sign in sign up
<<
Home , Systems neuroscience, Xylaria

2013 NEWSLETTER

MORE NEWS AND INFORMATION AT BIOLOGY.UOREGON.EDU BiologyAnimals as

INSIDE 2 From the Department Head 2 In the News 2 Meet Santiago Jaramillio Alaska Oregon Research Training Alliance (AORTA) interns and mentors, left to right: Shamaria Hale (intern), 4 Graduate Student Karen Carleson (intern), Kat Milligan-Myhre, Eric Johnson, Karen Guillemin, Brendan Bohannan, Dustin Carl Spotlight (intern), Annah Rolig, Clay Small, Raghuveer Parthasarathy, Tayesia Nick (intern), Matthew Jemielita, Ariel Royall. 5 Undergraduate Student Spotlight ach one of us is an facilities that are pioneering colonization of the gut in E for millions advances in gnotobiology real time. These innovative 5 ABLE Conference of microorganisms that (the technology of rearing experiments generate large 6 Follow the Fungi live on our bodies and in animals with defined consortia datasets that serve as the basis 8 Biology Platinum our digestive tracts. The of microbes), live imaging, for developing and testing University of Oregon is genomics, and bioinformatics. novel theoretical models of home to a new NIH-funded The META Center host-microbe interactions. National Center for research program builds on Major missions of the META is a publication Biology devoted to studying a long tradition at the UO Center are to train the next of the University of Oregon Biology these ecosystems. Directed of excellence in zebrafish generation of systems biologists Department of Biology by biology professor Karen research, dating back to the and increase the diversity of Department Head Guillemin, the Microbial seminal work of the late scientists in this field. So the Bruce Bowerman Ecology and Theory of George Streisinger. For their center hosted its first cohort of Business Manager Animals (META) Center investigations, META Center Alaska Native undergraduate Shelley Elliott for studies scientists use gnotobiotic interns this summer through how animals coexist with their fish, both zebrafish and its Alaska Oregon Research Editor resident microbes. stickleback, that are grown Training Alliance (AORTA). Lynne Romans The center brings together in sterile conditions and The four interns spent an Designer twelve UO faculty members then associated with defined intensive ten weeks carrying UO Design and Editing and affiliated students and microbes. The ability to out original research in the Services postdoctoral fellows from grow large populations of META Center. Each intern Printing the biology, physics, and genetically defined fish in isolated and characterized UO Printing and Mailing mathematics departments controlled environments and novel fish-associated bacteria, Services to establish a new field of with known microbes allows had hands-on exposure to host-microbe systems biology. researchers to ask questions the technologies of the four The center is divided into that are not possible in human META Center cores, and made three research areas that focus studies. And the fact that these valuable contributions that will on the assembly, dynamics, fish are optically transparent further the research mission of and evolution of host- when they are developing the META Center. microbe systems. Research makes it possible to image For more information, visit is supported by four core the events of microbial meta.uoregon.edu biology.uoregon.edu/facebook FROM THE DEPARTMENT HEAD Achievements and Visions

he number of under- majors. For more information, IN THE NEWS T graduates majoring in see smart.uoregon.edu. biology and marine biology In addition to these exciting The 2013 Guggenheim Fellow for is now nearly 1,000 students, advances and improvements, prior achievement and exceptional which represents a doubling this last year we also promise was awarded to Jessica in size over the past ten years. conducted a ten-year external Green, associate professor for the Promising new developments review of the effectiveness Institute of Ecology and Evolution. will ensure that the increasing of our teaching and research Green, a biologist, ecologist, and engineer, joined the UO faculty in enthusiasm for biology will programs. The review panel of 2007 and specializes in biodiversity result in an exceptionally highly accomplished biologists theory and microbial systems. She exciting and stimulating from four different educational is codirector of the Biology and the educational experience. institutions produced an Built Environment Center. We recently received exceptionally complementary An Early Research Career Award approval from the College a new centralized program and stimulating report was given to Cris Niell, Institute of Arts and Sciences for an for promoting undergraduate that includes suggestions of . Niell studies the extensive renovation of our research in faculty labs. This for how we can further function and development of neural biology office that will expand program, called UO-SMART improve our education and circuits for visual processing. He and improve the space we use (Scientific Mentorship and research missions. Faculty has helped pioneer methods to label synapses in the brain and manipulate for our undergraduate advising Research Training in biology), members will examine individual . program. The renovations will is overseen by our curriculum the recommendations increase the amount of space coordinator, Cristin from the external review Bruce Bowerman, in the Institute available for peer advising and Hulslander. It includes an panel and formulate a of Molecular Biology, was named a provide office space for both annual undergraduate research plan for implementing fellow of the American Association for the Advancement of Science. of our faculty advisers, Pat symposium and awards more improvements. I look Bowerman was selected for his Lombardi and Jana Prikryl. for outstanding research forward to describing these pioneering contributions in C. These renovations should achievements. This new new goals and our plan for elegans developmental genetics, be completed by spring of program, which simplifies and future changes in our next including studies on the mechanisms 2014 and represent the first improves opportunities for newsletter. of Wnt signaling, asymmetric cell division, meiosis, and cytokinesis. substantial improvement in students to gain experience our office and advising space in cutting-edge research, is Bruce Bowerman Scott Bridgham, professor of in decades. Second, after two fundamental for enriching [email protected] biology and environmental studies, years of planning, we have the experience of our biology was named a fellow of the Society of Wetland Scientists. In addition, Professor Bridgham is the director of the newly launched Environmental Science Institute. The institute is an Meet Santiago Jaramillo interdisciplinary research organization that includes faculty members and riven by an interest in in Barak Pearlmutter’s Brain graduate students from environmental intelligent machines, and Computation Lab at the studies, biology, geology, D geography, anthropology, and other Santiago Jaramillo started National University of Ireland, disciplines. The institute promotes his research career as an Maynooth. His doctoral work interdisciplinary collaboration in the engineer in Colombia. Seeking focused on theories to explain environmental sciences and provides inspiration from biological how attention modulates shared research facilities. For details, systems, he turned to the neural signals in order to visit esi.uoregon.edu. study of the . improve perception. After working for the Center A summer at the Marine for Neuromagnetism, headed Biological Laboratory in by Rodolfo Llinás at NYU, Woods Hole persuaded 2 he went to complete his PhD him to use animal models UO DEPARTMENT OF BIOLOGY Groundbreaking! Janis Weeks funded for research in global health and development

iology professor Janis IN THE NEWS B Weeks was awarded a prestigious Grand Challenges Eric Selker, Institute of Molecular Explorations research grant Biology, is the 2013 Outstanding from the Bill and Melinda Scientist of the Oregon Academy of Gates Foundation (BMGF), Science. The academy noted that entitled “- Selker’s name has appeared on 130 peer-reviewed research articles, based platform for STH (soil- many of which are often cited by transmitted helminth) drug other scientists. discovery.” This is the first BMGF grant ever awarded to Bill Cresko, Institute for Ecology and Evolution, was selected to the University of Oregon. Shawn Lockery that integrates Janis Weeks with staff of an HIV/ receive a Fund for Faculty Excellence AIDS clinic in rural Zimbabwe. In Two to three billion of the the fields of microfluidics and Award. Designed to further the UO’s world’s poorest people are neurophysiology to record 2012, 1,000 clients were enrolled in strategic commitment to improve infected by soil-transmitted neuromuscular signals from the program with another 2,000 on its academic quality and reputation, helminths (worms) such as nematode worms while a waiting list. recipients are chosen on the basis of hookworm and whipworm. testing potential anthelmintic human worm infections. scholarly impact and contributions. However, few treatments (antiworm) drug candidates. Weeks’s global health Helen Neville was are approved for human In 2011, Lockery and Weeks research is motivated in part among three U.S. professors chosen use and existing drugs are formed a biotech company, by her firsthand experiences in to receive the William James Fellow failing due to increasing drug NemaMetrix, to help make Africa. She is a member of the Award. Recipients are honored for resistance in the parasites. this technology available to UO African Studies Program their lifetime of significant intellectual contributions to the basic science of These infections, which researchers worldwide. and teaches biology courses for psychology. Neville is internationally cause chronic malnutrition The BMGF project aims undergraduates on infectious renowned for her groundbreaking and anemia, have especially to adapt the microfluidic and parasitic diseases of research on the plasticity of the devastating impacts on technology, initially Africa. Several undergraduates developing brain. the physical and cognitive developed in the nonparasitic are also members of her lab New graduate specialization in development of children. nematode, C. elegans, for use research team. For more neuroscience: Anchored in the Weeks’s research utilizes with parasitic nematodes, to information, visit neuro. biology and psychology departments, a patent-pending technology accelerate the development of uoregon.edu/ionmain/htdocs/ the graduate specialization in invented by biology professor new, improved drugs to treat faculty/weeks.html. neuroscience has two overriding objectives. The first is to produce innovative, intellectually critical, and experimentally skilled with an interdisciplinary outlook. The second is to foster interdisciplinary research at the intersection between in his studies of neural the Institute of Neuroscience, together with theoretical and systems neuroscience and . This graduate information processing, and where molecular biology computational approaches, to specialization will establish for the as a postdoctoral fellow meets systems neuroscience study the perception of sounds first time a common curriculum with Anthony Zador at Cold and psychology. under changing contexts. across the in biology Spring Harbor Laboratory, Santiago’s group will focus Outside the lab, Santiago and psychology. he developed techniques on the neuronal circuits that spends his time on volleyball continued on page 6 to investigate the effects of mediate behavioral flexibility courts, as guest guitarist in attention and expectation in and selective attention. His his friends’ bands, and with the auditory of rodents. research uses state-of-the-art his girlfriend Anja, a cancer Coming from a multi- techniques for monitoring biologist with whom he shares disciplinary background, and manipulating neuronal a passion for podcasts and SantiagoFALL 2013 is excited NEWSLETTER to join activity in behaving mice, playing Frisbee at wine tastings. 3 GRADUATE STUDENT SPOTLIGHT Michael Kyweriga

