Aishwarya Prakash, Ph.D.

Assistant Professor of Oncologic Sciences

2016-03-09 Aishwarya Prakash resized.jpg

 

USA Mitchell Cancer Institute
1660 Springhill Ave.
Mobile, AL 36604
(251) 410-4915
aprakash@health.southalabama.edu

 

Professional Profile

Primary Interests:
- Mitochondrial Disease and Cancer
- Oxidative DNA Damage and Repair
- Enzyme Binding and Kinetics
- Structural Biology including Macromolecular X-ray Crystallography and Small Angle X-ray Scattering

Education and Training:

- Ph.D., Cancer Research, University of Nebraska Medical Center (UNMC, Mentor: Dr. Gloria Borgstahl). 2005-2010
- B.S., Biotechnology, with a Minor in Chemistry, The University of Nebraska at Omaha (UNO). 2003-2004
- A.A.S., Biotechnology, Collin County Community College District (CCCCD), Plano, Texas. 2001-2002

Professional Appointments and Experience:
- Assistant Professor of Oncologic Sciences, Mitchell Cancer Inst., Mobile, Ala., 2016-present
- Post-doctoral researcher, University of Vermont (UVM, Mentor: Dr. Sylvie Doublié). 2010-2016 
- Guest instructor: Macromolecular Structure of Proteins and Nucleic Acids, UVM course MMG240. 2014
- Graduate Student Teaching Assistant for Cell Biology, UNMC Course BRTP 822. 2007
- Graduate Student Tutor for incoming Cancer Research Graduate Program Students, UNMC. 2006
- Research Technician; UNMC, PI: Dr. Tatiana Bronich, Nanoparticle Drug Delivery. 2005
- Summer Research Student, UNMC, PIs: Drs. Alexander Kabanov and Tatiana Bronich. 2004
- Teaching Assistant, UNO, Courses: beginning Algebra and College Algebra. 2003-2004
- Student Research Associate, Mary Kay Inc. Research and Development, Dallas, TX. 2002
- Teaching Assistant/Tutor, Mathematics Laboratory, CCCCD, TX. 2001-2002 

Research Support:

Active
1K99ES024417 – 01 Prakash, Aishwarya, PI. 08/01/14 – 07/30/19. 12 calendar
NIH/NIEHS $85,743
Repair of Environmentally and Endogenously Induced Oxidized Mitochondrial-DNA Damage   

Completed
- J. Walter Juckett Fellowship (Prakash, A., Fellow) 07/01/12-06/30/14 --10.8 calendar The Vermont Cancer Center  $50,000          
- Presidential Fellowship (Prakash, A., Graduate student)   07/01/09-06/30/10 -- 12 calendar University of Nebraska Medical Center $21,000          
- Graduate Studies Fellowship (Prakash, A., Graduate student)  07/01/07-06/30/09 -- 12 calendar University of Nebraska Medical Center $21,000          
- Incoming Graduate Fellowship (Prakash, A., Graduate student) 07/01/05-06/30/06 --12 calendar University of Nebraska Medical Center $21,000          

Specialized Training
- RapiData Fundamentals in Crystallography, Brookhaven National Labs, Long Island, N.Y., 2012
- Principles and Methods in Light Scattering, Wyatt Technology, Santa Barbara, Calif., 2007
- Eppley Institute (UNMC) Short Course: Stem Cells in Cancer and Development, 2006; Ubiquitin and Cancer, 2007; Metabolic Regulation of Human Malignancies, 2008; MicroRNA and Cancer, 2009; Metastasis and the Tumor Environment, 2003.
- Certified Nursing Assistant, Omaha, Neb., 2003 

Professional Recognition and Awards:
- K99/R00 NIH Pathway to Independence Award – NIEHS, 2014   
- J. Walter Juckett post-doctoral fellowship, The Vermont Cancer Center, 2012
- Norman and Bernice Harris Award in Cancer Research, Eppley Cancer Institute, 2010
- Berndt Graduate Student Travel Award, UNMC, 2009
- NIH Graduate Student Research Festival Travel award, NIH Nov. 12-13, 2009
- Summa Cum Laude Graduate, University of Nebraska at Omaha, Dec. 2004, (GPA 3.8)  2004
- International Students’ Scholarship, University of Nebraska at Omaha 2003-2004 
- Regent Scholarship for Excellence in Academics, University of Nebraska at Omah,a 2003-2004 
- Dean’s List, University of Nebraska at Omaha, 2003-2004 
- Nominee for Student Employee of the Year, University of Nebraska at Omaha,  2003-2004 
- Emerging Scholar in Math Award, Collin County Community College District (CCCCD), Texas,  2002
- The Pamela Justice Scholarship for Women in Math and Natural Sciences, CCCCD, Texas, 2002
- The Edward Bock Scholarship for proficiency in Math, CCCCD, Texas, 2002
- Dean’s List/ President’s List, CCCCD, Texas, 2001-2002
- Math World Honor for Young Mathematicians – All India competition, Bangalore, India,1999

Scientific Conferences Organized:
- Elected Chair, Gordon Research Seminar (GRS), Mutagenesis, 2016

Publications:

