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IGERT FACULTY


Maciek Antoniewicz
Chemical Engineering

The Antoniewicz lab for Metabolic Engineering and Systems Biology works on a wide range of topics in modern life sciences including Biofuels and Diabetes, where we apply techniques such as Metabolic Flux Analysis, Stable-isotope Labeling Experiments, e.g. 13C, 2H, 18O, and Tandem Mass Spectrometry to study cellular systems. The primary goal of our research efforts is to provide a comprehensive understanding of the function and regulation of complex biological processes that emerge through the interaction of genes, proteins, and metabolites at multiple metabolic and genetic regulatory levels. To achieve this, we develop novel experimental and computational tools to quantify cellular physiology and apply genome-wide models of cellular interactions to interpret the large sets of biological data generated from these technologies.

Our interests range from looking at model microbial systems, i.e. Saccharomyces cerevisiae and Escherichia coli, to investigations of mammalian cells such as hepatocytes, adipocytes and myocytes. Beyond large-scale identification of interactions and transcriptional control of network operations in isolated cells, we develop technologies for studying disease phenotypes at the whole organism level. Our results find applications in many areas including industrial biotechnology, e.g. metabolic engineering of microbial cells for the production of biofuels and biochemicals, and medicine, in particular, investigations of human metabolic disorders such as Type-2 Diabetes.



Brian Bahnson
Chemistry and Biochemistry

Structural Enzymology. We are focusing on a group of human HDL and LDL associated enzymes that have direct links to atherosclerosis. Also, one of the systems currently under study is also a promising catalyst for the detoxification of organophosphate neurotoxins. We use a combination of protein expression, site-directed mutagenesis, kinetics, homology modeling and x-ray crystallography to understand the relationship between structure and function for these systems, with goal of either inhibiting detrimental activities or designing more specific catalytic activities.



Thomas Beebe
Chemistry and Biochemistry

Probing receptor interactions on neurons and other cell surfaces directly with the AFM; Development of micropatterned biomaterials and controlled surfaces for cell-surface interactions; Molecule corrals and nanostructures for molecular control; XPS, TOF-SIMS, AFM and other surface-sensitive techniques.



Daniel Carson

Biological Sciences

The extracellular matrix plays key roles in developing tissues, maintenance of tissue function and pathological states such as cancer. Our lab is particularly interested in the role that proteoglycans, mucins and their corresponding binding proteins play in mammalian reproduction and cartilage function. Transgenic mouse models as well as a variety of biochemical and molecular biological approaches are used to study these questions.



Carlton Cooper
Biological Sciences

Bone metastasis is a debilitating complication of advanced prostate cancer. My research focuses on the role cell adhesion plays in prostate cancer preferential metastasis to bone. Presently, we are seeking to identify the cell adhesion molecules (CAMs) involved and how they are regulated by components of the bone microenvironment. In addition, we are interested in the contribution of prostate cancer adhesion to bone matrix components to chemosensitivity and cell survival.



Patricia DeLeon

Biological Sciences

We are interested in candidate or novel genes that play a role in spermatogenesis, epididymal sperm maturation, and fertilization. A major focus is the "germ-cell specific" hyaluronidases of which the Sperm Adhesion Molecule 1 (SPAM1) is the best characterized. Molecular genetic approaches, including gene targeting and transgenesis, are being used to gain insights into the mechanisms leading to sperm dysfunction and male infertility associated with the over-expression of this gene. We are also studying the post-transcriptional control of murine Spam1 as a model of spermatid-expressed genes.



Melinda Duncan

Biological Sciences

Our group is interested in the molecular control of vertebrate eye development and blinding eye disease. Most of our investigations study this process during in the ocular lens, a simple epithelium comprised of two general cell types, lens epithelial cells that maintain the ability to proliferate, and terminally differentiated lens fiber cells which derive from the epithelium. The lens is a particularly good tissue for the study of cellular differentiation since the two cell types are spatially separate and morphologically dissimilar. Further, since abnormalities in lens development do not affect the survival of laboratory animals, it is possible to genetically manipulate pathways controlling lens formation without fear of lethality.



