Biology2 0 13 N E W S L E T T E R

INSIDE

2 From the Department Head

2 In the News

2 Meet Santiago Jaramillio

4 Graduate Student Spotlight

5 Undergraduate Student Spotlight

5 ABLE Conference

6 Follow the Fungi

8 Biology Platinum

Biology is a publication of the University of Oregon Department of Biology

Department Head Bruce Bowerman

Business Manager Shelley Elliott

Editor Lynne Romans

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M O R E N E W S A N D

I N F O R M AT I O N AT

B I O L O G Y. U O R E G O N . E D U

Animals as Ecosystems

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Each one of us is an ecosystem for millions

of microorganisms that live on our bodies and in our digestive tracts. The University of Oregon is home to a new NIH-funded National Center for Systems Biology devoted to studying these ecosystems. Directed by biology professor Karen Guillemin, the Microbial Ecology and Theory of Animals (META) Center for Systems Biology studies how animals coexist with their resident microbes.

The center brings together twelve UO faculty members and affiliated students and postdoctoral fellows from the biology, physics, and mathematics departments to establish a new field of host-microbe systems biology. The center is divided into three research areas that focus on the assembly, dynamics, and evolution of host-microbe systems. Research is supported by four core

facilities that are pioneering advances in gnotobiology (the technology of rearing animals with defined consortia of microbes), live imaging, genomics, and bioinformatics.

The META Center research program builds on a long tradition at the UO of excellence in zebrafish research, dating back to the seminal work of the late George Streisinger. For their investigations, META Center scientists use gnotobiotic fish, both zebrafish and stickleback, that are grown in sterile conditions and then associated with defined microbes. The ability to grow large populations of genetically defined fish in controlled environments and with known microbes allows researchers to ask questions that are not possible in human studies. And the fact that these fish are optically transparent when they are developing makes it possible to image the events of microbial

colonization of the gut in real time. These innovative experiments generate large datasets that serve as the basis for developing and testing novel theoretical models of host-microbe interactions.

Major missions of the META Center are to train the next generation of systems biologists and increase the diversity of scientists in this field. So the center hosted its first cohort of Alaska Native undergraduate interns this summer through its Alaska Oregon Research Training Alliance (AORTA). The four interns spent an intensive ten weeks carrying out original research in the META Center. Each intern isolated and characterized novel fish-associated bacteria, had hands-on exposure to the technologies of the four META Center cores, and made valuable contributions that will further the research mission of the META Center.

For more information, visitmeta.uoregon.edu

Alaska Oregon Research Training Alliance (AORTA) interns and mentors, left to right: Shamaria Hale (intern), Karen Carleson (intern), Kat Milligan-Myhre, Eric Johnson, Karen Guillemin, Brendan Bohannan, Dustin Carl (intern), Annah Rolig, Clay Small, Raghuveer Parthasarathy, Tayesia Nick (intern), Matthew Jemielita, Ariel Royall.

2 UO DEPARTMENT OF BIOLOGY

Achievements and VisionsFROMTHEDEPARTMENTHEAD

The 2013 Guggenheim Fellow for prior achievement and exceptional promise was awarded to Jessica Green, associate professor for the Institute of Ecology and Evolution. Green, a biologist, ecologist, and engineer, joined the UO faculty in 2007 and specializes in biodiversity theory and microbial systems. She is codirector of the Biology and the Built Environment Center.

An Early Research Career Award was given to Cris Niell, Institute of Neuroscience. Niell studies the function and development of neural circuits for visual processing. He has helped pioneer methods to label synapses in the brain and manipulate individual neurons.

Bruce Bowerman, in the Institute of Molecular Biology, was named a fellow of the American Association for the Advancement of Science. Bowerman was selected for his pioneering contributions in C. elegans developmental genetics, including studies on the mechanisms of Wnt signaling, asymmetric cell division, meiosis, and cytokinesis.

Scott Bridgham, professor of biology and environmental studies, 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 interdisciplinary research organization that includes faculty members and graduate students from environmental studies, biology, geology, geography, anthropology, and other disciplines. The institute promotes interdisciplinary collaboration in the environmental sciences and provides shared research facilities. For details, visit esi.uoregon.edu.

Meet Santiago Jaramillo

T he number of under-graduates majoring in

biology and marine biology is now nearly 1,000 students, which represents a doubling in size over the past ten years. Promising new developments will ensure that the increasing enthusiasm for biology will result in an exceptionally exciting and stimulating educational experience.

