Wanek School of Natural 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

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Blackledge Lab Website

The Blackledge lab is interested in understanding and manipulating bacterial behavior and pathogenesis using small molecules and peptides. Specifically, we are interested in identifying novel small molecules that combat bacterial biofilm formation, antibiotic resistance, and bacterial persistence. We use a wide variety of techniques from organic synthesis to microbiology and biochemistry to answer these questions. Currently, there are three main projects in the Blackledge lab:

1. Understanding the role of the PASTA kinase Stk1 in S. aureus
Eukaryotic-like serine/threonine kinases (eSTK) were first described in bacteria approximately 27 years ago. The penicillin-binding protein and serine/threonine associated (PASTA) kinases are a subset of eSTKs found in numerous gram-positive pathogens and mycobacteria that feature a single transmembrane region linking the cytoplasmic kinase domain to extracellular penicillin-binding protein domain. The extracellular penicillin binding domain is hypothesized to bind cell wall precursor muropeptides as a monitor of cell wall homeostasis. Pathogenic bacteria have co-opted this sensing mechanism to respond to antibiotics, such as β-lactams, that also bind in the extracellular domain of PASTA kinases. Because of their role in homeostasis and virulence regulation, this family of kinases has been identified as an attractive drug target for novel therapeutics that address bacterial virulence and antibiotic resistance. The Blackledge lab has identified several small molecules that inhibit Stk1. We are utilizing these molecules as chemical probes to elucidate novel regulatory functions of Stk1 and develop a more comprehensive model for resistance and virulence gene regulation in S. aureus.

2. Drug repurposing to combat antimicrobial resistance and biofilm formation
We are now living in a post-antibiotic era. Bacteria are developing resistance to our current therapeutic arsenal at a rate that far outpaces our ability to create new treatments. The Review on Antimicrobial Resistance estimates that by 2050 antibiotic resistant infections will kill someone every three seconds. Compounding the problem of antibiotic resistance is the propensity of pathogenic bacteria to form biofilms, which provide a persistent reservoir of infection in patients. Antibiotic treatments alone are inefficient at eradicating or fully preventing bacterial biofilms and can contribute to the enrichment of resistant strains of bacteria. Compounds that disarm bacterial biofilm formation and resistance mechanisms have potential as novel therapeutics. In an effort to identify such compounds, we turned to FDA-approved drugs as a rich source of well-studied molecules with known safety and bioavailability profiles. We hypothesize that this drug repurposing approach will provide us with lead compounds for development and could even identify approved compounds that could rapidly be deployed in the clinic. To date we have identified four FDA-approved drugs capable of potentiating antibiotics and inhibiting biofilm formation in resistant strains of Staphylococci.

3. Bacterial toxin-antitoxin systems as novel antibacterial targets
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.
Dr. Keir Fogarty
Assistant Professor
Biophysical Chemistry

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Fluorescence as a Tool for the Study of Molecular Interactions

The Fogarty Lab’s research focus lies in the field of fluorescence science. We have built a laser-based, single molecule fluorescence (SMF) instrument, developed methodologies for the new chemistry department fluorometer, and have aided in the development of fluorescence microscopy resources at HPU. This diverse array of fluorescence technologies provides the opportunity for unique experimental methodologies that can impact a diverse array of research fields. For example, we currently have collaborations in biochemistry (HIV), organic catalysis, and the creation of novel fluorescent molecules.

Research Projects:
1) Investigating Human Tat Specific Factor 1's Role in HIV-1 Nucleic Acid Binding. This project is a collaboration with the Miller lab at HPU and focuses on the interaction of HIV-1’s genome with human Tat-SF1, a protein which is part of gene regulation in humans. In previous research, Dr. Miller found that Tat-SF1 also plays a role in HIV-1 infection in humans. Without the Tat-SF1 protein, HIV-1 infections are impossible. Tat-SF1 protein is a nucleic acid interacting protein, meaning it interacts with our DNA genome, and indirect evidence indicates that it is likely to interact with HIV-1’s genome as well. We aim to elucidate the specific interaction between Tat-SF1 protein and the HIV-1 genome using a suite of biochemical and fluorescence-based methods.

2) Exploration of Light Sensitive Compounds as Catalysts in Organic Synthesis. This project is a collaboration with the Geyer (WFU), Lundin, and Wommack labs (HPU). Many drug compounds, plastics, and other commercially useful materials are created using catalysts to drive chemical reactions. Catalysts are “helper materials,” that promote, or ease, chemical reactions which are difficult to normally use. Thus, catalysts are incredibly important commercial materials: there is a never-ending effort to devise novel catalysts and understand how they work so that they can be used to generate commercially-relevant compounds cheaply and effectively. In recent years, photo-catalysts, or catalysts which translate light into energy to drive reactions, have been increasing in commercial significance. Our collaboration seeks to create novel photo-catalytic materials and characterization methods to impact the field of photo-catalysis.

3) Synthesis and Characterization of Covalently-Linked Fluorescent Dye Polymers for Bio-labeling and Photo-physical Applications. This project is a collaboration with the Lundin lab at HPU. We design novel fluorescent dimers by linking together fluorescent molecules, such as rhodamine B, in intelligently designed ways to quantitatively explore how intramolecular geometry impacts fluorescence performance. This project involves synthesis of the novel molecules, characterization of the molecules via the suite of fluorescence instrumentation at our disposal, and theoretical simulation of the molecules to gain mechanistic insight into their fluorescent behavior. Our goal is to design smart fluorescent materials using the intelligent design principles that our basic research produces.
Dr. Todd Knippenberg
Associate Professor
Physical / Computational Chemistry

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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
Associate 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. 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.

Chemistry at HPU

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