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:


 

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.



Thesis Title: Investigations of the structural changes in proapoptotic peroxidase- active cardiolipin-bound cytochrome c and liquid-gel phase transitions in liposomes using solid state NMR spectroscopy 

Graduation Date: November 30, 2016

 

Research Interests: 

Abhishek performed structural and dynamical measurements on cytochrome c (cyt-c) in its lipid-bound state. Cyt-c is primarily known for its role in the electron transfer pathway but it also plays an important role in intrinsic apoptosis. A required step in this process is the peroxidation of mitochondrial lipid cardiolipin (CL). A crucial open question is regarding the structural changes in the bound protein that allow its covalently bound heme to catalyze the peroxidation of CL acyl chains in the membrane core. He used solid-state NMR methodology to study the structure and dynamics of both the CL bound cyt-c as well as the vesicles themselves using samples mimicking the proapoptotic conditions that trigger cyt-c’s peroxidase activity.  These methods were complemented with various spectroscopic methods, including fluorescence based peroxidase assays, to correlate the function and structure of the bound cyt-c.

 

Education: 

Bachelor’s of Science in Biochemistry, Temple University, Philadelphia, 2011


PhD Advisor: Dr. Patrick CA van der Wel

 

Current Location:  Analyst with Highmark Inc., Pittsburgh, PA


 Publications:

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:

 

 



Photo of Muwen Ben Kong

Thesis Title: Single-Molecule Studies of Rad4-Rad23 Reveal a Dynamic DNA Damage Recognition Process

Graduation: June 30, 2017

 

Research Interests: 

Our lab studies the nucleotide excision repair (NER) pathway in DNA repair. Ben's thesis project looked at the mechanism of DNA damage recognition by yeast NER protein Rad4-Rad23, using single-molecule techniques such as our DNA tightrope assay with quantum dot labeled proteins, as well as atomic force microscopy (AFM).

 

 

 

Education: 

B.A. Physics, Knox College 2008

M.S. Physics, CMU 2010


PhD Advisor: Dr. Bennet Van Houten

Current Location: postdoc in Eric Greene lab, Columbia University (New York, NY) (per Oct 2017)

 

 

Email: muwenkon{AT}pitt.edu


Publications: