Spindle microtubule, microtubule motor and kinetochore mechanics for accurate chromosome segregation. We are also developing new fluorescence microscopy and electronic imaging methods for assays of protein function in living cells.
We are engaged in studying the molecular biology of the human parvovirus adeno-associated virus (AAV) with the intent to using this virus for developing a novel, safe, and efficient delivery system for human gene therapy.
We have three main areas of research focus: (1) Nucleotide excision repair: The only known mechanism for the removal of bulky DNA adducts in humans. (2) DNA damage checkpoints: Biochemical pathways that transiently block cell cycle progression while DNA contains damage. (3) Circadian rhythm: The oscillations in biochemical, physiological and behavioral processes that occur with the periodicity of about 24 hours.
Our long term goals are to better define mechanisms of chronic intestinal inflammation and to identify areas for therapeutic intervention. Research in our laboratories is in the following four general areas: 1) Induction and perpetuation of chronic intestinal and extraintestinal inflammation by resident intestinal bacteria and their cell wall polymers, 2) Mechanisms of genetically determined host susceptibility to bacterial product,. 3) Regulation of immunosuppressive molecules in intestinal epithelial cells and 4) Performing clinical trials of novel therapeutic agents in inflammatory bowel disease patients.
Cell adhesion controls cellular functions implicated in human disease, e.g. cancer. FAK, a tyrosine kinase, is a major component of this signaling pathway. We study the function and molecular mechanisms by which FAK controls these events.
My lab is interested in mechanisms that (1) fine tune gene expression and (2) coordinate transcription and RNA processing in eukaryotes. Our work is based on molecular, genetic and biochemical analysis of the suppressor of sable gene of Drosophila.
Movement control and neuroplasticity in able-bodied humans and humans with neurological dysfunction are the focus of research program. More specifically, would like to understand the basic interaction of spinal circuits and supraspinal systems and adaptability of these interactions during upper limb movements and locomotion. Studies to understand this interaction include anatomical (dissection and MRI), electrophysiological (EMG and reflex) and biomechanical studies to identify the neuromuscular elements that interact with spinal circuits, and what principles govern their coordination. Studies are also underway to understand plasticity of spinal circuits, including those underlying stretch reflexes in both able-bodied humans and humans with spinal cord injury. These studies utilize operant conditioning of reflexes that may be useful for the functional training of newly formed connections in spinal cord injured patients if regeneration can be induced. The operant conditioning studies will also be useful in determining the relationship of spinal circuits and voluntary movement.
Genome instability is a major cause of cancer. We use the model organism Drosophila melanogaster to study maintenance of genome stability, including DNA double-strand break repair,
meiotic and mitotic recombination, and characterization of fragile sites in the genome. Our primary approaches are genetic (forward and reverse, transmission and molecular), but we are also using biochemistry to study protein complexes of interest, genomics to identify fragile sites and understand the regulation of meiotic recombination, fluorescence and electron microscopy for analysis of mutant phenotypes, and cell culture for experiments using RNA interference.
Research interests center around interactions between xenobiotic compounds (ambient and indoor air pollutants as well as food allergens) and the immune system and consequent effects on infectious and allergic disease. The laboratory has developed several rodents models of infetious and allergic disease. The focus is to understand the effects that exposure to environmental agents may have on both local and systemic immune responses, the underlying mechanisms associated with these effects, the consequent impact on susceptibility to disease, and the relationship between rodent data and human health effects.
Our laboratory is involved in studies to determine the mechanisms and proteins involved in the migration of alloreactive and regulatory T cells to organs involved in graft-versus-host disease after stem cell transplantation using mouse models.
The primary research projects in my lab span topics from evolutionary genetics to behavioral ecology. Prior, current and future projects of mine focus on theoretical studies of speciation and reinforcement but include work on mate choice, learning and imprinting, aposematic coloration, and brood parasitism. My main goal is to use mathematical models to integrate rigorous evolutionary theory with hypotheses explaining behavioral and ecological patterns and phenomena.
The lab relies on murine genetic approaches to study the roles of the INK4/ARF tumor suppressor locus in human cancer and aging. At present, the lab has two main focuses:
Stem Cell Aging:
Cancer and degenerative diseases are much more common in old people than young. Although this has been well-recognized in clinical medicine for decades, scientists do not agree as to why this occurs. Recently, work from several labs including our own has shown that humans age, in part, because important regenerative cells lose their capacity to divide with the passage of time. That is, the tissues and organs from old people are less able to replace and regenerate lost or damaged cells than the corresponding tissues and organs from young people. Our lab has studied mechanisms that underlie this age-dependent failure of cell division; in fact, we have shown the surprising result that cellular programs that function to prevent cancer untowardly also calls aging. Specifically, cellular “senescence” is now believed to be of major importance in the process of aging. Senescence refers to a permanent growth arrest induced in formerly dividing cells by the activation of genes that prevent cancer. The good news in this system is that the normal functioning of these ‘tumor suppressor genes’ prevents cancer; the bad news is that these same genetic events appear to cause aging by activating cellular senescence.
