Research Interests:

The Dahl group primarily interested in studying and understanding the mechanical properties of the nucleus and actin cytoskeleton. I primarily use confocal microscopy, to study biophysical characteristics of force mechanotransduction through particle tracking, immunofluorescence, and FRET tension-sensor measurements. Cellular forces have been identified to play critical roles in the cell life cycle, but how the cell interprets and propagates mechanical perturbation is largely unknown. We endeavor to develop a better understanding of how force plays pivotal roles in determining cell fate.

Education:

BS Biophysics, Loyola University Chicago, December 2014

PhD Advisor:  Kris Noel Dahl

Lab Address: 

Doherty hall
5000 Forbes Ave
Pittsburgh PA 15213

email:  

Klavreny@andrew.cmu.edu

Kil23@pitt.edu

Publications:

• Piperazine Derivatives Enhance Epithelial Cell Monolayer Permeability by Increased Cell Force Generation and Loss of Cadherin Structures, Shiyuan Zheng, Kirill Lavrenyuk, Nicholas G. Lamson, Katherine C. Fein, Kathryn A. Whitehead, and Kris Noel Dahl, ACS Biomaterials Science & Engineering 2020 6 (1), 367-374 , DOI: 10.1021/acsbiomaterials.9b01660

   

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:

• D. W. Bauer, A. Evilevitch. Influence of internal DNA pressure on stability and infectivity of phage lambda. Journal of Molecular Biology. 427 (20), 3189–3200 (2015)
• D. W. Bauer, D. Li, J. Huffman, Fred Homa, K. Wilson, J. Leavitt, S. Casjens, J. Baines, A. Evilevitch. Exploring the balance between DNA pressure and capsid stability in Herpesviruses and phages. Journal of Virology. 89 (18), 9288–9298 (2015)
• D. W. Bauer, J. B. Huffman, F. L. Homa, A. Evilevitch.  (2013) Herpes Virus Genome, The Pressure Is On. J. Am. Chem. Soc. 135, 11216-21

Research Interests:  

My area of research is using NMR spectroscopy to study the structure-function relationship of a member of a family of murine parasite proteins that mimic the function of the TGF-beta family of signaling proteins. 

Education:

B.S. in Chemical Engineering, North Carolina State University, Raleigh, NC, May 2012

M.S. in Biomanufacturing, North Carolina State University, Raleigh, NC, Aug 2014

PhD Advisor: Dr. Andrew Hinck

Lab Address: 

Department of Structural Biology
Room 2024, 3501 Fifth Ave
Pittsburgh, PA 15260

email: STW59 - AT - pitt.edu

Publications:

• White SE. Characterization of the Freeze/Thaw Stability of a Cell Culture-Derived Influenza A/PR/8/34 (H1N1) Virus Stock and the Production Impact thereof. Raleigh, NC: North Carolina State University; 2014

• Jakubek, R. S.; Handen, J.; White, S. E.; Asher, S. A.; Lednev, I. K. Ultraviolet Resonance Raman Spectroscopic Markers for Protein Structure and Dynamics. TrAC - Trends Anal. Chem. 2018, 103, 223–229.

• Jakubek, R. S.; White, S. E.; Asher, S. A. UV Resonance Raman Structural Characterization of an (In)Soluble Polyglutamine Peptide. J. Phys. Chem. B 2019, 123 (8), 1749–1763. 

• Jakubek, R. S.; Workman, R. J.; White, S.; Asher, S. A. Polyglutamine Solution-State Structural Propensity Is Repeat Length Dependent. J. Phys. Chem. B 2019 123(19), 4193-4203.

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:

• Sharaf, N. G.; Barnes, C. O.; Charlton, L. M.; Young, G. B.; Pielak, G. J., A bioreactor for in-cell protein NMR. J. Magn. Reson., 202 (2010) 140-146.
• Miklos AC, Li C, Sharaf NG, Pielak GJ. 2010. Volume exclusion and soft interaction effects on protein stability under crowded conditions. Biochemistry 49: 6984-6991.
• Sharaf NG, Poliner E, Slack RL, Christen MT, Byeon IJ, Parniak MA, Gronenborn AM, Ishima R. The p66 immature precursor of HIV-1 reverse transcriptase. Proteins. 2014; 82(10):2343-52
• Sharaf, N. G., and Gronenborn, A. M. 19F-Modified Proteins and ¹⁹F-Containing Ligands as Tools in Solution NMR Studies of Protein Interactions. Methods in Enzymology 2015; 565:67-95
• Sharaf NG, Ishima R, Gronenborn AM. Conformational Plasticity of the NNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study. Biochemistry. 2016 Jul 19;55(28):3864-73>
• Sharaf NG, Brereton AE, Byeon IL, Andrew Karplus P, Gronenborn AM. NMR structure of the HIV-1 reverse transcriptase thumb subdomain. J Biomol NMR. 2016 66(4):273-280
• Sharaf NG, Xi Z, Ishima R, Gronenborn AM. The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site. Proteins. 2017 doi: 10.1002/prot.25383 (in press)

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