David R. Hayworth College of Arts and Sciences

Faculty Research Interests

Dr. Brian Augustine
Materials Science and Nanoscience

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Research in the Augustine laboratory is highly interdisciplinary bridging the disciplines of chemistry, physics, engineering and biology. We are interested in the surface science of materials that have potential applications in biomedical devices. Understanding the surface chemistry of polymers is critical to control and manipulate biological materials in a biomedical device. We use a variety of microscopy, spectroscopy and microfabrication technologies to control polymeric thin films, and to understand their morphology and chemistry.

Au and Pt Film Adhesion To Polymeric Surfaces

Metal adhesion to polymer surfaces is critical for a variety of device technologies such as sensors, lab-on-a-chip, and displays. Au and Pt are commonly used interconnnect metals, but are notoriously difficult to stick to most surfaces since these metals are so inert. We have been developing a methodology to pre-treat poly(methyl methacrylate) (PMMA) surfaces with halogenated organic solvents which increases the Au adhesion by a factor of five compared to untreated or O2 plasma treated surfaces. (Adv. Funct. Mater. (2013) DOI: 10.1002/adfm.201201955)

Nanocomposite Polymer Crystallization Kinetics

Nanocomposite thin films composed of PMMA and polyhedral oligomeric silsequioxane (POSS-MA) exhibit properties that are hybrid between a traditional organic polymer like PMMA and an inorganic oxide like SiO2. POSS-MA has properties that can be controled based on the amount of POSS that is incorporated into the PMMA backbone. We have studied how an O2 plasma environment affects the surface wetting properties of POSS-MA films (Langmuir 2007)and are currently studying the crystallization kinetics of POSS-MA in-situ and in real-time using AFM. (Langmuir (2007) DOI: 10.1021/la063180k)

Microfluidic Device Fabrication

We collaborate with researchers at James Madison University and the Unversity of Virginia to fabricate and characterizate microfluidic devices for biomedical applications. (Anal. Chem. (2011) DOI: 10.1021/ac200292m)
Dr. Meghan Blackledge
Assistant Professor
Bioorganic chemistry

The Blackledge lab is seeking to understand and manipulate bacterial behavior and pathogenesis using small peptides and peptidomimetics. We are currently investigating bacterial toxin-antitoxin systems as novel targets for antibiotics and antibiotic adjuvants. Toxin-antitoxin systems are two or more closely related genes that encode a protein “toxin” and a corresponding “antitoxin”. When the toxin and antitoxin are bound together, the bacterial cells proceed normally through growth and colony formation. However, under certain stress conditions, the antitoxin will be destroyed and the toxin initiates activity that ultimately results in death of the bacterial cell.

Our lab is seeking to more fully understand the molecular basis of interactions between specific toxins and antitoxins by using small peptide mimics of the antitoxin. By understanding these molecular interactions, we can design and synthesize novel molecules with the potential to act as antibiotics or as protective antibiotic adjuvants, additives to an already available antibiotic that can protect “good” bacteria from being eliminated during antibiotic treatment. To achieve these goals, research in the Blackledge lab relies heavily on organic synthesis, peptide synthesis, and biochemical and microbiological assays.
Dr. Keir Fogarty
Assistant Professor
Biophysical Chemistry

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Fluorescence as a Tool for the Study of Biochemical Equilibrium

Traditional biochemical methods study biomolecular behavior through purification and study in a test tube. Unfortunately, “test tube” methods remove the biomolecules from their native environment; biochemical processes are often dependent on extremely complex feedback mechanisms of the cellular environment. Is it possible to investigate a complex system in living cells? The answer lies in fluorescence based studies. Once tagged with a fluorescent label, such as yellow fluorescent protein (YFP), all of the information necessary to decode a biomolecule’s behavior is contained within the fluorescent data. Fluorescence intensity is linearly related to concentration. Protein localization can be determined using imaging methods. The size of protein complexes can be determined using fluorescence brightness analysis.

Research Questions:
1) In a test tube, the fluorescence intensity of a labelled biomolecule is directly proportional to the concentration. In a cell, the fluorescence intensity can also be impacted by cellular organelles and morphology. How do we account for these factors when analyzing biomolecular concentration in cells?

2) To investigate biochemical equilibrium in cells, it is necessary to measure a system at a variety of concentrations with ample statistical weight. Cellular variability in a population renders this difficult; how do we know that a measurement performed in a sub-region of a cell of one size and shape is functionally equivalent to the same measurement performed in sub-regions of other cells exhibiting variable size, shape, and cell-cycle stage? Is it possible to normalize cellular populations?

3) In cells, reaction rates are dependent on a variety of factors; such as the concentration of the reacting species, the availability of cofactors, and the transport/diffusion of molecules to reaction-sites. How can we globally track time-dependent processes occurring in cells?
Dr. Todd Knippenberg
Assistant Professor
Physical / Computational Chemistry

My research is focused on the study of tribology, or the study of friction. I’m interested in the creation and application of new computer algorithms and potential energy functions to better understand friction at the atomic level. A recent potential energy function [Knippenberg, et al. J. Chem. Phys. 136:164701,(2012)] has been developed to study carbon-, hydrogen-, and oxygen-containing systems. Current research is being conducted on friction in the presence of water, which is vital to understanding how water contributes to wear, and the simulation of novel coatings that help reduce wear.
Dr. Heather Miller
Assistant Professor

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My research interests are in the biochemistry of gene expression, particularly the processes of transcription and splicing. My work centers on a human transcription-splicing factor, Tat specific factor 1 (Tat-SF1). This relatively understudied protein has proposed functions in transcription, alternative splicing, and polyadenylation of human genes. Furthermore, this protein not only functions in human gene expression, but is a host factor for human immunodeficiency virus (HIV) and influenza virus. Undergraduates performing research in my lab are able to gain experience in human cell culture, RNA purification, reverse transcription-quantitative PCR, RNA immunoprecipitations, and other techniques to help decipher Tat-SF1's role in both cellular and HIV-1 gene expression.

