Control of Gene Expression and Cellular Programming|
Molecular mechanisms of aging and caloric restriction |
Assistant Professor of Physiology The Baur lab is interested in the basic mechanisms that lead to aging. Age is the most important risk factor for many of the diseases affecting Western society today, including cancer, cardiovascular disease, and neurodegenerative disorders. |
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Role of adaptors in regulation of transcriptional activation in yeast and humans |
Daniel S. Och University Professor, Department of Cell & Developmental Biology Our research focuses on regulation of the nuclear genome in mammals and model organisms. The long strands of nuclear DNA are associated with packaging proteins, called histones, into a structure known as chromatin, akin to the way thread is organized around a spool. We are particularly interested in changes in this chromatin structure via chemical modification of the histone proteins, and how attachment of certain chemical groups onto the histones leads to altered chromatin function. These targeted structural changes are conceptually like the unraveling of the thread to reach specific, buried sections. We are also fascinated by functional changes in chromatin, caused by these histone modifications, that persist through cell division from one cell into two daughter cells; these persistent, or epigenetic, changes are of particular interest because they are key to normal and abnormal growth: they occur during organismal development into multicellular tissues and organs, and are typically disrupted during abnormal reversal of tissue specialization and growth control as in cancer, as well as during aging of cells and individuals. |
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Molecular basis for intracellular signaling in vascular biology |
Professor of Medicine, Pathology and Laboratory Medicine, and Pharmacology Most of the work we are currently doing is devoted to understanding the molecular basis for platelet activation in vivo. Individual projects are looking at the role of heterotrimeric G proteins in initiating platelet activation, low molecular weight GTP-binding proteins in fostering integrin activation, and Eph kinases in maintaining platelet activation. The actual studies are being done in vitro using isolated human platelets and transfected cell systems, and in vivo using genetically engineered mice. |
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Genetic and mechanistic studies of viral-host interactions |
Assistant Professor of Microbiology Research in the Cherry lab is aimed at identifying cellular factors that
regulate viral pathogenesis, including both those factors hijacked by
viruses for replication and those innate anti-viral mechanisms used by
the host to combat the invader. To identify these factors we are taking a
genetic approach by screening for factors that impact viral
replication. To this end, we are using the model genetic organism
Drosophila. This allows us to use a wide-variety of techniques to
identify these genes including both high-throughput RNA interference
screens in cell culture, and forward genetic screens in animals.
Moreover, we are also screening for host factors in human cells using
high-throughput RNA interference screening technologies. We are using
these approaches to study a number of arthropod-borne RNA viruses,
including the flavivirus West Nile virus, the alphavirus Sindbis and the
bunyavirus Rift Valley Fever virus. These are the three major families
of viruses that are important human pathogens transmitted by mosquitoes
to humans. By screening in both hosts- insect and human- we hope to gain
a more comprehensive understanding of the host factor requirements of
these pathogens. We are currently characterizing the roles of candidate
genes already uncovered by using molecular biological and cell
biological techniques and have discovered factors involved in viral
replication and innate immunity. By combining these methodologies, and
using a variety of viruses, we hope to gain a comprehensive
understanding of the interplay between the host and pathogen in a
complex and dynamic setting. Taking advantage of forward genetics and
functional genomics in will allow us to use these unbiased and global
methodologies to identify many important and novel host factors that
modulate virus-host interactions. Moreover, the more viral-host pairs
that we study, the better our understanding of pathways and processes
essential to pathogens, and the more equipped we will be to develop
anti-viral treatments. |
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Nuclear transport, hnRNP complexes, RNA-binding proteins, spinal muscular atrophy |
Isaac Norris Professor of Biochemistry & Biophysics, Howard Hughes Medical Institute Investigator The research efforts of the Dreyfuss laboratory are presently focused on four interrelated topics:
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Regulation of chromatin structure and its impact on human diseases |
Assistant Professor of Biochemistry & Biophysics The Fan lab is interested in understanding the mechanisms of epigenetic regulation. Epigenetics describes the process by which a specific transcriptional program, induced by a signal, is maintained and inherited through cell divisions without the necessary presence of the original signal. Chromatin structure holds the secrets of epigenetic regulation. To dissect the mechanisms of epigenetic regulation, our research is focused in two main directions. First, we study how ATP-dependent chromatin remodelers regulate chromatin structure and how defects in these activities can lead to disease. Currently, we are using CSB (Cockayne Syndrome complementation group B) as a model protein to understand the function of ATP-dependent chromatin remodeling in DNA repair, aging and cancer. Second, we wish to understand how epigenetic regulatory mechanisms influence cancer cell self-renewal and differentiation, mechanisms that might impact the programming and reprogramming capacity of cancer cells. Results from our studies will, therefore, not only shed light on fundamental mechanism of epigenetic regulation, but will provide novel insights into the causes and mechanisms of disease. |
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Mechanisms that drive and control chromosome motions in mitosis |
Assistant Professor of Physiology |
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Investigating the enzymatic basis for diversity generation in the immune system and pathogens; enzyme mechanisms, chemical biology, protein evolution |
Assistant Professor of Medicine, and Biochemistry & Biophysics Our laboratory focuses on the enzymatic generation of genomic diversity. We utilize a broad array of approaches, including biochemical characterization of enzyme mechanisms, chemical synthesis of enzyme probes, and biological assays spanning immunology and virology to study this central tactic in the constant battle between our immune system and pathogens. From the host immune perspective, the generation of genomic diversity is used as both a defensive and an offensive weapon. On the one hand, host mutator enzymes such as Activation-Induced Cytidine Deaminase (AID) seed diversity in the adaptive immune system by introducing targeted mutations into the immunoglobulin locus that result in high affinity antibodies (somatic hypermutation) or altered isotypes (class switch recombination). Related deaminases of the innate immune system can directly attack retroviral threats by garbling the pathogen genome through mutation, as accomplished by the deaminase APOBEC3G, which restricts infection with HIV. Immune mutator enzymes, however, also pose a risk to the host, as overexpression or dysregulation have been associated with oncogenesis. From the pathogen perspective, alteration in key antigenic determinants at a rate that outpaces immune responses is a potent means for evasion. Further, rapid mutation may allow for the development of resistance to antimicrobials. Our research program aims to understand mutator enzymes and pathways in the immune system and pathogens. We further aim to harness these diversity-generating systems for directed evolution of proteins. Additionally, we apply chemical biology to decipher and target these pathways, to impede the development of multidrug-resistance in pathogens or prevent the neoplastic transformations that can result from genomic mutation. |
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Cellular osmoregulation, stress-induced gene expression, C. elegans genetics |
Assistant Professor of Physiology I am interested in the molecular mechanisms by which animal cells sense and respond to environmental stressors. My lab approaches these questions using genetic, genomic, and biochemical approaches in the nematode C. elegans. Currently, the lab is focused on defining the molecular mechanisms underlying the osmotic stress response. The cellular osmotic stress response is essential for all forms of cellular life, but the molecular events that underlie this process have never been genetically dissected in animals. The soil dwelling nematode C. elegans offers numerous experimental advantages for these studies, such as forward and reverse genetic tractability, transparent body architecture, simple transgenic methods, and a highly annotated complete genome sequence. The lab is currently addressing two important problems using this system: 1) The role of protein damage in activation of osmosensitive signaling pathways. To chronically adapt to hypertonic stress, all organisms accumulate organic osmolytes, which are non-ionic, osmotically active solutes such as glycerol, trehalose, and sorbitol, that balance osmotic gradients and stabilize protein structure. Worms accumulate the organic solute glycerol to adapt to hypertonicity. The C. elegans genome encodes two glycerol-3-phosphate dehydrogenase (gpdh) genes, which catalyze the rate limiting step in glycerol biosynthesis. Worms expressing a gpdh-1:GFP transgene exhibit no GFP expression under standard lab culture condition. However, rapid GFP expression is induced following exposure to hypertonic stress. Since other stressors do not affect the expression of gpdh-1:GFP, this reporter function as a specific in vivo monitor for the activation state of signaling pathways controlling osmosensitive gene expression. Using genome-wide RNAi screening approaches, we have identified at least 122 gene knockdowns that result in the constitutive activation of gpdh-1:GFP expression. The majority of these genes normally function to regulate protein folding, protein synthesis, and protein degradation. These data have suggested the hypothesis that the accumulation of specific types of misfolded proteins, which is a major consequence of hypertonic stress, functions as a signal to activate osmosensitive signaling pathways in animals. Currently, we are testing if hypertonicity disrupts protein stability and if accumulation of destabilized and aggregating proteins can directly activate osmosensitive gene expression. 2) Signaling pathways that regulate osmosensitive gene expression. The signaling events that regulate osmotic stress responses have been best explored using genetic and genomic approaches in bacteria, yeast, and plants. Using osmosensitive gpdh-1:GFP as a phenotype, we have begun to apply these methods to molecularly dissect the osmotic stress response in C. elegans. Forward genetic screening has identified numerous loss-of-function and gain-of-function mutants that regulate gpdh-1 expression. Using a quantitative large object flow cytometer (the “Worm Sorter”), we are performing both RNAi and forward genetic screens to identify the kinases, transcription factors, and other novel signaling molecules that transduce osmotic stress signals. Using genetic approaches such as epistasis and suppression, we will assemble this pathway to understand how, when, and where these genes act relative to one another. In the future, the application of these approaches to other stress response pathways, such as heat shock and oxidative stress, should allow us to build an integrative picture of environmental stress signaling. |
