Faculty Research Interests

Dr. Catharina Coenen

My research focuses on the action of the hormone auxin in plant growth and development and in the interaction between plant roots and soil microbes.  My students and I have been characterizing the role of auxin in mycorrhiza, an agriculturally and ecologically important symbiotic association between plant roots and fungi.  We have also begun to explore auxin as a communication signal between plant-protective bacteria and the roots these bacteria colonize.  These projects have implications for organic agriculture, because the fungi and bacteria we study reduce the need for toxic fungicides and fertilizers.

The methods my students use to study auxin responses include genetics, molecular, biochemical and physiological experiments.  As long as you enjoy working with plants, fungi, or bacteria, there are lots of different experimental approaches to choose from.  Even if you may not be interested in staying in plant research in the long term, you will find valuable techniques and analysis methods to learn here that transfer to other systems.

Dr. Alice Deckert

My general research interests lie in the area of interfacial chemical kinetics.  My investigations of interfacial kinetics utilize assembled systems such as Langmuir-Blodgett (LB) films and self-assembled monolayers (SAM).  These films consist of well-ordered mono- or multilayers and can be fabricated from almost any amphiphillic molecule.  The ordered nature of these films provides a unique opportunity to study reactions in organized media.

We employ several analytical techniques to monitor reactions.  These include, UV-visible spectroscopy, ATR-FTIR, surface-enhanced Raman spectroscopy (SERS), microgravimetry and surface plasmon resonance (spr).

My primary interest is in reactions between the surface of the film and molecules from the solution or gas phase.  In this case only one reactant is “organized” or constrained while the other reactant is free to move in three-dimensions.  An understanding of this class of reactions is important when designing chemical sensors or biosensor technology.

Recent senior projects:

  • “Oxygen binding of myoglobin immobilized on self-assembled monolayers”
  • “Investigation of the kinetics for activation of 4-mercaptobenzoic acid with N-hydroxysuccinimide and 1-[3-(dimethylamino)propyl]-3]ethylcarbodiimide hydrochloride and displacement by histidine”
  • “Kinetics of DNA duplexing and denaturation studied using surface plasmon resonance”
  • “Kinetic investigation of glucose oxidase binding to a gold organosulfur self-assembled monolayer using surface plasmon resonance (spr) and contact angle (CA)”

Dr. Ivy Garcia

RNA plays a crucial structural and catalytic role in a variety of important cellular processes. They are synthesized as single-stranded chains and must fold into defined complex structures, like proteins, to accomplish their diverse functions. Structural versatility is a challenge for most RNAs due to the difficulty of reaching the native folding state. Hence, protein cofactors are usually necessary to stabilize or modulate RNA folding. One type of RNA protein cofactors are the ubiquitous DEAD-box proteins. DEAD-box proteins are essential in all aspects of RNA metabolism including pre-mRNA splicing, ribosome biogenesis, RNA interference, translation, mRNA transport, and decay. These motor proteins modulate RNA-RNA, RNA-protein, and/or protein-protein interactions by utilizing nine conserved motifs to convert RNA binding and ATP hydrolysis into distinct conformational changes. As part of the helicase superfamily 2 (SF2), DEAD-box proteins are formally putative RNA helicases. However, ATP driven unwinding of RNA duplexes has only been illustrated for few proteins. The main focus and motivation of my research has been to biochemically understand the structural interactions and the role that proteins play in RNA catalysis and folding in eukaryotic RNA metabolism.

Dr. Brad Hersh

Though virtually all cells in an animal contain the same DNA sequences, different cell types (e.g., muscle cells and nerve cells) have distinct physical properties.  These differences are achieved during growth and development of the organism by switching on and off specific sets of genes within the common DNA sequence.  My research focuses on identifying and characterizing the DNA sequences that control when, where, and at what level gene expression is switched on and off in the developing animal body.  The long term goal of my research is to understand the mechanisms by which Hox proteins, involved in shaping the head-to-tail patterning of all animals, regulate their target genes.  We use the fruit fly, Drosophila melanogaster, to examine the DNA sequences that respond to the Hox protein Ultrabithorax and either activate or repress gene expression the Drosophila hindwing.  The lab uses molecular biological techniques to generate variants of sequences shown to be important for gene expression, and then tests the function of these variants in transgenic animals by looking at fluorescent reporter gene activity.  In addition, we are interested in identifying the genes that are important for morphological differences between insect species so that we may understand evolutionary changes that occur in the developmental processes that produce animal shape.

Dr. Tricia Humphreys

My research focuses on the obligate human pathogen Haemophilus ducreyi, the causative agent of the sexually transmitted disease chancroid.  Like other genital ulcer diseases, chancroid facilitates the acquisition and transmission of HIV.  The long term goal of my research is to understand host-pathogen interactions between H. ducreyi and humans.  Projects in my lab examine this interaction from the bacterial side of the interaction, including defining differences between the recently described two classes of H. ducreyi.  Class I and class II H. ducreyi are known to differ in outer membrane components, but not much is known about genetic differences.  Students in my lab discovered that the two classes have multiple point mutations in key virulence genes (pal, wecA, lspA2) as well as a gene commonly used to understand phylogenetic relationships (recA).  When these genes are used to generate phylogenetic trees, the class I and II strains split consistently into two groups.  Future research will focus on studying phylogenetic relationships using housekeeping genes and mutli-locus sequence analysis.

