Cell nucleus, lamins, nuclear lamina


 

We study mechanical and rheological properties of the nucleus. In deciphering the structural and mechanical elements of the cell's nucleus we hope to determine roles of epigenetic regulation, stem cell differentiation, aging pathologies and cancer metastases. Mechanical regulation of cell and tissue function is poorly understood but is a fascinating area of study. Our research focuses on molecular, organelle, cellular and multicellular length scales over time, and we use a combination of spectroscopic, imaging, image informatics, biophysics and computational approaches.

 

 

 

 


Education

PhD 2004, University of Pennsylvania

Postdoctoral Training

Johns Hopkins University School of Medicine, Department of Cell Biology


 

Carnegie Mellon University
Department of Chemical Engineering
Doherty Hall 2100C
5000 Forbes Ave. 
Pittsburgh, PA 15213

Phone: (412) 268-9609 
Fax: (412) 268-7139

E-mail: krisdahl@cmu.edu 

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High-resolution cryo-EM of macromolecular assemblies


Our research is focused on structure and function of macromolecular assemblies using three-dimensional cryo-electron microscopy (cryoEM), combined with biochemical, biophysical and molecular biology methods. CryoEM is a powerful tool for structure determination of large protein complexes and macromolecular assemblies, and their conformational changes to provide structural snapshots along dynamic processes. Research efforts in our lab are currently directed to two areas in biology: (I) HIV pathogenesis, particularly HIV capsid assembly, maturation, and interactions with host cell factors; (II) molecular mechanisms of signal transduction in bacterial chemotaxis. We are also developing technologies to bridge the gap in single molecule imaging, by integrating optical and electron imaging methods (correlative microscopy), and working at the interface of nanotechnology and biology.


Education

PhD 1998, University of Virginia, Molecular Biophysics

Postdoctoral Training

1998-2000 National Institute of Health, NIDDK
2000-2002 National Institute of Health, NCI


 

Department of Structural Biology
University of Pittsburgh
3501 5th Avenue
Pittsburgh, PA 15260

Phone: (412) 383-5907
Fax: (412) 648-8998

E-mail: pez7@pitt.edu

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Bioorganic chemistry 


 

Research in the Wipf Group focuses on the total synthesis of natural products, organometallic and heterocyclic chemistry, combinatorial, medicinal and computational chemistry. At the center of this research program is the study of chemical reactivity and the use of synthesis to augment the chemical toolbox and develop new therapeutic strategies. A major emphasis involves the efficient preparation of polyfunctionalized nitrogen-containing building blocks for biological screening and natural product target-directed synthesis. The discovery of fundamentally new reaction pathways is stimulated by exploratory studies of transition metal complexes, in particular zirconocenes.

 


 

Education

PhD 1987, University of Zürich, Switzerland

Postdoctoral Training

1988-1990, University of Virginia


 

Department of Chemistry
University of Pittsburgh
Parkman Avenue, CSC 1301
Pittsburgh, PA 15260

Phone: (412) 624-0787
Fax: (412) 624-8606

E-mail: pwipf@pitt.edu

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NMR of ion channels & low-affinity drug action


 

Research efforts in Dr. Xu's group are directed to three projects: (1); membrane protein structures and dynamics by NMR; (2); low-affinity drug interaction with membrane proteins, and (3); gene and stem cell therapy for brain protection and revitalization after cardiac arrest and resuscitation. The current focuses are as follows. For Project 1, NMR is used to determine the transmembrane domain structures of the human glycine receptor, which is the primary inhibitory receptors in the spinal cord and responsible for a wide range of diseases. The long-term goal is to provide the structural basis for novel design of drugs that are disease specific and devoid of side effects. For Project 2, experimental and theoretical approaches are combined to study how low affinity neurological agents, such as alcohol and general anesthetics, exert their effects on the central nervous system at the molecular level. The goal is to shed new lights on the great unsolved mystery of modern medicine: the molecular mechanisms of general anesthesia. For Project 3, new gene therapy strategies are being developed to target a special event called reperfusion injury after cardiac arrest and resuscitation. Recently, Dr. Xu's group combines gene therapy with stem cell therapy using a non-controversial source of stem cells, in an effort to stop and reverse the neuronal loss and to rebuild neuronal circuitry after reperfusion from prolonged cardiac arrest or stroke.

Students in Dr. Xu's laboratory have the opportunity to learn a variety of modern techniques, including expression and purification of membrane proteins, immunohistochemistry, high-resolution nuclear magnetic resonance imaging and spectroscopy, imaging reconstruction, 3-D protein structure calculation, and molecular dynamics simulations.

 

 


 
Education

PhD 1990, State University of New York

Postdoctoral Training

University of California at San Francisco

 

 


Department of Anesthesiology
University of Pittsburgh
Biomedical Science Tower 3, Room 2048
3501 Fifth Avenue
Pittsburgh, PA 15260 

Phone: (412) 648-9922 
Fax: (412) 648-8998

E-mail: xuy@anes.upmc.edu  

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Amyloid structure & assembly


 

Aggregate structure. The protein aggregates associated with Alzheimer's Disease, Huntington's Disease, and other diseases tend to be highly ordered structures possessing, so far as we can establish, the same degree of packing specificity normally found in globular proteins. The structure of the amyloid fibril is both intriguing and mysterious. These assemblies can form from a number of different proteins which differ widely in amino acid sequence, size, and secondary structural features of the native state. The structure of amyloid is obscure because its polydispersity, size, insolubility, and inability to form diffraction quality crystals renders ineffective the normal techniques for solving protein structure. We use standard techniques like CD, FTIR, and EM (in the lab of John Dunlap at UT); to study the gross morphology of these aggregates. We attempt to get at finer structural points by adapting other methods previously applied to globular proteins. For example, we are mapping the secondary structural features of Ab amyloid fibrils using hydrogen-deuterium exchange as assessed by mass spectrometry. We have also used limited proteolysis of fibrils to determine which parts of the Ab peptide are intimately involved in the b-sheet network of the fibril. We are also characterizing a unique set of monoclonal antibodies that have the ability to bind to a conformational epitope presesnt on amyloid fibrils. On-going projects include the use of scanning mutagenesis techniques coupled with fibril formation assays to map the tolerances of each residue position of the peptide for various structural changes. In collaboration with Dr. Ying Xu at Oak Ridge National Labs, we are building and testing models of fibril structure based on this and other experimental data.

Fibril assembly and inhibition. We are interested in fibril assembly mechanism, kinetics and thermodynamics. From a basic, theoretical point of view, very little is known about the basis of fibril stability. The observation that many proteins that normally fold into stable, monomeric structures can nonetheless form amyloid fibrils suggests that the rules governing fibril packing and stability may be somewhat relaxed compared to the rules for globular proteins. On the other hand, amino acid replacements in amyloidogenic peptides can significantly alter fibril formation. We want to understand these constraints as another way to study fibril structure. From a practical point of view, learning about the "hot spots" for fibril stabilization should tell us what places to target in inhibitor design. We have developed and optimized a number of assays for following fibril formation that we routinely use to assess the kinetics and thermodynamics of fibril formation and to screen for inhibitors, both in the Alzheimer's Ab system and in the Huntington's Disease polyglutamine system.

The basis of aggregate cytotoxicity. When bacteria produce inclusion bodies filled with densely packed, misfolded recombinant proteins, they often suffer very little from the presence of these abnormal structures outside of perhaps a slight diminution in growth rate. Particular protein aggregates can have devastating consequences, however, to human biology. We are interested in the mechanisms by which cells die or become dystrophic in response to aggregates. The mechanism we are particularly interested in has been called the "recruitment" or "sequestration" mechanism. The idea is that the loss of the major amyloid component (Ab, for example); is not the problem, but rather it is the loss to the local environment of other proteins when these molecules become entrapped in the growing amyloid deposit. Particularly good evidence for this mechanism exists in the polyglutamine system, where cellular proteins containing short polyglutamine sequences can be observed to co-aggregate in the cell with the expanded polyglutamine-containing protein forms inclusions. We are studying polyglutamine aggregation in vitro to develop the biophysical underpinnings of this mechanism, and are also studying what happens when polyglutamine aggregates made in vitro are introduced into cells.


 
Education

PhD 1973, University of California, Berkeley 

 

Postdoctoral Training


Max Planck Institute for Experimental Medicine in Goettingen, Germany
Yale University


Department of Structural Biology
University of Pittsburgh
Biomedical Science Tower 3
3501 5th Avenue
Pittsburgh, PA 15260

Phone: (412) 383-5271
Fax: (412) 648-9008

E-mail: rwetzel@pitt.edu 

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