Tufts University  |  School of Arts and Sciences  |  School of Engineering  |  Find People  | 
   

News

The Biology department would like to welcome Dr. Erik Hoel, who started as a Research Assistant Professor at Allen Discovery Center.
Dr. Erik Hoel completed his postdoctoral training with Rafael Yuste at Columbia University. He uses information theory and causal analysis to explore the biological basis of consciousness and understand the nature of emergence. Part of this research is on how complexity and information theory can be used to track or measure the neural difference between consciousness and unconsciousness, using data from cutting-edge neuroscientific methodologies. The goal is to develop a formal measure of consciousness that can be empirically verified and is medically useful. A second aspect of his research is to understand how causal structure changes across scale, and how information theory metrics can capture and quantify the emergence of macroscale causal structure. The goal is to improve causal model choice in scientific fields, as well as solve long-standing problems in neuroscience, such as identifying the fundamental functional unit of the mammalian brain. He is pursuing this by causally analyzing the cortex from the microscale of individual neurons to the mesoscale of neural ensembles to the macroscale of brain regions.
Dr. Hoel will be based at the Allen Discovery Center, room 335.
We are exceptionally lucky to have a scientist of Dr. Hoel's caliber in our ranks, and look forward to years of exciting scientific interactions with him.

Professor Barry Trimmer and his colleague Vishesh Vikas have been awarded a new NSF grant as part of the National Robotic Initiative entitled 'M3SoRo: Mobility and Morphing using Modular Soft Robots.'

Throughout October 2018, Professor Barry Trimmer is serving as a Distinguished Visiting Fellow of the Scottish Informatics and Computer Science Alliance (SICSA) in Edinburgh.

Congratulations to Biology Ph.D. candidate Charles van Rees, who won 'Best Paper' at the 2018 Conference of The Waterbird Society. In August 2018, members of Tufts University's Reed Lab and Romero Lab traveled to Vancouver, Canada and attended the Waterbird Society annual conference. They also attended the 27th International Ornithological Congress, which provides a platform for ornithologists around the world to meet and share up-to-date research, along with conservation accomplishments and concerns. The Congress occurs every four years, and is considered the oldest and most prestigious of meetings for avian scientists.

Congratulations to Ph.D. candidate Avalon Owens, who won the Founders Memorial Award for the best student or postdoc paper at the 2018 Animal Behavior Society Meeting held in Madison, Wisconsin.

Congratulations to members of the Mirkin Lab, whose paper "The mechanisms of genetic instability caused by (CGG)n repeats in an experimental mammalian system" was recently published in Nature Structural & Molecular Biology. The paper is also referenced in a News & Views feature.

Congratulations to Dr. Michael Romero, who received a Presidential Award for Excellence in Science, Mathematics & Engineering Mentoring, on June 25, 2018.

Congratulations to Dr. Benjamin Wolfe on his new appointment to the Eileen Fox Aptman and Lowell Aptman Professorship at Tufts University, effective May 18, 2018.

Congratulations to Allan Chen, a Tufts Biology graduate student, along with Jaclyn Dunphy, Neuroscience, who earned third place in the Gordon Institute's $100K New Ventures Competition. They pitched their idea for Cabin Labs, a pharmaceutical company engineering a safe medicine for chronic pain, and were awarded some seed money to begin their venture. Congratulations to both Allan and Jaclyn.

Congratulations to Ph.D. student Jessica Rozek. This week, Jessica received the national AbbVie Immunology Scholarship ($15,000), which is awarded to exceptional students living with inflammatory diseases. Persons with disabilities are disproportionately underrepresented in STEM as graduate students, and in the workforce. Her diagnoses of both Crohn's Disease and Autoimmune Hepatitis have encouraged her to become a voice and advocate for graduate students and young scientists with chronic illnesses.

Congratulations to the Freudenreich Lab on the recent publication of their paper in GENETICS about ISW1 and triplet repeat expansion. Their work was a featured this past week on the SGD blog "Trouble with Triplets", and they made an exciting video animation of the work.