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Gene regulation; protein crystallography; structural basis of recognition |
Professor of Biochemistry & Biophysics The major objective of our research is to understand how proteins respond to metabolites and regulate transcription. Our work has focused on the repressor of bacteriophage lambda and the lac operon of E. coli. For almost half a century, these two systems have served as the paradigm for understanding gene regulation. The primary focus of our lab has been to provide detailed structural information on these two systems. |
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Mechanism and consequences of regulated alternative splicing |
Associate Professor of Biochemistry & Biophysics, and Genetics Recent insight into the human genome has revealed that most genes encode multiple distinct protein isoforms through the process of alternative pre-mRNA splicing. My laboratory is focused on understanding the biochemical mechanisms and regulatory networks that control alternative splicing in response to antigen-challenge of the human immune system. Recently we have identified ~150 genes that exhibit an alteration in isoform expression in response to T cell stimulation. Through our initial work on the regulated splicing of the protein tyrosine phosphatase CD45, we have identified the regulatory sequence, proteins that controls activation-induced isoform expression of CD45 as well as exons in several other genes essential for T cell function. This work is on-going as we seek to understand the mechanism of this regulation at molecular and atomic detail. We are also expanding our focus to include additional networks of co-regulated splicing events in T cells. Together these studies are providing new insights into the mechanisms and consequences of RNA-based gene regulation in the cellular response to environmental stimuli. |
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X-ray crystallography, chromatin regulation, tumor suppressors, oncoproteins, kinases, aging, structure-based inhibitor design |
Wistar Professor of Biochemistry and Biophysics The laboratory uses a broad range of molecular, biochemical and biophysical research tools centered on X-ray crystal structure determination to understand the mechanism of macromolecular recognition and post-translational histone and protein modifications in the regulation of gene expression, chromatin and epigenetics. The laboratory is particularly interested in gene regulatory proteins and kinases that are aberrantly regulated in cancer and age-related metabolic disorders such as type II diabetes and obesity, and the use of high-throughput small molecule screening and structure-based design strategies towards the develop protein-specific small-molecule compounds to treat such diseases. |
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Embryonic transcriptional regulation; fate specification; cell lineages; C. elegans; microscopy |
Assistant Professor of Genetics |
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Structural biology; transcription; protein-DNA interactions; heat shock response |
Associate Professor of Biochemistry & Biophysics |
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Systems biology; developmental biology; non-coding RNA |
Assistant Professor of Bioengineering The Raj lab studies the biology of single cells. The primary motivation for studying biological processes on a cell-by-cell basis is the fact that even genetically identical cells can behave very differently. Many of these differences arise as a consequence of the developmental process, whereby some cells are directed to become, for example, liver cells while others become skin cells. We aim to understand these differences at the molecular level. One of our primary experimental tools is a method we have developed for detecting individual RNA molecules via fluorescence microscopy, yielding very precise, quantitative data about RNA abundance and localization within single cells. One application of this method is the visualization of non-coding RNAs. Recently, researchers have made the exciting discovery that much of the genetic material that was previously thought to be “junk” DNA is actually converted into RNA molecules, and some of these non-coding RNA molecules appear to have direct functional roles in development. We are directly visualizing and localizing these molecules in their cellular context to decipher the mechanisms by which they operate, including potential roles in stem cell differentiation. Another area in which cellular heterogeneity is important is cancer. We are producing RNA expression maps throughout tumor sections at single cell resolution to measure spatial variation in expression during tumor formation and development. We anticipate that such studies will lead to new diagnostic tools as well as a deeper understanding of cancer biology. |
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Protein engineering; synthetic biology; cell-fate decisions |
