border left blue header line border right
INBRE logo header text
header bottom
 
  Mentored Summer Program Research Areas  
spacer

Mentors at UAF

UALR  |  UAMSBack

1UARK

Biophysical and Biochemical Approaches to Study Ras-Related Protein Interactions
Paul D. Adams, PhD
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

Our research interests are focused on understanding structure and function of Ras-related proteins involved in signal transduction processes involved in the onset of diseases such as cancer and COPD. The Ras proteins presently being studied in the laboratory include Cdc42 (Cell division cycle 42) and Rheb (Ras homology enriched in brain), both of which are involved in a wide range of cellular processes including cell cycle progression, cytoskeletal organization, protein trafficking, and secretion. The goal of our research is to develop approaches to study molecular details of these proteins, and their interaction with effectors. We use several biophysical and biochemical techniques, including site-directed mutagenesis, multi-dimensional NMR spectroscopy for use in protein structure determination as well as dynamics, steady-state and time-resolved fluorescence spectroscopy, isothermal titration calorimetry, differential scanning calorimetry, protein expression and purification procedures, circular dichroism spectroscopy, structural analysis of proteins using molecular dynamics simulations in our approaches.

2UARK

Development of Photoactive Transition Metal 5-Membered Ring Quinone Methideanalogs
Potential Anti-cancer and Anti-tumor Drug Design
Neil Allison, PhD
Department of Chemistry & Biochemistry, University of Arkansas, Fayetteville

The quinone methide moiety has been reported to be possible bioreductive alkylators of DNA as well as alkylators of nucleic acid bases. A goal of the Allison research group is to study the preparation and chemistry of 5-membered ring quinone methide analogs that are bonded to a transition metal. In contrast to quinone methides, we can vary the metal and ligands to control reactivity.

Pre-requisite courses: Organic Chemistry I and II

Bioinformatics students:  No

3UARK

Bioseparation Systems Design
Robert R. Beitle, PhD & Ralph Henry, PhD
Ralph E. Martin Department of Chemical Engineering, and Department of Biological Sciences, University of Arkansas, Fayetteville

This joint project between biological science (Ralph Henry) and chemical engineering (Robert Beitle) introduces a new and powerful concept by which recombinant proteins of commercial, therapeutic, or academic interest may be isolated when affinity tail technology is used to dictate purification. Work will focus on the optimization of protein purification via the technique of Immobilized Metal Affinity Chromatography (IMAC). We have cataloged genomic proteins of Escherichia coli that bind chelated metal ions during IMAC. Based on our results it has been established that eight proteins constitute over 50% of the potential contaminating genomic proteins of E. coli. When these eight are eliminated or mutated via genetic means the purification process will be greatly improved. Anticipated benefits would include but not be limited to reductions in (i) the regiment of chromatography, (ii) column capacity loss due to contaminating protein adsorption, and (iii) complexity of elution protocols since the number of proteins to be resolved are less.  Such an effort to date has not been documented in literature.

 

Students are sought with background in (i) molecular biology, (ii) chemical or biological engineering, or (iii) math sciences. Specific tasks would likely be (i) collecting proteome data, (ii) scaling the lMAC process to larger systems, or (iii) modeling the system.

Pre-requisite courses: None

Bioinformatics students: Yes

4UARK

Quantitative Proteomic Analysis of the Protein Complexes Functioning in Programmed Cell Death

Yuchun Du, PhD
Department of Biological Sciences, University of Arkansas, Fayetteville

Mass spectrometry based quantitative proteomics involves using stable isotope to differentially label proteins or peptides, and mass spectrometry to compare the relative abundance of the proteins in different samples. Research in Du laboratory focuses on using multidisciplinary approaches including techniques from quantitative proteomics, biochemistry and cell biology to identify and characterize protein complexes that play critical roles in programmed cell death. 

Pre-requisite courses:  None

Bioinformatics students:  Yes

5UARK

Development of Photoactivated Ruthenium Complexes to study Biological Electron Transfer
Bill Durham, PhD & Frank Millett, PhD
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

This laboratory is involved in developing novel photoactivated ruthenium complexes to study biological electron transfer reactions. Currently mitochondrial electron transfer in several proteins involved in the electron transport chain, including cytochrome c, cytochrome oxidase, and cytochrome bc1 is being studied.