We recently received approval from the College of Arts and Sciences for an extensive renovation of our biology office that will expand and improve the space we use for our undergraduate advising program. The renovations will increase the amount of space available for peer advising and provide office space for both of our faculty advisers, Pat Lombardi and Jana Prikryl. These renovations should be completed by spring of 2014 and represent the first substantial improvement in our office and advising space in decades. Second, after two years of planning, we have

a new centralized program for promoting undergraduate research in faculty labs. This program, called UO-SMART (Scientific Mentorship and Research Training in biology), is overseen by our curriculum coordinator, Cristin Hulslander. It includes an annual undergraduate research symposium and awards for outstanding research achievements. This new program, which simplifies and improves opportunities for students to gain experience in cutting-edge research, is fundamental for enriching the experience of our biology

majors. For more information, see smart.uoregon.edu.

In addition to these exciting advances and improvements, this last year we also conducted a ten-year external review of the effectiveness of our teaching and research programs. The review panel of highly accomplished biologists from four different educational institutions produced an exceptionally complementary and stimulating report that includes suggestions for how we can further improve our education and research missions. Faculty members will examine the recommendations from the external review panel and formulate a plan for implementing more improvements. I look forward to describing these new goals and our plan for future changes in our next newsletter.

Bruce Bowermanbowerman@uoregon.edu

INTHENEWS

D riven by an interest in intelligent machines,

Santiago Jaramillo started his research career as an engineer in Colombia. Seeking inspiration from biological systems, he turned to the study of the human brain. After working for the Center for Neuromagnetism, headed by Rodolfo Llinás at NYU, he went to complete his PhD

in Barak Pearlmutter’s Brain and Computation Lab at the National University of Ireland, Maynooth. His doctoral work focused on theories to explain how attention modulates neural signals in order to improve perception.

A summer at the Marine Biological Laboratory in Woods Hole persuaded him to use animal models

FALL 2013 NEWSLETTER 3

INTHENEWS

Eric Selker, Institute of Molecular Biology, is the 2013 Outstanding Scientist of the Oregon Academy of Science. The academy noted that Selker’s name has appeared on 130 peer-reviewed research articles, many of which are often cited by other scientists.

Bill Cresko, Institute for Ecology and Evolution, was selected to receive a Fund for Faculty Excellence Award. Designed to further the UO’s strategic commitment to improve its academic quality and reputation, recipients are chosen on the basis of scholarly impact and contributions.

Neuroscientist Helen Neville was among three U.S. professors chosen to receive the William James Fellow Award. Recipients are honored for their lifetime of significant intellectual contributions to the basic science of psychology. Neville is internationally renowned for her groundbreaking research on the plasticity of the developing brain.

New graduate specialization in neuroscience: Anchored in the biology and psychology departments, the graduate specialization in neuroscience has two overriding objectives. The first is to produce innovative, intellectually critical, and experimentally skilled neuroscientists with an interdisciplinary outlook. The second is to foster interdisciplinary research at the intersection between systems neuroscience and cognitive neuroscience. This graduate specialization will establish for the first time a common curriculum across the neurosciences in biology and psychology.

continued on page 6

B iology professor Janis Weeks was awarded a

prestigious Grand Challenges Explorations research grant from the Bill and Melinda Gates Foundation (BMGF), entitled “Neurophysiology-based platform for STH (soil-transmitted helminth) drug discovery.” This is the first BMGF grant ever awarded to the University of Oregon.

Two to three billion of the world’s poorest people are infected by soil-transmitted helminths (worms) such as hookworm and whipworm. However, few treatments are approved for human use and existing drugs are failing due to increasing drug resistance in the parasites. These infections, which cause chronic malnutrition and anemia, have especially devastating impacts on the physical and cognitive development of children.

Weeks’s research utilizes a patent-pending technology invented by biology professor

Shawn Lockery that integrates the fields of microfluidics and neurophysiology to record neuromuscular signals from nematode worms while testing potential anthelmintic (antiworm) drug candidates. In 2011, Lockery and Weeks formed a biotech company, NemaMetrix, to help make this technology available to researchers worldwide.