Randall Duncan

Biological Sciences

The primary focus of my research is the study of signal transduction mechanisms involved in the response of musculoskeletal cells to mechanical and hormonal stimulation, concentrating on Ca2+ signaling. This line of research can be divided into three major themes; 1) Mechanotransduction: defining the mechanisms involved in the initial response of musculoskeletal cells to mechanical stimulation, 2) Cytomechanics: examining the mechanical parameters of the cells important in adaptation and return to responsiveness of the cells following chronic mechanical loading and 3) Hormonal Synergy: discerning the mechanisms behind the interaction of calciotropic hormones and mechanical stimulation.



Cynthia Farach-Carson

Biological Sciences

Role of calcitropic hormones in the bone remodeling process, primarily on bone-forming osteoblasts. Interplay between hormonal and mechanical factors in bone health and disease. Role of bone matrix in the progression of cancer following metastasis from primary sites, such as prostate, to bone. Heparan sulfate proteoglycans in bone and cartilage.



Eric Furst

Chemical Engineering

Our research interests lie at the intersection of three major themes: The structure, rheology and phase behavior of complex fluids, such as colloidal and biopolymer systems; Cellular mechanics and movement, including cell rheology and the behavior of cytoskeletal biopolymers and structures; and Interfacial phenomena as they relate to understanding and controlling colloidal interactions and stability. By applying new tools based on single-polymer visualization, microrheology and optical trapping, we have an unprecedented ability to guide the assembly, deform structures, measure stress and study dynamics at a microscopic scale to better understand and control material and biological properties and responses.



Pamela Green

Department of Plant and Soil Sciences and College of Marine Studies

Regulation and Function of RNA: Combining biochemical, molecular genetic, and genomic approaches. Messenger RNA is of critical importance to cells as the key intermediate in gene expression and its abundance usually dictates the amount of protein produced from a gene. Rates of synthesis and degradation both contribute to the abundance of mRNAs, although less is known about how the latter (mRNA stability) is controlled. Interestingly, some genes produce RNA rather than protein as their final product and investigators are just beginning to unravel the roles of such "noncoding RNAs." The Green lab addresses fundamental questions about the control of mRNA stability, RNA-degrading enzymes, and the functional genomics of noncoding RNAs, mainly in the model plant Arabidopsis, but also in yeast and marine organisms.



Xingiao Jia

Materials Science and Engineering

The overall goal of our research is to design and synthesize biomimetic materials with controlled architectures and functionalities for biomedical applications. The first area aims at engineering artificial extracellular matrices (ECM) that are not only reconfigurable and adaptable, but also exhibit desired mechanical properties that are conductive to tissue growth. The second research area is soft tissue engineering, with an emphasis on vocal fold tissue regeneration. We are evaluating vocal fold biomechanics at both cellular and tissue levels. We are also studying vocal fold ultrastructure from molecular level up to macroscopic scale. This knowledge will be applied to the design of functional vocal fold substitute materials.



Murray Johnston

Chemistry and Biochemistry

Protein characterization by mass spectrometry. Multidimensional peptide and protein separations coupled to mass spectrometry; high throughput proteomics using two dimensional gel electrophoresis and mass spectrometry; protein identification, structure elucidation and de novo sequencing by mass spectrometry; matrix-assisted laser desorption ionization, electrospray ionization, and tandem mass spectrometry methodology.



Kristi Kiick

Materials Science and Engineering

Protein based materials; de novo design of artificial protein polymers; protein-saccharide self-assembling hydrogels; drug delivery matrices; biopolymer processing; light-emitting biopolymers. Protein engineering methods provide a powerful synthetic method for producing polymeric materials whose structure and composition are precisely controlled. Our group utilizes a combination of protein engineering and chemical strategies to design and synthesize novel macromolecules for applications in biology and materials science. Potential applications include toxin neutralization, mediation of chemotactic events, drug delivery, growth factor delivery for biomaterials applications, light-emitting diodes, and self-assembled materials.



Eric Kmiec

Biological Sciences

The research focus of this laboratory, centers on the development of novel DNA or RNA molecules that can direct genetic changes in the chromosomes of mammalian cells and animal models. We use biochemical and genetic tools to study the mechanism by which these changes occur and how the cell regulation this process. Presently, the vector of choice is a single-stranded DNA oligonucleotide that mediates the correction of single base mutations using the endogenous DNA repair and recombination activities. The repair of single base mutations by these oligonucleotides is being tested as a gene therapy approach for several inherited disorders.



Jung-Youn Lee

Plant & Soil Science

Intercellular communication is fundamental to every living organism for their survival. Both animals and plants have evolved unique systems that provide cytoplasmic passageways for ions, metabolites and small signaling molecules between cells. In plants, the cytoplasmic channels are called plasmodesmata. Fascinatingly, plasmodesmata have the additional capacity to mediate trafficking of macromolecules such as proteins and various forms of RNA. We are exploring the molecular mechanisms and players involved in macromolecular trafficking through plasmodesmata to better understand the role of plasmodesmata in this event and in plant growth and development.



Abraham Lenhoff

Chemical Engineering

Applied protein biophysics; fundamentals of separations processes; protein interactions with surfaces and in solution; protein thermodynamic properties and phase behavior; crystallization and precipitation; fundamentals of protein chromatography.


Kelvin H. Lee
Chemical Engineering

With the right tools, one can identify the genetic basis for many different phenotypes or disease states. Our research laboratory is focused on the development of next generation tools for protein expression profiling and the use of existing tools applied to specific problems in biomolecular engineering and medicine. Our current areas of focus include: 1) the use of proteomics in support of a passive immunization clinical trial for the treatment of Alzheimer's disease; 2) the study of enhanced heterologous protein secretion in bacterial and mammalian cells including a detailed understanding of protein translation; and 3) the development of nanoscale materials and technologies for protein separation. We rely heavily on computational methods as well as biological mass spectrometry and we actively pursue both gel-based as well as shotgun-based proteomics approaches.



Li Liao

Computer and Information Sciences

We are interested in developing computational tools-particularly by incorporating the domain specific knowledge - to solve biological problems. Our current research is focused on detecting the sequential and structural features of proteins, and using them to identify and understand relationships among proteins. Our work includes graph-theoretic clustering algorithms to tackle multi domain proteins; support vector machines combined with pair wise similarity and phylogenetic information to detect more remote homology; and hidden Markov models to predict transmembrane protein topology.



Blake Meyers

Plant & Soil Science

We work in two areas of plant molecular biology. We use a novel technology called 'massively parallel signature sequencing' for genome-wide transcriptional analysis of mRNA and small RNAs in Arabidopsis and rice. This requires a number of bioinformatics tools and approaches for handling and analyzing the data. We have described novel patterns and types of gene expression, and we are experimentally validating these results. The second research project is characterizing the function and evolution of two families of Arabidopsis genes. Sequence similarities, inferences from animal innate immune signaling systems, and gene clusters suggest that these two families of genes function in plant disease resistance signaling. These plant proteins may be components of an ancient host defense system that evolved prior to the divergence of plants and animals.



Ulhas Naik

Biological Sciences

Our research interest is to understand the molecular mechanism of signal transduction involved in cardiovascular disease and cancer. Cell-cell interactions and cell-extracellular matrix interactions play key roles in these diseases. One of our research interests is studying the molecular mechanisms involved in platelet aggregation (initiation of thrombus). Understanding the signaling events involved in this process may help develop remedies that target myocardial infarction and stroke. Another area of interest is to elucidate the role of cell adhesion molecules belonging to the immunoglobulin superfamily in tumor-induced angiogenesis. Our studies routinely involve cell and molecular biological techniques as well as knock-out animal models to better understand the molecular mechanisms involved in pathological angiogenesis.



Sharon Neal

Chemistry and Biochemistry

Our goals are to develop multidimensional fluorescence techniques and multivariate data analysis methods to monitor dynamic interactions in microheterogeneous biological media, such as model membranes and membrane bound or associated proteins using multi-state, microenvironment-sensitive probes. We are combining a variety of fluorescence measurements, including spectral, photokinetic, anisotropy and energy transfer measurements, into multidimensional methods for simultaneous monitoring of multiple excited-state interactions between probe molecules and biological systems. Currently, we are using these methods to investigate temperature-induced changes in mixed lipid aggregates (bicelles) and chemically induced changes in proteins.