Pre-requisite courses: None

Bioinformatics students:  Yes

6UARK

Early Endosome Trafficking in Fungal Pathogenesis
Martin J. Egan, PhD
Department of Plant Pathology, University of Arkansas, Fayetteville

The main focus of the Egan lab is to understand the role of microtubule-based early endosome trafficking in the infection-related development, and pathogenesis of filamentous fungi. Filamentous fungi are responsible for devastating diseases of agriculturally important food crops, and cause life threatening infections of immunocompromised humans. Our group use the rice blast fungus, Magnaporthe oryzae, and the opportunistic human pathogenic fungi, Aspergillus fumigatus, and A. nidulans, as model systems for dissecting the molecular mechanisms of disease. We are using cell biological and molecular genetic approaches to understand the importance of microtubule-dependent early endosome motility in host perception, signal transduction, and the initiation of the pathogenic program.
Prerequisite Courses: None
Bioinformatics Students: Possibly      

7UARK Genetics of Senescence and Genomic Analysis of Gene Expression
William J. Etges PhD
Department of Biological Sciences, University of Arkansas, Fayetteville

Our lab group focuses on the genetic and environmental determinants of variation in biodemography using a Drosophila model system. We are assessing sequenced genomes with microarrays and nextgen transcriptomics to understand patterns of gene expression associated with aging, how these functional gene clusters vary through the life cycle, and are influenced by major environmental factors. We plan on assessing expression patterns with qPCR as well as determining the roles of known gene families on adult behavior and sensory perception.
Pre-requisite courses: Introductory Biology
Bioinformatics students: Yes

8UARK

Miniature Biosensors and Bioassays

Ingrid Fritsch, PhD

Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

Research in the Fritsch lab involves bioanalytical chemistry. It includes interfacing various materials that are suitable for miniature biosensors and bioassays with selected biological compounds. Projects include immobilization of molecules onto surfaces, studies of stability of activity, microfluidics to achieve automation and manipulate nanoliter to picoliter volumes and electrochemical detection of pathogens and biomarkers important in medical diagnostics and environmental applications.  In certain cases, we write computer simulations that can be used in combination with experiments to better understand results and design new biosensor and bioassay devices.

Pre-requisite courses:  Freshman Chemistry & Organic Chemistry

Bioinformatics students:  Yes

9UARK

Molecular Biology of Plant Immunity

Fiona L. Goggin, PhD

Department of Entomology, University of Arkansas, Fayetteville.

The Goggin laboratory uses molecular and genomic tools to study the mechanisms through which plants defend themselves against attack by insects and other herbivores.  The ultimate goal of this work is to identify means of enhancing herbivore resistance in crop plants in order to reduce yield losses and pesticide usage.  Our laboratory can offer training in standard techniques for gene expression analysis (eg. quantitative RT-PCR) as well as techniques to suppress expression of genes that have been selected for functional analysis (eg. virus-induced gene silencing). web site: http://entomology.uark.edu/3926.php.

Pre-requisite courses: None

Bioinformatics students:  Possibly

10UARK

Improving Detection of Alzheimer’s Disease

Christa N. Hestekin, PhD

Ralph E. Martin Department of Chemical Engineering, University of Arkansas, Fayetteville

Alzheimer disease is a debilitating neurodegenerative disorder affecting more than 30 million people worldwide.  Although exact nature of how Alzheimer disease progresses is still not completely understood, there are significant indications that it involves the aggregation of the B-amyloid (AB) protein, specifically the ~40 residue hydrophobic proteins.    The B-amyloid monomers are not harmful and must aggregate in order to become neurotoxic.  However, it is still unclear what level of aggregation (10s – 1000s of monomers) is the key toxic form.  Some recent studies have suggested that the oligomeric (3-20 mers of 4.3 kDa) forms may be the most important.   The small size of these oligomers makes them more challenging to separate and to visualize.  In addition, any detection method for Alzheimer’s disease must also be able to detect AB protein at physiologically relevant levels (pM).   Microchannel electrophoresis offers the potential to sensitively analyze small samples of material (from a sources such as CSF) to determine the degree of aggregation and its involvement in the progression of Alzheimer’s disease.  In this project, sample conditions such as salt, pH, and the presence of other proteins on amyloid beta aggregation will be tested.

