Working closely with the many interdisciplinary programs on campus: The BIMO Program, the Neuroscience Program, the Environmental Studies Program and the BiGP Program, the Biology Department’s goal is to provide students with the opportunity to do hands-on, one-on-one research with a professor in addition to offering state of the art academic courses. To that end the department had 20 honors students working in faculty labs this past year. Of these, 9 were inducted into the Sigma Xi Honors Society. For the academic year 2012-2013, the department has 26 students who will be doing honors work. The department is committed to providing a positive research and learning experience for all biology students. As a result of this commitment, several of our students were awarded grants or fellowships to pursue their studies after graduation. Anna Szymanski received a Stratton Fellowship to further her studies. The department also has approximately 40 students doing summer research, either here at Williams or off campus. Emma Rickles and Kathleen Higgins will be working at the Whitehead Institute. Funding for summer research comes from various sources including individual research grants and Division funding. At least half of the biology faculty has outside research funding from either NSF or NIH. This funding allows many students to travel to professional meetings throughout the year giving poster presentations on their research at Williams. One of Professor Swoap’s students, Uttara Partap ‘13 received an undergraduate research fellowhip from the American Pyhsiological Society for 2012. On December 2, 2011, a number of BIOL and/or BIMO alumni (Ellen Crocker ’06, Esa Seegulam ’06, Erica Dwyer ’03, and Erin Troy ’01) returned to campus to share their post-graduate research experiences with students. Through a poster presentation and panel discussion they gave current students an opportunity to learn firsthand about life as a graduate student.
Each year at graduation, the Biology Department awards prizes to several outstanding majors, Jack Berry and Hannah Wilson each received the Benedict Prize in Biology. Sara Dorsey received the Dwight Botanical Prize. Tarjinder Singh received the Conant-Harrington Prize for exemplary performance in the biology major, and Lauren Goldstein-Kral received the William C. Grant, Jr. Prize for demonstrating excellence in a broad range of areas in biology.
The Biology Department continued to participate in the Class of 1960 Scholars program. In addition to the returning alumni who were sponsored by the Class of 1960 Scholars program, the department invited Dr. Pam Silver from Harvard Medical School and Dr. Jerry Wilkinson from the University of Maryland to be a Class of 1960 Scholar speakers.
Class of 1960 Scholars in Biology
|Sora Kim||Marissa Thiel|
|Henry Su||Geordie Lonza|
|Elizabeth Hwang||Grace LaPier|
Professor Marsha Altschuler continued her research on chromosome copy number control in the ciliate Tetrahymena thermophila assisted by independent study students Tom Kuriakose ’12 in the Fall and Bryan Chow ’13 in the Spring and first year students Achala Chittor ’15 and Chris Seitz ’15 during WSP. During Fall semester 2011 she taught a tutorial (BIOL218T DNA, Life, and Everything) which explored a wide range of DNA-related topics including synthetic biology, language evolution, and human genetic diversity. During Spring 2012 she taught a new course for non-majors, BIOL132 The Human Genome--in the course students had the opportunity to synthesize a bit of their own DNA via PCR, to search segments of Professor Altschuler’s genome for variants linked to disease susceptibility, and to discuss the ethical issues associated with personal genome information.
Professor Art has been on a full-year sabbatical during academic year 2011-2012 working on the 75-years of data collected in the Hopkins Memorial Forest permanent plot system. The summer of 2011 marked the completion of re-inventorying the permanent plot system in the Hopkins Memorial Forest, a research collaboration with a group of 11 undergraduates: Abigail Martin’11, Eric Outterson ’12, Claudia Corona ’12, Amelia Simmons ‘13, Mark Lyons ’13, Sarah Rowe ’13, and Gordon Smith ’13, Julio Luquin ’13, Wade Davis ’14, Julieanne Fontana ‘15, and K.B. DiAngelo ’13, each of whom worked 10 weeks on the project. This research segued into my sabbatical that has been spent working with Chris Warren (OIT) on building up the web-based Hopkins Forest database and query retrieval system, Sharron Macklin on establishing the Hopkins Forest Geographic Information System, and with Paul Smernoff, Networks & Systems Administrator on a file sharing system for the 25-member Hopkins Forest Alumni Research Network to produce papers using the 75-year data collection. Professor Art offered a summer 3-day course for K-12 teachers in the Hopkins Memorial Forest in July, 2011 as part of the Museum Institute for the Teaching of Science Program offered through the Berkshire Museum. The course was based on how to tell the integrated “forest” from the individual “trees” and involved12 teachers from schools across Berkshire County. Professor Art also led two Alumni Travel ecological field trips, one to Southeast Alaska – Glacier Bay in August, 2011, and one to the Serengeti and the great migration in January, 2012.
Associate Professor Lois Banta continued her research on the soil bacterium Agrobacterium tumefaciens. This plant pathogen is best known for its unique ability to deliver DNA and proteins to host plant cells, thus stably altering the genetic makeup of the plant and causing crown gall tumors (“plant cancer”) to form at the infection site. One major goal of the lab’s current research is to characterize the host defense responses elicited by the bacterium. Honors students Greg McElroy (’12) and Lauren Goldstein-Kral (’12), along with Naomi Patterson (’15) and post-doctoral fellow Janis Bravo, pursued this line of investigation, which is funded by a $415,000 grant from the National Science Foundation (NSF) awarded to Professor Banta. Connor Dempsey (’13), Nicole Lou (’13), and Audrey Kwon (’13) also contributed to this research project over the summer of 2011. At the annual international Crown Gall Conference, held this year in Madison, WI, Janis Bravo presented a poster, and Lois Banta presented a talk on this research. During the academic year, Grace LaPier (’13) and Abbi Davies (’13) used site-directed mutagenesis to create new T6SS mutants. Independent Study student Hannah Wilson (’12) concluded the lab’s exploration of a novel mechanism for transcriptional regulation of a subset of the virB genes, which encode a multi-protein complex responsible for the delivery of the DNA and several virulence factor proteins to host cells.