Associate Professor of Bioengineering The Sarkar laboratory utilizes both experimental and computational methods to quantitatively understand fundamental biomolecular (e.g., binding, catalysis) and cellular (e.g., signaling, trafficking, gene regulation) processes. We seek to understand and manipulate the operation of biomolecular networks, and consequently cellular behavior, by integrating novel molecular design strategies into a cell engineering framework. Current applications range from controlling cell fate decisions to engineering novel therapeutic ligands, receptors, and signaling networks to generating molecular devices for use in synthetic biology. |
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Regulation of beneficial or neuropathogenic prions and amyloids by protein-remodeling factors, molecular chaperones, and small molecules |
Assistant Professor of Biochemistry & Biophysics Life demands that proteins fold into elaborate structures to perform the overwhelming majority of biological functions. We investigate how cells achieve such successful protein folding. In particular, we seek to understand how cells prevent, reverse, or even promote the formation of prion and amyloid fibers. |
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Cancer proteomics; structure-function of membrane associated proteins: protein chemistry and mass spectrometry |
Wistar Institute Professor of Biochemistry & Biophysics Our research group primarily focuses on proteomics of human diseases and structure-function of protein-protein interactions. We are currently pursuing two structure-function projects that primarily utilize biophysical methods, such as isothermal titration calorimetry and sedimentation equilibrium, and mass spectrometry to probe protein structures, protein-protein interactions and function. One project involves the giant membrane skeletal protein spectrin, a human actin crosslinking protein that plays a key role in stabilizing the plasma membrane in most cell types. Current studies focus on the proteotypical spectrin tetramers found in human red blood cells and their role in membrane purturbations caused by hereditary hemolytic anemia mutations. Another project involves structure-function analysis of peroxiredoxin 6, an antioxidant enzyme with glutathione peroxidase activity and phospholipase activity, which plays a critical role in protecting lung and other tissues from damage due to oxidative stress |
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Structural biology; protein-protein interactions; x-ray crystallography |
Jacob Gershon-Cohen Professor of Medical Science We are interested in understanding on a structural and biochemical level how DNA and RNA molecules are maintained and processed by living cells. In addition to the mechanisms and regulation of genome replication and transcription, this includes processes such as DNA repair, site-specific and homologous recombination, transposition, condensation of chromosomes, chromosome pairing and segregation, and RNA trafficking and splicing. Our approach is to establish three-dimensional models of macromolecular assemblies relating to a particular biological question using X-ray diffraction methods and to then develop mechanistic and functional models that can be tested experimentally. |
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Cancer cell metabolism, nutrient sensing
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Assistant Professor of Cancer Biology Our laboratory is interested in understanding how nutrient metabolism interfaces with signaling and transcriptional networks, with a current focus on metabolic regulation of the epigenome. Diseases such as cancer and diabetes are characterized by significant epigenetic and cell metabolic alterations. Chromatin modifications such as histone acetylation are sensitive to changes in nutrient metabolism, although the contribution of metabolism to epigenetic regulation in normal physiology or in disease states is not known. Current goals of our research include defining the molecular mechanisms that link cellular metabolism to the epigenome and investigating the functional significance of this interaction in cancer and metabolic diseases. |
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Glycoproteins; lysosomal enzymes; storage diseases; gene transfer into brain |
Professor of Pathology & Medical Genetics Dr. Wolfe’s laboratory studies gene transfer and neural stem cells in the brain. Two general approaches for transferring genes to the brain are being investigated: 1) Direct transduction of brain cells in vivo is studied using vectors derived from herpesvirus (HSV), adeno-associated virus (AAV), and lentiviruses; and 2) Ex vivo gene transfer is being studied using lentiviral vectors and neural stem cells for specific properties of repopulation after transplantation. Efforts are also directed toward understanding of the molecular and cellular mechanisms of brain cell dysfunction leading to the deficits in mentation. These studies include: 1) Gene expression array and proteomic analyses in subregions of the brain in animal models; and 2) Development of induced pluripotent stem cells from human patients, which allow analysis of diseased and control human neural cells that otherwise could not be done. Areas of current research include: 1) fate of viral vectors in different neuronal pathways; 2) molecular determinants of viral surface proteins affecting gene distribution; 3) biochemical properties of engineered therapeutic proteins in neurons; 4) engineering neural stem cells to improve bio-distribution; 5) development of imaging methods to monitor gene expression in vivo; 6) functional changes in disease and responses to therapy; 7) genomics and proteomics analysis of cellular changes in disease; 8) translational research to evaluate barriers to scaling up treatments to large mammalian brains. |
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