Melanoma and Murine Models of Cancer:
Because of the important role of p16INK4a in preventing melanoma, the lab has long been interested in this particularly deadly form of skin cancer. Specifically, we are interested in using genetically engineered models of cancer to study melanoma genetics. We have shown a role for the p16INK4a-RB and ARF-p53 tumor suppressor pathways in repressing this important human cancer in response to RAS-RAF activation. We have generated highly faithful models of human melanoma, and have used these to study novel therapeutics. We have also discovered a novel human melanoma sub-type based on expression profiling, and have identified a new therapeutic target (CD200) for treatment of melanoma.
My work is centered upon the characterization of the large mucin gene products and the complexes they make which are essential for the formation of the mucus gels vital for epithelial protection and function. This work is focused around the human lung where there are many human diseases including asthma, cystic fibrosis, and chronic bronchitis in which these glycoconjugates are centrally implicated. Our studies are broad ranging and seek to build up a picture of the chemistry of these complex phenotypes, the network of their interactions that constitutes a mucosal surface and the mechanisms of their biosynthesis, assembly and secretion. The laboratory is established with a wide range of methods including MALDI and ESI mass spectrometry, electron and atomic force microscopy, hydrodynamics, theoretical molecular dynamics and a variety of surface physics tools.
Regulator of G-protein signaling (RGS) proteins accelerate the GTPase activity of G-alpha subunits and thereby act as critical negative regulators of hormone and neurotransmitter signaling via G protein-coupled receptors. Our lab first recognized the existence of these critical signaling regulators in 1996. We continue to study their structural and functional diversity, as well as their roles in physiological and disease processes, including immunity, oncogenic transformation, and pain processing.
Our lab examines cytoskeletal dynamics, the molecules that regulate it and the biological processes it is involved in using live cell imaging, in vitro reconstitution and x-ray crystallography. Of particular interest are the microtubule +TIP proteins that dynamically localize to microtubule plus ends, communicate with the actin network, regulate microtubule dynamics, capture kinetochores and engage the cell cortex under polarity-based cues.
Dr. Smiths research interests are in correlating pharmacokinetics and metabolism of drugs with their pharmacodynamics and toxicity. Research efforts in this area include in vitro studies and in vivo animal experiments aimed at understanding mechanisms of processes that influence drug disposition and toxicity. Where possible, transitional studies in human subjects are conducted to demonstrate clinical relevance and the potential application to humans. A primary emphasis in the laboratory is the process of glucuronidation, the major Phase II metabolic pathway where the sugar, glucuronic acid, is coupled to drugs and other xenobiotics.
Correction of genes with mutant pathologies (gene therapy); construction of animal models of human genetic diseases to facilitate better studies of the resultant pathology and develop new modes of treatment.
Work in my laboratory is directed at the role of neuronal growth factors in the development and regeneration of axons. We employ sensory neurons of the DRG as a model system. Sensory neurons are unique in elaborating a peripheral axon that regenerates readily after injury and a central axon projecting in the spinal cord that does not. This work is directly relevant to a major NINDS goal of achieving spinal cord repair.
My primary research area is computational geometry, in which one studies the design and analysis of algorithms for geometric computation. Computational geometry finds application in problems from solid modeling, CAD/CAM, computer graphics, molecular biology, data structuring, and robotics, as well as problems from discrete geometry and topology. Most of my work involves identifying, representing, and exploiting geometric and topological information that permit efficient computation. My current focus is on applications of computational geometry in Molecular Biology and Geographic Information Systems (GIS). Examples of the former include docking and folding problems, and scoring protein structures using Delaunay tetrahedralization.
I study the ultimate and proximate factors controlling flexibility in reproductive behavior. Using songbirds as a system, I use field and laboratory studies to investigate the ecological cues regulating reproductive flexibility, the neural integration of these cues, and the neural mechanisms precipitating adaptive behavioral outcomes. Of particular interest is the study of courtship and mate-choice behavior and how the songbird brain integrates ecological and social information. I am also interested in how the timing of reproduction, reproductive effort, and family planning are controlled. I use high performance liquid chromatography for the measurement of central catecholamines and immunocytochemistry and microscopy for quantifying neuropeptides and the expression of immediate early genes as markers of neural activity.
Our laboratory studies signal transduction systems controlled by heterotrimeric G proteins as well as Ras-related GTPases using a variety of biophysical, biochemical and cellular techniques. Member of the Molecular & Cellular Biophysics Training Program.
We are combining biochemistry and molecular biology to study protein synthesis in mammalian mitochondria. Factors required for the initiation and elongation steps of have been cloned and detailed protein chemistry is being carried out to study their properties. Mutations of several of these proteins are lethal in humans and these mutations are being studied to study the interactions of these factors with ribosomes and the structures of these factors bound to ribosomes are being examined using cryoelectron microscopy. Chemical probing is being used to explore the structures of mitochondrial mRNAs. The tRNAs in mammalian mitochondria are quite unusual and mutations in them can cause human diseases. The underlying defects in these tRNAs are being probed at structural and biochemical levels providing an understanding of how the mutations lead to human disease.