During the fall semester, Professor Banta taught the lab-intensive capstone course for the Genomics, Proteomics, and Bioinformatics program. The course focuses on one model system, the Ras/MAPK signal transduction pathway, and its role in the development of colon cancer. Highlights of the course this year included using quantitative real-time PCR to probe the contributions of inflammation to human colon cancer. In the spring term, Professor Banta taught an upper-level elective in Microbiology. The students in this course over the past few years are among the first undergraduates in the nation to carry out a metagenomics project, surveying the full spectrum of bacteria found in a given ecological niche; the class this year focused on pond sludge from Woods Hole, MA and from local agricultural sites.
During this academic year, Professor Banta served as a panelist for the National Science Foundation, and as a reviewer for Journal of Bacteriology, The Plant Cell, and Molecular Plant Physiology. She was named to the Editorial board for the journal Frontiers in Plant-Microbe Interaction. Within Williams, she served on the Biochemistry/Molecular Biology advisory committee, the Bioinformatics, Genomics and Proteomics advisory committee, the Environmental Studies advisory committee, and as departmental seminar coordinator; she also served as coordinator for the Global Health track of the International Studies Area of Concentration and for the college-wide program in Public Health. Finally, she is Secretary/Treasurer of the Williams College Chapter of the national science honor society Sigma Xi.
Derek Dean continues to work with colleagues to further develop the biology lab program. For example, the infamous “Fly Lab” in the Genetics course has been redesigned: in the past, this lab had students map known eye color mutations in the fruit fly, Drosophila melanogaster. While this was an effective teaching tool for the fundamentals of genetics, it involved students analyzing very well-characterized mutations, so little new information was uncovered. This past year, the lab was redesigned to include original research. Students mapped wavy, a mutation affecting the morphology of the fly wing. While this mutation has been known and maintained since the 1930s, it has not been determined which gene is affected by the mutation. The location of the gene has been narrowed down to about 500,000bp of DNA on the X-chromosome, and this fall, we hope to identify the wavy gene within that region. In addition to course development, Dean continues to use fly genetics to research how metabolism affects seizure disorders. Daniel Nachun (’12), Derek Dean’s most recent honors student, did an excellent job importing a neurophysiology technique into the lab, and this technique is being used to top off their findings for a manuscript. Nachun will be attending the Neuroscience Ph.D. Program at UCLA this fall.
Assistant Professor Tim Lebestky joined the department in the summer of 2011. The Lebestky lab utilizes the genetic model system of Drosophila melanogaster for the study of behavioral genetics and molecular neurobiology techniques to understand arousal and sensory integration. Animals use their senses to learn about their immediate environment, parse the relevant information, and react in a meaningful way. These concepts also translate into human biology, as imbalances in arousal and sensory gating are linked to pathologies, such as insomnia, attentional disorders, autism, and anxiety. Dr. Lebestky chaperoned two undergraduates on a week-long research trip to UCLA (Jack E. Berry and Chansoo Lee). Students learned biology techniques and computer-programming strategies for creating visual stimuli patterns for Drosophila behavior experiments (August 2011). He also mentored 3 honors thesis students (Sameer Aryal, Jack Berry, Nathaniel Kastan), one independent study student (Chansoo Lee), two volunteer researchers (Jenni Ginsberg, Zach McKenzie), and one Summer Science Student in the fall semester (Racquel Gibson). Dr. Lebestky gave two invited lectures at the University of Kansas and also Brandeis University. He also submitted a manuscript to GENETICS, and attended two meetings, the Drosophila Neuroscience Conference, and also the New Neuroscience Faculty Symposium at Cold Spring Harbor Labs. In the Fall semester, Dr. Lebestky created a new course: Biol 407, the Neurobiology of Emotion, and then taught Biol 310, Neural Development and Plasticity in the Spring of 2012. Both the lab and lecture portions of the Biol310 course represent a new version of the course, with all new lab experiments and new directions for lectures on neural plasticity.
During this past year Professor Dan Lynch was on leave during the fall semester. In the spring he taught BIMO/BIOL/CHEM 322 Biochemistry II Metabolism lecture and two laboratory sections while a third lab section was taught by Visiting Assistant Professor Jon Snow. Lynch continued his research on plant sphingolipid biochemistry but he switched from working with the flowering plant Arabidopsis thaliana to the moss Physcomitrella patens. The moss provide certain advantages over Arabidopsis in studies of sphingolipid metabolism and function. Students working in the lab included Mike Essman, a thesis research student in the biology department who began his project during winter study to generate and characterize moss plants with decreased levels of phytosphingosine, the predominant long-chain base in the moss. In addition, Karyn Moss completed a senior thesis project working with professors Lynch and Swoap to characterize the lipid profiles in selected fat depots of calorically restricted mice. Lynch served as a review panel member at the NSF in the fall and as a reviewer for manuscripts submitted to several scientific journals
Assistant Professor Manuel Morales taught Animal Behavior during the spring semesters of 2011 and 2012. A highlight for students is the all-day field trip to the Bronx Zoo. Morales was on leave during the Fall 2011 Semester.
Luana Maroja has two additional lines of research this year. The first, in collaboration with K. Wallin from U. of Vermont, is related to the impact of winter climate change in Northeastern forest; more specifically how the invertebrate fauna is affected by reduced snow pack in winter. With two students (K. Oliva ’15 and N. Horowitz ’14) Maroja has developed microsatellite genetic markers for a tiny snail abundant in our forests and will investigate the population genetics of the species. The second project is part of a collaboration with Prof. Joan Edwards that aims at combining population dynamics with population genetics to investigate the effects of isolation and climate change (past and current) in the populations of arctic plants on Isle Royale in Lake Superior. With the help of three students (O. Calzada ’12, H. Matheny ’12 and T. Singh ’12) Maroja also developed microsatellites for these endangered plants.
In addition to these new lines of investigation, Maroja has also completed part of her postdoctoral work on the Heliconius butterfly genome, which shows that hybridization was responsible for the spread of adaptive coloration genes and was published in the journal “Nature.” During the summer, Maroja will present a lecture at the Science lunches reporting these interesting results. Maroja will also be participating in the Evolution 2012 conference in Ottawa in July, taking four students (Hart ’14, Horowitz ’14 , T. Miller ’15, and Oliva ’15) who will present three posters.
In Fall 2011, Maroja taught Genetics 202 for the 1st time and together with D. Dean she has changed the fly lab, which now is an original research project that includes modern genetic techniques, such as the use of p-elements to map unknown traits (a curly wing gene that has not been mapped). She also wrote an academic manuscript describing the lab she developed for her evolution class (students sequence their own DNA and learn about phylogenetic tree building and human evolution) that has been accepted for publication on “Evolution: Outreach and Education.” Also in the fall, Maroja also participated on an NSF grant review panel on Evolutionary Biology and presented an invited graduate student seminar at the University of Vermont.
Martha Marvin continues to investigate the role of small heat shock proteins in embryonic development of the zebrafish, in an ongoing collaboration with former Williams professor Lara Hutson. This family of proteins protects embryos from environmental stress, but also serve essential developmental roles. Dr. Marvin is particularly interested in the role of a tissue called the yolk syncitial layer; it does not directly give rise to the brain, heart or viscera but is essential to pattern and guide the development of these embryonic tissues. A specialized region of the YSL, Kupffer’s vesicle, contains cilia that move fluid in one direction to break the embryo’s bilateral symmetry. Paloma Marin ’12 demonstrated that reducing Hspb7 causes the loss of a cilia component that is essential for their movement. Mark Springel ’12 showed that loss of Hspb7 in the yolk syncitial layer causes severe and prolonged heart defects, including malformed valves and small ventricular chambers, due to defective migration of the layer of cells that will form the heart. Dr. Marvin teaches the laboratories for Neuroscience 201 and also taught a lab section of Physiology, Biology 205. She advised two honors students this year. She also co-taught a Winter Study course called Project BioEyes, which trains Williams students to teach genetics and development, and also engages local 4th and 11th grade students to scientific investigation.
Associate Professor Claire Ting taught a capstone course in the fall semester on Life at Extremes: Molecular Mechanisms (BIOL 414), which explored the physiological and molecular survival kits organisms have evolved that permit them to acclimate to environmental stresses and to thrive in extreme environments, such as the deep sea. In the spring semester she taught the Biology Department core course, The Organism (BIOL 102). Through lectures, discussions of original research papers, and laboratories, this large, introductory course encouraged students to explore how one cell becomes a multicellular organism through the process of development and how evolution results in the rich biological diversity on earth.
During the year, Professor Ting continued to pursue her National Science Foundation funded research on photosynthesis in the ecologically important marine cyanobacterium Prochlorococcus. This blue-green bacterium is one of the most abundant photosynthetic organisms on the planet and is an important carbon sink. Research in her laboratory aims to establish how differences at the genomic level translate into physiological advantages in photosynthetic capacity and in tolerance to environmental stress. In addition to laboratory work, her group has conducted field work in the Sargasso Sea, which is an open ocean region where Prochlorococcus thrives. This past year her laboratory continued to work with the bacterioplankton samples they collected from Sargasso Sea waters for metagenomic and metatranscriptomic analyses. Undergraduate students who participated in research in her laboratory this past year included Ellen Beauchamp ’12 (NSF summer research assistant, honors thesis student), Melany Funes ’14 (NSF summer research assistant), Adena Hernandez ’12 (honors thesis student), and Alyson Barrett ’14 (research assistant). In addition, Christie Black ’15 and Catherine Pang ’14 joined the Ting Laboratory as BIOL 22 Introduction to Biological Research students during Winter Study, and continued as research assistants during the spring. Kris Anderson continued as an NSF-funded research technician in the laboratory. With support from the National Science Foundation, Ellen Beauchamp ’12 and Melany Funes ’14 joined Professor Ting at the Department of Energy Joint Genome Institute (DOE JGI) User Meeting on Genomics of Energy and Environment in Walnut Creek, California and participated in a Prochlorococcus Team Meeting is Asilomar, California during the spring semester.
In order to raise awareness about current environmental issues associated with the oceans and its inhabitants, and about the challenges associated with stewardship of the oceans, Professor Ting organized a Williams College Oceans Symposium during the spring semester. This interdisciplinary symposium, which was sponsored by the Center for Environmental Studies, included seven events that took place throughout the spring semester and encouraged interactions across disciplines and between the College and wider community.
Heather Williams continued her work on the cultural evolution of song in two Savannah sparrow populations, one in Williamstown and one on Kent Island in the Bay of Fundy. She presented some of this work at a Science Center lunch in the fall. She supervised three summer research students. Ryan Buchanan ’14 used surgical techniques to place implants containing muscimol over a brain area important for the production of learned bird song. Ai Tran ’12 investigated changes in circulating hormones in young male songbirds raised without song tutors. Kate Foley ’12 asked whether song syntax is innate or learned. She continued her summer work as an honors thesis and used operant learning techniques to train naive young males with artificially generated variable syntax songs to try to determine whether young zebra finches can learn a variable syntax or whether the species-typical fixed syntax has an innate basis. Williams served on a panel for the National Science Foundation and as part of a committee that reviewed the Neuroscience program at Mount Holyoke College, and as a peer reviewer for several journals.
During the fall semester, Professor Steve Zottoli taught BIOL 304, Neurobiology. In thespring he was on leave. A long-term goal of the Zottoli laboratory is to understand the neuronal basis of behavior and the recovery of behavior after spinal cord injury. He uses identified neurons in the goldfish as a ‘model system’. Sonja Boatman ’12 and Melinda Wang ’14 worked as Research Assistants studying vestibular and lateral line efferent neurons in the goldfish. Zottoli was a co-author on a paper entitled: “Regeneration in the era of functional genomics and gene network analysis,” that was published in the Biological Bulletin, Volume 221, pp. 18-34. Professor Zottoli continues to conduct summer research at the Marine Biological Laboratory in Woods Hole, MA where he is an Adjunct Scientist in the Cellular Dynamics Program. Professor Zottoli continues as a Life Trustee of The Grass Foundation.
Larry Zipursky, UCLA, HHMI
Co-sponsored with Neuroscience
“Cell Recognition, Molecular Specificity and Constructing Neural Circuits”
Warren Abrahamson, Bucknell University
“Host Plants, Herbivores, & Natural Enemies: A Medley of Questions and Approaches”
Pam Silver, Harvard Medical School
1960s Scholar Lecture
“A Chemical Biology Approach to Understand Host-Parasite Interactions”
Zhen Yan, University of Virginia
“Molecular and Signaling Mechanisms of Skeletal Muscle Adaptation”
Jerry Yin, University of Wisconsin, Madison
“Memor, Sleep, Sick Flies and Fiesty Badgers – Really?”
Kerry Woods, Bennington College
“Imagined Forests: Preconceptions and Realities of Old-Growth”
Margaret Rubega, University of Connecticut
“Feeding Mecanics in Birds: We Know Less Than You Think”
Wendy Garrett, Harvard School of Public Health
“Disease-associated and Beneficial Gut Microbiota in Colitis and Colorectal Cancer”
Miriam Cremer, Basic Health International
“Cervical Cancer Prevention in Rural El Salvador”
Jerry Wilkinson, University of Maryland
1960s Scholar Lecture
“Sexual Selection, Genomic Conflict and Reproductive Isolation in Stalk-Eyed Flies”
Rachel Brewster, University of Maryland Baltimore County
“Getting the Brain Into Shape: Mechanisms of Neural Tube Morphogenesis”
Art, Hank. Tuesday Science Lunch – What We Know (and Don’t Know) About an Enigmatic Woodlot in the Hopkins Forest. December, 2011.
Lebestky, Tim. Tuesday Science Lunch – Be My Fruit Fly Valentine – February 2012
Swoap, Steve. Tuesday Science Lunch - Some Mammals Are Really Cool – October 2011
Williams, Heather. Tuesday Science Lunch – Cultural Evolution: Is Bird Song Like Language? - October 2011
Hank Art. Seventh Annual Forest Summit – “Woodlot History in the Hopkins Memorial Forest, Williamstown, MA” – Holyoke Comm. College, October, 2011
Lois M. Banta, Janis E. Bravo, Lauren Goldstein-Kral(’12), Audrey Kwon(’13), Nicole Lou(’13), Connor Dempsey(’13), Greg McElroy(’12), Helen Cha(’11), and Rosalia Deeken. Modulation of Basal Defenses in Arabidopsis thaliana by Agrobacterium tumefaciens. Oral presentation at the 32nd Annual Crown Gall Conference (Madison, WI, Nov. 2011)
Janis E. Bravo, Audrey Kwon(’13), Nicole Lou(’13), Rosalia Deeken, and Lois M. Banta. Effect of the A. tumefaciens Type 6 Secretion System on Basal Defense Responses in Arabidopsis thaliana. Poster presentation at the 32nd Annual Crown Gall Conference (Madison, WI, Nov. 2011)
Elizabeth Hart (’14), J. Jing (’14), Z.M. McKenzie (’14), L.S. Maroja. Song differences, male courtship intensity and cuticular hydrocarbons in a cricket hybrid zone.. EVOLUTION 2012 – Ottawa, Canada. Poster presented by student.
Kim Oliva (’15), Nina Horowitz (’14), H. Yurchenco, P. Templer, K.F. Wallin, L.S. Maroja (LPA1). Effects of Winter Climate Change on Terrestrial Snails (Zonitoides arboreus) in a Northern Forest Ecosystem., EVOLUTION 2012 – Ottawa, Canada. Poster presented by students.
T. Miller (’15), L.S. Maroja, D.C. Smith, E. Maclary. Don’t put all your eggs in one basket: chorus frogs distribute offspring in multiple pools.. EVOLUTION 2012 – Ottawa, Canada. Poster presented by student.
Dean D.M. and L.S. Maroja. Adapting the fly lab for primary research in the genetics classroom. 53rd Annual Drosophila Research Conference March 7-11, 2012. Poster presented by Dean.
Davey J.W., Baxter S.W., Maroja L.S. , Kapan D.D., Jiggins C.D., Blaxter M. Scaffolding the Heliconius melpomene genome with RAD Sequencing. International Conference on Quantitative Genetics in Edinburgh. Presentation by Davey.
Maroja L.S. Invited graduate student seminar. University of Vermont. September 9, 2011. Barriers to Gene Exchange, Hybrid Zones and Speciation.”
Lahvic, J., Davis, L., Hutson, L.D. and Marvin, M.J. HspB7 and HspB12 Are Necessary for Normal Left-Right Asymmetry. 9th International Conference on Zebrafish Development and Genetics, Madison, WI. June, 2010 (poster)
Lahvic J. and Marvin, M.J. HspB7 and HspB12 are necessary for normal left-right asymmetry. North East Society for Developmental Biology, Woods Hole, MA, April 2010. (talk, delivered by Jamie Lahvic)
Marin P. and Marvin, M.J. Small heat shock protein Hspb7 is required for function and morphogenesis of Kupffer’s Vesicle cilia. North East Society for Developmental Biology, Woods Hole, MA, April 2012. (poster)
Springel, M.W. and Marvin, M.J. Cardiac morphogenesis in zebrafish depends upon the small heat shock protein Hspb7. North East Society for Developmental Biology, Woods Hole, MA, April 2012. (poster)
Springel, M.W., Ji, Y., Zuflacht, J., Marin, P., Lahvic, J., Hutson, L.D., Amack, J., and Marvin, M.J. Cardiac laterality, migration and morphogenesis depend upon small heat shock proteins. 10th International Conference on Zebrafish Development and Genetics, Madison, WI. June, 2012 (poster)
Morales, M.A. gave an invited talk to the Department of Ecology and Evolutionary Biology at the University of Connecticut in March 2012.
Morales, M.A. 2011. Phenology of mutualism: altitudinal variation in survival and benefit of an ant-tended treehopper. 96th Annual Meeting of the Ecological Society of America.
Morales, M.A and A. F. G. Zink. 2012. Mechanism of agreggation in an ant-tended treehopper. 97th Annual Meeting of the Ecological Society of America.
POSTGRADUATE PLANS OF BIOLOGY DEPARTMENT MAJORS
|Isaac Abodunrin, Jr.|
|Amlak Bantikassegn||Research Assistant, Yale University.|
|Francesca Barrett||Research Assistant, Zon Lab, Boston Children’s Hospital|
|Ellen Beauchamp||Research Technician at Dana-Farber Cancer Institute in Boston, MA and then I plan to apply to graduate school in 2 years|
|Stella Berke**||Working in strategy consulting in Boston, MA at a small firm called OC&C|
|Jack Berry||Working as a research technician in the department of neurosurgery at Stanford Medical School|
|Olivia Delia||Leading a high school backpacking trip for Overland in the Spanish Pyrenees and Swiss Alps, and in the fall heading to France to teach middle school and/or high school English|
|Elizabeth Dorr||Working as an admissions counselor for Sea Education Association/SEA Semester in Woods Hole, MA.|
|Amanda Esteves-Kraus||Teaching biology at the Hackley School in Westchester, NY.|
|Katelyn Foley||Working at Mass General Hospital.|
|Lauren Goldstein-Kral||Working for Teach for America in Hartford, CT.|
|Gregory Johnson**||Research Assistant in Developmental Neuroscience Beth Israel Deaconess Medical Center Boston, MA.|
|Nathaniel Kastan||Working in Dr. Greenberg’s neuro lab at Harvard Medical School.|
|Thomas Kuriakose||High school math in Mississippi with the Mississippi Teacher Corps|
|Donna Lee||M.D. at University of Rochester School of Medicine and Dentistry|
|Stephen Maier, II|
|Paloma Marin||Teach for America teaching science in a low-income, urban school in Los Angeles. I was selected to be a 2012 Amgen fellow (funded by the biotechnology company of the same name), a fellowship awarded to 100 math and science major accepted corps members. I plan to do TFA for 2 years before applying to medical school|
|Hannah Matheny||I accepted a six-month Fellowship position with the Clinic for the Rehabilitation of Wildlife (C.R.O.W) on Sanibel Island, Florida. I am planning on applying to veterinary school this summer for matriculation in the fall of 2013|
|Gregory McElroy||Working as a research assistant at Boston University in the Pulmonary Center|
|Nikola Mirkovic**||Post-bac premedical program at William Patterson University; coaching high school football and wrestling|
|Sylvia Molina||Research Assistant in the University of New Mexico.|
|Daniel Nachun**||Attending a Ph.D. program in Neuroscience at University of California, LA|
|Nina Piazza||I am going to spend a year teaching science, music, and English at a rural elementary school in Yongfeng, China, after which I will be attending medical school at the University of Rochester.|
|Estefany Reyes||Working as a research assistant in the lab of Dr. Mark Boldin at the Beckman Research Institute (Part of the City of Hope Cancer Hospital) in Duarte, CA.|
|Kate Shaper**||Teaching AP Biology and AP English to high school students at the ChenYin Private Academy in Shanghai, China|
|Tarjinder Singh||Hershel-Smith Fellow, completing a MPhil in Biological Sciences at the University of Cambridge|
|Mark Springel**||Working as a Research Assistant at Children’s Hospital, Boston MA|
|Anny Szymanski||Pursuing a Master’s in Marine Biology at the University of Alaska in Fairbanks, AK|
|Hannah Wilson||Teaching and doing public health work in Africa.|
The role of DopR neuronal circuits in regulating endongeous arousal in D. melanogaster
Endogenous arousal can be defined as the internally generated periodic changes in behavior that underlie the circadian cycle of sleep and wakefulness. A balanced level of endogenous arousal is fundamental to many behaviors. Unstimulated locomotor activity reflecting sleep-wake transitions can be measured to quantify endogenous arousal. The neurotransmitter Dopamine has been implicated in mediating endogenous arousal in D. melanogaster. It has been suggested that Dopamine regulates sleep and wakefulness by acting on DopR, the fly ortholog of the human Dopamine D1 receptor. We investigated the role of DopR-expressing neuronal circuits in regulating endogenous arousal by expressing the nonspecific cation channel Transient receptor potential channel (TrpA1) in different subsets of DopR-expressing neurons. The sleep-wake changes resulting from raising the temperature to 31°C allowed us to characterize the functions of different DopR circuits in regulating sleep and wakefulness. Our results confirm that there exist multiple DopR-expressing neuronal circuits regulating endogenous arousal in Drosophila. Our results also suggest that the mushroom body has a central role in regulating sleep and wakefulness.
Characterization of the Nitrogen Utilization Strategies and Carbon Fixation Mechanism of Prochlorococcus
The marine cyanobacterium Prochlorococcus survives in a wide variety of open ocean environments. Dominating the subtropical and tropical oceans between the surface waters and depths of 200 meters, concentrations of this microorganism can reach 105 cells per milliliter. To date, the genomes of twelve different strains of Prochlorococcus have been completely sequenced. Strains differ in their physiology and cellular structure, genome size and content, and abundance in the water column. Such structural, physiological, and genomic differences are likely to impact strategies for acclimation to environmental conditions and to shape the distribution and population dynamics of Prochlorococcus within the oceans. In this study, I specifically examined the nitrogen utilization strategies and carbon fixation mechanism of Prochlorococcus strains. The dynamics of these processes are of particular interest due to the significant role Prochlorococcus plays in global primary production.
When cultures of the MED4 and MIT9313 strains of Prochlorococcus were grown under low environmental nitrogen conditions, the two strains responded differently. I observed differences in growth rate, chlorophyll concentration per cell, and the maximum quantum efficiency of Photosystem II between the strains under the two conditions. This is consistent with the physiological, structural, and genomic differences between MED4 and MIT9313, and it supports our hypothesis that strains have evolved different nitrogen utilization strategies to deal with low nitrogen conditions.
Prochlorococcus contains a Carbon Concentrating Mechanism (CCM), which includes a microcompartment called the carboxysome. This microcompartment is surrounded by a protein shell and increases the efficiency of carbon fixation by concentrating carbon dioxide in a small area near the enzyme RuBisCO. Using bioinformatic tools, I characterized the proteins that constitute the carboxysome shell. The chromosomal organization and amino acid sequences of these proteins are highly conserved. Furthermore, calculations of the ratio of nonsynonymous to synonymous nucleotide changes indicated that the gene encoding the CsoS3 protein is under negative selection. However, there are numerous amino acid changes in CsoS3 that differentiate Prochlorococcus from other cyanobacteria and which separate several clades of Prochlorococcus from each other. Further information about nitrogen utilization and carbon fixation in Prochlorococcus is likely to be determined via gene expression analyses of genes under different environmental conditions in different strains. I began this work by optimizing an RNA isolation and qRT-PCR protocol which will be used in future experiments in our laboratory.
Host Plant Defenses and Their Modulation by the Agrobacterium tumefaciens T6SS are under Light and/or Circadian Control
Agrobacterium tumefaciens is a gram-negative soil bacterium that induces Crown Gall Disease in a broad range of primarily dicotyledonous hosts. Crown Gall Disease is caused by the transfer of T-DNA from a bacterial tumor-inducing (Ti) plasmid into the host plant through the Type IV Secretion System (T4SS). The T-DNA is stably incorporated into the host genome and results in tumor growth and the production of opines that serve as a food source for the bacterium. Gram-negative bacteria, such as Agrobacterium tumefaciens, can form other types of secretion systems in addition to the T4SS. One of these is the Type VI Secretion System (T6SS). A strain of A. tumefaciens (#20) was created in which the entire T6SS was deleted. In comparing Arabidopsis thaliana plants infected with wildtype (#58) or mutant (#20) A. tumefaciens, the mutant bacteria are less successful at promoting tumorigenesis. We hypothesized that A. tumefaciens secretes an effector through the Type VI Secretion System (T6SS) that suppresses host defense responses. The overarching goal of this thesis is to test this hypothesis.
Recent findings have suggested a circadian component to plant defenses, but there is limited research in this field. This thesis examines whether the effect of the bacterial T6SS on Arabidopsis plants is influenced by the plant circadian clock. Plant defense regulators, plant defense genes, and bacterial virulence genes were analyzed with respect to time of inoculation. Our results showed no time-of-day dependence for the induction of known regulators of plant defenses by wildtype or #20 mutant A. tumefaciens, but induction of At2g17740, a downstream plant defense gene, did show fluctuations based on the time of inoculation. Further, expression of At2g17740 was different between plants infected with wildtype or #20 mutant bacteria and those differences were dependent on the time of day. Bacterial virulence genes showed fluctuations based on the time of day in a pattern similar to the pattern of plant defense gene induction. These bacterial genes did not show light-sensitivity, so their fluctuations can be attributed to an effect of the plant on the bacteria and not to an effect of light on the bacteria. The fluctuations in both plant defenses and bacterial genes were disrupted by exposure to constant light. This disruption supports the idea that plant defenses and associated bacterial virulence are under light and/or circadian control.
Photosynthetic Responses of Prochlorococcus to Environmental Stresses
The marine cyanobacterium, Prochlorococcus, can be found thriving in a diverse range of environmental conditions in terms of nutrients, temperature and light levels. In this study, the effects of high light intensity were characterized in Prochlorococcus strains MED4 and MIT9313. We hypothesized that different strains of Prochlorococcus have evolved different molecular responses to light stress. By examining chlorophyll production and cell division after 48 hours of exposure to light stress we found that while MIT9313 was profoundly affected by the high irradiances, MED4 was not. A two-hour light stress experiment was also performed, and the effects of this short term light stress on chlorophyll production, cell division, and the quantum efficiency of Photosystem II were characterized. After a two hour light stress, both MIT9313 and MED4 exhibit a decrease in the quantum efficiency of Photosystem II, though the decrease was greater for MIT9313. From these results, it is apparent that MED4 and MIT9313 have evolved different mechanisms for acclimating to high light intensities. In particular, MED4 appears to have the ability to rapidly repair any damage resulting from exposure to high irradiance levels. Decreases in the quantum efficiency of Photosystem II in MED4 following exposure to short term light stress are not a result of irreversible damage to the photosynthetic apparatus, and MED4 cells are able to continue dividing and to retain their chlorophyll even following 48 hours of exposure to light stress. Examining the different responses of Prochlorococcus strains to environmental stresses is important for understanding the population dynamics and distribution of this genus in the world oceans.
