Biochemistry and Molecular Biophysics Graduate Group

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pixel Cell Signaling and Intracellular Trafficking

Charles S. Abrams, M.D.

Phospholipid signaling pathways in platelets and lymphocytes

Professor of Medicine
912 Biomedical Research Building II/III
Tel: 215-898-1058 / Fax: 215-573-7400
Email: abrams@mail.med.upenn.edu
Abrams department website

The Abrams laboratory is focused on phospholipid signaling in hematopoietic cells. Ongoing projects are directed at understanding the roles of pleckstrin and lipid kinases in platelets and leukocytes. Pleckstrin (p47) was once solely known as an early marker of platelet activation; more recently it has been noted to contain the prototypic Pleckstrin Homology motif. Over the past half dozen years, work derived from our laboratory has demonstrated that pleckstrin plays a dominant role in the reorganization of the platelet, and lymphocyte, cytoskeleton. Furthermore, the laboratory has established these effects are regulated by pleckstrin phosphorylation, require critical lipid-binding residues contained with the amino-terminal Pleckstrin Homology domain, and have implicated an effector for this process to be the small GTP-binding protein, Rac. It has also cloned a ubiquitously expressed paralog, pleckstrin 2, although its mechanism of regulation is unknown. Additional work from the Abrams laboratory has helped define the role ofphospholipid kinases in the pathway that is initiated by G-protein coupled, and T-cell, receptors and ultimately leads to actin reorganization. These studies use molecular and cellular biologic techniques to examine blood cell biology, and involve expression mutagenesis, single cell microinjection, genetic library screening, and murine homologous gene targeting ("gene knock-out").

 

Yair Argon, Ph.D.

Quality control of protein folding in the cell by molecular chaperones

Professor of Pathology & Laboratory Medicine; Chief, Division of Cell Pathology
816B Abramson Research Center
Tel: 267-426-5131 (office) / 267-426-5130,29,28 (lab) / 267-426-5346 (administrator)
Fax: 267-426-5165
Email: yargon@mail.med.upenn.edu
Email: ARGONY@email.chop.edu
Argon lab website

Orchestrating protein folding in the cell is a key process underlying the expression of membrane receptors and secreted proteins. Inefficient folding leads to inappropriate protein-protein interactions, inability to transport proteins from the ER to the Golgi complex, and is the molecular basis of many diseases. The molecular chaperones in the ER govern proper folding and assembly, recognize misfolded proteins and either improve folding or direct them to degradation. Our work focuses on two molecular chaperones, BiP and GRP94.

 

Joel S. Bennett, M.D.

Regulation of integrin function

Professor of Medicine
914 Biomedical Research Building II/III
Tel: 215-573-3280 / Fax: 215-573-7039
Email:bennetts@mail.med.upenn.edu
Bennett ITMAT webpage

Integrin function is essential for normal platelet adhesion and aggregation and participates i n the formation of the arterial thrombi that are responsible for heart attacks and strokes. The activation state of platelet integrins is regulated by platelet agonists, but the structural basis for this regulation is not known. Our studies indicate that helix-helix interactions involving the transmembrane and membrane-proximal cytoplasmic domain segments play an essential role in regulating the function of both beta 1 and beta 3 integrins. The current focus of the laboratory is to use biophysical and molecular biologic techniques to characterize these interactions in detail and to use this information to design potential anti-thrombotic agents.

 

Shelley L. Berger, Ph.D.

Role of adaptors in regulation of transcriptional activation in yeast and humans

Daniel S. Och University Professor of Cell & Developmental Biology
9-125 Smilow Center for Translational Research
Tel: 215-746-3106 (office) / Fax: 215-746-8791
Email: bergers@upenn.edu
Berger Cell & Dev Bio page; Epigenetics website

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. 

 

Ben E. Black, Ph.D.

Chromosome segregation; chromatin structure; epigenetic centromere specification; hydrogen/deuterium exchange

Associate Professor of Biochemistry & Biophysics
913A Stellar-Chance Labs
Tel: 215-898-5039 (office) / Fax: 215-573-7058
Lab: 912 Stellar Chance Laboratories
Tel: 215-898-4476 (lab)
Email: blackbe@mail.med.upenn.edu
Black department webpage

Dr. Black's laboratory is interested in how particular proteins direct accurate chromosome segregation at mitosis. 

