- Academic English Studies (ESL)
- Biochemistry/Molecular Biology
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Biology faculty lead overseas programs designed especially for Biology majors, offering the opportunity to earn elective credit toward the Biology major while studying overseas. The most recent program was to East Africa fall 2013, led by Prof. Clifton. Prof. Binford is leading a program to New Zealand spring 2015.
The focus on investigative skills in Lewis & Clark’s biology courses prepares students well to undertake independent research projects. Over half of all biology majors at Lewis & Clark become involved in research. Some students work as assistants to or collaborators with a Lewis & Clark faculty member for a summer, a semester or longer. Some students earn credit for this work (Biology 244 or 499) and others receive support from faculty research grants or from the John S. Rogers Undergraduate Summer Research Program. Other students carry out their own completely independent projects, with a Lewis & Clark biology professor as their mentor. Some spend a summer doing research at another college, university, or research institution, e.g., through the National Science Foundation’s Research Experiences for Undergraduates (REU) program. Students with strong research skills and a GPA of at least 3.5 are invited to conduct an honors thesis during their senior year, a year-long independent investigation that culminates in a written thesis, an oral presentation to the department, and a defense to department faculty.
All Biology faculty encourage undergraduate participation in their research programs. Undergraduates co-author faculty research publications and presentations at regional and national meetings.
Here are a few examples of recent senior theses and student-faculty collaborative research that have been published in scientific journals or presented at meetings. Asterisks identify student co-authors:
- Barrett, A.* and Hermann, G.J. (2016) A Caenorhabditis elegans homologue of LYST functions in endosome and lysosome-related organelle biogenesis. Traffic 17:515-535.
- Delahaye, J.L., Foster, O.K.*, Vine, A.*, Saxton, D.S.*, Curtin, T.P.*, Somhegyi, H.*, Salesky, R.*, Hermann, G.J. (2014) C. elegans HOPS and CCZ-1 mediate trafficking to lysosome-related organelles independently of RAB-7 and SAND-1. Mol. Biol. Cell 25:1073-1096.
- Hermann, G.J., Scavarda, E., Weis, A.M., Saxton, D.S., Thomas, L.L., Salesky, R., Somhegyi, H., Curtin, T.P., Barrett, A., Foster, O.K., Vine, A., Erlich, K., Kwan, E., Rabbitts, B.M., Warren, K. (2012) C. elegans BLOC-1 functions in trafficking to lysosome-related gut granules. PLoS ONE 7 (8): e43043.
- Claire A. Fassio*, Brett J. Schofield*, Robert M. Seiser, Arlen W. Johnson and Deborah E. Lycan (2010) Dominant Mutations in the late 40S biogenesis factor Ltv1 Affect Cytoplasmic Maturation of the small ribosomal subunit in S. cerevisiae. Genetics 185: 199-209.
- Zobel-Thropp, P.A., *Bodner, M.R., Binford, G.J. 2010. Comparative analyses of venoms from American and African Sicarius spiders that differ in sphingomyelinase D activity. Toxicon. 55:1274-1282.
- *Duncan, R.P., *Rynerson, M.R., Ribera, C.., Binford, G.J. 2010. Diversity of Loxosceles spiders in Northwestern Africa and molecular support for cryptic species in the Loxosceles rufescens lineage. Molecular Phylogenetics and Evolution. 55:234-248.
- *Levitte, S., *Salesky, R., *King, B., *Coe Smith, S., *Depper, M., *Cole, M., Hermann, G.J. 2010. A C. elegans model of orotic aciduria reveals enlarged lysosome-related organelles in embryos lacking umps-1 function. FEBS J. 277:1420-1439.
- Kennedy, P.G. and *L.T. Hill. 2010. A molecular and phylogenetic analysis of the structure and specificity of Alnus rubra ectomycorrhizal assemblages. Fungal Ecology 3: 95-104.
- Kennedy, P.G., *Schouboe, J.L., *Rogers, R.H., *Weber, M.G., and Nadkarni, N.M. 2010. Frankia and Alnus rubra canopy roots: an assessment of genetic diversity, propagule availability, and effects on soil nitrogen. Microbial Ecology 59: 214-220.
- Clifton, K.E., *Dubey E.M., *Woodburn E. 2009. A quantitative assessment of reef fish distribution and abundance within near-shore reef habitats of Yap State, F. S. M. J Ocean Science Foundation 2:1-29.
- *Bischoff-Mattson, Z., Mattson, D. 2009. Effects of simulated mountain lion caching on decomposition of ungulate carcasses. Western North American Naturalist, 69(3)343-350.
