Evolutionary Biology and Genomics; Karen Barnard-Kubow, Assistant Professor of Biology: Dr. Barnard-Kubow’s lab focuses on the question of how genetic diversity is generated and maintained from the level of populations to species, and up through communities. Students will have the opportunity to work on one of two main projects in the lab. The first project is focused on developing metabarcoding protocols to characterize the community structure of zooplankton communities in the Belle Isle rockpools in Richmond, VA. Students would assist with sampling zooplankton communities in the field, carrying out initial community characterization under the microscope, generating metabarcoding data through PCR and next generation sequencing (big data), and analysis of data using bioinformatics. The second project is focused on using the plant species Campanula americana to examine the role of co-evolution between the nuclear and cytoplasmic (mitochondria and chloroplast) genomes in driving genetic incompatibility and the formation of new species. Students will have the opportunity to test hypotheses regarding the genomic signatures of co-evolution by analyzing genomic data (big data) using a combination of command line tools and programming in R (bioinformatics). Students may also assist in identification and genotyping of new populations of our model plant system, Campanula americana (the American Bellflower), though a combination of field work and basic molecular biology.  

Structural Biochemistry and Enzymology; Chris Berndsen, Associate Professor of Chemistry & Biochemistry: Dr. Berndsen’s lab focuses on describing the structure and mechanism of plant beta-amylases through a hybrid computation-biochemical approach. REU students will purify proteins and assay activity followed by collecting X-ray data on their selected protein in a variety of conditions. Where structural information is limited, students will use bioinformatic approaches to identify similar sequences/structures, to predict structure, and then study the dynamics. Students will combine their experimental results with their computational studies to connect changes in structure to mechanism and function. Most data sets are analyzed using R programming and Python is used to script the setup and execution of simulations and modeling.

Neural Control Movement; Corey Cleland, Associate Professor of Biology: The goal of our research is to understand the strategies by which sensory information is used by the central nervous system in mammals to plan movement. We attack the problem using a simple model system, the nociceptive withdrawal response in the rat. Currently we use diverse techniques – behavioral, electrophysiological, surgical, computational and computer simulations. REU students will participate in behavioral studies, in which we use high-speed video and sophisticated analysis software to quantify the movement of the rat’s tail in response to a heat stimulus. Our results will help us to understand the strategies by which animals use sensory information to plan movements and may lead to improvements in the treatment of movement disorders.

Restoration Ecology Within Southern Appalachia; Heather Griscom, Associate Unit Head of Biology: Research in Dr. Heather Griscom’s lab focuses on identifying barriers to plant regeneration and changes in biomass and diversity in forest ecosystems. Currently, this research has been focused on quantifying changes in tree/soil carbon and biodiversity within cattle pastures and restored riparian buffers in the Shenandoah Valley. Students will have the opportunity to develop an independent research project investigating different aspects of the interplay between riparian buffer restoration/land management practices and changes in biodiversity and soil microbial community functioning. Students will receive hands on experience conducting field work and ecological surveys while also developing laboratory and quantitative analysis skills. Students will have the opportunity to participate in each step of the scientific process from literature review to data analysis and communication of their results. Research will focus on current ecological theory and how this theory can be applied in restoration projects to improve the efficacy of these land management practices.  

Quantitative Cell-Substrate Mechanobiology; Kristopher Kubow, Assistant Professor of Biology: Cells in your body are in a reciprocal relationship with their surrounding tissue: they both derive information from and have the ability to change their local environment. Dr. Kubow's lab investigates how these interactions between cells and their environment impact cell migration and new tissue formation. Students will design projects investigating different aspects of the interplay between mammalian cell migration and extracellular matrix (ECM) synthesis. Students will conduct experiments using in vitro cell-substrate model systems, high-content light microscopy with digital imaging (big data), quantitative image processing (image analysis), and computational analysis (R programming).

Microanatomy, ecology and immunology of the gastrointestinal tract; Bisi Velayudhan, Assistant Professor of Biology: Dr. Velayudhan’s lab explores the influence of diet on gut mucosal structure, gut microenvironment, mucosal immunity and behavior using mice model. Students will design individualized, independent projects involving histological analysis of the gastrointestinal tract, to determine changes in the gut microflora, and conduct behavioral tests, using histological and image analyses. Behavioral studies also involve off-line video tracking. Students will incorporate high-content light microscopy imaging (big data), quantitative image processing (image analysis), and computational analysis.

Mechanosensation and Molecular Dynamics Simulation; Nate Wright, Assistant Professor of Chemistry & Biochemistry: Dr. Wright’s lab focuses on the molecular underpinnings of muscle diseases.  We are currently interested in how a specific mutation, obscurin R6669H, causes dilated cardiomyopathy in people.  We will approach this question from both a computational and a wet-lab experimental angle.  First, we will use fluorescence anisotropy to see if this mutation alters how tightly the mutated protein binds to its cellular target.  Next we will model how this mutation affects the structure and function of the parent protein using both MD and SMD.  This work will interface with a larger project with a collaborator, who is using mouse models to explore this mutation on an organismal level.  Together, this medically relevant project will give students training in a large range of computational, biochemical, and molecular biological techniques.