Research in Biology

Student Research

Research is at the heart of biology and, for that matter, of all disciplines in the sciences. For that reason, the Biology curriculum is designed around our belief that the best way to learn science is to do science. In other words, all Biology students are immersed in research experiences throughout their coursework; all Biology students experience the excitement and satisfaction of doing research. Starting in Bio 110 (Biological Investigations), Biology students learn the skills that biologists use to acquire new knowledge: how to pose testable hypotheses, design observational and experimental studies, interpret data critically, and communicate the results of their investigations in written form and as oral presentations and posters. After Bio 110, they develop these skills further in upper-division courses, asking and answering their own research questions in systems that range from DNA molecules and cellular development to bird behavior and forest ecology.

Beyond the research projects that all students undertake as part of their coursework, there are also opportunities to engage in lengthier and more independent research experiences. All Biology faculty encourage undergraduate participation in their research programs. Opportunities vary in scope and depth, and students are welcome to discuss research opportunities during any part of their time at Lewis & Clark. Early on, a student may serve as an apprentice in a faculty research program for a semester, either on a volunteer basis or by earning practicum credit (Biology 244). Later, they may assume a more collaborative role with a faculty research partner for a semester, a summer, or longer, either for credit (Biology 499) or with financial support from a faculty research grant. Some students carry out their own completely independent projects, with a Lewis & Clark biology professor serving as their mentor. And Biology majors with strong research interests and a GPA of at least 3.5 are invited to conduct a year of senior research, which culminates in a written thesis, an oral presentation to the department, a defense to department faculty, and the opportunity to graduate with honors in Biology.

In summers, the John S. Rogers Undergraduate Summer Research Program offers, on a competitive basis, 10-week paid research internships with Lewis & Clark faculty from throughout the sciences. Other students 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. In either opportunity, students work collaboratively with a faculty mentor to design and execute an independent research project. Each semester we offer information sessions on how to find these opportunities and develop a competitive application.

Student researchers regularly co-author research publications and make presentations at regional and national meetings of professional societies. Here is a sampling of some recent student-authored publications, followed by descriptions of faculty research programs. Asterisks identify student authors.

  • *Brandt, J.N., *Voss, L., *Rambo, F.M., *Nicholson, K., *Thein, J.R., *Fairchild, L., *Seabrook, L., *Lewis, D., *Guevara-Hernandez, L., *White, M.L., *Sax, L., *Eichten, V., *Harper, L., and Hermann, G.J. (2022) Asymmetric organelle positioning during epithelial polarization of C. elegans intestinal cells. Developmental Biology 481:75-94
  • Voss, L., Foster, O.K., *Harper, L., Morris, C., Lavoy, S., *Brandt, J.N., *Peloza, K., *Handa, S., *Maxfield, A., *Harp, M., *King, B., *Eichten, V., *Rambo, F.M., and Hermann, G.J. 2020. An ABCG transporter functions in Rab localization and lysosome-related organelle biogenesis in Caenorhabditis elegans. Genetics 214:419-445.
  • Brockway, N. L, Z. T. Cook*, M. J. O’Gallagher*, Z. J. C. Tobias, M. Gedi*, K. M. Carey, V. K. Unni, Y. A. Pan, M. R. Metz, and T. A. Weissman. 2019. Multicolor lineage tracing using in vivo time-lapse imaging reveals coordinated death of clonally related cells in the developing vertebrate brain. Developmental Biology 453:130-140.
  • Morris, C.*, Foster, O.K.*, Handa, S*., Peloza, K., Voss, L.*, Somhegyi, H*., Jian, Y., Vo, M. V., Harp*, M., Rambo, F.M.*, Yang, C. and Hermann, G.J. 2018. Function and regulation of the C. elegans Rab32 family member GLO-1 in lysosome-related organelle biogenesis. PLOS Genetics. 14(11):e1007772.
  • *Cook ZC, Brockway NL, Tobias ZJC, *Pajarla J, *Boardman IS, *Ippolito H, *Nkombo Nkoula S, & Weissman TA. 2019. Combining near-infrared fluorescence with Brainbow to visualize expression of specific genes within a multicolor context.  Molecular Biology of the Cell, Feb 15;30(4):491-505. doi: 10.1091/mbc.E18-06-0340. Epub 2018 Dec 26. PMID: 30586321. Cover issue. 
  • *Lowenstein E.G., Velazquez-Ulloa N.A. 2018. A fly’s eye view of natural and drug reward. Frontiers in Physiology. Vol. 9 Article 407.
  • *#Morris, M., *#Shaw, A., *Lambert, M., *Perry, H.H., Lowenstein, E., *Valenzuela, D., Velazquez-Ulloa, N.A. 2018. Effect of developmental nicotine exposure on brain size and the dopaminergic system of Drosophila melanogaster. BMC Developmental Biology 18(1):13. doi: 10.1186/s12861-018-0172-6. #equal contribution.
  • *Clements, H. and P. Bierzychudek. 2017. Can the Persistent Seed Bank Contribute to the Passive Restoration of Urban Forest Fragments After Invasive Species Removal? Ecological Restoration 35(2): 156-166.
  •  *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.
  • *Cosgrove J, Agnarsson I, Harvey M, Binford G. 2016. Pseudoscorpion diversity and distribution in the West Indies: sequence data confirms single island endemism for some clades, but not others. Journal of Arachnology 44(3):257-271.
  • Lajoie, D. M., Roberts, S. A., Zobel-Thropp, P. A., *Delahaye, J. Bandarian, V., Binford, G. J., and Cordes, M. H. J. 2015 Variable Substrate Preference Among Phospholipase D Toxins From Sicariid Spiders. J. Biological Chemistry. 17:10994- 11007.
  • Esposito LA, Bloom T*, Caicedo-Quiroga L, Alicea-Serrano AM, Sánchez-Ruíz JA, May-Collado LJ, Binford GJ, Agnarsson I. 2015. Islands within islands: Diversification of tailless whip spiders (Amblypygi, Phrynus) in Caribbean caves. Mol Phylogenet Evol. 93:107-17.
  • Marra MH, *Tobias ZJC, *Cohen HR, Glover G, Weissman TA.  2015. In vivo time-lapse imaging in the zebrafish lateral line: A flexible, open-ended research project for an undergraduate neurobiology laboratory course.  Journal for Undergraduate Neuroscience Education, Jul 7;13(3):A215-24. eCollection 2015 Summer.
  • *Hamling KR, *Tobias ZJC, Weissman TA.  2015. Mapping the development of cerebellar Purkinje cells in zebrafish. Developmental Neurobiology, Feb 4 doi: 10.1002/dneu.22275
  • *Young, A and Clifton, K.E. 2015. Tardigrades inhabit lichen and moss in Smith Rock State Park, Oregon. Bull. Cal. Lichen Soc. 22(2), 48 - 53. 
  • 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.
  • McHugh, A.*, P. Bierzychudek, C. Greever*, T. Marzulla*, R. VanBuskirk and G. Binford. 2013. A molecular phylogenetic analysis of Speyeria and its implications for the management of the threatened Speyeria zerene hippolyta. Journal of Insect Conservation 17(6): 1237-1253.
  • 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.

