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Biology Faculty Research Interests

  • Colin Saldanha

    Department Chair

    Hormones are profound modulators of brain structure and function; with influences that span the lifetime of an organism. The muti-faceted and pluripotent neural effects of steroids require that a specific hormone be delivered to the right target at precisely the right time. Members of my laboratory and I are curious as to how this process occurs. We have discovered that estrogen is synthesized in synaptic boutons and in astroglia (a type of non-neuronal cell in the brain). This compartment- and cell-specific hormone provision may be responsible for the effects of estrogen on learning, memory, neural degeneration and perhaps neuroprotection and repair.

I received my PhD from the University of Virginia in the field of molecular cell biology. Specifically, I studied the mechanisms underlying the regulation of intracellular trafficking in the endomembrane system. My work focused on the identification and examination of Secretory Carrier Membrane Proteins (SCAMPs), a family of integral membrane proteins that are highly conserved from invertebrates to humans. I continued my research during post-doctoral fellowships at Harvard Medical School, and The University of Pennsylvania. I am currently teaching Bio 372 and 373 (Human Anatomy and Physiology) as well as Bio110 (General Biology).

For an organism to survive, the genome, the complete set of DNA in any cell, must be stably maintained and correctly regulated. The fundamental question I am addressing is: How is genome architecture established and maintained in healthy cells and how does it go awry in disease? To address this question I am using a unicellular eukaryote, the ciliate Oxytricha trifallax, as a model system for the role of epigenetics - information on the DNA molecule but outside the DNA sequence - in controlling genome architecture. I currently have funding from NIH to study the role of the DNA repair protein DNA-PKcs in cytosine DNA methylation, and to search for new drugs affecting DNA methylation in hopes of discovering epigenetic cancer therapies.

I am broadly interested in molecular evolution and empirical population genetics. The main research focus of my lab is on the functional significance of genetic variation in protein-coding genes. We are particularly interested in synonymous variation, as it may impact translational accuracy and/or efficiency, as well as mRNA splicing and stability. The main ongoing projects in my lab include: 1) experimental manipulation of codon bias in bacteria, 2) analysis of codon usage in hemimetabolous and holometabolous insect genomes, 3) synonymous mutation rates in proto-oncogenes and tumor suppressor genes, and 4) transcriptome profiling of cave and surface populations of the freshwater amphipod Gammarus minus, with an aim toward identifying genes undergoing divergent modes of natural selection in the two habitats.

Dr. Connaughton's research interests encompass the disciplines of developmental biology (nervous system development) and neurobiology. Specifically, she is interested in examining the relation between visually-guided behaviors in larval teleosts and maturation of retinal neurons, circuits, and receptor mechanisms. She is also interested in examining how the development of neural connections could be altered due to mutations or drugs. She has performed experiments that address behavioral/ ecological questions, as well as those that employ cell biology techniques to examine retinal circuitry in both developing and adult retinal tissue.

Dr. DeCicco-Skinner's research interests include cancer biology, cell biology, and immunology. Specifically, her research is focused on studying two of the major inflammatory pathways in the cell, MAPK and NF-kB, to identify how these pathways become inappropriately regulated as a normal cell transitions into a cancerous state. Her research uses a variety of immunological and molecular biology techniques in two separate cancer model systems, squamous cell carcinoma and multiple myeloma.

My research is on the ecology and evolution of groundwater-dwelling crustaceans, especially amphipods and isopods. The amphipod Gammarus minus is an especially useful model organism because subterranean and surface populations with different morphologies exist, allowing for comparative studies. Current ongoing projects include: 1. Long-term monitoring of population dynamics of the amphipod Stygobromus tenuis potamacus and the isopod Caecidotea kenki from a seepage spring in George Washington Memorial Parkway. 2. Determinants of community structure in karst springs. This project examines the interactions of size-selective predation by fish and sexual selection on the body size of populations of the amphipod Gammarus minus, and the cascading effect of body size variation among populations on macroinvertebrate community structure in karst springs of West Virginia and Virginia. 3. Hybridization among surface and cave populations of the amphipod Gammarus minus for a QTL analysis of traits associated with cave adaptation. 4. Molecular phylogeography, and genetic adaptations to the subterranean environment, of different species of groundwater crustaceans, in collaboration with David Carlini.

