Projects 2012
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.
Emma Coddington, Assistant Professor of Biology
My lab investigates how hormones, through their impact on neurons, modify behavior. We study the clasping behavior of rough skin newts, Taricha granulosa, to unravel the neural mechanisms of hormone action. The hormones of particular interest are clasp-inhibiting hormones such as stress hormones (Corticosterone) and clasp-enhancing hormones (vasotocin). We know that these hormones impact specific hindbrain neurons that control clasping through the regulation of cannabinoid neurotransmitters. Past research by students has used confocal imaging to examine specific questions about how stress impacts vasotocin signaling. For example, Erin McEvoy and Sarah Sonnenfeld discovered that cannabinoids block endocytosis of vasotocin receptors in the hindbrain, and revealed a brand new mechanism by which hormones act to modify neural control of behavior. This summer students will use the new confocal microscope and/or electrophysiology to continue Erin and Sarah’s work.
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).
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.
Scott Pike, Associate Professor of Environmental and Earth Sciences and Archaeology
Archaeological geology focuses on using geologic techniques and methodologies to investigate archaeological questions. My research interests focus on the synergistic interactions of past societies with their dynamic physical environments. One avenue of research I am currently pursuing is the development and application of on-site, real-time geochemical surveys at archaeological sites. With the use of a portable X-ray fluorescence spectrometer (pXRF), the chemical constituents of any solid material can now be measured in the field. The near-immediate output produced by the pXRF opens the door for new and innovative opportunities to explore, identify and interpret the geochemical signatures of past cultural activities. As the technology is relatively new at archaeological field sites, a major is to develop transferable pXRF protocols and procedures that can be adopted at other archaeological sites around the world.
This summer, research will be carried out at the Ness of Brodgar excavations at the Heart of Neolithic Orkney UNESCO World Heritage Site in Orkney, Scotland. Willamette University is the only non-UK based school associated with this important archaeological site. In fact, last February, the British Museum identified the Ness of Brodgar as the Archaeological Research Project of the Year.
Prior to departure for Scotland, students will undertake background reading on the physics of flouresence as well as published reports of geochemical studies of archaeological, colluvial and pedological materials. Students will also develop skills in using the pXRF by undertaking small research projects in Oregon. While in Scotland, the student researcher will work and live alongside other Willamette students who will be participating in Willamette’s Archaeological Field School.
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 - careful observation of natural systems - 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
Using a thermotolerant, equatorial perennial plant, tree tobacco, the Tallman lab studies the effects of heat stress on plant thermotolerance and growth. Recent findings from the lab indicate that heat stress makes plant cells insensitive to auxin, the plant hormone that causes individual plant cells to increase in size; auxin is also required for plant cells to divide. Using cultured plant cells, the lab has discovered that heat reduces production of the important signaling gas nitric oxide which is known to be required for auxin signaling in plants. The lab is currently investigating whether heat blocks auxin-regulated gene expression in intact plants and how heat might affect the levels and/or activities of enzymes that affect nitric oxide production.