 

Lawrence Brass, M.D., Ph.D.

Molecular basis for intracellular signaling in vascular biology

Professor of Medicine, Pathology & Laboratory Medicine, and Pharmacology
Associate Dean and Director, Combined Degree and Physician Scholar Program School of Medicine
913 Biomedical Research Building II/III
Tel: 215-573-3540 / Fax: 215-573-2189
Email: brass@mail.med.upenn.edu

Combined Degree Program

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.

 

 

Maya Capelson, Ph.D.

Nuclear organization of chromatin and its role in gene regulation and cell differentiation

Assistant Professor of Cell & Developmental Biology
9-101 Smilow Center for Translational Research
Tel: 215-898-0550 (office) / 215-573-7548 (lab)
Email: capelson@mail.med.upenn.edu
Capelson department webpage

We are interested in how the genome is organized inside the nucleus, and how this organization contributes to functional regulation of gene activity. Spatial organization is mediated by interactions between specific regions of the genome and protein components of nuclear structural scaffolds, such as the nuclear envelope. Entire chromosomes, large chromatin domains and specific genes have been reported to occupy particular places in the nuclear three-dimensional space, in a manner that is correlated with their expression status. Such organization represents a potentially widespread mechanism of gene regulation since specifying the relative position of the DNA template inside the nucleus could influence the probability or kinetics of all possible reactions that are carried out on that template, such as transcription, silencing or replication. Yet many of the basic principles of how particular genomic loci are targeted to and affected by distinct nuclear scaffolds remain obscure. Our goal is to understand how these interactions are determined, how they can change in development or disease states, and how they influence the establishment and inheritance of gene expression patterns.

 

Bohdana M. DIscher, Ph.D.

Translating signaling pathways of G-protein coupled receptors into electronic read-outs with nanoscale field effect transistors

Research Assistant Professor of Biochemistry & Biophysics
901C Stellar-Chance Labs
Tel: 215-898-5668 Fax: 215-898-0465
Email:bohdana@mail.med.upenn.edu
Discher department webpage

We are investigating the interactions of GPCRs with single wall nanotubes (SWNTs) and graphene and how the different modes of these interactions affect the conductivity of the carbon-based field effect transistors (FETs). We have established that we can reproducibly detect activation of olfactory GPCRs on SWNTs. Now we are extending our studies to non-olfactory GPCRs and graphene. Our goal is to convert the conformational variations of the receptors into distinct real-time electronic signals. This technology will help us to decipher the complex responses of the receptors. We aim to correlate these responses with intracellular signaling events and with their regulatory role in health and disease.

 

Roberto Dominguez, Ph.D.

Actin cytoskeleton, structural biology

Professor of Physiology
728 Clinical Research Building
Tel: 215-573-4559 / Fax: 215-573-5851
Email: droberto@mail.med.upenn.edu
Dominguez Lab Page

Structure Biology of the Actin Cytoskeleton
The actin cytoskeleton plays an essential role in multiple cellular functions, including cytokinesis, vesicular trafficking and the maintenance of cell shape and polarity. The driving force for these processes is the dynamic remodeling of the actin cytoskeleton into supramolecular functional networks. Remodeling of the cytoskeleton is a tightly regulated process, which involves hundreds of actin-binding and signaling proteins. The main focus of the research in our lab is to understand the molecular basis for how protein-protein interaction networks bring together cytoskeleton scaffolding, nucleation, elongation, and signaling proteins to accomplish specific cellular functions. Another area of significant interest is the study of large multi-domain proteins that connect the actin cytoskeleton to the cell membrane, and sense or induce membrane curvature.

Our primary research tool is protein X-ray crystallography. The atomic snapshots resulting from crystal structures provide a wealth of knowledge, but lack information about the dynamic aspects of protein-protein interaction. To obtain this kind of information we also use a host of other approaches, including mutagenesis, bio-informatics, and biophysical methods such as isothermal titration calorimetry (ITC), multi-angle light scattering (MALS), small and wide angle X-ray scattering (SAXS/WAXS). The lab collaborates with cell biologists and electron microscopists to study actin cytoskeletal proteins in the cellular environment.

 

Gideon Dreyfuss, Ph.D.

Nuclear transport, hnRNP complexes, RNA-binding proteins, spinal muscular atrophy

Isaac Norris Professor of Biochemistry & Biophysics
Howard Hughes Medical Institute Investigator
328 Clinical Research Building
Tel: 215-898-0398, 215-898-0172 / Fax: 215-573-2000
Email: gdreyfuss@hhmi.upenn.edu
Dreyfuss Lab Homepage / Dreyfuss Departmental Page / Howard Hughes Medical Institute Page

The research efforts of the Dreyfuss laboratory are presently focused on four interrelated topics:

  1. The transport of proteins and RNAs between the nucleus and the cytoplasm
  2. The molecular function of SMN (Survival of Motor Neurons), the protein product of the Spinal Muscular Atrophy (SMA) disease gene
  3. The structure and function of the hnRNP proteins, with particular focus on the role of these proteins in the formation and function of mRNA
  4. Novel phage display methods for identification of interacting proteins.

 

Hua-Ying Fan, Ph.D.

Regulation of chromatin structure and its impact on human diseases

Assistant Professor of Biochemistry & Biophysics, and Genetics
9-133 Smilow Center for Translational Research
Tel: 215 573-5705 (office)
Email: hfan@mail.med.upenn.edu
Fan departmental webpage

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.

 

Kathryn M. Ferguson, Ph.D.
Graduate Group Chair

Structural biology, growth factor receptor signaling, molecular mechanisms of protein-protein interactions

Associate Professor of Physiology
364 Clinical Research Building
Tel: 215-573-1207 (office) / 215-746-2816 (lab)
Email: ferguso2@mail.med.upenn.edu

We are interested in understanding molecular mechanisms that regulate receptor signaling at and across membranes. We continue our long-standing interest in the regulation of the Epidermal Growth Factor Receptor (EGFR) family of receptor tyrosine kinases (RTKs), and also expand our study to several other families of RTKs. Rekindling an early interest in pleckstrin homology domains, we are also investigating the role of lipid binding modules in several settings. To address these questions we use a combination of biophysical, structural, biochemical and cellular approaches.

 

Benjamin Garcia, Ph.D.

Quantitative proteomics for analysis of chromatin structure and function

Presidential Associate Professor of Biochemistry & Biophysics
9-124 Smilov Center for Translational Research
Tel: 215-573-9423 (office)/ 215-573-9422 (lab)
Email: bgarci@mail.med.upenn.edu
Garcia Department page

 

 

Mark Goulian, Ph.D.

Two-component signaling, bacterial regulatory circuits

Edmund J. and Louise W. Kahn Endowed Term Professor of Biology
204F Carolyn Lynch Laboratory
Tel: 215-573-6991 (office) 215-898-5135 (lab) / Fax: 215-898-2010
Email: goulian@sas.upenn.edu
Goulian web site

Our research is focused on two-component signaling in bacteria. Two-component systems are regulatory circuits that mediate responses to diverse environmental signals and play a central role in regulating many aspects of bacterial physiology. In their simplest form, these circuits are composed of an upstream sensor kinase and a downstream response regulator. The response regulator is usually a transcription factor, although in some instances it controls other cellular processes such as protein degradation, protein localization, or flagellar motor switching. Depending on the circuit, additional phospho-transfer steps or additional regulatory proteins may be involved in the signal transduction process. Two-component systems provide an excellent context in which to study cell signaling. These systems tend to be relatively simple, with a small number of components; they can be found in genetically tractable, well-studied organisms; and there are many examples of such systems  that can be used for comparing and contrasting designs (E. coli K-12 alone contains roughly 30 two-component systems). Our research applies techniques from genetics, molecular biology, fluorescence microscopy, and mathematical modeling to explore the design principles underlying two-component systems. We have been particularly interested in the mechanisms that maintain fidelity in transducing and processing signals. We are developing new techniques to measure signaling activity, both across populations and at the level of the single cell, in order to formulate and test quantitative models. We are also engineering networks within E. coli in order to build novel circuits and to explore the general design constraints and schemes for cell signaling.

 

 

Ekaterina L. Grishchuk, Ph.D.

Mechanisms that drive and control chromosome motions in mitosis

Assistant Professor of Physiology
675 Clinical Research Building
Office: (215) 746-8178 / Fax: (215) 573-2273
Email: gekate@mail.med.upenn.edu
Grishchuk department website

Our goal is to understand the molecular mechanisms that produce force and accuracy for mitotic chromosome motions during cell division. With biophysical, cell biological and computational approaches we study the specialized protein complexes, which function as efficient nanomachines capable of providing durable attachments between chromosomal kinetochores and the assembling and disassembling ends of microtubules. There are no man-made or natural macro-devices that function analogously to these coupling protein complexes, so uncovering the corresponding mechanisms is both challenging and exciting. Current research is focused on kinesin motor CENP-E and the microtubule-binding protein complex Ndc80, which are studied with Total Internal Reflection Fluorescent microscopy and advanced laser trapping techniques. Rigorous understanding of how the kinetochores attach to the dynamic microtubule ends should ultimately assist developing novel and more specific anticancer drugs.

 

 

Roland G. Kallen, M.D., Ph.D.

Structure, function, and regulation of expression of ion channel

Professor of Biochemistry & Biophysics
913B Stellar-Chance Labs
Tel: 215-898-5184, 898-8348 / Fax: 215-573-7058
Email: rgk@mail.med.upenn.edu
Kallen Departmental Page

The action potential responsible for muscle contraction involves the voltage-gated sodium channel. We are studying the conformations of parts of the molecule in the activated, inactivated, closed states, determining the architecture of sites of drug and toxin binding for rational drug design, and elucidating the regulation of the expression of these proteins during development and in disease states.

 

 

Rahul M. Kohli, M.D., Ph.D.

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
502B Johnson Pavilion
Tel: 215-662-2359 / Fax: 215-349-5111
Lab: 509 Johnson Pavilion / Tel: 215-614-0163
Email: rkohli@upenn.edu
Kohli lab website

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.

 

 

Michael Lampson, Ph.D.

Chromosome segregation in mitosis and meiosis, biosensors for mitotic kinases

Assistant Professor of Biology
204-I Carolyn Lynch Laboratory
Tel: 215-746-3040
Email: lampson@sas.upenn.edu
Lampson lab website

Our research addresses molecular mechanisms that maintain genomic integrity during cell division. The replicated chromosomes are physically segregated at each division to create two genetically identical daughter cells. Segregation errors lead to loss or gain of whole chromosomes in the daughter cells, or aneuploidy, which is strongly associated with human cancer, developmental disease, and infertility.  A complex and highly dynamic cellular machinery ensures accurate chromosome segregation. While many of the key components have been identified, we now face the challenge of understanding how the system is controlled. Using high-resolution light microscopy, combined with molecular perturbations introduced by RNAi or with small molecule inhibitors, we are examining key processes in cell division in real time in living cells. Research in the lab is currently focused in two directions, as detailed below.

First, mitotic kinases and phosphatases are critical for the regulation of cell division, and we are developing probes based on fluorescence resonance energy transfer (FRET) to examine signaling networks at specific intracellular structures in living cells. A core project in the lab is to examine signaling at the centromere, the site on each chromosome that attaches to the mitotic spindle.  Accurate chromosome segregation requires that each replicated chromosome pair attaches to spindle microtubules in the correct configuration, so that sister chromosomes are pulled in opposite directions at anaphase. Attachment errors must be (1) detected, to activate the spindle checkpoint, and (2) corrected before anaphase onset. Both processes depend on signaling at individual centromeres. We showed how the mitotic kinase Aurora B acts as a tension sensor to regulate microtubule interactions (Liu et al. 2009). Building on these findings, we are developing models for site-specific signaling networks, involving both kinases and phosphatases, that control cell division.

Second, we are addressing the question of why female fertility decreases with age. The best evidence to date is that the decreased fertility is due to an increase in the production of aneuploid eggs by older females (both human and mouse), which clearly points to chromosome segregation defects as an underlying cause. We are using mouse oocytes as a model system to understand the defects leading to aneuploidy. Our goal is to focus on basic molecular mechanisms involved in meiotic chromosome segregation, such as the spindle checkpoint, kinetochore function, and cohesion, but the relevance for reproductive health is obvious. This project provides an opportunity to study cell division in a system that has clear importance for human health, the mammalian oocyte, but that has received relatively little attention compared to some other model systems. We will address both the age-associated increase in aneuploidy, which is currently quite mysterious, and basic mechanisms of meiosis

 

Matthew J. Lazzara, Ph.D.

ErbB-mediated cell signaling

Assistant Professor of Chemical & Biomolecular Engineering
371 Towne Building
Tel: (215) 746-2264 / Fax: (215) 573-2093
Email: mlazzara@seas.upenn.edu

The Lazzara Lab is interested in the dynamics of receptor-mediated cell signaling processes and the impact of those processes on cellular decision making. A special area of emphasis is the ErbB family of receptor tyrosine kinases. In this area, we are working to develop novel quantitative insights into the determinants of ErbB receptor endocytosis rates and the connections between receptor trafficking properties and downstream signaling dynamics. We are also working to develop quantitative understanding of the determinants of cellular sensitivity to ErbB-targeted therapeutics used in the treatment of cancer. To address these issues, we implement a combination of experimental and computational approaches. A second area of interest for our group is receptor-mediated signaling in the glomerulus and proximal tubule of the nephron and associated issues of macromolecular transport in this physiological setting.

 

Virginia M.-Y. Lee, Ph.D.

Pathobiology of Alzheimer's and Parkinson's disease

Professor of Pathology & Laboratory Medicine
Director, Center for Neurodegenerative Disease Research
The John H. Ware 3rd Professor in Alzheimer’s Research
3 Maloney Building, Hospital of the University of Pennsylvania
Tel: 215-662-6427 / Fax: 215-349-5909
Email: vmylee@mail.med.upenn.edu
CNDR Webpage

Dr. Virginia M.-Y. Lee’s research interest focuses on tau, a-synuclein and amyloid beta precursor protein (APP), and their roles in the pathobiology of neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson’s disease (PD), and frontotemporal dementias (FTD). In particular, we wish to determine the pathogenesis of senile plaques, Lewy bodies and neurofibrillary tangles because these are major lesions found in the brains of AD patients and other neurodegenerative diseases. Information obtained from research program may shed light on how neurons degenerate in AD and PD and lead to a better understanding of the etiology of these diseases. A multi-disciplinary approach (including biochemical and molecular studies of neuronal culture systems, animal models and human tissues obtained at autopsy) is used in the laboratory to address these research issues in common with these neurodegenerative diseases. Our other research efforts focus on an increased understanding of the normal functions of tau, synucleins, and APP.

 

Mark A. Lemmon, Ph.D.

Biochemistry/biophysics of intermolecular interactions of growth factor receptor signaling

George W. Raiziss Professor of Biochemistry & Biophysics
322A Clinical Research Building
Tel: 215-898-3072 / Fax: 215-573-4764
Email:mlemmon@mail.med.upenn.edu
Lemmon Departmental Page / Lemmon Lab Page

Research Interests of the Lemmon Lab:
Signaling by receptor tyrosine kinases from the ErbB/HER family
EGF receptor signaling in Drosophila
Membrane recruitment by phosphoinositide-binding domains
Dynamin-family large GTPases in intracellular trafficking

 

Paul A. Liebman, M.D.

G-protein-receptor-arrestin mechanisms; visual signal transduction

Professor of Biochemistry & Biophysics
260 Anatomy-Chemistry Building
Tel.: 215-898-6917 / Fax: 215-573-8093
Email: liebmanp@mail.med.upenn.edu
Liebman Departmental Page

 

 

Kristen W. Lynch, Ph.D.

Mechanism and consequences of regulated alternative splicing

Professor of Biochemistry & Biophysics, and Genetics
909B Stellar-Chance Labs
Tel: 215-573-7749 (office); 215-573-7756 (lab)
email: klync@mail.med.upenn.edu
Lynch Lab

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.

 

Michael S. Marks, Ph.D.

Molecular mechanisms of intracellular protein transport and organelle biogenesis

Professor of Pathology & Laboratory Medicine
1107B Abramson Research Center
Children's Hospital of Philadelphia and University of Pennsylvania
Tel: 215-590-3664 (office); 215-590-3944 (lab)
Email: marksm@mail.med.upenn.edu

The secretory and endocytic pathways of eukaryotic cells are compartmentalized into distinct membrane-bound organelles and vesicular structures, each with its own characteristic function and macromolecular composition. We study how proteins and protein complexes are assembled, modified, and sorted to the appropriate compartments, and how these processes contribute to the biogenesis of specific organelles and suborganellar structures.

