Projects 2013
David Altman, Assistant Professor of Physics
Generation of force is critical for various cellular processes. Central to many of these processes are motor proteins, proteins that use the cell's chemical energy to create directed motion. Myosins are a family of motor proteins that generate motion along the filamentous protein actin using the energy of ATP hydrolysis. Single-molecule studies of myosin motors have led to a detailed understanding of their force-generating mechanism. However, an understanding of how a myosin functions also requires an understanding of how the motor is regulated by its cellular environment. The goal of this research is to elucidate how forces that a myosin experiences in the crowded and dynamic environment of the cell regulate its function.
To mimic the forces felt by a motor in the cell, we will use an optical trap system capable of applying forces of varying magnitude and direction to individual motors. This system will be used to study a class I myosin predicted to perform different functions in different cellular systems. We will test the hypothesis that external forces regulate the motor's function.
In addition, we will use a retinal pigment epithelium (RPE) primary tissue culture system to study the role of myosins in RPE phagocytosis. The RPE is a single cell layer situated just outside the retina. One of the functions of the RPE is the daily phagocytosis of rod outer segments (ROS) shed by adjacent photoreceptor cells as part of the cycle of photoreceptor renewal. ROS phagocytosis is essential for retina function, and defects in this process result in progressive retinal degradation. We will use fluorescence microscopy and optical trapping to study the roles of myosins 6 and 7 in this process.
Karen Arabas, Professor of Environmental & Earth Sciences
ZERI: Zena Ecological Restoration Initiative
This project focuses on habitat restoration activities at Willamette University’s 300-acre Zena Forest. The Zena Ecological Restoration Initiative (ZERI) incorporates both research and management activities. ZERI guides our efforts managing and monitoring invasive and non-native plant species, and increasing native-prairie, oak woodland and riparian structure, function, and species diversity. Students on the ZERI team will work in both the field and lab, setting up long-term monitoring plots, collecting understory and overstory vegetation data, analyzing tree core data, manipulating the ZERI database, generating publication quality graphs and tables, and working on a short project of their own. Students also have the option of continuing to work on the project as paid research assistants during the 2013-2014 academic year. In this way, ZERI extends beyond the summer and Willamette faculty: students will be part of an interdisciplinary team that has coalesced around the work at Zena, and that includes land managers, professional foresters, private landowners, fish and wildlife experts, and plant ecologists. As part of the team, students will work alongside experts to design the restoration project, implement it, collect, analyze, interpret data, and communicate the findings (both in report form and as peer-reviewed publications).
GLIMPSE: Geographic Landscape Inquiry through Multiproxy Studies in Ecology (Funding Pending)
Although boreal and subalpine forests contain almost half of all global terrestrial carbon, the role of these forests in the global carbon system is complex and not well understood because of temporal and spatial complexities in the way these ecosystems respond to climate. As a result we are not able to accurately predict the role of these systems in the global carbon cycle and their influence on future climate change. This project will investigate the linkages among climate, disturbance, and subalpine forest productivity in the Lakes Basin Area of the Eagle Cap Wilderness, Oregon, where global and regional climate trends are strongly expressed at the local scale as proxy evidence in tree rings and lake sediments. We will generate a multi-proxy, millennial-scale data set from the area to answer the fundamental question: what role will subalpine forests play in the global carbon system of the future? Working collaboratively with faculty and students from several predominantly undergraduate institutions, as well as local high school teachers and experts from several major research universities, Willamette students will develop a multi-species network of tree-ring chronologies from which forest productivity and climate will be reconstructed. This is a year-long project: there will be two weeks of summer field work in the Eagle Cap collecting tree ring, fire history, charcoal and pollen data. Students on the GLIMPSE team will also work through the school year (2013-2104) to process and analyze the tree ring chronologies.
Haiyan Cheng, Assistant Professor of Computer Science
Estimation of partially observable dynamic phenomena, such as weather or macroeconomic systems, is an important problem in the physical and social sciences. We have complete solutions to simple versions of such problems, and a variety of incomplete solutions to the more complex types, when the chance elements of the phenomena do not follow the "bell-shaped" curve that captures the so-called normal statistical distribution. Depending on the area of application, the solutions are called data assimilation procedures, or filters, and come in various flavors such as ensemble filters, particle filters, and four-dimensional variational filters or methods.
My current research project is to improve the function of particle filter method by tackling the particle degeneration problem. The outcome of the research will lead to improved nonlinear forecast simulation models. For this SCRP project, the participating students will start with critical literature reading to understand the background and research problem, followed by algorithm implementation and numerical simulations and analysis. The research activities will enhance students' programming proficiency and problem solving ability. Diverse fields of applications of the underlying algorithm such as geoscience, artificial intelligence, finance will provide students with motivation and perspective for future research career.
Andrew Duncan, Associate Professor of Chemistry
Information to come...
Jason Duncan, Assistant Professor of Biology
The transport of proteins, mRNA transcripts and organelles within a cell facilitates their localization to discrete cellular domains. This is especially critical in neurons: chemical messages synthesized in the cell body must be delivered through the axon to the distant synapse. This distance poses a significant challenge for the neuron, as the length of the axon is orders of magnitude the width of the cell body. The neuron employs a microtubule-based transport system to actively transport these chemical messages along its entire length. In Drosophila melanogaster larvae, the segmental nerve is ideal for studying axonal transport. Segmental nerve bundles emerge from the brain and bilaterally innervate the body wall musculature of each larval segment. They are easily accessible, narrow, extremely elongated and the microtubules within the axon are polarized, thus transport occurs in intrinsically defined directions. Research conducted in my lab will employ a genetics based approach in Drosophila to identify novel components of microtubule-based axonal transport. The identification of genes involved in axonal transport in Drosophila is facilitated by the fact that mutants defective in the process have a characteristic crawling defect in which the larval tail flips upwards, and transported synaptic vesicles accumulate as axonal clogs in the axons. Participation in this research will provide undergraduate students with a broad exposure to laboratory techniques in Genetics, Neurobiology and Molecular and Cell Biology.
Alison Fisher, Assistant Professor of Chemistry
Plants exchange hundreds, if not thousands, of diverse volatile (gaseous) organic compounds (VOCs) with the air around them. Although we generally can't see it, plants emit millions of tons of reactive organic carbon into the air each year, significantly impacting the chemistry of the lower atmosphere. As a result of the environmental impacts of VOC emissions from plants, the atmospheric processes these compounds participate in have been the subject of intense research for the last two decades. The biological questions surrounding these emissions have received less attention and, as a result, are less well understood. Students collaborating with me this summer will use classic biochemistry techniques combined with modern molecular genetic methods to answer some of the outstanding questions about plants and the volatile compounds they make.
1. How does the volatile hormone ethylene influence the timing of plant flowering?
Ethylene (ethane; C2H4) is a volatile plant hormone that affects virtually every developmental process in plants, from seed germination and root hair growth to fruit ripening and the senescence of leaves and flowers. Its role in the timing of plant flowering, the critical developmental switch from vegetative growth to reproductive growth, is not well understood. We are using reverse transcription coupled with quantitative polymerase chain reaction (RT-qPCR) to analyze ethylene's regulation of key flowering time genes in two model plants: Arabidopsis thaliana (thale cress) and Ipomoea nil ‘Violet' (Japanese morning glory). Furthermore, we are using chromatin immunoprecipitation (ChIP) assays to address the role of epigenetics in ethylene's regulation of flowering time in these model plants.
2. Why do plants make isoprene?
Isoprene is the most abundant reactive VOC produced by plants and, despite almost twenty years of research on isoprene production, why plants make it is still a matter of intense debate. With our collaborators at Portland State University, we are exploring the use of moss as a model system to better understand biogenic isoprene production. To this end, we are using classic protein chemistry methods and gas chromatography to isolate and characterize an isoprene-producing enzyme (isoprene synthase) from the model moss Campylopus introflexus (heath star moss).
Susan Kephart, Professor of Biology
NSF funded Camassia Research Position
Prof. Susan R. Kephart & Dr. Kathryn Theiss
Plants show astounding diversity floral color, shape, and scent, so decoding these traits and their functions is like solving a good mystery! It is challenging yet essential to the practices applied daily in agriculture, conservation, and medicine. The undergraduate students who join our team will use novel approaches and discovery-driven hypotheses to compare the morphology, pollinators, and ecological niches of camas (Camassia) and rush lilies (Hastingsia). While conducting field work in several states, we will track flowering times, observe the responses of pollinators to experimentally manipulated and natural flowers, and design crossing experiments among species. Students must be prepared to work and hike under varied field conditions in wet or dry meadows and woodlands. Student effort typically spans a major part of the mid May-July field season, with some options negotiable. There are also opportunities for split summer and academic year positions or to extend research through the academic year via a research thesis or other options.