Current Biology Research Programs:

Dr. Kellar Autumn

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.

Dr. Paulette Bierzychudek

My research focuses on conservation and restoration biology, especially for plants and insects, and combines field data with mathematical models and statistical analysis. My most recent work has investigated how an urban forest recovers after invasive plant species have been removed; this work has taken place in Riverview Natural Area, a city-owned park adjacent to the Lewis & Clark campus. We have found that herbaceous plant species return naturally, but that trees and shrubs are much slower to recruit. Students in my Ecology class have been exploring conifer regeneration patterns in Portland’s many other urban parks. My students and I have also collaborated with the Oregon Nature Conservancy to help develop plans to conserve the threatened Oregon silverspot butterfly. We’ve collected demographic data on Viola adunca, the butterfly’s food plant, to evaluate how violets respond to mowing and prescribed burning. We’ve also studied the movement patterns of caterpillars searching for food. We used this information to model the likelihood of caterpillar host-finding success in different densities and distributions of host plants.

Dr. Greta Binford

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.

Dr. Kenneth Clifton

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. With that background, my research has recently shifted to issues of conservation and how marine protected areas influence the population ecology and demography on coral reefs in Tanzania and Panama.

Dr. Greg Hermann

Over the past 3 decades the field of developmental biology has undergone a striking transformation due to the application of modern cellular, biochemical, genetic, and molecular approaches, which has uncovered the mechanisms that specify cell fate. I am interested in how a group of cells that become specified to become part of a tissue or organ generates the cellular architecture that gives them their function. Studies in my lab address this question by focusing on the formation and differentiation of specialized cell-type specific compartments called lysosome related organelles (LROs). In humans, LROs carry out key functions within skin, lung, and blood cells. While much is known regarding the functions of LROs, for example pigment synthesis by melanosomes and blood clotting by platelet dense granules, the mechanisms involved in their construction remain poorly understood. Defects in these processes underlie a number of human genetic diseases. We are discovering and analyzing the function of genes controlling the formation of LROs in the model organism, Caenorhabditis elegans, whose homologues function similarly in humans. .

Dr. Margaret Metz

My research program is driven by an interest in understanding species coexistence, particularly the processes that maintain the diversity of forests. My projects in the old-growth forests of southwestern Washington, the coastal forests of California, and the Amazonian rainforests of eastern Ecuador are field-based and long-term, and draw on a wide variety of rigorous, quantitative tools to address our research questions.

Dr. Sharon Torigoe

The diversity of cellular functions in multicellular organisms is driven by the regulation and control of gene expression, and there are myriad pathways that underlie differentiation and specialization of cells. Gaining a deeper understanding of these pathways will not only contribute to our knowledge of biology but also to regenerative medicine, for which we hope to produce replacement cells and tissues by reprogramming a patient’s own cells. In my lab, my students and I investigate how gene regulation is determined by sequences in the genome, particularly the “junk” DNA that does not correspond to a protein. We utilize molecular biology and biochemistry approaches to characterize these sequences and how they are interpreted in the cell. Currently, projects are focused on the regulation of genes in the context of stem cells.

Dr. Norma Velazquez Ulloa

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.