A major goal is to understand the nature of the cellular machinery involved in protein sorting and organelle biogenesis through genetic, cellular and biochemical approaches. Our efforts in this area focus on the generation of lysosome-related organelles, which are specialized endosome-derived structures found only in certain cell types. Our favorite model system for mechanistic studies is the melanosome - the pigment organelle in melanocytes - but we are extending our findings to additional organelles in platelets / megakaryocytes, lung epithelial cells and dendritic cells of the immune system. These organelles provide useful models for understanding how genetic diseases alter sorting processes required for organelle formation and subsequent physiological function. Additionally, fibrillar structures within melanosomes resemble amyloid that forms under pathological conditions such as Alzheimer and Parkinson diseases, and their benign formation serves as a basis for understanding how things go wrong in disease.

 

Benjamin L. Prosser, Ph.D.

Mechano-signaling in the heart

 

Assistant Professor of Physiology
726 Clinical Research Building
Tel: 215-746-1488 / Fax: 215-573-2071
Email: bpros@mail.med.upenn.edu
Prosser Physiology website

We utilize super-resolution and high-speed live cell imaging, manipulation of cell mechanics, electrophysiology, and molecular biology to gain insight into:
1. Transmission of mechanical stress through the microtubule cytoskeleton.
2. Stress-dependent production of reactive oxygen species and regulation of calcium signaling.
3. Mechano-signaling as a therapeutic target for muscular dystrophy in heart and skeletal muscle.

 

Ravi Radhakrishnan, Ph.D.

Computational structural biology and systems biology; cell membrane mediated trafficking; targeted drug delivery; cancer signaling

 

Associate Professor of Bioengineering, and Biochemistry & Biophysics
540 Skirkanich Hall
Tel: 215-898-0487
Email: rradhak@seas.upenn.edu
Radhakrishnan lab website

Radhakrishnan directs a computational research laboratory with research interests at the interface of chemical physics and molecular biology. The goal of the computational molecular systems biology laboratory is to provide atomic and molecular level characterization of complex biomolecular systems and formulate quantitatively accurate microscopic models for predicting the interactions of various therapeutic agents with innate biochemical signaling mechanisms. The lab specializes in several computational algorithms ranging from techniques to treat electronic structure, molecular dynamics, Monte Carlo simulations, stochastic kinetic equations, and complex systems analyses in conjunction with the theoretical formalisms of statistical and quantum mechanics, and high performance computing in massively parallel architectures.

 

Brian M. Salzberg, Ph.D.

Multiple-site optical recording; excitation-secretion coupling; neural networks

Professor of Neuroscience, and Physiology
234 Stemmler Hall
Tel.: 215-898-2441 / Fax: 215-573-2015
Email: bmsalzbe@mail.med.upenn.edu
Salzberg Neuroscience Web page

Certain substances, when bound to the membranes of neurons, cardiac and skeletal muscle, salivary acini, and other cells, behave as molecular indicators of membrane potential. The optical properties of these molecules, most notably fluorescence and absorbance, vary in a linear fashion with potential and may, therefore, be used to monitor action potentials, synaptic potentials, or other changes in membrane voltage from a large number of sites at once, without the necessity of using electrodes. Our laboratory is engaged in the development of more sensitive probes, extending the technology associated with their use, and in using these molecular voltmeters for optical recording of membrane potential from hitherto inaccessible regions of single neurons such as axon and neuroendocrine terminals and axonal and dendritic processes, and from many sites simultaneously in small assemblages of neurons and electrical syncitia, in order to study the spatial and temporal patterning of activity. Also, we are using dynamic high bandwidth atomic force microscopy to monitor extremely rapid mechanical events in nerve terminals and elsewhere in order better to understand neurosecretion.

 

Phong Tran, Ph.D.

Cytoskeleton organization and cellular pattern formation

Assistant Professor of Cell & Developmental Biology
1009 Biomedical Research Building II/III
Tel: 215-746-2755 / Fax: 215-898-9871
Email: tranp@mail.med.upenn.edu
Tran Cell and Developmental Biology Homepage

The Tran lab is interested in understanding how positional information is generated within the cell by the cytoskeleton. For example, their previous studies in fission yeast have shown that bundles of microtubules can set up a spatial map for the cell to know where to grow and where to position its nucleus.