Babatunde Ogunnaike

Chemical Engineering

Our research efforts are organized around the general theme of first understanding the dynamic behavior of complex systems through mathematical modeling and analysis, and then exploiting this understanding for novel designs and improved operation. The particular complex systems of interest range from polymer reactors, particulate processes and extruders, to biological systems on the cellular, tissue, and organ levels. When sufficient fundamental knowledge is available, we develop and employ dynamic “mechanistic” models; when more data is available than fundamental knowledge, we apply probability theory and statistics for efficient data acquisition and “empirical” model development.



Darrin Pochan

Materials Science and Engineering

We are exploring the rules underlying the molecular design and self-assembly of unique biopolymeric and bioorganic-inorganic hybrid materials. Biomaterials are being constructed via the design and self-assembly of polypeptide molecules taking advantage of the large tool box of inter/intramolecular interactions and molecular conformations available in peptides. Ultimately, secondary structure phase transitions and specific interactions sensitive to their environment will produce materials whose structure, and consequent function, will be sensitive to desired environmental cues. A variety of microscopy (transmission and scanning electron, optical, laser scanning confocal and atomic force/surface probe) and scattering (small- and wide-angle x-ray and neutron) techniques are used to elucidate bulk, solution, and thin film structures. In addition, the cell and tissue level biological properties (e.g. biocompatibility/cytotoxicity) of materials are assayed in a new cell culturing lab located in the Delaware Biotechnology Institute.



John Rabolt

Materials Science and Engineering

The Rabolt group investigates the assembly of engineered proteins into fibers to create novel biomimetic materials. The group is expert at development of vibrational spectroscopic methods for "real time" probing of the evolution of microstructure in commercially melt spun and electrospun fibers. They collaborate with Bruce Chase (DuPont) and Richard Ikeda (Adjunct Professor - MSE and DuPont - Retired)] to study commercially important systems.


Christopher Roberts

Chemical Engineering

Research in Dr. Roberts’ laboratory is centered on bio-physical chemistry and modeling of protein degradation; both in solution and in amorphous solids typical of commercial protein products. There is particular emphasis on understanding protein aggregation and other degradation routes from the perspective of interactions between non-native proteins, solvent-mediated and solute-mediated forces, the interplay between chemical and physical degradation routes, and the influence of conformational state on reactivity.


Anne Robinson
Chemical Engineering

Our laboratory is taking two approaches to increase our understanding and ability to control molecular interactions and cellular functions: 1) Examining proteins in isolation to identify important interactions in folding and assembly in an effort to control those interactions to optimize this process. 2) Identifying interactions in the cell that control protein expression, and altering the interactions to maximize production of functional proteins. Our research is focused on expression of membrane proteins (G-protein coupled receptors), characterization of the stress response in yeast, and characterization and reversal of misfolded proteins (antibodies and membrane proteins).



Joel Schneider

Chemistry and Biochemistry

Our research entails the de novo design of functional peptides and proteins. Ongoing efforts are highly interdisciplinary and span historically disparate disciplines of science such as materials science, inorganic and organic chemistries, chemical synthesis and biophysics. As chemists, we are not limited to the naturally occurring amino acids in our designs and we often incorporate non-natural residues, which we design and synthesize, into peptides and proteins to impart unique structural and functional properties. General design strategies for the preparation of peptide-based antibiotics, recognition motifs for protein folding specificity, peptide and organoarsenical-based probes, as well as bio-inspired materials are actively being pursued in the Schneider Lab.



Erica Selva

Biological Sciences

Posttranslational modification of extracellular molecules has recently been shown to play a crucial role in the temporal and spatial regulation of signal transmission by altering extracellular receptor-ligand interactions. The objective of my research is to use Drosophila melanogaster as a model system to study the function of posttranslational changes that influence developmentally critical signaling events.