Dr. Ann Kleinschmidt

The major focus of the projects carried out in my laboratory relate to understanding the mechanisms that control gene regulation. My research focuses on an investigation of the regulation of plant peroxidase genes in the Brassica rapa Wisconsin Fast Plant model system. Peroxidases play a diversity of roles in plants, including involvement in resistance to pathogens, removal oxidative compounds, wound healing, and growth and development. In a related plant, Arabidopsis thaliana, 73 different peroxidase cDNA clones have been identified, and very little is known about how the products of these genes specifically function, or what regulates their expression or activity. In my lab, we are currently isolating and characterizing cDNA clones for peroxidases expressed in Brassica rapa and in the non-native species Alliaria petiolata. These sequences are used to design primers for RT-PCR analyses gene expression in various plant tissues during the course of normal development or conditions where development is altered by changes in growth conditions. In addition to the gene expression analysis, we have been investigating how mutations affect the enzymatic activity and structure of a cytosolic ascorbate peroxidase from Pisum sativum. As the cDNA sequences for peroxidases from Fast Plants are completed, we will also be cloning those into bacterial expression systems to allow analysis of their enzymatic activity.

Recent senior projects:

  • “Purification and characterization of a flower bud specific peroxidase.”
  • “Characterization of expression patterns at the mRNA and protein level in wild type and floral mutants of a flower bud specific peroxidase.”
  • “Development of an expression and purification system for ascorbate peroxidase and characterization of mutations altering the APX cation-ligand site Asparagine182”
  • “The Effects of an Ethephon Induced Stress Response on Specific Peroxidase Expression in Brassica rapa Leaf Tissue”
  • “The Effects of Infection by a Fungal Pathogen, Leptosphaeria maculans on Specific Peroxidase mRNA Levels in Brassica rapa

Dr. Shaun Murphree

Research in the Murphree group focuses mainly on synthetic methodology, particularly through the use of sulfones. For example, the sulfone-based reagent 2,3-dibromo-1-(phenylsulfonyl)-1-propene, or DBP, reacts with 1,3-diketones to form 2,4-disubstituted furans, a structural motif found in some naturally occurring products of biological and industrial interest.

Ongoing projects are exploring the synthetic utility of this methodology, as well as the chemistry of other novel sulfonyl-substituted small molecules.

An additional research interest involves the development of more environmentally benign modifications of classical industrial syntheses through the use of catalytic methods.

Dr. Margaret Nelson

I am interested in the way in which signal transduction pathways allow cells to interpret and respond to external cues during development. My research is currently focused on the role that two proteins, FbxA and FbiA, play in the development of Dictyostelium discoideum. FbxA is a member of an evolutionarily conserved protein family that regulates cell behavior by targeting specific components of signal transduction pathways for degradation. Malfunctions in this degradation system have been implicated as a potential causative agent in several human diseases, including Alzheimer’s disease, Parkinson’s disease, and cancer. Data from former comp projects suggest that FbiA may be a target of FbxA-mediated degradation. Proteins homologous to FbiA are found in a wide array of eukaryotes, including fungi, plants, C. elegans, Drosophila, mice, and humans. The function of these FbiA homologues is, however, unknown. Hence, further characterization of FbiA’s role in Dictyostelium development may shed light on the function of this conserved protein family.

Work in the near future will address questions such as: (i) when and where the FbiA protein is expressed, (ii) what signaling pathway(s) are responsible for the complex, developmentally regulated pattern of fbiA RNA expression, (iii) why the absence of FbiA disrupts pattern formation, and (iv) whether FbxA & FbiA interact in a biologically relevant fashion. Depending upon the project you choose, you might employ any of the following techniques: restriction digests, agarose gel electrophoresis, plasmid & genomic DNA preps, PCR, introduction of recombinant DNA molecules into cells (bacteria, Dictyostelium), cell propagation and sterile technique (bacteria, Dictyostelium), protein purification, protein gels, Western blots, histochemical staining, phase contrast microscopy, immunofluorescent microscopy, bright-field microscopy (stereozoom scope), and digital photography.

Recent senior projects:

  • Dictyostelium fbiA mRNA expression analysis via in situ hybridization”
  • “Characterizing the relationship between the proteins FbxA and FbiA in Dictyostelium discoideum
  • “Regulation of FbiA protein levels via ubiquitination-mediated proteolysis in Dictyostelium discoideum
  • “Characterization of Dictyostelium discoideum mutants overexpressing FbiA”
  • “Creating and Characterizing the fbiA mutant in Dictyostelium discoideum

Dr. Marty Serra

Physical Biochemistry – Development of models to predict the stability of RNA structure from sequence.  Small synthetic RNA oligomers are studied by optical melting to determine their thermodynamic stability. The effect of sequence on the stability of the RNA is used to develop models to predict the structure of naturally occurring RNAs.