Congratulations to Dr. Kate Mirkin for receiving a "Tufts Teaching with Technology Award" in recognition of her outstanding use of technology in the classroom. Educational Technology Services requested that students throughout the university nominate individuals "whose use of technology has had a markedly positive impact on their learning and engagement in a Tufts course." The IT Governance Sub-Committee on Teaching and Learning then selected the honorees. Kate will receive her award on the first day of the university-wide teaching conference on May 21, 2018. Congratulations to Dr. Mirkin, from everyone in the Biology department.

The awardees and honorable mentions for the 2018 NSF Graduate Research Fellowship Program competition have been announced. The NSF received over 12,000 applications, and made 2,000 award offers. Congratulations to Gabriela Garcia from the Orians Laboratory, who was awarded a fellowship this year.

Congratulations to Prof. Dany Spencer Adams, principal investigator at the Tufts Center for Regenerative and Developmental Biology and research professor in the Department of Biology, who has been named editor-in-chief of the new journal Bioelectricity. "We are on the threshold of a transformation in the intellectual and technical strategies used in the biosciences, as ever more researchers begin to explore the biophysical phenomena that act synergistically with the biochemical," said Adams in an announcement about the journal. "That makes this an exhilarating moment in the progression of bioelectricity studies, from a small specialty to an internationally recognized topic of great significance to biology and medicine."

Tufts Biology was ranked 5th in the nation by College Factual. The general biology program was ranked 5th out of 820 programs, nationwide. This makes general biology at Tufts a Top 5 program in the United States. Read more >

Congratulations to Biology Ph.D. candidate Charles van Rees, who was the recipient of a Fulbright Award to do a post-doctoral fellowship next year in Spain. He also attended a World Wetlands Day celebration in Hawaii to receive a Certificate of Commendation for Dedication and Service to Hawaiian Conservation from the State of Hawaii House of Representatives.

Tufts biologist Benjamin Wolfe and his research were featured in National Public Radio's 'The Cheese Does Not Stand Alone: How Fungi and Bacteria Team Up for a Tastier Rind". The article describes how bacteria use fungal "highways" in cheese to spread, affecting the flavor.

Congratulations to Sarah Dykstra, a post doc in the Biology Department who was co-organizer of a recent highly successful career development symposium. Learn more about the Boston Symposium on Careers and Collaboration in Science (B-SOCCS).

Research completed in Dr. Sergei Mirkin's lab was featured in a December 2017 article in Tufts Now: New process could be key to understanding complex rearrangements in genome. This approach from Tufts-led researchers could lead to new diagnostic and treatment techniques for many cancers and genetic disorders. Learn more about The Mirkin Lab >

Dr. Elizabeth Crone's work on monarch butterflies was recently featured in a Northwest Public Radio article 'Monarch Butterflies Are Disappearing, But They May Be Saved, Researchers Say.'

Congratulations to Dr. Michael Levin, who received a $1.86M grant award from DARPA's Microsystems Technology Office, for a proposal he submitted earlier this year titled "Somatic computation via bioelectricity for novel life-time learning machines." Dr. Levin was the primary investigator for this grant, and he collaborated with two co-investigators: Josh Bongard (University of Vermont) and Sara Walker (Arizona State University). Learn more about this DARPA program >

MD/PhD candidate Alex Neil in the Mirkin lab, found that mutations in the flap endonuclease (Rad27/FEN1) result in the dramatic increase in (GAA)n repeat expansions in vivo, which led him to propose a new mechanism for repeat instability involving lagging-strand template-switch during DNA replication. This work was done in collaboration with the Tainer labs at Lawrence Berkeley National Laboratory and UT M.D. Anderson Cancer Center, the Grasby lab at University of Sheffield and the Hamdan lab at King Abdullah University of Science and Technology. Learn more >

Former Graduate Student Allen Su and Professor Catherine Freudenreich, of the Tufts Department of Biology, recently published the following paper in the Proceedings of the National Academy of Sciences. In the paper, Su and Freudenreich show that that R-loop-induced deamination of cytosines is responsible for causing chromosomal breaks at an expanded CAG repeat sequence, as well as loss of repeat units (contractions). R-loops are structures that form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Expanded CAG repeat tracts are the cause of several human diseases, including Huntington's disease and myotonic muscular dystrophy. Su and Freudenreich were able to show that the repeat contractions were caused by base excision repair, a pathway used in other circumstances to repair damaged DNA bases. Intriguingly, the R-loop dependent double-strand breaks were caused by the MutL gamma endonuclease, which is known to recognize structured DNA and cause nicks, defining a new mechanism for how R-loops can generate DNA breaks. The results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. Read the paper >

Congratulations to Michael Romero, who has received a five year NSF award "ABR: Melding Mathematical and Theoretical Models of Stress" totaling $1,025,381!