- Bierzychudek, P., Warner, K.A., *McHugh, A., *Thomas, L. 2009. Testing the host-finding ability of a monophagous caterpillar in the field. Ecological Entomology, 34:632-637, pdf available from first author
- Binford, G.J., *Bodner, M.R., Cordes, M.H.J. ,*Baldwin, K.L. ,*Rynerson, M.R., Burns, S.N., and Zobel-Thropp, P. A. 2009. Molecular evolution, functional variation and proposed nomenclature of the gene family that includes sphingomyelinase D in sicariid spider venoms. Molecular Biology and Evolution. 26(3):547–566.
- Binford, G.J., *Callahan, M.S., *Bodner, M.R., *Rynerson, M.R., Berea NuÃ±ez, P., *Ellison, C.E., and *Duncan, R.P. 2008. Phylogenetic relationships of Loxosceles and Sicarius spiders are consistent with Western Gondwanan vicariance. Molecular Phylogenetics and Evolution. 49:538-553.
- *Rabbitts, B.M., *Kokes, M., *Miller, N.E., *Kramer, M., Lawrenson, A.L., *Levitte, S., *Kremer, S., *Kwan, E., *Weis, A.M. and Hermann, G.J. 2008. glo-3, a novel Caenorhabditis elegans gene, is required for lysosome-related organelle biogenesis. Genetics 180:857-871.
- *Currie, E., *King, B., Lawrenson, A.L., Schroeder, L.K., Kershner, A.M.*, Hermann, G.J. 2007. Role of the C. elegans multidrug resistance gene, mrp-4, in gut granule differentiation. Genetics 177:1569-1582.
- *Duncan, R.P. Autumn, K.A. Binford, G.J. 2007. Convergent setal morphology in sandcovering spiders suggests a design principle for particle capture. Proc. Royal Soc. B.1629:3049-3056. Featured in Research Highlights Nature 418:758
- *Schroeder, L.K., *Kremer, S., *Kramer, M.J, *Currie, E., *Kwan, E., Watts, J.L., Lawrenson, A.L., Hermann, G.J. 2007. Function of the Caenorhabditis elegans ABC transporter PGP-2 in the biogenesis of a lysosome-related fat storage organelle. Mol. Biol. Cell 18:995-1008.
- Autumn, K. and *Hansen, W. 2006. Ultrahydrophobicity indicates a nonadhesive default state in gecko setae. Journal of Comparative Physiology A-Sensory Neural & Behavioral Physiology.
- Seiser, R.M., *Sundberg, A., *Wollam, B.J., Zobel-Thropp, P., *Baldwin, K., *Spector, M.D., and D. Lycan. 2006. Ltv1 is required for efficient nuclear export of the ribosomal small subunit in Saccharomyces cerevisiae. Genetics 174: 679-691.
- *Tomaro, L. 2006. Apparent predation of juvenile coho salmon (Oncorhynchus kisutch) by prickly sculpins (Cottus asper) is an artefact of trapping methodology. Marine and Freshwater Research. 57: 513–518.
- *Hansen, W. R. and K. A. Autumn. 2005. Evidence for self-cleaning in gecko setae. Proceedings of the National Academy of Sciences 102(2): 385-389.
- Kearney, M., *Wahl, R., and K. Autumn. 2005. Increased capacity for sustained locomotion at low temperature in parthenogenetic geckos of hybrid origin. Physiological and Biochemical Zoology 78(3):316-324.
Current Biology Research Programs:
Our research focuses on biomechanics, physiology, and evolution of animal locomotion. A central project in the Autumn Lab is the study of adhesive setae in geckos and the design of biologically inspired adhesive nanostructures and climbing robots. In 2002 we discovered the molecular mechanism of adhesion in geckos and and in 2005 showed that the adhesive setae on their toes form the first known self-cleaning adhesive. We also study the effects of running speed, temperature, body size, and phylogeny on aerobic metabolism in geckos and other lizards. In 1999 we found that geckos have evolved metabolic fuel economy 2 to 3 times greater than that of other legged animals, which permits activity at very low temperatures. In 2005 we discovered that, contrary to predictions, all-female gecko clones have greater aerobic capacity, and can outperform their sexual relatives.
My students and I have been collaborating with the Oregon Nature Conservancy to develop a plan for managing Oregon’s Cascade Head preserve, which hosts one of the last remaining populations of the threatened Oregon silverspot butterfly. We’ve collected demographic data on Viola adunca, the butterfly’s food plant, in order to evaluate how the violet population responds to mowing and prescribed burning. In addition, we’ve studied the movement patterns of caterpillars searching for food. We’re using this information in a model to predict the likelihood of host-finding success in different densities and distributions of host plants. These predictions will guide the Nature Conservancy’s management of the preserve. In independent projects, students are exploring patterns of genetic variation among the butterflies and their host plants. In addition to this project, we’ve been starting to explore conifer regeneration patterns in Portland’s many urban parks.
The chemical richness and diversity of spider venom cocktails make them interesting subjects for understanding how evolution generates novelty. My research program uses integrative, evolutionary approaches to better understand patterns of diversity in spider venoms. In my lab, students have the opportunity to participate in evolutionary analyses of spider venoms at all levels of the process. This includes collecting a range of spiders in the field, doing protein analyses of the venoms, and using molecular approaches to study the genes that code for the venom proteins. Students also analyze the effects of venoms on insect prey and observe spider foraging behavior. These data help to better understand the role venom plays in immobilizing prey and how that varies across spider species. My research has discovered that the toxin in brown recluse venom is also present in venoms of closely related Sicarius spiders. This means this toxin likely originated in an ancestor of these two types of spiders. This helps us better understand the range of species related to the brown recluse that is capable of causing lesions when these animals bite people and may help to facilitate development of broadly effective treatments.
My field studies of behavior examine the environmental and social determinants of dispersion: where do organisms occur, how do they interact, and does this influence the timing and intensity of reproduction? Working primarily in coral reef habitats, my students focus on species of fish and algae that show intermittent bursts of reproductive activity. This research provides insight into the ecological factors that ultimately generate patterns of distribution and abundance within tropical marine habitats. We are also examining the effects of greenhouse gasses on the ability of marine seaweeds to build their calcified skeletons.
Studies in my lab focus on two aspects of organogenesis: the formation of specialized organelles that in part define organ function and programmed cell death which sculpts organ morphology. We are studying these processes in the soil nematode Caenorhabditis elegans. C. elegans has emerged as a powerful system to identify and characterize genes controlling important evolutionarily conserved developmental processes. Students in my lab have discovered C. elegans genes controlling the formation of intestinal specific lysosomes whose homologues in humans are implicated in Hermansky-Pudlak syndrome. Further studies in the nematode C. elegans should lead to greater insights into the cause and treatment of this human genetic disease.
Our research focuses on how ribosomal subunits are assembled in higher cells. We use the yeast S. cerevisiae as a model organism to study this essential and highly conserved process. Ribosomes are among of the largest and most complex macromolecular machines assembled in cells. In eukaryotes, the 40S and 60S subunits are assembled in the nucleus from rRNA and over 80 ribosomal proteins that must be imported from the cytoplasm is a stepwise process that occurs co-transcriptionally. The subunits are processed and modified in the nucleoplasm and then exported through nuclear pores in a process requiring the nuclear export receptor, Crm1. Export of the large subunit is known to require an adapter protein and two additional export receptors besides Crm1. In contrast, no analogous adapter has been identified for the small subunit, nor have export receptors besides Crm1 been identified. Eight non-ribosomal proteins are added to the 40S subunit late in nuclear assembly and cycle between the nucleus and the cytoplasm. We are working to understand how some of these proteins function in the final steps of 40S export and processing so that the subunit is competent for protein synthesis. You can read a student co-authored paper on this here.
My research program is driven by an interest in understanding species coexistence, particularly the processes that maintain the diversity of forests. My projects are field-based and long-term, and I draw on a wide variety of rigorous, quantitative tools to address my research questions. I have ongoing research programs in both temperate and tropical forests.
I am interested in how drugs of addiction modulate behavior. During my postdoctoral work, I characterized several effects of long-term nicotine exposure on the common fruit fly, Drosophila melanogaster. I found similarities between the effects of nicotine in flies and the effects of nicotine in other model organisms as well as in humans. In the future, I plan to use the genetic and molecular tools available for Drosophila research to identify new genes, cellular and molecular mechanisms for drug-induced behaviors.
Dr. Tamily Weissman-Unni
My lab is interested in the neural circuitry that underlies behavior. Specifically, how does connectivity develop in the young brain and how do mature connections generate behavior?
Brain function relies upon the precise organization of many neural circuits. Although we are beginning to understand important properties of simple circuits, we know little about how complex circuits form and how their mature properties underlie behavior. This is largely because the complexity of most brain circuits prevents their complete examination using traditional labeling or recording methods. Due to the generation of a new powerful approach (“Brainbow”), we can now label populations of cells in many different colors, allowing us to visualize multiple individual components of a complex circuit in unprecedented detail. We have applied this approach to the translucent developing zebrafish nervous system, where individual synapses can be visualized over time within the living animal. Using this combined approach, we are testing how an important circuit within the cerebellum, the mossy fiber-to-granule cell synapse, develops and functions. These studies, along with dynamic imaging and recording of neuronal activity, will allow us to quantify the developmental circuit properties of a complex pathway and begin to determine what types of information are being compared in this pathway to generate appropriate behavior. The combination of two powerful approaches – Brainbow and zebrafish – allows us to ask these detailed questions about a complex circuit in the brain of a living, intact animal.