Microtubule architecture and dynamics are influenced by both plus- and minus-end microtubule-associated-proteins. A long-term goal, then, is to understand what role these proteins play in the establishment and maintenance of cellular spatial domains by microtubules. The Tran lab plans to: 1) identify the molecular components of the microtubule organizing centers, 2) define the interactions of known microtubule-associated-proteins with the microtubule ends and the roles of these proteins in bringing about proper nuclear positioning and cellular pattern, and 3) develop and apply advanced optical imaging and analysis methods to the yeast system.

High resolution optical imaging and analysis techniques, use of the green fluorescent protein and its variants as non-invasive fluorescent biosensors, and the model organism Schizosaccharomyces pombe with its well-defined shape, size, and genetic tractability constitute ideal, proven tools for studying cellular spatial organization and regulation.

 

David F. Wilson, Ph.D.

Integration of metabolism; oxidative phosphorylation; neuroregulation

Professor of Biochemistry & Biophysics
901A Stellar-Chance Labs
Tel: 215-898-6382 / Fax: 215-573-3787
Email:wilsondf@mail.med.upenn.edu
Wilson Biochemistry & Biophysics Page

My research is on the regulation of cellular and tissue metabolism in vivo, with particular focus on the role of oxygen in tissue energy metabolism. This program covers several different tissues, including brain, liver, heart, and eye, and involves several models of ischemia/hypoxia and reoxygenation.  We have developed an optical method for noninvasive measurement of oxygen, based on oxygen dependent quenching of phosphorescence, and are utilizing this technology for quantitative determine the oxygen dependence of tissue metabolism and function. 

 

John H. Wolfe, V.M.D., Ph.D.

Glycoproteins; lysosomal enzymes; storage diseases; gene transfer into brain

Professor of Pathology & Medical Genetics
Director, Walter Flato Goodman Center for Comparative Medical Genetics,
School of Veterinary Medicine and Stokes Institute, Children's Hospital of Philadelphia
502G Abramson Building (CHOP)
Tel: 215-590-7028 (office) / 215-590-7029 (lab) / Fax: 215-590-3779
Email: jhwolfe@vet.upenn.edu
Wolfe lab website

Animal homologs of human genetic diseases are used as test systems for gene transfer by viral vectors or stem cell therapies focused on the central nervous system. The include ex vivo gene transfer using genetically modified neural stem cells and direct injection of herpes, adeno-associated and lentivirus vectors. The studies involve transport within neural systems of proteins and/or vectors, properties of transduction for different cell types and various subregions of the brain, modification of therapeutic proteins for improved bioavailability, gene and protein array analysis of mechanisms of pathology and as biomarkers for pathology and response to therapies, stem cell development including diseased human iPSCs, and MRI and PET strategies for non-invasive monitoring of therapies.

 

Zhaolan (Joe) Zhou, Ph.D.

Epigenetic control of genome function in brain development and disease

Assistant Professor of Genetics
452A Clinical Research Building
Tel: 215-746-5025 / Fax: 215-573-7760
Email: zhaolan@mail.med.upenn.edu
Zhou lab website

A fundamental question in biomedical research is how the brain executes genetic programs while maintaining the ability to adapt to the environment. The underlying molecular mechanisms are not well understood, but epigenetic regulation, mediated by DNA methylation and chromatin organization, provides an intricate platform bridging genetics and the environment, and allows for the integration of intrinsic and environmental signals into the genome and subsequent translation of the genome into stable yet adaptive functions in the brain. While we can now profile genome-wide DNA methylation at single-base resolution, how the methylome is established and maintained, and how the cells interpret the methylome to affect gene expression and chromatin structure remain poorly understood. Moreover, recent studies have challenged the stability of the methylome in postmitotic neurons and have coupled changes in DNA methylation at specific loci to adaptive behaviors. We are interested in understanding how DNA methylation is coded and decoded genome-wide but with locus-specificity in neurons. Given the high abundance of hydroxymethylcytosine in the brain, we are also interested in understanding the role of the methylome in establishing and maintaining neuronal identity and the molecular mechanisms by which the methylome modulates genome function in the brain.