Dave Bauer

Thesis title: "Influence of internal genome pressure for viral particle infectivity and stability"

Defense date: April 2015

Research interests:

Genome packaging during virus replication is an ATP-dependent process, resulting in a thermodynamically unstable state of packaged viral DNA. This energetically unfavorable confinement of the microns-long DNA molecule creates a large internal pressure inside the virus. The effects of tight genome confinement has previously been studied for multiple bacterial viruses. Recently, using a novel experimental assay, we have provided the first measurement of this DNA pressure within a eukaryotic herpesvirus, HSV-1. Dave's project focused on calorimetric investigations of internal pressure for specific viral systems, as well as comparative studies between evolutionarily diverse viruses. This experimental approach can uncover general physical properties of viruses that regulate viral infectivity.

Prior education:

B.S. Biology; B.S. Physics, Rowan University, Glassboro, NJ

 

Current location:

Research Scientist at Cybergenetics in Pittsburgh, PA

PhD Advisor: Dr Alex Evilevitch

 

Publications:

 

Naima Sharaf

Thesis Title: Solution NMR studies of HIV-1 reverse transcriptase

Graduation Date: Nov 21, 2016

 

Research Summary: 

Naima used solution NMR as a  method to study protein structure and dynamics. Standard NMR experiments use protein uniformly labeled with NMR active nuclei, such as 15N, 13C and 2H.  Each nucleus reports on its surrounding environment and the ability to obtain structural information depends on being able to resolve, and unambiguously assign all resonance frequencies to unique nuclei. However, for large proteins (> 30 kDa) resonance overlap properties render this process difficult. Naima's goal was to help develop NMR methods to study large proteins in solution. Towards this goal, she applied selective labeling methods to study the structure and dynamics of the 118 kDa HIV-1 reverse transcriptase, a major drug target in the treatment of HIV-1 infection. The NMR spectra of RT produced by these labeling methods contain less resonance overlap since only a few residues are labeled.

Education: 

Chemistry (biochemistry track) University of North Carolina at Chapel Hill  

PhD Advisor: Dr Angela Gronenborn

Current Location: Postdoctoral associate in the Rees lab at CalTech / HHMI.

 

Publications:

Inventor in a provisional patent titled: Device for particulate NMR samples in a fluid.

Ryan Slack

Research Interests:

I study the structural basis of dimerization and maturation of HIV-1 reverse transcriptase (RT).  This viral enzyme is a primary target in the current treatments for HIV-1 infection.  The biologically active form of the enzyme requires dimerization of the RT subunits and proteolytic processing of one of these subunits.  Little structural data currently exists regarding the mechanisms of these dimerization and maturation processes which could provide attractive therapeutic targets for future antiretroviral therapies.  Our lab uses solution nuclear magnetic resonance (NMR) spectroscopy to determine structures of viral enzymes, and integrate our structural understanding into further mechanistic and functional studies.

Education: 

B. Sc. in Biophysics, Centenary College of Louisiana, 2006

PhD Advisor: Dr. Rieko Ishima

Lab Address: 
Room 1037
Biomedical Science Tower 3
3501 Fifth Ave.
Pittsburgh, PA 15260

email: rls128{AT}pitt.edu

Publications:

 

Jacob Spiegel

Research Interests:

While at the University of Pittsburgh I've had the opportunity to work on a number of projects across several fields.

From 2013 to 2017 I worked with Dr. Roger Hendrix researching fundamental phage biology. I worked on two projects while in his lab. I studied non-canonical ribosome translation in bacteriophage ΦHau3, in which the ribosome bypassed a 10 nucleotide region and continued translation downstream. My other project was crystallizing and studying the chaperone tail assembly proteins in bacteriophage λ.

Following the passing of Dr. Roger Hendrix, I join the lab or Dr. Jacob Durrant, working on computation biology with focuses in computer-aided drug design (CADD), Molecular Dynamics, and program development. My dissertation focuses on the development of the genetic algorithm for de novo computer-aided drug design, AutoGrow4, and its application to poly(ADP-ribose) polymerase 1 (PARP-1).

 

 

 

Education:

Biomedical Engineering BE, State University of New York at Stony Brook, 2013

PhD Advisor: Dr. Jacob Durrant

Lab Address:

A318 Langley Hall

 

 

email: jspiegel[at]pitt.edu

Publications:

  • Spiegel, J.O., Durrant, J.D. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J Cheminform 12, 25 (2020). https://doi.org/10.1186/s13321-020-00429-4

  • Ropp, P.J., Spiegel, J.O., Walker, J.L. et al. Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. J Cheminform 11, 34 (2019). https://doi.org/10.1186/s13321-019-0358-3

David Punihaole

Thesis title: Molecular Structural Insights of Polyglutamine-rich Amyloid-like Fibrils using UV Resonance Raman Spectroscopy

Graduation date: June 2016

MBSB PhD Advisor: Dr Sanford Asher (Dept. Chemistry; University of Pittsburgh)

 

Research Interests: 

David worked on the development of UV Resonance Raman (UVRR) spectroscopic methods to study amyloid fibril structure and aggregation kinetics.  UVRR is exquisitely sensitive to protein/peptide conformations and can be used to selectively probe the electronic structure of UV-absorbing chromophores. 

His my main research focus was the aggregation mechanism(s) of polyglutamine (polyQ) peptides and how they lead to amyloid fibril formation.  There are at least nine neurodegenerative diseases associated with expansions in polyQ repeat segments of proteins.  These simple polyQ peptides are useful model systems for studying the fundamental biophysics of larger, more complicated polyQ rich protein systems. Another focus was on the development of instrumentation for use in studying new biological systems with UVRR.  For this, he worked on creating a high-resolution, high-throughput UV double monochromoter to study biologicals with ~200 nm-excited UVRR and on refurbishing a picosecond Nd:YAG laser so that it can directly probe picosecond dynamics of model peptides and organic molecules.

Current location: postdoctoral researcher in the Frontiera lab at the University of Minnesota.

Education:     

B.S., Molecular Biology/Biochemistry, University of Pittsburgh, 2009
Ph.D., Molecular Biophysics & Structural Biology, University of Pittsburgh, 2016

Publications:

 

 

  1. Abhishek Mandal
  2. Muwen Ben Kong
  3. Benjamin Himes
  4. Rebecca Eells