Student research associates join a multi-institutional collaborative team linked to undergraduates at two other universities nationwide. Your input is expected in developing the study, analyzing and interpreting data, and writing reports. You will work alongside peers, and faculty mentors as we learn and share the best practices of science, from poster design to talks & scientific writing.
Broad goals: In addition to exploring species boundaries, we aim to extend understanding of the ecological and cultural value of plants today and for indigenous peoples, develop new keys for identifying rare and common plants, and contribute insights that will improve conservation efforts.
Melissa Marks, Assistant Professor of Biology
My research concerns the genetics, physiology, ecology, and evolution in populations of aquatic bacteria (Caulobacter crescentus). Since its initial isolation, C. crescentus has been propagated and studied in many laboratories throughout the world. During this time, a number of notable phenotypic changes evolved in lab strains of this species, including changes in outer membrane structure that confer increased resistance to predators (bacteiophage) and changes in transport proteins that result in improved survival rates. In my lab, student researchers and I will collaborate to (1) analyze the biochemical composition of outer membranes from strains with different phenotypes, (2) map the gene(s) responsible for differences in outer membrane phenotype, (3) assess the relationship between outer membrane phenotype and susceptibility to phage infection, (4) assess the genetic interaction between related nutrient transport genes and survival rates, and (5) measure fitness advantages and tradeoffs conferred by these nutrient transport alleles.
Brandi Row, Associate Professor of Exercise Science
As we age, reductions in muscle strength, muscle power, gait, and balance function can increase the risk of sustaining an injurious fall. My overall research program is focused on 1) improving these aspects of function in older adults through exercise interventions aimed at improving strength, power, gait, and balance function, 2) on quantifying age-related changes in biomechanical and neuromuscular aspects of gait and balance function, and 3) on relating laboratory-based measures of function in older adults to clinically-feasible proxy tests of physical function. My current research projects involve studying the medial-lateral control of gait, which is particularly challenging with aging, and reduced control of this aspect of gait is linked to increased fall risk. Acceleration magnitude and variability measures of the trunk, indicators of the medial-lateral control of gait, have been shown to improve with increased balance and gait functionfollowing a training program, but continued work needs to be done to identify gait acceleration thresholds that distinguish between individuals of varying levels of fall risk. My current projects involve 1) a validation analysis of medial-lateral gait acceleration during walking overground and during walking on a treadmill, in order to determine whether it would be appropriate to use treadmill gait to make trunk accelerometry measurements in seniors, and 2) to compare gait acceleration measures with other indicators of fall risk. Students working on these projects would gain experience working with older adults to collect data in laboratory and off-campus locations, possibly learning how to write computer programs in Matlab to process the data (if the student would like to learn these computer programming skills), and learning how to analyze and interpret gait accelerations and fall risk.
Chris Smith, Assistant Professor of Biology
Coevolution is a process of reciprocal evolutionary change, through which two or more species adapt to each other. Coevolution may be involved in an enormous variety of ecological interactions, from African gazelles trying to outrun cheetahs, to the origin of new flu strains each year. Work in our lab examines coevolution in an obligate pollination system - the interaction between the Joshua tree (Yucca brevifolia) and the yucca moths that are their exclusive pollinators. Both the moths and the trees are entirely dependent on one another for reproduction, and morphological features of the moths and the flowers that they pollinate fit together like a lock and key. Our lab seeks to understand whether and how reciprocal natural selection - as opposed to other, non-adaptive evolutionary processes - have produced the remarkable fit between this iconic desert plant and the insects on which it relies. We combine the traditional tools of field biology - field research in the Mojave Desert - with manipulative experiments, population genetics, and genome-wide-association studies to measure natural selection using both direct and indirect approaches.
Gary Tallman, Professor of Biology
Many perennial plants that live in hot climates have evolved to survive heat extremes. It is assumed that the seemingly modest temperature increases of 5-6ºC predicted to accompany the next century of global climate change will have little effect on these plants. With funding from the National Science Foundation, members of the Tallman lab are studying the effects of 5-6ºC temperature increases on plant cells growing near their thermal survival limits. Results from the lab indicate that 5-6ºC temperature increases block the action of a critical growth hormone, auxin, that at lower temperatures activates genes required for plant cells to divide and grow. The lab is attempting to determine 1) whether 5-6ºC temperature increases block auxin’s ability to activate genes for cell division and growth in intact plants; and 2) whether temperature increases block auxin action by inhibiting one particular enzyme called a Rac GTPase, an important player in the chain of events leading to auxin-activated gene readout.