Biofilms are densely-packed communities of bacteria, encased in a self-synthesized polymeric matrix, growing attached to a tissue or surface. Biofilm is the predominant mode of growth for bacteria in most natural, industrial and clinical environments. Biofilm formation causes major problems ranging from industrial corrosion and biofouling to chronic or nosocomial infections. Kaplan's lab is studying the detachment and dispersal of cells from bacterial biofilms. The emphasis of his research is the use of biofilm matrix- degrading enzymes as potential antibiofilm therapies for the treatment and prevention of various human, animal and plant infections. Kaplan's lab is currently funded by grants from the National Institute of Allergy and Infectious Diseases and from the U.S. Department of Defense.

Dr. Krogan is a developmental biologist interested in how gene regulation guides the formation of complex tissues and organs in eukaryotes. The proper arrangement of these structures usually requires precise spatial control of fate- specifying genes, involving both transcriptional activation and repression. Research in his laboratory concentrates on the transcriptional regulation of floral organ formation and stem cell function in the model plant Arabidopsis thaliana. His work relies on a variety of techniques, including molecular biology, genetic and genomic approaches. His research aims to contribute to our understanding of how complex patterns form in eukaryotes, and can lead to strategies for improvement of agronomically important crops.

Dr. Schaeff's main research interests are conservation biology, molecular ecology and behavior. She uses molecular DNA techniques in conjunction with behavioral data to investigate gene flow patterns within and between populations (e.g., right whales and gray whales), determine mating strategies (e.g., penguins, right whales), and understand the evolutionary significance of various behaviors (e.g., fostering). She is also conducting a number of studies on fluctuating asymmetry to determine whether morphological asymmetry is a useful tool for assessing population health in endangered species (right whales, manatees, Sable Island ponies) and recently began studying mate choice in gays and lesbians.

Dr. Tudge is primarily a reproductive biologist with particular interests in the reproductive biology of invertebrates. His research focuses on the reproductive cells and associated structures, evolutionary mechanisms, and reproductive behaviors of marine decapod crustaceans. He also has experience dealing with other invertebrate and vertebrate groups and his knowledge of reproduction in crustaceans can be directly applied to other taxa. He uses this interest in crustacean reproduction to investigate the evolutionary history (phylogeny) of particular crabs in the marine environment.

Colin Saldanha

Dr. Saldanha



Zebrafish neurons

Zebrafish neurons (see Dr. Connaughton's research)




Biofilm (see Dr. Kaplan's research)



Oxytricha triffallax

The Bracht lab investigates the process of genome rearrangement in the ciliate Oxytricha trifallax. During genome rearrangement, this remarkable organism pieces together its genome from pieces much as one might assemble a jigsaw puzzle.