Pre-requisite courses: None

Bioinformatics students: No

11UARK

Molecular Adaptations to Life at High pH: Virulence Genes of the Intestinal Pathogen Clostridium Difficile
Mack Ivey, PhD
Department of Biological Chemistry, University of Arkansas, Fayetteville

Research in the Ivey laboratory focuses on the biochemical and genetic mechanisms by which bacteria respond to their ionic environment. Microbiological, molecular genetic and biochemical techniques are used in the investigation of an unusual ATP synthase isolated from a bacterium that lives in extreme environments. A second project involves the molecular characterization of ion transporters and other potential virulence determinants in the intestinal pathogen Clostridium difficile.

Pre-requisite courses: None

Bioinformatics students:  Yes

12UARK

Biophysics of Membrane Channels
Roger Koeppe, PhD  

Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

To study the biophysics of membrane channels, the synthesis, labeling and purification of membrane-active peptides are used. Protein/lipid structural and dynamic interactions are analyzed using deuterium magnetic resonance spectroscopy, circular dichroism spectroscopy, and other methods.

Pre-requisite courses: None

Bioinformatics students:  No

13UARK

Regulation of Microbial Stress Responses
Jeff Lewis, PhD
Department of Biological Sciences,  University of Arkansas, Fayetteville

Our lab focuses on the genetic and biochemical underpinnings of stress defense. All organisms experience environmental stress and must rapidly adapt to changing conditions. These stress responses are remarkably complex, coordinating multiple levels of sensing, signal transduction, and global regulatory networks. Thus, stress research feeds into nearly all aspects of cell biology, with implications for human disease, microbial pathogenesis, and the evolution of regulatory networks. Our group takes advantage of natural variation within wild microbial populations to perform comparative genomics of stress responses. We use this powerful approach, in combination with classical genetics and biochemistry, to identify and characterize novel stress regulatory pathways and mechanisms of stress defense.
Pre-requisite courses: None
Bioinformatics students: Yes

14UARK

Mechanisms of Candida albicans pathogenesis and the development of antifungal therapeutics
David S. McNabb, PhD
Department of Biological Sciences, University of Arkansas, Fayetteville

The McNabb laboratory has two major areas of research: 1) to examine the mechanisms by which the CCAAT-binding factor regulates the expression of numerous genes involved in respiration, iron uptake and utilization, and the oxidative stress response in the human opportunistic pathogen Candida albicans; 2) to develop small peptides that display fungicidal activity and to dissect the mechanism(s)-of-action of these peptides with the long-term goal of identify novel therapeutics for treatment of fungal infections.  Approaches include standard molecular genetic techniques, EMSAs to study protein-nucleic acid interactions, gene expression analysis via Northern blotting, RT-PCR and gene reporter assays, high-throughput screening of antifungal peptides, and minimum inhibitory concentration assays to quantify the fungicidal activity of peptides.

Pre-requisite courses: None
Bioinformatics students: No

15UARK

Mitotic Chromosome Segregation in Yeast
Inés Pinto, PhD

Department of Biological Sciences, University of Arkansas, Fayetteville

The main goal of Dr. Pinto’s research is to understand how chromatin structure affects chromosome segregation. The budding yeast Saccharomyces cerevisiae is used as a model system. This lower eukaryote offers the advantage of being amenable to many types of analyses, including cell biology, molecular genetics and biochemical techniques. A multi-disciplinary approach is used to investigate the role that chromatin plays in the basic process of cell division.

Pre-requisite courses: Introductory Biology

Bioinformatics students:  No

16UARK

Genomics, and Metabolic Diseases using Poultry

Doug Rhoads, PhD

Department of Biological Sciences, University of Arkansas, Fayetteville

The Rhoads laboratory uses advanced methods of genome analysis to identify, and map genes involved in development of genetic diseases affecting chickens.  Our main focus at present are Pulmonary Hypertension Syndrome, and Bacterial Chondronecrosis with Osteomyelitis.  Both of these are focused on chicken diseases that model medical issues in humans. We have projects using genomic in chickens to understand the disease and genomics in bacteria to understand the evolution of pathogenesis.  This project uses PCR, DNA sequencing, bioinformatics, Next Generation Sequencing, and qPCR to characterize genes and gene regions through sequence and expression analysis.

