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Graduate Program in Cell and Molecular Biology
Paul D. Adams- Protein Biochemistry and Biophysics
Our research is focused on understanding the molecular details of constructs of Ras proteins that are known to have altered cell signaling potential. Mutants or abnormal expression of Ras proteins have been found to alter these proteins’ roles in normal cell-signaling function. Our approaches, using biochemical and biophysical techniques, are expected to help us delineate the processes by which changes in Ras-related proteins and their interactions with regulators and targets affect various important signal transduction pathways.
Jamie I. Baum – Nutritional Science
Our research is focused on the role of dietary protein in metabolic health through the lifecycle using research models ranging from molecule to man. We are particularly interested in the role of the branched-chain amino acid leucine, and how it can regulate energy metabolism, thereby altering body composition and susceptibility to obesity and metabolic disease. We use C2C12 muscle cell line to identify the molecular mechanisms involved in leucine’s regulation of energy metabolism. We use immunoprecipitation and Western blotting techniques to measure protein levels and gene expression via rt-PCR. In addition, we use nutrition intervention studies to determine role of dietary protein during obesity. Techniques include metabolic assays using plasma, body composition, and measurement of genes related to obesity and energy metabolism in skeletal muscle and adipose tissue. Finally, we conduct human intervention trials to determine the impact of protein intake (both quantity and quality) on energy metabolism, body composition, metabolic biomarkers and satiety.
Robert Beitle – Bioprocess Engineering
We employ an interdisciplinary environment including molecular biology, advanced fermentation, and novel bioseparation methods to isolate proteins of therapeutic of commercial value. In particular, our team investigates methods of high-cell density fermentation (fed batch in particular) for product expression and novel affinity techniques for the simplification of product isolation. Techniques include: DNA manipulation and PCR, fermentation (batch, fed batch, and continuous), liquid chromatography, ultrafiltration / diafiltration, and aqueous two phase extraction. Mathematical models are used when appropriate to describe a process or part of the bioprocess.
Yuchun Du – Proteomics analysis of cancer
Research in my laboratory focuses on using multidisciplinary approaches including techniques from quantitative proteomics, biochemistry, and molecular and cell biology to identify and characterize the proteins that are involved in radiation or drug-resistance of pancreatic cancer cells. We are also working on studying the molecular mechanisms underlying the activation of an important proapoptotic protein called Bax. Techniques include mammalian cell culture, molecular cloning, gene overexpression, RNAi-based gene silencing, SDS-PAGE, Western blotting, real-time-PCR, protein expression/purification, mass spectrometry analysis, etc.
Gisela F. Erf – Avian Immunology
We are using cellular and molecular techniques to examine fundamental aspects of innate and adaptive immune system development and function in chickens. The research includes experimental manipulation of the animal, tissue collection and in situ as well as ex vivo analyses. Techniques include histology, immunohistochemistry, cell culture, cell population analysis by flow cytometry, laser-capture microdissection and gene-expression analysis both at the protein (e.g. ELISA) and RNA (e.g. real-time RT-PCR) level.
Ingrid Fritsch – Microelectrochemical Sensing
Our research is focused on fundamental and applied studies toward the development of micro total analysis systems for portable environmental chemical analysis and point-of-care diagnostics. Chemical sensing is central to these goals, where investigations include finding ways to handle a small sample in an automated fashion, to capture or identify analytes in the sample, and to transduce that recognition event into an electrical signal. The projects involve microfabrication and electrochemical patterning of materials and biorecognition molecules on a chip, protein and DNA-hybridization microarrays interfaced to electrochemical detection, novel microelectrochemical strategies for detection of small molecules, and microfluidics controlled with magnetic fields.
Fiona L. Goggin - Molecular Plant Defense
We use molecular and genomic approaches to understand plants’ “immune” responses against insect pests to enhance these defenses in crop plants to reduce usage of pesticides. Techniques include DNA and RNA isolation, gene expression analysis by realtime RT-PCR and microarrays, manipulation of plant gene expression through virus-induced gene silencing, utilization and hybridization of T-DNA and transposon mutants, electrical penetration graph analysis of insect feeding, olfactometer assays of insect host choice, and other bioassays to evaluate the impact of plant traits on insect survival, reproduction, and behavior.