The BMGF project aims to adapt the microfluidic technology, initially developed in the nonparasitic nematode, C. elegans, for use with parasitic nematodes, to accelerate the development of new, improved drugs to treat

Groundbreaking!Janis Weeks funded for research in global health and development

human worm infections.Weeks’s global health

research is motivated in part by her firsthand experiences in Africa. She is a member of the UO African Studies Program and teaches biology courses for undergraduates on infectious and parasitic diseases of Africa. Several undergraduates are also members of her lab research team. For more information, visit neuro.uoregon.edu/ionmain/htdocs/faculty/weeks.html.

Janis Weeks with staff of an HIV/AIDS clinic in rural Zimbabwe. In 2012, 1,000 clients were enrolled in the program with another 2,000 on a waiting list.

in his studies of neural information processing, and as a postdoctoral fellow with Anthony Zador at Cold Spring Harbor Laboratory, he developed techniques to investigate the effects of attention and expectation in the auditory system of rodents.

Coming from a multi-disciplinary background, Santiago is excited to join

the Institute of Neuroscience, where molecular biology meets systems neuroscience and psychology.

Santiago’s group will focus on the neuronal circuits that mediate behavioral flexibility and selective attention. His research uses state-of-the-art techniques for monitoring and manipulating neuronal activity in behaving mice,

together with theoretical and computational approaches, to study the perception of sounds under changing contexts.

Outside the lab, Santiago spends his time on volleyball courts, as guest guitarist in his friends’ bands, and with his girlfriend Anja, a cancer biologist with whom he shares a passion for podcasts and playing Frisbee at wine tastings.

4 UO DEPARTMENT OF BIOLOGY

Michael Kyweriga

GRADUATESTUDENTSPOTLIGHT

Iam not what you would you would call a traditional

student. Unlike most students at the University of Oregon, I enlisted in the U.S. Navy after high school. While serving as a hospital corpsman treating sick and injured U.S. Marines, I found myself increasingly interested in human physiology and psychology. I was especially interested in human cognition, and a question burned in my brain: How does a three-pound fatty blob of cells in our head drive our life and experiences? Five years later I received my honorable discharge and I used my GI Bill to obtain a bachelor’s degree in psychology with a minor in biology at UC Santa Cruz.

During my undergraduate studies, I became hooked on the idea that all of our cognitions are based on physical neuronal systems. After graduation, I was accepted into the UO Summer Program for Undergraduate Research (SPUR). I worked in Paul Dassonville’s visual cognition lab studying human susceptibility to visual illusions. While in the program, I met many students from around the world. We bonded over our strong interests in science, technology, and Oregon’s

beautiful outdoor recreation. It still remains my favorite summer of all time. As a SPUR scholar, the collaborative atmosphere fostered by brilliant scientists impressed me. I was particularly drawn to the research of Mike Wehr and his mechanistic stance that neurons drive our thoughts and behavior.

The following year, I was accepted into the biology PhD program and I soon joined Wehr’s lab. How neural circuits function in the cortex has remained an elusive problem in systems neuroscience. While the cortex is primarily composed of excitatory neurons, approximately 20 percent are inhibitory neurons and their role is poorly understood.

Scientists have long known that a sound wave originating from the right side of the body will stimulate the right ear drum more than the left one. These eardrum movements are converted into an electrical signal and then compared in your brain. This way you can detect where a sound is coming from even if you can’t see it. My work has revealed a novel role of inhibitory cells in the processing of sound location cues in the auditory cortex. While inhibition has little to no role in processing

sounds originating from the side of the head, I have demonstrated that it plays a strong role in the processing of sounds that originate from the front of the head.

In addition to my research, I have also had the opportunity to mentor undergraduates and teach lab sections. Throughout my education, I have had the good fortune of gifted mentors who got me excited about science and supported my goals. I aspire to pay this forward, sharing my passion for science with young minds and being the best mentor and teacher that I can be. Soon I will graduate and move on to a postdoc or two. I will miss hiking Oregon’s trails, tide pooling on the coast, and yelling “O!” at Autzen Stadium. In the future, I will have my own lab and utilize the recent advent of new genetic techniques that allow researchers to turn neurons on and off with lasers in living animals. With this technique and the collaboration of colleagues, I will continue to investigate the role of inhibition in cortical circuits and learn exactly how our neurons work together to make us who we are.

Kyweriga is the 2013 recipient of the Biology Teacher Recognition Award.

“Throughout my

education I have had the

good fortune of gifted

mentors who got me

excited about science and

supported my goals.”