Welcome to Biology. Norah Warchola is a new lecturer in the Department of Biology, where she has been a part-time lecturer since 2016. She received her B.S. in biology and her Ph.D. in ecology and evolution from Stony Brook University. Previously, she was a postdoctoral research associate at Harvard and at Tufts, studying Fender's blue butterfly and Bartram's Scrub-Hairstreak butterfly. A member of the Ecological Society of America, she has published in the Journal of Applied Ecology and the Journal of Insect Conservation.

"When we factored in climate change along with all the other threats to shorebirds, we found that 47 of the 49 species we evaluated were at a higher risk of extinction than scientists previously believed," says Michael Reed, a professor of conservation biology at Tufts University. Scientists and conservationists team up to protect imperiled migratory shorebirds. Read more >

Rachel Bonoan, PhD Student looks for clues into honey bee colony declines using hives on the Grafton Campus.

Well done to Gina Mantica, a PhD Student who recently had an article published in the Boston Globe. The article is a result of a science communication workshop that she attended this summer.

Congratulations to Prof. Elizabeth Crone, who has recently been invited to become an external member of the Finnish Academy of Science and Letters. She was invited to accept the nomination as an external member in recognition of her outstanding academic merits.

New Weapon to Fight Dangerous Infections
Tufts researchers find drugs already approved for other uses in people help frogs survive deadly E. coli by changing their cells' electrical charge. This paper was written by Jean-Francois Pare, Ph.D., and Dr. Michael Levin joined by Christopher J. Martyniuk of the Center for Environmental and Human Toxicology and Department of Physiological Sciences, University of Florida Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville.

Congratulations to Fallon Durant and Dr. Michael Levin, whose research has just come out in New Scientist. Fallon's paper also got the cover of the issue, featuring a homage to M. C. Escher's art. Also key contributors from our department were Junji Morokuma, Kate Williams, and Dany Adams.

Congratulations to Dr. Eric Tytell, whose NSF Career award "BIOMAPS: Comparative analysis of locomotor biomechanics and control in fishes" got funded in the amount of $910K for the next five years. This prestigious award is a testament of Eric's recognition by the scientific community.

Congratulations to Dr. Ben Wolfe, whose research proposal for NSF MCB Systems and Synthetic Biology was approved for funding.

Prof. Ben Wolfe received a grant from National Institute of Food and Agriculture/USDA totaling $387,783 to study "Linking patterns with processes in phyllosphere microbiome assembly".

Prof. Mimi Kao together with Prof. Ani Patel from Department of Psychology were selected to receive a Tufts collaborates grant.

Congratulations to graduate student Kaylinnette Pinet who presented her research at a conference sponsored by the Society for Developmental Biology (Woods Hole, MA). Her poster was awarded first prize in the graduate poster award competition.

New research led by Tufts University shows that the invasive European paper wasp, Polistes dominulus, plays a role in facilitating sour rot disease in the absence of other insects.
Wasps and wine: paper wasps found to contribute to sour rot grape disease, a scourge of wine industry

Congratulations to Simran Kausha, who has been selected to receive 2017 Graduate School of Arts and Sciences, Outstanding Contributions to Undergraduate Education Award.

Congratulations to Mitch McVey, who has been selected to receive 2017 Graduate School of Arts and Sciences, Faculty Mentoring Award.

Dr. Levin and Allen Discovery Center at Tufts use artificial intelligence to gain insight into the biophysics of cancer
Artificial intelligence uncovers new insight into biophysics of cancer. Read more >

Professors Levin and Adams publish new book
Professors Levin and Adams have published a new book titled 'Ahead of the Curve: Hidden breakthroughs in the biosciences'. Michael Levin is the Vannevar Bush Professor, Department of Biology, and the director of the Allen Discovery Center at Tufts and Tufts Center for Regenerative and Developmental Biology, Tufts University. Dany Spencer Adams is a research associate professor, Department of Biology, and Tufts Center for Regenerative and Developmental Biology affiliate, Allen Discovery Center at Tufts, Tufts University.

