Dr. Noah Fierer of the University of Colorado at Boulder, and Dr. Rob Dunn of North Carolina State University. Congratulations Anne!