FALL 2013 NEWSLETTER 5

Brianna McHorse

UNDERGRADUATESTUDENTSPOTLIGHT

M y first two years as a biology major were

spent trying out the different flavors of science offered and working in everything from zebrafish to climate change labs. Evolution and ecology drew my interest, especially anything involving mammals, but for some time I remained unsure whether research was truly a good fit for me. Luckily, a simple summer data-entry task would set me on the path toward my current interests and plans to build a career in academic research.

The project involved looking up mammalian sleep patterns for my honors college and research adviser, Samantha Hopkins. Since we needed data for every mammal possible, I received a crash course in phylogenetics and massive Excel spreadsheets—two things I remain fond of, despite hours spent hunting down information and offset errors in the spreadsheet. I began working with Assistant Professor Hopkins again when I decided to

study horses for my senior honors thesis. Together, we designed the project where I examined several specific questions about the assumed relationship between “conformation,” or the external shape of the horse’s body parts, and its suitability for competition. This research helped me win a Goldwater Scholarship, which allowed me to spend my final year focusing on the thesis and other research projects.

A side effect of working in a paleontology lab turns out to be a growing interest in paleontology. One of those projects included studying the functional morphology of fossil camels from the mid-Miocene (approximately fifteen million years ago) of eastern Oregon. The paper from this work is currently in revision and will likely be published soon. I’m also very excited about several other projects that I hope to finish up and publish before I leave!

In the fall I will join the Department of Organismic

and Evolutionary Biology at Harvard University as a PhD student and NSF Graduate Research Fellow. My proposed research will use my undergraduate experience as a launching point. I plan to build three-dimensional musculoskeletal models of horse legs to test modern performance hypotheses, as well as to investigate the adaptive significance of the evolutionary change from three toes to one toe.

Ultimately, I would love to become a professor—it combines the best of teaching and research, both of which I enjoy, although I hear being a professor would be easier with about eight more hours in the day. I am immensely grateful for all the opportunities I’ve had to work with incredible teachers and researchers at the University of Oregon, within and outside of the biology department, and I am excited to see what my academic future brings.

“This research helped

me win a Goldwater

Scholarship, which

allowed me to spend my

final year focusing on the

thesis and other research

projects.”

2014 ABLE Conference at the University of Oregon

DEP

ARTMENT OF BIOLOG

Y

UN

IV

ERSITY OF OREGO

N

ABLE 2014 More than 200 biology laboratory

instructors from all across the U.S. and Canada will converge on the UO June 17–20, 2014, to attend the thirty-sixth annual Association for Biology Laboratory Education (ABLE) workshop and conference. The conference will be hosted by

Carl Stiefbold, biology career senior instructor and ABLE second vice president with financial support in the form of a program grant from the UO College of Arts and Sciences and generous financial and staff support from the UO Department of Biology.

6 UO DEPARTMENT OF BIOLOGY

INTHENEWS

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.

Ashley Bateman, Institue of Ecology and Evolution PhD candidate, has received the Clarence and Lucille Dunbar Scholarship This scholarship recognizes high achieving undergraduate and graduate students in the areas of biology, chemistry, computer and information science, human physiology, geological sciences, mathematics, physics, or psychology.

Daniel Thomas, IEE PhD candidate, has earned the NSF East Asian and Pacific Summer Institute Fellowship and the William R. Sistrom Award for Excellence in Microbiology. Dan recently received the Oregon Mycological Society Scholarship for Graduate Research as well.

Roo Vandegrift, PhD candidate, also received an NSF’s East Asia and Pacific Summer Institute Fellowship in addition to the Mycological Society of America Graduate Fellowship and the Cascade Mycological Society Outstanding Research Project Scholarship. Roo is also an NSF Graduate Research Fellowship awardee.

continued from page 3

Daniel Thomas and I (Roo Vandegrift) spent

the summer in Taiwan this year as participants in the NSF East Asia and Pacific Summer Institute. This gave us the opportunity to spend the summer working with Yu-Ming Ju, the world expert on the taxonomy and identification of fungi in the family Xylariaceae, and his wife Monica Hsieh, who heads the molecular phylogenetic side of the lab at Academia Sinica in Taipei.

