Graduate Faculty Research Interests
MS in Biochemistry and Molecular Biology
Visit the MS in Biochemistry and Molecular Biology program page for more information about how to apply, curriculum, and outcomes.
Biochemistry and molecular biology of parasitic protozoa, particularly Cryptosporidia sp., and Human African Trypanosomes (HAT). My research has resulted in the development of a new class of compound, the oxaboroles, to treat HAT that is currently in phase II clinical trials in Africa. I am also developing a novel culture system to facilitate the screening of novel compounds for the treatment of cryptosporidosis.
The electrical activity of nerve cells underlies brain function. This electrical activity arises when ions (e.g. calcium) surge into or out of nerve cells through ion channels - specialized proteins embedded in the cell’s membrane. There are hundreds of different ion channels that control brain functions such as vision, hearing, memory formation, neurotransmitter release, and muscle control. Not surprisingly, many neurological and cardiovascular diseases are caused by mutations in ion channels. One of our main interests is to investigate how mutations alter ion channel function: Does the mutant channel not open? Does it open faster than normally? Is it not desensitizing as it should? Can the difference between normal and mutant channels explain human disease? rsuing these questions not only helps us understand human disease, but may also point to cures. Indeed, 20% of all drugs target ion channels. Thus, another area of interest in my laboratory is neuropharmacology. We study the behavior of different ion channels in the presence of drugs, plant extracts or other chemicals. Students are guided through literature searches, some bioinformatics, cutting edge molecular biology tools, pharmacology and, most importantly, electrophysiology, giving rise to an exciting journey of research for the benefit of humankind.
My research is at the interface of molecular ecology and ecological genetics. That is, I use molecular tools to understand ecology, and I study how genomes evolve in response to the environment. More specifically, I am interested in how freshwater fish polations adapt to environmental stressors, including hypoxia and pollution. I am most interested in questions revolving around the role of phenotypic plasticity in adaptation, and how phenotypic plasticity evolves, through examination at both the molecular and phenotypic levels.
Effects of Bromelia pinguin (Bromeliaceae) on soil ecosystem function and fungal diversity in the lowland forests of Costa Rica
Understanding the interaction between mycobacteria and small molecules produced by the human immune response.
The nature and regulation of the various cellular processes of fertilization, including the development of fertilization competence, gamete signaling, sperm-oocyte fusion, the oocyte to embryo transition, and production of an eggshell to protect the developing embryo in Caenorhabditis elegans.
Significant variations in digestive tissue oxytocin (OT) concentration have been observed in fasting male rats when compared to controls. The following experimental groups are employed: ab lib (full access to feed and water) fasted with subsequent food
Understanding the biochemistry of DNA-processing enzymes. His lab studies the enzyme topoisomerase IA an enzyme of prokaryotic organisms which manages the supercoiling generated during transcription.
Many proteins that control cell division are involved in cancer development. The phosphorylation state of the Retinoblastoma protein (Rb) regulates the ability of this protein to control cell proliferation.
Vertebrate behavior and sensory ecology with a focus on animal communication. The objective of my research program is to increase our understanding of how both proximate and ultimate factors, including adaptations facilitating the detection and assessment of biologically relevant sensory information, can shape the communication systems of animals.
The regeneration of sensory systems, with emphasis on sensory hair cells. These cells transduce mechanical forces in the inner ear into electrical signals that can be received and interpreted by the brain, and are responsible for our senses of hearing and balance. Hair cells are delicate and can be damaged or destroyed by loud noises and certain medicinal drugs. In humans and other mammals these cells are not naturally regenerated, leading to hearing loss. Fishes and other non-mammalian vertebrates, however, naturally regenerate hair cells throughout life. Dr. Steiner uses the zebrafish as a model system to understand the cellular and molecular processes that enable hair-cell regeneration in such animals, with the goal of identifying new routes to inducing hair-cell recovery in the human ear. His group utilizes the tools of molecular biology, advanced microscopic imaging, and large-scale gene expression analysis to reveal and characterize genes that regulate regeneration.
The symbiosis of the Hawaiian Bobtail Squid and the bioluminescent bacteria, V. fischeri in the hope of shedding some light on human bacterial infections.