Website:http://www.uark.edu/ua/drhoads

Pre-requisite courses: Cell Biology; Genetics

Bioinformatics students:  Yes

17UARK

Artificial Enzyme Mimics
Susanne Striegler, PhD
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

The laboratory project focuses on synthesizing and evaluating galactonoamidines as transition state   analogs and templates for artificial enzyme mimics. A combination of biochemical, synthetic and material science including spectroscopy, calorimetry and synthesis will be used to prepare and characterize templated microgels as catalysts for the selective hydrolysis and synthesis of glycosidic bonds.
Pre-requisite courses: None

Bioinformatics students:  No

18UARK

3-Dimensional Structural Analysis of Protein-Ligand Complexes
Joshua Sakon, PhD

Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

Detailed structural studies of medically relevant proteins can reveal subtle features concerning the interaction of the protein and its binding partners. From this information, lead compounds may be developed using structure-based drug design methodology. Techniques include protein isolation, protein crystallization and structural characterization using x-ray crystallography.

Pre-requisite courses: None

Bioinformatics students:  Yes

19UARK

Transgenic Approaches to Control Aflatoxins in Corn

Department of Plant Pathology

Ronald J. Sayler, PhD

The Sayler lab also develops transgenic plants, yeast and bacteria in order to test the efficacy of novel transgenes in preventing the accumulation of aflatoxins in crop plants.  Aflatoxins are produced by the fungus Aspergillus flavus and are the most potent naturally occurring carcinogen known to man.  The end goal of this work is to reduce aflatoxin contamination in harvested crops and improve the safety of food made from these crops.  Our lab can offer training in standard nucleic acid analysis techniques including DNA extraction, primer design, both conventional and real-time Q-PCR.  Our laboratory also can offer training for protein biochemistry including ELISA, SDS-PAGE and western blot analysis. Web site: http://plantpathology.uark.edu/2308.htm

Pre-requisite courses: None

Bioinformatics students:  Possibly

20UARK

Medicinal Chemistry and Chemical Biology of Antitumor Natural Glycoconjugates
Wei Shi, PhD
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

Our research objective is to discover and optimize pharmaceutically-relevant molecules derived from natural small-molecule glycoconjugates for treating life-threatening diseases, including, but not limited to, cancer. We employ interdisciplinary techniques (organic synthesis, cellular and molecular biology, and proteomics) to understand the mechanism, utility, and function of these naturally-occurring molecular hybrids, thereby facilitating rational design of next generation of chemical entities with improved efficacy. Website: https://comp.uark.edu/~weishi/index.html.
  Pre-requisite courses: None
Bioinformatics students:  No

21UARK

In Vivo Microdialysis Sampling Studies for Monitoring Signaling Molecules

Julie Stenken, PhD

Department of Chemistry & Biochemistry Chemical Biology, University of Arkansas

Our bioanalytical chemistry laboratory focuses on making direct measurements as well as improving the ability to make measurements within awake and freely moving mammalian systems. Microdialysis sampling is a widely used and successful sample collection method to obtain analytically-clean samples from very complex matrices such as mammalian tissues, bioreactors, or environmental samples.  There are numerous potential projects that could be tailored for students and faculty within the Arkansas INBRE program.  Our current major focus has been aimed towards improving peptide and protein sampling using the microdialysis sampling approach.  Systems of interest include: 1. Detection of cytokines and matrix metalloproteinases in situ within wound sites.  2. Modulation of cytokines and MMPs during wound healing. 3. Measurement of neuropeptides related to addiction. 4. Measurement of peptides and proteins (e.g., insulin, leptin) related to obesity and metabolic syndrome.  Common analytical techniques frequently used in this laboratory include ELISA, HPLC, flow cytometry-based immunoassays, and mass spectrometry.  