Development of Twelve Polymorphic Loci in Primula mistassinica
Molecular markers, like microsatellites, allow biologists to explore the genetic characteristics of a population. Microsatellites are highly variable DNA regions that enable fine-scale analyses of population genetics, such as calculations of genetic diversity and genetic distance. Using microsatellite markers, we hope to investigate the historical movements of Primula mistassinica, a distylous, self-incompatible diploid plant native to Alaska and the boreal forests of Canada. We designed twelve primer pairs that amplify polymorphic microsatellite loci in this species. These loci can be used to explore the relationships between a population of P. mistassinica on Isle Royale, MI, and more northern (Arctic) populations. Arctic plant populations shifted their range after the last ice age, but disjunct populations of some Arctic species exist far south of their typical range. They could be the relic of the northward migration of the plants or the result of a more recent colonization event. Studying historical plant movements can offer valuable insight as to the survival prospects of current plant populations, which face the pressures of global, anthropogenic climate change.
Arabidopsis thaliana seedling pattern recognition defense activation by bacterial Type VI secretion during infection by Agrobacterium tumefaciens
Arabidopsis thaliana, like all plants, lacks circulating immune cells and thus requires a range of defensive responses against pathogenic bacterial threats. Ultimately, for these defenses to function, the plant must first recognize the presence of an invading bacterium. Agrobacterium tumefaciens is a soil dwelling gram-negative plant pathogen that causes crown gall disease. It is primarily recognized by the EFR receptor in Arabidopsis, initiating plant defense. Data in this thesis suggest that the presence of a functional Type VI secretion system (T6SS) in Agrobacterium dampens plant defenses, but that in the absence of a functional EFR receptor, this T6SS may trigger alternate plant defenses. This finding may lead to the identification of a novel Pattern Recognition Receptor (PRR) in Arabidopsis that recognizes some aspect of the bacterial T6SS. Growth inhibition, anthocyanin production, and expression of defense gene transcription factors were used as metrics for plant defense activation in seedlings. The method of infection, degree of light-stress, and the timing of infection relative to circadian rhythms have different effects on the Arabidopsis defense response.
Small Heat Shock Proteins and Kupffer’s Vesicle Cilia: An Early Role for hspb7 in D. rerio Left-Right asymmetry
Small heat shock proteins are low-molecular weight chaperones intended to protect cells from stresses such as heat or oxidative stress. hspb7 has been implicated in the establishment of left-right asymmetry in zebrafish. This thesis takes a closer look at the earliest asymmetric event in the zebrafish embryo: nodal flow at the level of Kupffer’s vesicle. Kupffer’s vesicle is the zebrafish equivalent of the mammalian ventral node, responsible for triggering asymmetric gene expression via its monocilia. Strong knockdown of hspb7 leads to defects in morphology of KV as well as ciliary defects, pointing to a possible role of hspb7 early in the LR-asymmetry pathway.
Characterization of Microsatellite Markers in Arctic Disjunct Populations of Sagina nodosa (Caryophyllaceae), Isle Royale, Michigan
We investigated the population history and structure of Sagina nodosa populations in Isle Royale National Park by developing and characterizing eight novel microsatellite markers using next-generation sequencing technology. This is the first study to develop microsatellite markers of a plant in the Sagina genus. We characterized the 8 polymorphic markers on 29 individuals belonging to 7 island subpopulations in the northeastern tip of Isle Royale, and performed preliminary analyses to quantify the genetic variation, and population structure of Sagina nodosa. From our preliminary analysis of the genotyped population, we found that every locus significantly deviated from Hardy-Weinberg Equilibrium (HWE) with a p-value of less than 0.001 when treating the entire Isle Royale region as single population. If each island is treated as a unique subpopulation, no locus significantly deviated from HWE following Bonferroni correction. The pairwise FST values between islands range from 0.0486 to 0.3668, while 13 out of the 18 pairwise comparisons all had values that exceed an FST of 0.15. The multilocus estimate of FST was found to be 0.2073. Our preliminary population-level analysis of S. nodosa in Isle Royale suggests an underlying population substructure exists that limits gene flow across island populations. With these novel markers, we hope to genotype the remainder of the 103 samples from Isle Royale and additional individuals in the surrounding Lake Superior region and analyze the results using a landscape genetics framework. The optimized methods outlined in this thesis can serve as the basis for low cost, rapid development of microsatellite markers for small disjunct plant populations.
TRPM8 is necessary for cool sensation but is not required for torpor
The integration of ambient temperature sensation with internal thermoregulation is crucial to the livelihood of mammals. TRPM8, a thermo-TRP channel on peripheral neurons, is involved in sensing cool temperatures (18-26°C) and eliciting thermoregulatory responses. The current study hypothesized that TRPM8 (-/-) mice would engage in thermoregulation in response to environmental cool on a different time scale than control mice: experiencing a decrease in body temperature before engaging in a thermoregulatory response. In addition, because wild type mice enter torpor at ambient temperatures within the TRPM8 activity range, the hypothesis predicted that TRPM8 (-/-) animals would not enter torpor at temperatures within the TRPM8 activity range. TRPM8 (-/-) and (+/-) mice were exposed to warm and cool temperatures over 24 hour periods, during which metabolism was measured using indirect calorimetry, and body temperature and heart rate using EKG telemetry. TRPM8 (-/-) mice experienced a larger drop in body temperature (-1.8 ± 0.1 °C) than TRPM8 (+/-) mice (-1.0± 0.4 °C) (p<0.05) during ambient cooling from 30°C to 20°C, and also experienced a larger increase in body temperature (2.3±0.1°C) than control animals (1.3±0.1°C) as ambient temperature changed from 20°C to 30°C. TRPM8 (+/-) and (-/-) animals and wild type animals were fasted at a series of ambient temperatures while their metabolism, heart rate, body temperature, and activity level were measured. All animals, regardless of genotype, entered torpor at ambient temperatures below 26-27°C. This demonstrated no difference in torpor behavior between control and TRPM8 (-/-) mice. Lastly, mice that were either fed ad libitum, 60% calorically restricted, or fasted, were given the choice between a 20°C ambient area and a 30°C ambient area over the course of the 12 hour dark phase. TRPM8 (-/-) mice spent more time (0.40 ± 0.03) in the cool area than TRPM8 (+/-) mice (0.26 ± 0.03) when fed, but when calorically restricted or fasted, there was no significant difference between the groups. These data show that when calorically restricted, a significant phenotype of TRPM8 (-/-) is abated. Together, these data suggest that while TRPM8 is necessary for normal cold sensation, it is not required for normal torpor bouts, and that during a fast, cool sensation is upregulated in both TRPM8 (+/-) and (-/-) mice.
