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IBiS REU Program in Biomolecular Science

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Pipetting in the PCR lab

Summaries of Research Labs Involved

Dr. Bonnie Bratina, Microbial Ecology. Students in Dr. Bratina’s lab investigate microbial community diversity and interactions. Currently her lab is studying nitrification and denitrification in the sediments of the Upper Mississippi River in conjunction with the local Upper Midwest Environmental Sciences Center and examining microbial interactions with the manganese biogeochemical cycle in temperate and Antarctic lakes. Organisms involved in these processes are identified by sequencing their 16S rRNA using this data to create molecular phylogenies.

Dr. Scott Cooper, Molecular Biology Students in Dr. Cooper’s lab use molecular techniques to understand the effects of hibernation on blood clotting - ground squirrels that hibernate have increased blood clotting times to prevent clots from forming as their hearts slow and blood pressure drops.  We are trying to understand how the squirrels regulate primary and secondary hemostasis to accomplish this.  This has direct medical applications in organ transplants, storage of blood products like platelets, and treatment of hypothermia.

Dr. Nick DowneyCell Biology.  Dr. Downey’s research focuses on the parasite Trypanosoma brucei. Trypanosomes have only one mitochondrion and the mitochondrial DNA (mtDNA) is attached to the flagellum of the cell.  Students in his lab work to understand the connection between the flagellum and this mtDNA. The link is proposed to be the method used by the trypanosome to segregate its mitochondrial genome (and it’s mitochondrion). Students use bioinformatics approaches to identify candidate proteins that may be involved in mitochondrial segregation and mtDNA replication. The location of candidate proteins is observed using fluorescence microscopy.  Students disrupt gene expression with RNA interference and infer protein function from the phenotype of the cell. We hope this will identify new approaches to develop effective anti-trypanosomal drugs.

Dr. Anne Galbraith, Molecular Genetics.  Students in Dr. Galbraith’s lab study the control of meiosis.  Their current focus is on the meiotic roles of CDC7 and DBF4, two genes whose protein products are known to be interact at G1/S of the mitotic cell cycle in order to initiate DNA replication.  Because of their known mitotic role, the lab is trying to determine whether these two genes are also required for DNA replication during meiosis.  A variety of methods are being performed to test this hypothesis. For example, mutant alleles of the CDC7 and DBF4 genes are being examined for their ability to undergo DNA replication during meiosis using flow cytometry. In related experiments, biochemistry and molecular genetics are used to see if the two proteins are expressed at the same time and interact during DNA replication in meiotic cells.  In addition, other proteins that interact with the Cdc7 protein during meiosis will be identified so that their relationships can be ultimately characterized as well.  Western blot of flagellar proteins

 Dr. Mike Hoffman, Virology.  Students in Dr. Hoffman’s research lab are investigating several steps in the replication cycle of human parainfluenza virus type 3 (HPIV3), a common cause of respiratory tract infections such as bronchitis and pneumonia. One area of focus is understanding the sequences involved in regulating transcription and replication of the HPIV3 genome. In this research, students make mutations in the viral genome and then determine the effects of these mutations on viral transcription, genome replication and virus viability. A second area of research focuses on understanding how HPIV3 virus particles are assembled and released from infected cells.  In this research, students use a combination of genetic engineering, biochemistry, and cell biology to characterize interactions between the matrix protein and other HPIV3 proteins. Such interactions are important in the assembly of virus particles.  In a similar manner, interactions between the matrix protein and cellular proteins are studied to understand how the matrix protein triggers release of virus particles from infected cells. 

Dr. David Howard, Cell Biology.  Students in Dr. Howard’s research lab study how cells control movement.  Most students investigate the regulation of eukaryotic flagellar motility, using the model organism Chlamydomonas reinhardtii. The signal transduction pathway used to control flagellar beating is not well understood for any organism.  Students are using biochemistry to purify the novel form of the enzyme PKA, which somehow plays a key role in control.  Following purification will determine its protein sequence. Students are also cloning and determining the expression pattern of a putative PKA gene. To determine the role of this novel PKA and of specific dynein motor proteins in live cells, students are using high speed video microscopy and image analysis to precisely measure flagellar beating in various mutants and inhibitor-treated cells.  This latter project is particularly well-suited for students who have little experience in molecular biology techniques because they can participate in experimental design and collect publishable data with minimal training. 