2016 List of 10 Top Science Books
Congratulations to Sara Lewis, whose book Silent Sparks made it onto the 2016 list of 10 Top Science Books @ Science News.

Tufts researchers uncover possible source of genetic error behind a dozen debilitating diseases
Tufts University researchers have discovered a possible explanation for the occurrence of a genetic error that causes over a dozen neuromuscular and neurodegenerative disorders, including Huntington's disease, myotonic dystrophy and forms of spinocerebellar ataxia. Jane Kim, Ph.D., who was a research assistant professor in Professor Mirkin's lab when the research was conducted and who is the paper's first author, said the model suggests answers to two questions that have puzzled researchers. The findings are published in Nature Structural & Molecular Biology. Read More >

Two McLaughlin Lab research assistants won first prize and Graduate student gives talk
Two undergraduate research assistants in the McLaughlin lab, Justine Epiney (Summer Scholars Award 2016) and Hannah Harris (Russell L. Carpenter Summer Internship 2016) presented their research at a conference co-sponsored by the Society for Developmental Biology & International Society for Development (Aug. 4-7th; hosted in Boston, MA). Their poster won first prize for the Undergraduate Best Poster competition! At this same meeting - PhD candidate, Kyle Jewhurst, was the only graduate student selected to give a talk in a special Regeneration/Repair session of this meeting.

Two Lily Glidden Award Recipients Named
The Department of Biology congratulates Katherine Kurth and Xinruo (Amy) Guo for being selected recipients of the Lily Glidden Award. Katherine Kurth, a masters student in the Conservation Medicine program, will be using her award to travel to Botswana to participate in an EcoTraining camp, and Xinruo Guo, an undergraduate student, will be traveling to Tokyo, Japan to participate join an ongoing research program.

The Lily Glidden Award
Lily Glidden ended her last adventure in Kaeng Krachan National Park, Thailand, January, 2014 at the age of 24. She was traveling and observing the wildlife in southeast Asia after completing an internship in southern China. Lily planned to pursue a life as a biologist or a veterinarian, but after graduation from the Washington Wilderness School in 2008 and from Tufts University in 2012, she pursued other dreams for the next two years, taking internships and positions that brought her closer to the wildlife she loved. She spent time in the western U.S. working with coyotes, wolves, and other mammals, and in southern China collecting and tagging bamboo pit vipers for relocation. Between jobs, Lily explored the natural world on her own terms, often backpacking alone into the farthest wilderness she could find. She loved to laugh and her infectious personality inspired others. Read more >

The Russell L. Carpenter Fund for Teaching and Research in Biology
Please enjoy this recently created document about The Russell L. Carpenter Fund for Teaching and Research in Biology at Tufts University. It was established in 1983 by Dr. Cynthia McFadden and Dr. Russell F. Carpenter in honor of their father, distinguished Tufts alumnus and Professor of Zoology, Russell LeGrand "Bud" Carpenter, A24, H77. Learn more about The Russell L. Carpenter Fund for Teaching and Research in Biology.

The Department of Biology published the first edition of its Newsletter
This Newsletter is for Biology alumni and was distributed via email. We hope to include news from past undergraduates and graduate students in future issues.


Faculty Highlights

Congratulations to Mitch McVey for his promotion to the Full Professor rank.

Dr. Ben Wolfe was selected to be the Bernstein Faculty Fellow for 2016-2017!
This is an award given to a junior faculty member who is a few years into his research moves on to a new project. As a Fellow, Ben becomes the recipient of a prestigious faculty development program sponsored by prominent members of the Tufts community to foster the work of outstanding faculty members.