Jin-Woo Kim – Bio/Nano Technology
Biomaterials, including DNA, proteins, and cells, are well optimized through evolution, exhibiting unique recognition, transport, catalytic, and replication properties. The integration of such pre-engineered biomaterials into nano systems would lead to the realization of the next generation bio/abio hybrid engineered systems for applications ranging from MEMS/NEMS-based micro/nano fluidic systems, to bioelectronic or biosensing systems. Currently, we are in the process of developing a series of nano biohybrid devices through stable and ‘controllable’ interfaces between bio and abio materials at the nanoscale, using bio/nano technology tools, including molecular cloning, bioseparation, atomic force microscopy, transmission electron microscopy, and micro/nanofabrication among others.
Roger Koeppe – Membrane Biochemistry & Biophysics
The research projects in my group are focused on understanding the functional interactions of lipids and proteins in biological membranes. We are interested in the molecular mechanisms for regulating cell signaling and the activities of ion channels and other membrane proteins. Potential mechanisms include physical features such as lipid bilayer thickness and transmembrane helix tilt, in addition to chemical interactions such as ligand/receptor binding. Our main methods involve solid-phase peptide synthesis, molecular modeling and biophysical techniques including solid-state NMR spectroscopy, fluorescence and circular dichroism.
Kenneth L. Korth – Plant Molecular Biology
We are using tools of molecular biology and genomics to understand plant defense responses to insect pests. The work focuses on production of terpene secondary metabolites and formation of mineral crystals that deter chewing insects. In order to measure gene expression and metabolite levels and characterize gene function, we utilize RT-PCR, RNA blots, gas chromatography, enzyme assays, and production of transgenic plant materials.
Michael Lehmann – Genetics of Development and Metabolism
We use the model organism Drosophila melanogaster to study evolutionarily conserved genes that control development and energy metabolism. Techniques include the creation of transgenic flies to study gene function in whole animals, mutagenesis, fluorescence microscopy, recombinant DNA technology, RNA and protein detection (PCR, microarrays, Western blots), and metabolic assays.
David S. McNabb- Biochemistry and Molecular Biology
My research group is focused on understanding the coordinate transcriptional regulation of genes involved in respiration, iron and heme metabolism in the yeast Candida albicans. We routinely use standard molecular techniques to: 1) identify cis-acting promoter elements in target genes via gene reporter assays; 2) generate specific gene knockout mutants of C. albicans; 3) to examine mRNA expression by RT-PCR or Northern blot studies; and 4) evaluate the DNA-binding activity of specific transcription factors to target promoters using electrophoretic mobility shift assays. We employ whole genome microarray studies to obtain a more comprehensive view of the regulatory pathways controlled by specific transcription factors in C. albicans.
Andy Pereira – Plant Stress Biology
My research group works on plant abiotic stress to understand the mechanisms underlying drought resistance, water use efficiency and high temperature tolerance. We work primarily with rice but use other plants where necessary. Our research uses a) functional genomics techniques such as transcriptome analysis with RNA-Seq and quantitative RT-PCR, knockout mutants and overexpression transgenic lines, protein-protein and protein-DNA interaction; b) Physiological analysis testing for drought, water use efficiency, temperature sensitivity and salinity; c) Bioinformatics analysis for RNA-Seq and genome resequencing data, gene coexpression networks and gene motif analysis.
Ines Pinto- Yeast molecular genetics to study chromatin function.
We are using the baker's yeast Saccharomyces cerevisiae, to study chromatin function, with emphasis in histone proteins and their interacting factors. We use genetic, molecular and biochemical approaches to understand the function that chromatin plays in chromosome segregation, in particular the role that histones and other centromere-associated proteins play in the attachment and proper segregation of chromosomes during cell division. Common techniques are ChIP, PCR, cloning, knockouts, expression tagging, and rtPCR.
Douglas D. Rhoads - Molecular Genetics and Genomics
We use molecular genetics to dissect developmental aberrations in the cardio pulmonary system and in the gonad in the chicken. Phenotyped animals are sampled for DNA and RNA which is subjected to further molecular analyses to understand how particular genes and alleles contribute to complex phenotypes. Techniques include DNA and RNA isolation, PCR genotyping, DNA sequencing, gene expression analyses by realtime quantitative PCR, statistical analyses, and genome level bioinformatics.