Course Prerequisites:   Freshmen Chemistry

Bioinformatics Students:  Yes  

22UARK

Post-translation Oxidation and Effects on Protein Activity, Stability, and Structure
Wesley Stites, PhD
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

The leading cause of premature death in smokers is cardiovascular disease. Diabetics also suffer from increased cardiovascular disease. This results, in part, from the hypercoagulable state associated with these conditions. However, the molecular cause(s) of the elevated risk of cardiovascular disease and the prothrombotic state of smokers and diabetics remain unknown. It is well known that oxidative stress is increased in both conditions. More generally, aside from smoking, aging and diseases such as diabetes are also well known to be accompanied by oxidative stress and many complications of these conditions appear related to this stress. Oxidative stress has been shown to be linked to oxidation of methionine side chains in proteins to the sulfoxide form. Methionine sulfoxide formation has also been shown to affect the biological activity of proteins in blood coagulation and may be a general regulatory mechanism. However, no systematic effort has been made to survey the human proteome for this oxidative modification nor to determine how it changes with age, disease state, or smoking status. This is, in part, due to the fact that it is fairly difficult to detect this modification. We have established methods to screen for this modification and are building a database of proteins more oxidized in smokers than in non-smokers.  We are also examining the effects on this modification on enzymatic activity.

Pre-requisite courses: None

Bioinformatics students:  Yes

23UARK

Structure, function and interactions of cytokines
Suresh Kumar Thallapuranam, PhD
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

My research group is focused on understanding the structure, function, folding and interaction(s) of fibroblast growth factors (FGFs).  Using protein engineering techniques, we are currently engaged in developing a new class of FGFs which have higher thermal stability and enhanced wound healing activity. In addition, the molecular mechanisms underlying the activation of the FGF receptor(s) are being investigated.  Another focus of my research group is to decipher the molecular events involved in the endoplasmic reticulum- Golgi independent, non-classical secretion of cytokines such as, FGF(s), vascular endothelial growth factor, and interleukins.  We are also actively working on in silico modeling of 3D structures of proteins and protein-ligand interactions. We use a wide array of structural biology, molecular biology, cell biology and computational techniques in our research.

24UARK

Mechanisms of Ionic Regulation in Fishes
Christian K. Tipsmark, PhD

Department of Biological Sciences, University of Arkansas, Fayetteville

My laboratory studies the physiological mechanisms that allow fish to live in a particular environment and how the endocrine system controls acclimation processes when the surrounding conditions change. Our studies are integrative and we use a variety of approaches including: organismal and organ biology, histology and cell and molecular biology. This multidisciplinary approach enables us to develop a broad and deep perspective on the environmental physiology of fish. 
Pre-requisite courses: None
Bioinformatics students: Yes

 

25UARK

Bioanalytical Mass Spectrometry

Charles L. Wilkins, PhD

Department of Chemistry & Biochemistry, University of Arkansas, Fayetteville

Our research involves development and use of advanced mass spectrometric methods for application in a variety of proteomics-related studies. Among those techniques are Fourier transform and matrix-assisted time-of-flight mass spectrometry. Recent research is exploring means of producing multiple-charged ions using a new ionization method under that involves sample conditions that make possible the use of electron capture dissociation (ECD) for effective protein analysis.

Pre-requisite Courses: Freshman Chemistry and Organic Chemistry

Bioinformatics students: Yes

26UARK

Visible Light Photoredox Catalysis and Sustainable (Green) Chemistry
Nan Zheng, PhD
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville

Research in my group is focused on the development of green or environmental sustainable methods for amine synthesis.  We are specifically interested in developing new reactions using environmentally friendly metals such as Fe and renewable sources such as air and sunlight.  One of our current research interests is to harvest synthetic potential of amine radical cations enable by visible light photoredox catalysis.
Pre-requisite courses: Organic Chemistry I and II
Bioinformatics students: No

 

 

 

 
 

The Arkansas INBRE is supported by a grant  from the National Institutes of Health

National Institute of General Medical Sciences (P20 GM103429).

Please contact Diane McKinstry regarding questions or comments about this site or our program.
For more information about the University of Arkansas for Medical Sciences visit http://www.uams.edu.

 
 
  blue footer line