Groundbreaking Research
Prof. Ben Wolfe
has been highlighted in Nature. Congratulations to Ben with this exceptional distinction. Read more >

The Tufts IGERT program in Soft Material Robots (led by PI and Director, Barry Trimmer) was the largest team contingent in the first International Grand Challenge in Soft Robotics (#softroboticsweek2016) that took place in Livorno, Italy in April. Ten students travelled to the week-long workshops and presentations then showed off their latest deformable robots in both manipulation and terrestrial trials. The Trimmer lab received a three year $610,000 grant from the NSF to study the "Neuromechanics of soft-bodied locomotion" and (with co-PI David Kaplan) another three year $616,724 NSF grant to develop "Biocomponent devices: developing actuators from insect muscles". During the summer the Trimmer lab (with Eric Tytell and co-PIs at Johns Hopkins and Cornell) began a five year $1,800,185 research project, funded by the Army Research Office to investigate "Dynamic tuning of instabilities for high power movements in deformable structures".

Dr. Trimmer also participated in the following international conferences:

  • Keynote Talk "Animal Model Systems for Soft Robots" at the Intelligent Autonomous Systems conference at Shanghai Jiao Tong University, Shanghai, China. 3-7 July 2016.
  • Plenary Talk "Non-Pneumatic Soft Robots: Design through Biomimetics" at the conference Towards Autonomous Robotic Systems (TAROS-16) at the University of Sheffield, UK. 28-30 June 2016.
  • Invited talk at the European Conference on Mathematical and Theoretical Biology (ECMTB 2016), University of Nottingham, UK. 11-15 July 2016. On "Biology and the Control of Soft Robots"
  • Invited talk "Real BioRobotics: Using Biology in Robots" at the UK-Japan Workshop on Bio-inspired Soft Robotics. Sydney Sussex College, University of Cambridge, UK. 14-15 July 2016.
  • In addition, it was announced in June that Soft Robots, a journal published by Mary Ann Liebert Inc., with Barry Trimmer as Editor-in-Chief was recognized as having the highest impact factor of all robotics journals.

Dr. Sara Lewis' opinion piece, "Are fireflies flickering out?" featured by CNN.

Michael Reed's groundbreaking studies featured
Michael Reed's groundbreaking studies on the role of climate change in shrinking of coastal birds populations was featured in National Geographic and Audubon.

Professor Sara Lewis' first book, "Silent Sparks: The Wondrous World of Fireflies" was published by Princeton University Press. For centuries, the beauty of fireflies has evoked wonder and delight. Yet for most of us, fireflies remain shrouded in mystery: how do fireflies make their light? What are they saying with all that flashing? And what do fireflies seek in a mate? Written for a general audience, this beautifully illustrated book uncovers the science behind the spectacle, revealing remarkable stories of passionate romance, treachery, and deadly poisons among these stunning ambassadors for Earth's natural magic.


Recent Publications

NuA4 initiates dynamic histone H4 acetylation to promote high-fidelity sister chromatid recombination at post-replication gaps. Nealia C.M. House, Jiahui Yang, Stephen Walsh, Jonathan Moy, C.H. Freudenreich (2014). Molecular Cell Sept. 18, 55(6). doi: 10.1016/j.molcel.2014.07.007. PMID: 25132173.

Chromatin modifications and DNA repair: Beyond double-strand breaks. Nealia C.M. House, Melissa R. Koch, Catherine H. Freudenreich. Frontiers in Genetics (Cancer Genetics), (2014). 05 September 2014 | doi: 10.3389/fgene.2014.00296.

RTEL1 Inhibits Trinucleotide Repeat Expansions and Fragility. Aisling Frizzell, Jennifer H.G. Nguyen, Mark I.R. Petalcorin, Katherine D. Turner, Simon J. Boulton, Catherine H. Freudenreich, and Robert S. Lahue. Cell Reports (2014). Volume 6, Issue 5, 13 March 2014, Pages 827–835; doi: 10.1016/j.celrep.2014.01.034. PMID: 24561255.

Tytell, E.D., Hsu, C.-Y., and Fauci, L.J. (2013). The role of mechanical resonance in the neural control of swimming in fish. Zoology in press. doi: 10.1016/j.zool.2013.10.011

Lobo, D., Solano, M., and Bubenik, G. A., (2014), A linear-encoding model explains the variability of the target morphology in regeneration, Journal of the Royal Society Interface, 11: 20130918

Lobikin, M., and Levin, M., (2014), Endogenous bioelectric cues as morphogenetic signals in vivo, chapter 15 in The Fields of Cells, edited by D. Fels and M. Cifra, in press