am not what you would beautiful outdoor recreation. sounds originating from I you would call a traditional It still remains my favorite the side of the head, I have student. Unlike most students summer of all time. As a SPUR demonstrated that it plays a at the University of Oregon, I scholar, the collaborative strong role in the processing of enlisted in the U.S. Navy after atmosphere fostered by sounds that originate from the high school. While serving as brilliant scientists impressed front of the head. a hospital corpsman treating me. I was particularly drawn In addition to my sick and injured U.S. Marines, to the research of Mike research, I have also had I found myself increasingly Wehr and his mechanistic the opportunity to mentor interested in human stance that neurons drive our undergraduates and teach physiology and psychology. thoughts and behavior. lab sections. Throughout I was especially interested The following year, I was my education, I have had in human cognition, and a accepted into the biology the good fortune of gifted question burned in my brain: PhD program and I soon mentors who got me excited How does a three-pound fatty joined Wehr’s lab. How about science and supported blob of cells in our head drive neural circuits function in my goals. I aspire to pay this our life and experiences? the cortex has remained an forward, sharing my passion Five years later I received elusive problem in systems for science with young minds my honorable discharge neuroscience. While the and being the best mentor and “Throughout my and I used my GI Bill to cortex is primarily composed teacher that I can be. Soon I education I have had the obtain a bachelor’s degree in of excitatory neurons, will graduate and move on good fortune of gifted psychology with a minor in approximately 20 percent are to a postdoc or two. I will biology at UC Santa Cruz. inhibitory neurons and their miss hiking Oregon’s trails, mentors who got me During my undergraduate role is poorly understood. tide pooling on the coast, excited about science and studies, I became hooked Scientists have long known and yelling “O!” at Autzen supported my goals.” on the idea that all of our that a sound wave originating Stadium. In the future, I will cognitions are based on from the right side of the body have my own lab and utilize physical neuronal systems. will stimulate the right ear the recent advent of new After graduation, I was drum more than the left one. genetic techniques that allow accepted into the UO Summer These eardrum movements are researchers to turn neurons on Program for Undergraduate converted into an electrical and off with lasers in living Research (SPUR). I worked signal and then compared animals. With this technique in Paul Dassonville’s visual in your brain. This way you and the collaboration of cognition lab studying can detect where a sound is colleagues, I will continue human susceptibility to coming from even if you can’t to investigate the role of visual illusions. While in see it. My work has revealed inhibition in cortical circuits the program, I met many a novel role of inhibitory cells and learn exactly how our students from around the in the processing of sound neurons work together to make world. We bonded over our location cues in the auditory us who we are. strong interests in science, cortex. While inhibition has Kyweriga is the 2013 technology, and Oregon’s little to no role in processing recipient of the Biology Teacher Recognition Award.