Baumler, D. J., L. M. Banta, K. F. Hung, J. A. Schwarz, E. L. Cabot, J. D. Glasner, and N. Perna. 2012. Using comparative genomics for inquiry-based learning to dissect virulence of Escherichia coli O157:H7 and Yersinia pestis. Cell Biology Education-Life Science Education 11:81-93.
L. M. Banta, E. J. Crespi, R. H. Nehm, J. A. Schwarz, S. Singer, C. A. Manduca, E. C. Bush, E. Collins, C. M. Constance, D. Dean, D. Esteban, S. Fox, J. McDaris, C. A. Paul, G. Quinan, K. M. Raley-Susman, M. L. Smith, C. S. Wallace, G. S. Withersand L. Caporale. 2012. Integrating genomics research throughout the undergraduate curriculum: A collection of inquiry-based genomics lab modules. Cell Biology Education-Life Science Education, in press.
D.M. Dean. (2012). Streamlined strategies to better visualize Southern blotting. American Biology Teacher. 74(4): 270-271.
D.M. Dean and J. Wilder (2011). The “Frankenplasmid” Lab: an investigative exercise for teaching recombinant DNA methods. Biochemistry and Molecular Biology Education. Sep-Oct;39(5):367-74. doi: 10.1002/bmb.20531. Epub 2011 Jul 25.
L.S. Maroja. HELICONIUS GENOMIC CONSORTIUM (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature doi:10.1038/nature11041.The evolutionary importance of hybridization and introgression has long been debated1. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression inHeliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2–5. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.
L.S. Maroja and J. Wilder. (in print). Where Do I Come From? Using Student’s Mitochondrial DNA to Teach About Phylogeny, Molecular Clocks, and PopulationGenetics. Evolution: outreach and Education. Abstract: Phylogenetic reconstruction, divergence times, and population genetics are critical concepts for a complete understanding of evolution. Unfortunately, students generally lack “tree-thinking” skills and are often unmotivated to explore these concepts using typical classroom exercises that feature taxa unknown to students or simulated datasets. To generate greater student interest, we have developed an affordable practical lab ($16 dollars per student) where students extract and sequence their own mtDNA and use it for exercises involving phylogenetic reconstruction (placement of own DNA into the world tree), divergence (speciation) time (comparing current student population with chimps, gorillas, and Neanderthal),and population genetics (demographic change calculation based on student’s sample). In contrast to traditional labs, we found that students were highly motivated and enthusiastic throughout the four-week activity. Students had a 100% rate of success in obtaining DNA sequences and their evaluations report high satisfaction with the learning outcome. Here we provide all details and datasets needed to run the lab and discuss a series of assessments and possible exercises.
L. Ferguson, L.S. Maroja, & C.D. JIGGINS. (2011). Convergent, modular expression of ebony and tan in the mimetic wing patterns of Heliconius butterflies. Development, Genes and Evolution 221: 297-308 The evolution of pigmentation in vertebrates and flies has involved repeated divergence at a small number of genes related to melanin synthesis. Here, we study insect melanin synthesis genes in Heliconius butterflies, a group characterised by its diversity of wing patterns consisting of black (melanin), and yellow and red (ommochrome) pigmented scales. Consistent with their respective biochemical roles in Drosophila melanogaster, ebony is upregulated in non-melanic wing regions destined to be pigmented red whilst tan is upregulated in melanic regions. Wing regions destined to be pigmented yellow, however, are downregulated for both genes. This pattern is conserved across multiple divergent and convergent phenotypes within the Heliconii, suggesting a conserved mechanism for the development of black, red and yellow pattern elements across the genus. Linkage mapping of five melanin biosynthesis genes showed that, in contrast to other organisms, these genes do not control pattern polymorphism. Thus, the pigmentation genes themselves are not the locus of evolutionary change but lie downstream of a wing pattern regulatory factor. The results suggest a modular system in which particular combinations of genes are switched on whenever red, yellow or black pattern elements are favoured by natural selection for diverse and mimetic wing patterns.
A.K. Surridge, S. Lopez-Gomollon, S. Moxon, L.S. Maroja, T. Rathjen, N.J. Nadeau, T. Dalmay & C.D. Jiggins. (2011). Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. BMC Genomics 12: 62doi:10.1186/1471-2164-12-62
Background: Heliconius butterflies are an excellent system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. miRNAs could act as regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races. Results: We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs were differentially represented in the libraries between colour pattern races. These candidates were tested further using Northern blots, showing that differences in expression were primarily due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified hme-miR-193 and hme-miR-2788; located 2380bp apart in an intergenic region. These two miRNAs are expressed in wings and show an upregulation between 24 and 72 hours post-pupation, indicating a potential role in butterfly wing development. A search for miRNAs in all available H. melpomene BAC sequences (~2.5Mb) did not reveal any other miRNAs and no novel miRNAs were predicted. Conclusions: Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages and may have important functions in butterfly wing development. Two miRNAs were located in the HmYb region and were expressed in developing pupal wings. Future work will examine the expression of these miRNAs in different colour pattern races and identify miRNA targets among wing patterning genes.
M.A. Morales. 2011. Model selection analysis of temporal variation in benefit for an ant-tended treehopper. Ecology. 92: 709-719.
J.H. Ness, M.A. Morales, E. Kenison, E. Leduc (’06), P. Leipzig-Scott, E. Rollinson, and B.J. Swimm (’09). 2012. Reciprocally beneficial interactions between introduced plants and ants are induced by the presence of a third introduced species. Oikos, In press.