Recent Faculty Publications

  • Carlini, D. B., Manning, J., Sullivan, P. G., Fong, D. W., 2009. Molecular genetic variation and population structure in morphologically differentiated cave and surface populations of the freshwater amphipod Gammarus minus. Molecular Ecology. 18, 1932-1945.
  • Cederlund, ML, ME Morrissey, T Baden, D Scholz, V Vendrell, L Lagnado, VP Connaughton, and BN Kennedy. 2010. Zebrafish Tg(7.2mab2112:EGFP)ucd2 transgenics reveal a unique population of retinal amacrine cells. Investigative Ophthalmology and Visual Science. In press.
  • Chapman, GB, R Tarboush, DA Eagles, and VP Connaughton. 2009. A light and transmission electron microscope study of the distribution and ultrastructural features of the peripheral nerve processes in the non-retinal layers of the zebrafish eye. Tissue Cell. 41: 286-298.
  • Connaughton, VP. 2010. Bipolar cells in the zebrafish retina. Visual Neuroscience. 16:1-17.
  • Connaughton, VP, A Bender, and R Nelson. 2008. Electrophysiological evidence of GABAA and GABAC receptors on zebrafish bipolar cells. Visual Neuroscience. 25(2): 139-154.
  • Connaughton, VP and R Nelson. 2010. Spectral responses in zebrafish horizontal cells include a tetraphasic response and a novel UV-dominated triphasic response. Journal of Neurophysiology. 104: 2407-2422.
  • D'Antonio JM,, (2010) Loss of Androgen Receptor-Dependent Growth Suppression by Prostate Cancer Cells Can Occur Independently from Acquiring Oncogenic Addiction to Androgen Receptor Signaling. PLoS ONE 5, e11475.
  • DeCicco-Skinner, KL, Trovato, EL, Simmons, JK, Lepage, PK, Wiest, J. (2010) Loss of Tumor Progression Locus 2 (TPL2) enhances tumorigenesis and inflammation in two-stage skin carcinoigenesis. Oncogene. 2010 Oct 11. [Epub ahead of print].
  • Fortunato CS, Carlini DB, Ewers E, Bushaw-Newton KL, 2009. Nitrifier and denitrifier molecular operational taxonomic unit compositions from sites of a freshwater estuary of Chesapeake Bay. Canadian Journal of Microbiology. 55, 333-346.
  • Hanson, N., M. Fogel, D.W. Fong, and S.E. MacAvoy. 2010. Marine nutrient transport: anadromous fish migration linked to the freshwater amphipod Gammarus fasciatus. Canadian Journal of Zoology 88: in press. DOI:10.1139/Z10-030
  • Hense, W., Anderson, N., Hutter, S., Stephan, W., Parsch, J., Carlini, D. B., 2010. Experimentally Increased Codon Bias in the Drosophila Adh Gene Leads to an Increase in Larval, But Not Adult, Alcohol Dehydrogenase Activity. Genetics. 184, 547-555.
  • Hutchins, B., D.W. Fong, and D.B. Carlini. 2010. Genetic population structure of the Madison Cave Isopod, Antrolana lira (Cymothoida: Cirolanidae) in the Shenandoah Valley of the eastern United States. Journal of Crustacean Biology 30(2): 312-322. DOI: 10.1651/09-3151.1
  • Lemaitre, R. Tudge, C.C. and McLaughlin, P.A. 2010. Preliminary study of the preungual process in the Paguroidea, with emphasis on the Paguridae (Crustacea: Decapoda: Anomura). Nauplius 18, 13-23.
  • Robles, R., Tudge, C.C., Dworschak, P.C., Poore, G.C.B., and Felder, D.L.. Molecular Phylogeny of the Thalassinidea Based on Nuclear and Mitochondrial Genes. In (J.W. Martin, K.A. Crandall, D.L. Felder, Eds.): Decapod Crustacean Phylogenetics. CRC Press, Boca Raton, 2009, pp. 309-326.
  • Tirelli, T., Silvestro, D., Pessani, D., and Tudge, C.C. 2010. Description of the male reproductive system of Paguristes eremita (Anomura, Diogenidae) and its placement in a phylogeny of diogenid species based on spermatozoal and spermatophore ultrastructure. Zoologischer Anzeiger 248, 299-312.
  • Tudge, C.C. Spermatozoal Morphology and Its Bearing on Decapod Phylogeny. In (J.W. Martin, K.A. Crandall, D.L. Felder, Eds.): Decapod Crustacean Phylogenetics. CRC Press, Boca Raton, 2009, pp. 101-119.
  • Zacharda, M., D.W. Fong, H.H. Hobbs, III, E. Piva, M.E. Slay, and S.J. Taylor. 2010. A review of the genus Traegaardhia (Acari, Prostigmata, Rhagidiidae) with descriptions of new species and a key to species. Zootaxa 2474:1-64.
  • Zagmajster, M, M.L. Porter, and D.W. Fong. 2010. Hydrozoans in subterranean freshwater habitats with new findings from North America. Speleobiology Notes: in press.