My laboratory at present is working on the vitamin K cycle and vitamin K-dependent proteins. The enzymes of the vitamin K cycle include, at a minimum two integral membrane proteins, both of which were purified and cloned by my laboratory. One, the vitamin K epoxide reductase is the target of warfarin for which 40 million prescriptions are written each year in the US alone. Polymorphisms in this gene are the best example to date of the use of genomics in molecular medicine. We are also interested in purifying any additional components of this cycle and trying to understand the ~50% of patients whose genotype is not informative about warfarin dose. In addition, we are interested in the mechanism of how factor VIIa works and the role of the extracellular matrix in coagulation.
Our laboratory is examining the role of histone post-translational modifications in chromatin structure and function. Using a combination of molecular biology, genetics and biochemistry, we are determining how a number of modifications to the histone tails (e.g. acetylation, phosphorylation, methylation and ubiquitylation) contribute to the control of gene transcription, DNA repair and replication.
Research interests involve metabolic interactions of essential microelements, especially trace metals, with toxic metals and metalloids that contaminate food chain and drinking water reservoirs. Research topics include: the interactions between selenium, an essential micronutrient, and arsenic, an environmental contaminant and human carcinogen; the enzymes and co-factors involved in the metabolism of arsenic and selenium; the mechanisms of arsenic- induced diabetes; and, the role of nutritional antioxidants and antioxidant enzymes in responses to the oxidative stress induced by exposure to environmental toxins, by viral infections or nutritional deficiencies.
My laboratory studies development and function of the human immune system and human liver, and HIV-1/HCV infection and immuno-pathogenesis. 1. Humanized mouse models to study human hamatopoietic stem cells (HSC), thymus and liver stem cells. 2. FoxP3 and regulatory T (Treg) cells in viral infection and immuno-pathogenesis. 3. Modeling immuno-pathogenesis and immuno-therapy of chronic HIV and HCV.
Research in my laboratory is directed toward achieving a better understanding of the mechanisms and pathogenesis associated with a variety of environmentally induced or genetically based birth defects. This information is then applied to development of preventative/ameliorative measures relative to these defects. Our interest in modeling human genetic malformation syndromes and opportunities for collaborative efforts with molecular geneticists who have produced transgenic mice and mice with targeted gene modification have proven productive in our attempt to better understand the developmental basis for a variety of malformations of the brain including anencephaly, holoprosencephaly, and hydrocephaly. Regarding teratogen-induced birth defects, our major emphasis is on Fetal Alcohol Spectrum Disorders (FASD). Currently, high resolution magnetic resonance imaging (MRI) is being utilized to identify, characterize, and correlate the craniofacial, ocular, otic and CNS dysmorphology that results from prenatal ethanol exposure at specific stages of embryogenesis. These studies are designed to inform human clinical research and to expand the diagnostic criteria for prenatal alcohol exposure.
I study complex traits using linkage, association, and genetic epidemiological approaches. Disorders include schizophrenia (etiology and pharmacogenetics), smoking behavior, and chronic fatigue.
The mechanical properties, force response and force generating mechanisms of biological systems is of great interest for physiological function, for tissue engineering and embryogenesis and for drug delivery. In collaboration with the Computer Science Department, we develop and apply new technologies for applying and measuring forces on single molecules, cells and tissue cultures. In collaboration with the departments of Mathematics, Computer Science, Chemistry and the UCN Cystic Fibrosis Center we are pursuing an integrated computational model of mucus clearance in the lung. Affiliated with the Molecular & Cellular Biophysics Training Program.
FFirst, we study the complex HIV-1 population that exists within a person. We use this complexity to ask questions about viral evolution, transmission, compartmentalization, and pathogenesis. Second, we are exploring the impact of drug resistance on viral fitness and identifying new drug targets in the viral protein processing pathway. Third, we participate in a collaborative effort to develop an HIV-1 vaccine. Fourth, we are using mutagenesis to determine the role of RNA secondary structure in viral replication.
My laboratory focuses on understanding mechanisms of carcinogenesis, with emphasis on the role of DNA damage and repair. During the last few years, we have developed ultra-sensitive and highly specific mass spectrometry methods for measuring the DNA and hemoglobin adducts of vinyl chloride, crotonaldehyde, ethylene oxide, propylene oxide, styrene oxide, butadiene, malondialdehyde, cis-platin and O6-methyldeoxy-guanosine, as well as slotblot methods for AP sites and oxidative DNA damage. These methods have been applied to understanding critical mechanisms in carcinogenesis, as well as undertaking molecular epidemiology studies of workers in the butadiene and reinforced plastics industries. We are also examining changes in gene expression associated with oxidative stress and environmental chemical exposure.