Steven C. Ricke - Foodborne Pathogen Microbiology
We are screening for natural antimicrobials against methicillin-resistant Staphylococcus aureus (MRSA) and some other foodborne bacterial pathogens such as Campylobacter jejuni, Salmonella, E. coli and Listeria monocytogenes. We also develop molecular and immunological methods for quantifying foodborne pathogens in a wide range of food matrices. This work employs molecular techniques such as DNA and RNA isolation, PCR, RT-PCR, genotyping, DNA sequencing, transcriptional profiling by microarrays, tissue culture, and bioinformatics.
Charles Rosenkrans, Jr. - Animal Genetics and Developmental Physiology
We are using molecular and physiological genetics to determine the mechanisms involved with growth and development of livestock. The work includes experimental manipulation of animal nutrition and toxicology, followed by isolation of tissues for DNA and RNA analysis. Techniques include DNA and RNA isolation, PCR genotyping, DNA sequencing and SNP identification, gene expression analysis by realtime PCR, statistical analyses, and bioinformatics
Mary C Savin- Microbial Ecology
We use molecular techniques to detect changes within environmental microbial communities in response to management practices. Management treatments in an organic orchard are altering nutrient cycling and availability. Only a small fraction of microorganisms from the environment are known and can be cultured, so we use of molecular techniques to investigate natural communities. We isolate total DNA from soil, and then use PCR-DGGE to investigate changes in community structure and target sequencing efforts to connect organisms involved in N transformations in plots with different organic amendments to affect soil structural properties and fluxes of N through the system.
Ron Sayler –Plant Pathology & Biotechnology
We are developing corn with resistance to a broad range of plant pathogens by using plant biotechnology. The work includes genetic engineering of the corn genome to express antimicrobial proteins. Techniques employed by this project encompass a broad range DNA, RNA, and protein analysis approaches PCR, RT-PCR, restriction digest, ELISA, and Western blot. Bioinformatics, statistical analyses, and fungal bioassays are also a routine part of our research. In addition, we employ plant tissue culture techniques for developing transgenic plants.
Shannon Servoss—Peptoid Based Diagnostics
We focus on the use of biomimetic materials with a poly-N-substituted glycine (peptoid) backbone for biomedical applications. Peptoids are easy and inexpensive to synthesize, and can be designed to form extremely stable secondary structures similar to proteins. In addition, peptoids are protease resistant decreasing the potential of an immune response. Projects in our lab include: peptoid-based microsphere coatings, peptoid-based antibody mimics for ELISA microarray, peptoid-based therapeutics for Alzheimer’s disease, antimicrobial agents, membranes for chiral separations, and targeted drug-delivery systems. Techniques include peptoid synthesis, high performance liquid chromatography, circular dichroism, scanning electron microscopy, and biochemical characterization methods.
Wesley E. Stites- Protein Biochemistry
This project is to better understand the modification of proteins by quinone electrophiles such as N-acetyl-p-benzoquinone, derived from acetaminophen, responsible for the lethal effects of acetaminophen overdose, and the urushiols found in poison ivy, responsible for their well-known effects. Very little is known about the basic chemistry of these modifications. Students will utilize organic and protein chemistry, advanced HPLC techniques, kinetics, NMR and mass spectrometry.
Suresh Kumar Thallapuranam – Biochemistry & Structural Biology
My research group is focused on understanding the structure, dynamics, stability, folding, and interactions of cytokines such as, the human acidic fibroblast growth factor and interleukin 1 alpha. We are also actively engaged in understanding the molecular mechanisms underlying the secretion of signal peptide-less proteins through the non-classical ER-Golgi independent pathway. In addition, development of novel methods for overexpression & purification recombinant proteins is a major area of interest in the group. We routinely use molecular biology, molecular modeling and biophysical techniques including multidimensional NMR spectroscopy.
Tyrone Washington – Muscle Physiology
My Exercise Muscle Biology Laboratory employs molecular biology techniques with in vivo and in vitro models examining muscle plasticity. Currently my laboratory is examining signaling within skeletal muscle induced by aging, obesity, regeneration, or altered loading, which can differentially regulate gene expression. Our research will provide information that can help in the development of counter measures for individuals with chronic wasting diseases, age-related loss of muscle mass, and obesity related muscle dysfunction.