Tat-SF1 is an HIV-1 host factor

HIV-1 relies heavily on host cell transcription, processing, and translation machinery to propagate. The virus is remarkable in that it encodes over 40 different mRNAs from a genome consisting of one single, 9kb strand. These mRNA isoforms are generated in part by alternative splicing. The prevailing hypothesis was that Tat-SF1 was a human transcription factor required for HIV-1 to transcribe its genome. However, this had yet to be formally tested in vivo. Using RNA interference (RNAi), I have demonstrated that Tat-SF1 is indeed utilized by HIV-1 to propagate, and that it alters the ratios of different HIV-1 mRNA isoforms. (Miller et al, 2009). The mechanism behind this is still unknown, and could be explained by a role in alternative splicing, altered stability, or export of HIV-1 RNA. We are currently investigating which of these roles Tat-SF1 plays. Furthermore, since the protein contains two RNA recognition motifs, undergraduate research are testing for a possible direct or indirect interaction with the HIV-1 RNA genome.

Tat-SF1 is a Human Transcription-Splicing Factor

Although the literature on Tat-SF1 has centered on this protein’s role in HIV-1 gene expression, the endogenous roles of Tat-SF1 remained mostly unknown. The human transcriptome was studied using specialized microarrays that reported on overall mRNA levels (changes in synthesis and/or degradation) as well as alternatively processed mRNA isoform levels. This large study provided vast amounts of information on Tat-SF1-regulated processes and identified over 500 human genes whose mRNA levels were altered by Tat-SF1 depletion (Miller et al., 2011). Gene ontology analyses pointed to many interesting pathways with evidence of Tat-SF1 intervention, including insulin-signaling, the cell cycle, and nucleic acid metabolism. Putative binding motifs were also identified within the thousands of genes that were analyzed. To date, this work contributes the most knowledge of how Tat-SF1 functions in human gene expression. My lab is currently investigating Tat-SF1's role in insulin signaling through glucose uptake assays in control and Tat-SF1 knockdown human cell lines.
Dr. Melissa Srougi
Assistant Professor

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Twitter: @DrSrougi

Inhibition of the Rho GTPase RhoB prevents apoptotic cell death after DNA damage. Visualization of the pro-apoptotic protein Bim by immunofluorescence in MCF-7 cells stably transfected with non-targeting shRNA (shvector) or shRNA targeted against RhoB (shRhoB) that were mock-treated or irradiated with 10 Gy and fixed 72 h later. (Srougi and Burridge, PLoS 2011).

My research interests are to understand how cancer cells acquire resistance to DNA damaging radio- and chemotherapeutic agents. I am particularly interested in uncovering how the Rho family of GTPases modulate the cellular response to genotoxic stress. Elucidating these signaling pathways may have significant therapeutic implications in the current treatment of cancer.

Questions Currently Under Investigation with Undergraduates:

1. How does loss of the DNA damage repair protein ATM affect Rho GTPase function?

2. Do agents that cause different types of DNA damage elicit similar pathways of Rho GTPase activation?

3. How are the guanine nucleotide exchange factors (GEFs; activators of Rho GTPases) regulated after DNA damage?
Dr. Andrew Wommack
Assistant Professor
Organic Chemistry

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Research in the Wommack Lab is focused on employing organic synthesis to access molecules of therapeutic interest. Specifically, we are interested in the total chemical synthesis of proteins related to amyotrophic lateral sclerosis (ALS) therapies and the investigation of antimicrobial peptides with novel bioisoteres. Undergraduates will gain experience in traditional flask chemistry as well as modern methods in flow chemistry to access target structures of high relevance.

Total Chemical Synthesis of ALS Therapeutics

ALS is a neurodegenerative disease that debilitates skeletal muscle neurons and eventually leads to nerve cell death. The causes for this degeneration are multifaceted and still an active area of research. The community is still without a cure for ALS and therapies are limited. One promising therapy target is the monoclonal antibody to CD40L (a broadly expressed member of the tumor necrosis factor family). In collaboration with ALS TDI, a non-profit biotechnology firm, we use an improved peptide synthesis approach to access protein fragments for a section of this antibody, or the active “nanobody.”

Synthetic Bioisoteres for Antimicrobial Peptide Engineering

Antimicrobial peptides (AMPs) are essential elements to the innate immune response in a diverse array of living systems. Our lab seeks to explore the structural elements in these evolutionary conserved defense molecules. Of particular interest to our research is the disulfide (cystine) bond, which is commonplace as a scaffold to the microbial affecting functionality. The disulfide bond is redox active at physiological intracellular potentials. This provides an outstanding question of what is the redox fate, and therefore structure, of the AMPs as they penetrate the cell? Our research will focus on the synthesis, structure, and function of AMPs that contain redox inert surrogates for the disulfide bond.

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