We developed an interest in the Xylariaceae while working in the cloud forests of Ecuador assisting Professor Bitty Roy’s research. While known to most people in the temperate zone by a single member, Xylaria hypoxylon, the candle-snuff fungus, this is a family of fungi with incredible diversity in the tropics. That diversity expresses itself through the proliferation of forms of fruiting bodies

Follow the FungiPhD candidates earn fellowship to do research in Taiwan

found mostly on decaying wood. These fungi are also some of the most common and ubiquitous endophytes—fungi that inhabit plant leaves without causing disease or other obvious harm—in the tropics. We wanted to answer this question: “What is a group of fungi that eats dead wood doing in living leaves?”

George Carroll, UO professor emeritus in biology, proposed more than a dozen years ago that some fungi might use an endophytic life stage as a means of “foraging” for food, hanging out in leaves until they fall, at which point they reap the benefits of increased dispersal distance and persistence in the environment. Indeed, this

might be what xylariaceous fungi are doing—biding their time to get to their preferred food. To test that hypothesis, we went to Taiwan to talk with the expert, and to run a field study that will hopefully help us answer this question.

In Taiwan, we worked with Yu Ming Ju to learn everything we could about the taxonomy and identification of these fungi, seeking his help with difficult specimens from Ecuador. We also worked in the lab with Monica Hsieh to learn molecular techniques for phylogenetic analysis, and shared our plans for high-throughput Illumina microbial community analysis with her. We obtained permission to work at the Fushan subtropical forest dynamics plot, one of the Smithsonian’s Long-Term Ecological Research (LTER) Network’s twenty-five-hectare plots.

This site in northern Taiwan is amazing: it ranges

Left: Shandao Temple carving. Right: Daniel and Roo with Yu-Ming Ju

When we try to pick out

anything by itself, we find

it hitched to everything else

in the universe.

—John Muir

FALL 2013 NEWSLETTER 7

INTHENEWS

Undergraduate scholarship recipients for 2013 includeKyla Martichuski: Mildred Braaten Archibald ScholarshipChristine Liu: Henry V. Howe ScholarshipDylan Hanes: CAS ScholarshipAmelia Fitch, Leif Rasmuson,David Adams, Michael Tomcal: Clarence and Lucille DunbarScholarshipsRuth Grenke: Henry V. Howe Scholarship

Undergraduate summer research awards from the SMART program for 2013 were given to Kyla Martichuski (Green lab), Hanna Moore (Phillips lab), and Clarissa Camarillo (Stankunas lab).For more information, visit smart.uoregon.edu.

To contribute to our scholarship funds, please send your check, payable to the UO Foundation, 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.

from between 600 and 700 meters elevation, and receives about four meters of rain a year. The wildlife at Fushan was astounding. We had troops of Formosan macaque monkeys, herds of barking deer, poisonous stinging caterpillars, and huge fuzzy caterpillars, as well as Taiwanese face spiders and many, many more amazing creatures. The plant diversity was incredible, particularly the ferns. And because it is part of a long term ecological monitoring program, we are able to correlate our data with masses of existing environmental and ecological data, and every tree in the twenty-five-hectare plot is uniquely tagged, with associated data available.

After two weeks of tromping around in the

Taiwanese rainforest, we returned to Taipei to process samples, extract DNA, and generally try to get as far along as we could before we needed to head home. But that doesn’t mean we didn’t get out a bit between bouts of work. We visited places all over Taiwan, including Taroko Gorge, which is often compared to the Grand Canyon, and certainly attracts at least as many tourists every year. We also took a trip to Li-Song hot springs, said to be some of the most beautiful in the world; we visited famous temples, including Shandao Temple in Taipei. To cap our summer off, we each took a week of vacation and enjoyed being on a tropical island.

Roo Vandegrift, author of this article, and Daniel Thomas are both PhD candidates in Bitty Roy’s lab.

Field site findsFrom left: Xylaria telfairii, Xylaria aff. anisolpuera

From top: Poisonous stinging caterpillar, Taiwanese face spider (Nephila pilipes)

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DEPARTMENT OF BIOLOGY

1210 University of Oregon Eugene OR 97403-1210

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

Left to right, front row, Michael Gottfredson, Bruce Bowerman, Ingrid Karson-Newman, and Annie Rogers; back row, Misty McLean-Schurbon, Andrew Louw, Marie Greig, Lynne Romans, Holly Lynn, and Shelley Elliott.

The biology office staff was awarded 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 affairs graduate fellow.

Biology Goes Platinum with Green Ways