4 UO DEPARTMENT OF BIOLOGY UNDERGRADUATE STUDENT SPOTLIGHT Brianna McHorse

y first two years as a study horses for my senior and Evolutionary Biology M biology major were honors thesis. Together, at Harvard University as spent trying out the different we designed the project a PhD student and NSF flavors of science offered and where I examined several Graduate Research Fellow. My working in everything from specific questions about the proposed research will use zebrafish to climate change assumed relationship between my undergraduate experience labs. Evolution and ecology “conformation,” or the as a launching point. I plan drew my interest, especially external shape of the horse’s to build three-dimensional anything involving mammals, body parts, and its suitability musculoskeletal models of but for some time I remained for competition. This research horse legs to test modern unsure whether research was helped me win a Goldwater performance hypotheses, truly a good fit for me. Luckily, Scholarship, which allowed as well as to investigate the a simple summer data-entry me to spend my final year adaptive significance of the task would set me on the path focusing on the thesis and evolutionary change from toward my current interests other research projects. three toes to one toe. and plans to build a career in A side effect of working Ultimately, I would love academic research. in a paleontology lab turns to become a professor—it The project involved out to be a growing interest combines the best of teaching looking up mammalian in paleontology. One of those and research, both of which I “This research helped patterns for my honors projects included studying enjoy, although I hear being a college and research adviser, the functional morphology professor would be easier with me win a Goldwater Samantha Hopkins. Since we of fossil camels from the about eight more hours in the Scholarship, which needed data for every mammal mid-Miocene (approximately day. I am immensely grateful allowed me to spend my possible, I received a crash fifteen million years ago) of for all the opportunities I’ve course in phylogenetics and eastern Oregon. The paper had to work with incredible final year focusing on the massive Excel spreadsheets— from this work is currently teachers and researchers at the thesis and other research two things I remain fond of, in revision and will likely be University of Oregon, within projects.” despite hours spent hunting published soon. I’m also very and outside of the biology down information and offset excited about several other department, and I am excited errors in the spreadsheet. projects that I hope to finish to see what my academic I began working with up and publish before I leave! future brings. Assistant Professor Hopkins In the fall I will join the again when I decided to Department of Organismic

LE 201 2014 ABLE Conference at the University of Oregon B ENT OF B 4 More than 200 biology laboratory Carl Stiefbold, biology career M IO A T L R O instructors from all across the senior instructor and ABLE A P G U.S. and Canada will converge second vice president with E Y D on the UO June 17–20, financial support in the form of

U 2014, to attend the thirty-sixth a program grant from the UO N N annual Association for Biology College of Arts and Sciences I V O G Laboratory Education (ABLE) and generous financial and staff E E RS R workshop and conference. The support from the UO Department ITY F O O conference will be hosted by of Biology.

FALL 2013 NEWSLETTER 5 Follow the Fungi PhD candidates earn fellowship to do research in Taiwan

IN THE NEWS continued from page 3

Holly Arnold, Institue of Ecology and Evolution PhD candidate, received the Gary Smith Summer Professional Development Award. The award is designed to support outstanding graduate students pursuing academic, professional development, or training enrichment opportunities. Arnold is using the award to participate in the Complex Systems Summer School at Santa Fe Institute. Left: Shandao Temple carving. Right: Daniel and Roo with Yu-Ming Ju

Ashley Bateman, Institue of aniel Thomas and I When we try to pick out might be what xylariaceous Ecology and Evolution PhD (Roo Vandegrift) spent fungi are doing—biding their D anything by itself, we find candidate, has received the Clarence the summer in Taiwan this time to get to their preferred and Lucille Dunbar Scholarship it hitched to everything else This scholarship recognizes high year as participants in the food. To test that hypothesis, achieving undergraduate and NSF East Asia and Pacific in the universe. we went to Taiwan to talk graduate students in the areas Summer Institute. This —John Muir with the expert, and to run a of biology, chemistry, computer gave us the opportunity to field study that will hopefully and information science, human spend the summer working found mostly on decaying help us answer this question. physiology, geological sciences, mathematics, physics, or psychology. with Yu-Ming Ju, the world wood. These fungi are also In Taiwan, we worked with expert on the and some of the most common Yu Ming Ju to learn everything Daniel Thomas, IEE PhD candidate, identification of fungi in the and ubiquitous endophytes— we could about the taxonomy has earned the NSF East Asian and family , and his fungi that inhabit plant leaves and identification of these Pacific Summer Institute Fellowship wife Monica Hsieh, who heads without causing disease or fungi, seeking his help with and the William R. Sistrom Award for Excellence in Microbiology. the molecular phylogenetic other obvious harm—in the difficult specimens from Dan recently received the Oregon side of the lab at Academia tropics. We wanted to answer Ecuador. We also worked in Mycological Society Scholarship for Sinica in Taipei. this question: “What is a group the lab with Monica Hsieh to Graduate Research as well. We developed an interest in of fungi that eats dead wood learn molecular techniques the Xylariaceae while working doing in living leaves?” for phylogenetic analysis, and Roo Vandegrift, PhD candidate, also received an NSF’s East Asia and in the cloud forests of Ecuador George Carroll, UO shared our plans for high- Pacific Summer Institute Fellowship assisting Professor Bitty Roy’s professor emeritus in biology, throughput Illumina microbial in addition to the Mycological Society research. While known to proposed more than a dozen community analysis with of America Graduate Fellowship and most people in the temperate years ago that some fungi her. We obtained permission the Cascade Mycological Society zone by a single member, might use an endophytic to work at the Fushan Outstanding Research Project Scholarship. Roo is also an NSF , the life stage as a means of subtropical forest dynamics Graduate Research Fellowship candle-snuff , this is a “foraging” for food, hanging plot, one of the Smithsonian’s awardee. family of fungi with incredible out in leaves until they fall, Long-Term Ecological diversity in the tropics. That at which point they reap the Research (LTER) Network’s diversity expresses itself benefits of increased dispersal twenty-five-hectare plots. through the proliferation distance and persistence in This site in northern of forms of fruiting bodies the environment. Indeed, this Taiwan is amazing: it ranges