Computational chemistry using sophisticated software such as GAMESS-US to derive the DFT geometry optimization for the calculation of molecular orbitals. Identification of active sites using HOMO and LUMO orbitals and docking experiments.
My current research interest focuses on microbial interactions with their environments and other microbes through cell surface proteins. The integration of molecular, chemical, and functional analyses is employed to understand how the environment affects the protein’s adherence property. Another area of interest focuses on the use of different amyloid-perturbing compounds to inhibit cell-to cell and cell-to-surface interactions. Understanding how the environment affects the amyloid region of the adhesion molecules is importance in shaping the medical treatment of biofilm formation.
My goal as a scientist is to study how enzymes and other proteins impact the growth of biologically relevant materials while mentoring undergraduate and masters students in both research and professional development. The study of biomineralization, or the mineralization processes of the living world, is a fascinating field that may offer insights into medicine and materials science. While many groups have studied the intrinsically disordered proteins (IDPs) associated with biomineralization, the investigation of the enzymes involved in such processes is relatively new and underrepresented in the literature. One exciting family of proteins, the silicateins, has been shown to both scaffold and catalyze the formation of intricate biosilica skeletal structures in sea sponges. Understanding how to manipulate the protein structure of silicateins to adopt new scaffolding or enzymatic properties and characterizing the silica precipitates from such systems would allow for students to gain hands-on experience: (1) expressing, purifying, manipulating, and characterizing proteins, (2) developing and refining silica mineralization assays in the absence and presence of proteins, (3) performing scanning and transmission electron microscopy along with atomic force microscopy and focus-ion beam milling, and (4) critically analyzing a complex and highly interdisciplinary data set in order to interpret results. The study of how silicatein and other biomineralization proteins impact the nucleation and growth of carbonates, phosphates, and silicates may enhance fundamental knowledge and translational applications in areas such as regenerative medicine and biomimetic materials.
Design and development of sensory systems for trace analytes that are of environmental, biological and forensic interest. Potential analytes include mercury, lead, zinc, copper, dioxins.
Computational chemist/biophysicist. Specializing in using molecular simulation and statistical mechanics to study the structure, dynamics and interactions in biomolecular systems.
Experienced in protein-ligand binding, free energy methods, structure-based drug design, Markov state model, protein dynamics, protein-protein interaction, nucleic acids simulation, force field development, scientific computing, programming and numerical algorithms.
Development of antimicrobial agents attached to different surfaces. Her research has resulted in the attachment of antimicrobial agents to military clothing, filtration systems, etc. Students involved in this research will be involved with the DNDi Open Source Program.
My research deals with monitoring the interaction of biomolecules (protein/enzymes) with the chemicals commonly found in the environment specifically the co-called emerging contaminants. I also work on the amyloid formation process screening different phenolics that inhibit the process for possible therapeutic remedies for degenerative diseases. These are all done using spectroscopic methods such as absorbance, fluorescence, IR and Raman.
Dr. Upmacis’ research focuses on investigating factors that lead to oxidative and nitrative stress under conditions of inflammation during disease states and also infections. Oxidative and nitrative stress occurs when there is an overproduction of reactive oxygen and nitrogen species that can act together to cause toxic effects in cells and contribute to inflammation. Recent research has examined the products formed when certain omega-3 polyunsaturated fatty acids, found in fish oils, scavenge oxygen. In addition, the effects of omega-3 polyunsaturated fatty acids and their oxidized products on parasite survival are under investigation.
Dr. Walczak's research interests include many aspects of theoretical and comtational nanophysics. His projects are related to sophisticated modeling and high-fidelity simulations of quantum transport phenomena as well as noise properties of molecular systems. Currently, he is working on multiscale transport theory and non- Fourier energy transfer with their applications in green nanotechnology and biophysics.
Hydrogel/lipid membrane assembly: modeling membrane system of cell; hydrogel nanoparticles, lipogels, nanofilms, liposomes. and lipid membrane synthesis manilation and characterization; synthetic and natural ionic reservoirs; bioanalytical devices, drug delivery and control release systems
Mohsen Shiri-Garakani, PhD
Chemistry and Physical Sciences
Quantum Spacetime, Unified Gravity, Foundations of Quantum Theory, Quantum Logic, History and Philosophy of Physics, Applications of Physics in Complex System Theory.