Dr. Tisha King-Heiden, Developmental Biology & Toxicology.  Research in Dr. King-Heiden's lab focuses on how pollutants and other environmental toxicants affect endocrine systems and vertebrate development. Using zebrafish as a model organism, students investigate how exposure to endocrine disruptors during early development affects sexual differentiation, reproduction, and health later in life (Developmental Basis for Adult Disease).  The current focus is on compounds that disrupt the function of normal male hormones.  Students evaluate the effects of potential endocrine disrupting compounds through behavior analysis, microscopy, and molecular biology.

REU students Josephine & Jacque performing surgery with Amy Cooper

Dr. Sumei Liu, Physiology. Dr. Liu's research focuses on understanding the enteric nervous system control of gastrointestinal functions in health and disease states. Goals are to understand the organization of the enteric nervous system, and to determine how enteric microcircuits and the activity of individual neurons within these circuits control motility, secretion, and epithelial barrier function of the gut. Current research projects include investigating the roles of enteric corticotropin-releasing factor (CRF) in stress-related gastrointestinal dysfunction and transient receptor potential channel in excitatory neurotransmission in the enteric nervous system.

Dr. Peg Maher, Physiology.  Students in Dr. Maher’s lab focus on how nutrients and hormones affect hunger and satiety in healthy individuals and those with metabolic and eating disorders. Students may work with cells, tissues, animal models, and/or humans. Students working in her lab have the opportunity to conduct numerous types of nutrition assessments, biochemical assays, in vitro and in vivo intervention studies, and epidemiological studies.

Dr. Aric Opdahl, Chemistry. Dr. Opdahl's research is centered on understanding structure-property relationships of bio-functionalized surfaces such as DNA and protein thin films, similar to the types commonly used in surface based diagnostics. Objectives of this project include understanding how surface interactions affect the activity of DNA probes and protein attached to gold surfaces. The lab primarily uses surface plasmon resonance (SPR) imaging spectroscopy, a label free technique to quantitatively characterize molecular interactions at or near the surface of a gold coated slide.

Dr. Kathryn Perez, Molecular Evolution.  Research in Dr. Perez's lab uses molecular biology techniques to determine the evolutionary relationships in animal species.  Students use DNA sequencing and bioinformatics to investigate the phylogeny of land snails.   Because many of these snails are endangered and/or serve as reporter species for the health of an ecosystem, understanding the phylogenetic relationships between species is important for managing ecosystems.  In addition, the taxonomy of many land snail groups is controversial, and students have the opportunity to clearly distinguish or even discover new species.

Dr. Anton Sanderfoot, Cell Biology. Dr. Sanderfoot's lab uses genetic, cell and molecular biological techniques to investigate the protein machinery involved in driving the secretory pathway of green plants. The lab uses the flowering plant Arabidopsis thaliana and the unicellular plant Chlamydomonas reinhardtii as model systems for identifying novel machinery and test beds for potential applications for crop plants. The lab also has an interest in the evolution and annotation of the protein machinery involved in vesicle trafficking, with a special interest in the novelty of the plant lineage as well as conservation across eukaryotes.

Dr. William Schwan, Microbiology.   Students in Dr. Schwan’s lab have the opportunity to work in one of four areas: type 1 pilus regulation in Escherichia coli, proline transporters in Staphylococcus aureus, detection of virulence factor genes in community-acquired S. aureus, and screening of natural products for antibacterial activity against clinically important bacterial species.  In this research, students will have the opportunity to grow and analyze different species of bacteria as well as use molecular-based (i.e. cloning, various types of polymerase chain reaction procedures, horizontal gel electrophoresis, Western blotting, Southern blotting, beta-galactosidase assays, etc.) and genetic (homologous recombination, transformation, transduction, conjugation) techniques. Some of the new, state-of-art equipment that they will be able to use will include a LightCycler for real time PCR and a phosphoimager.

Dr. Michael Winfrey, Microbial Physiology. Dr. Winfrey's lab focuses on discovery and characterization of novel antimicrobial agents from nut-bearing trees. Research students collect nuts and plant materials, prepare extracts, and test for antibacterial activity. If activity is found, the extracts are fractionated and the active chemicals purified and identified using a variety of analytical techniques. This research has the possibility of discovering new antibacterial drugs that may combat the growing problem of multi-drug resistant bacteria. A second project involves characterization of the microbial community in kefir grains. Kefir is a fermented milk known for his human health benefits. It is produced by a complex microbial community that aggregates into granules or “grains”. The approach is to clone the 16S rRNA genes from the grains, sequence the clones, and compare the sequences with known rRNA sequences to identify the microbial population. This will provide a much more comprehensive estimate of the total microbial community than the previously used culture techniques that are known to miss the majority of microbes in a sample.


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Last updated January 2011