6 UO DEPARTMENT OF BIOLOGY from between 600 and Taiwanese rainforest, we 700 meters elevation, and returned to Taipei to process IN THE NEWS receives about four meters samples, extract DNA, and of rain a year. The wildlife generally try to get as far along Undergraduate scholarship recipients at Fushan was astounding. as we could before we needed for 2013 include We had troops of Formosan to head home. But that doesn’t Kyla Martichuski: Mildred Braaten macaque monkeys, herds mean we didn’t get out a bit Archibald Scholarship of barking deer, poisonous between bouts of work. We Christine Liu: Henry V. Howe Scholarship stinging caterpillars, and huge visited places all over Taiwan, Dylan Hanes: CAS Scholarship fuzzy caterpillars, as well as including Taroko Gorge, which Amelia Fitch, Leif Rasmuson, Taiwanese face spiders and is often compared to the Grand David Adams, Michael Tomcal: many, many more amazing Canyon, and certainly attracts Clarence and Lucille Dunbar creatures. The plant diversity at least as many tourists every Scholarships Ruth Grenke: Henry V. Howe was incredible, particularly year. We also took a trip to Scholarship the ferns. And because it is Li-Song hot springs, said to be part of a long term ecological some of the most beautiful in Undergraduate summer research monitoring program, we are the world; we visited famous awards from the SMART program for able to correlate our data temples, including Shandao 2013 were given to Kyla Martichuski (Green lab), with masses of existing Temple in Taipei. To cap our Hanna Moore (Phillips lab), and environmental and ecological summer off, we each took a Clarissa Camarillo (Stankunas lab). data, and every tree in the week of vacation and enjoyed For more information, visit twenty-five-hectare plot being on a tropical island. smart.uoregon.edu. From top: Poisonous stinging is uniquely tagged, with Roo Vandegrift, author caterpillar, Taiwanese face spider To contribute to our scholarship associated data available. of this article, and Daniel (Nephila pilipes) funds, please send your check, After two weeks of Thomas are both PhD payable to the UO Foundation, tromping around in the candidates in Bitty Roy’s lab. to Department of Biology, 1210 University of Oregon, Eugene, Oregon 97403-1210. Designate the specific scholarship or fund you want to support on the check memo line.

Field site finds From left: Xylaria telfairii, Xylaria aff. anisolpuera

FALL 2013 NEWSLETTER 7 Nonprofit Organization U.S. Postage DEPARTMENT OF BIOLOGY PAID 1210 University of Oregon Eugene OR Eugene OR 97403-1210 Permit No. 63

Biology Goes Platinum with Green Ways he biology office staff was Tawarded the first-ever platinum-level green office certification. University president Michael Gottfredson delivered the platinum-level green office certificate to the Department of Biology. Bruce Bowerman, department head, accepted the award on behalf of the staff. The biology office has the highest level of achievement in the program. The Department of Biology met platinum standards by first meeting the program’s prerequisite and then exceeded standards, scoring “the highest of all participants to date” in the areas of energy, material management, transportation, and events, according to Andrew Louw, sustainability Left to right, front row, Michael Gottfredson, Bruce Bowerman, Ingrid Karson-Newman, and Annie Rogers; affairs graduate fellow. back row, Misty McLean-Schurbon, Andrew Louw, Marie Greig, Lynne Romans, Holly Lynn, and Shelley Elliott.

An equal-opportunity, affirmative-action institution committed to cultural diversity and compliance with the Americans with Disabilities Act. This publication will be made available in accessible formats upon request. ©2013 University of Oregon. DES1113-010s-D18226