Janine Sherrier

Plant and Soil Sciences

Our research focuses on the formation and function of a novel membrane in nitrogen-fixing root nodules, the symbiosome membrane. This membrane is derived from the plant plasma membrane and becomes specialized during root nodule development. Our goal is to understand how this unique membrane is formed and how its protein content influences nodule function. The results from this work will help us understand interactions of plants with soil microbes, development of plant tissues, and targeting of proteins within plant cells. Our group utilizes a wide spectrum of methods to study this fascinating membrane. These include biochemistry, molecular biology, cell biology, biotechnology, and classic botany.



Robert Sikes
Biological Sciences

My research is focused around the normal development of the mouse prostate and the development and progression of prostate cancer. Voltage-sensitive sodium channels (VSSCs) are transmembrane ion channels that open in response to membrane depolarization. My lab has been screening novel inhibitors of voltage-gated sodium channels (VGSC) for anti-tumor effects. Several lead compounds are now in preclinical animal testing The promising inhibitory results have shifted our attention on the biology of VGSCs in the metastatic phenotype. This includes cell motility and the role of VSSC in neuroendocrine differentiation of the prostate.


Daniel Simmons

Biological Sciences

Our laboratory is interested in the structure and function of the simian virus 40 tumor antigen (T antigen) and of cellular proteins that interact with it in virus infected and transformed cells. T antigen is a multifunctional phosphoprotein synthesized early in SV40 infection. It is required for virus DNA replication and for the regulation of viral gene expression in infected cells. The protein is also required for the induction and maintenance of malignant transformation of nonpermissive cells. By using a multifaceted biochemical and genetic approach, we are investigating the fine structure and activity of various functional domains of T antigen and correlating this information to the biology of SV40. Our present effort is focused primarily on T antigen's role in the initiation and elongation phases of SV40 DNA replication.



Millicent O. Sullivan

Chemical Engineering

The goal of our research is to design improved biomolecular strategies for therapeutic payload delivery to pre-determined cellular/sub-cellular locations. While a variety of drug and DNA packaging methods exist, what is missing are systematic studies of the processing and fate of these packages by and within cells, and a strong mechanistic link between materials design and the expected interactions within the extra- and intracellular environments. Materials evolution could render a delivered therapy ineffective, or conversely, might enhance drug transport or utilization. The emphases of our program: 1) To promote improved understanding of how the chemical and physical interactions between nanomaterials and the intracellular environment affect material stability, structure, and fate. We employ readily manipulable nanomaterial systems to systematically investigate how different material properties are affected by the environment. 2) To enable rational/predictive design of drug delivery nanomaterials by applying our understanding of the subcellular environment to pre-programming desirable material responses. These responsive biomaterials are applied to solving critical problems in drug/gene delivery.


Other FACULTY


Stephen Bernhardt

English

Professor Bernhardt's research interests center on visual rhetoric, computers and writing, workplace training and development, and the teaching of scientific and technical communication. As consultant to the pharmaceutical industry, he helps such companies as Pfizer, Schering-Plough, and AstraZeneca design large documentation sets, use global teams and technologies, deliver training programs, and improve written communication as a part of new drug development and registration.



Samuel Gaertner

Psychology

I am interested in intergroup relations and in particular, how prejudice, discrimination and intergroup conflict can be reduced. My current research explores the possibility that inducing the members of two groups to conceive of themselves as a single, more inclusive group or as subgroups within the same inclusive group structure (i.e., a dual identity), can harness cognitive and motivational processes that encourage more harmonious intergroup relations.



John Sawyer

Business Administration

Dr. Sawyer investigates the effects of individual characteristics and group processes on creativity and organizational innovation. His current research includes a qualitative and quantitative meta-analysis of creativity research and development of procedures for enhancing R&D productivity. Additionally he is currently investigating information sharing and integration in cross-functional, racially diverse decision making groups, and the impact of virtual teamwork on knowledge transfer and problem solving. Past empirical research on teams included the effects of social uncertainty on group member's allocation of time and effort to group tasks. Other published work includes studies of the effects of ambiguity and uncertainty on individual judgment processes and their impact on individual behavior, resource allocation decisions, work behaviors, work performance and attitudes.

IGERT :: Contact us :: University of Delaware, Newark, DE 19716 :: P302-831-3067 :: F302-831-1048