Peer-reviewed Publications

  1. Sjolund, A., Nemec, A.A., Paquet, N., Prakash, A., Sung, P., Doublié, S., Sweasy, J.B. “A Germline Polymorphism of Thymine DNA Glycosylase Induces Genomic Instability and Cellular Transformation”. (October 2014) Plos Genetics 10(11), e1004753 (2014).
  2. Prakash, A., Carroll, B.L., Sweasy, J.B., Wallace, S.S., Doublié, S. “ Genome and Cancer Single Nucleotide Polymorphisms of the Human NEIL1 DNA Glycosylase: Activity, Structure and the Effects of Editing”. DNA Repair 14:17-26 (2014).
  3. Prakash, A., Eckenroth, E.E., Imamura, K., Averill, A.M., Wallace, S.S., Doublié, S. “Structural Investigation of a Viral Ortholog of NEIL2/3 in Base Excision Repair”. DNA Repair. 12:1062-71 (2013).
  4. Lada, A. G., Waisertreiger, I. S. R., Grabow, C. E., Prakash, A., Borgstahl, G. E. O, Rogozin, I. B., and Pavlov, Y. I.  “Replication protein A (RPA) hampers the processive action of APOBEC3G cytosine deaminase on single-stranded DNA” PLoS ONE 6, e24848 (2011).
  5. Prakash, A., Natarajan, A., Marky, L. A., Ouellette, M. M., and Borgstahl, G. E. O. “Identification of the DNA binding domains of human Replication Protein A that recognize G-quadruplex DNA” J. Nucleic Acids 2011, Article ID 896947, 14 pages (2011).
  6. Prakash, A., Kieken, F., Marky, L. A., and Borgstahl, G. E. O. “Stabilization of a G-quadruplex from unfolding by Replication Protein A using potassium and the porphyrin TMPyP4” J. Nucleic Acids 2011, Article ID 529828, 13 pages (2011).
  7. Deng, X*., Prakash, A*., Dhar, K., Baia, G. S., Kolar, C., Oakley, G. G. and Borgstahl, G. E. O. “Human Replication Protein A-Rad52-ssDNA Complex: Stoichiometry and Evidence for Strand Transfer Regulation by Phosphorylation” Biochemistry 48, 6633-6643 (2009). Citations: 10

* These authors contributed equally to this work.

Review Articles
- Prakash, A., and Doublié, S. “Base Excision Repair in the Mitochondria”, Journal of Cellular Biochemistry, PMID: 25754732, (2015).

Book Chapters
- Prakash, A., Doublié, S., and Wallace, S. S. “The Fpg/Nei Family of DNA Glycosylases: Substrates, Structures and Search for Damage”, in Mechanisms of DNA Repair.  Paul W. Doetsch, Editor. Progress in Molecular Biology and Translational Science, (2012).
- Prakash, A., and Borgstahl, G. E. O. “The structure and function of replication protein A in DNA replication” Invited Review for “The Eukaryotic Replisome: a guide to protein structure and function” Publisher: Springer. Subcell Biochem. 62, 171-196 (2012).

Manuscripts in preparation
- Imamura, K., Eckenroth, B.E., Prakash, A., Fleming, A., Burrows, C.J., David, S.S., Wallace, S.S., and Doublié, S. “Structural analysis of a viral ortholog of human NEIL1 in complex with the further oxidation products of 8-oxoguanine”, in preparation.
- Prakash, A., Cao, V.B., Wallace, S.S., and Doublié, S. “Post-translational modifications in NEIL1”, in preparation.
- Prakash, A., Moharana K., Wallace, S.S., and Doublié, S. “Insight into the interaction between NEIL1 and PCNA”, in preparation.

Service:

Faculty of 1000 – Journal Evaluations
- Prakash, A., and Doublié, S. April 2013. Single pH buffer refolding screen for protein from inclusion bodies. Coutard B, Danchin EG, Oubelaid R, Canard B, Bignon C. Protein Expr Purif. 2012 Apr; 82(2):352-9.
- Prakash, A., and Doublié, S. January 2013. Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. Adhikary S, Cato MC, McGary KL, Rokas A, Eichman BF. DNA Repair (Amst). 2012 Dec 27.
- Prakash, A., and Doublié, S. October 2012. DIBER: protein, DNA or both? Chojnowski G, et. al. Acta Crystallographica Section D, October 2010. 
- Prakash, A., and Doublié, S. December 2011. Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank. Joosten RP et. al. Bioinformatics Oct 27, 2011.
- Prakash, A., and Doublié, S. August 2011. Protein crystallization facilitated by molecularly imprinted polymers. Saridakis, E et al. PNAS May 4 2011.
- Prakash, A., and Doublié, S. March 2011. How to read (and understand) Volume A of International Tables for Crystallography: an introduction for non-specialists. Dauter Z, Jaskolski M; Journal of Applied Crystallography July 2010.
- Prakash, A., and Doublié, S. January 2011. Look and see if it is time to induce protein expression in Escherichia coli cultures. KD Kelley, LQ Olive, A Hadziselimovic, CR Sanders; Biochemistry 2010 Jul 6 49 26:5405-7.  This evaluation was in the Structural Biology Faculty most viewed Top 10 list.

Presentations:

Poster Presentations

International Conferences
- Prakash, A., Galick, H.A., Carroll, B.L., Sweasy, J.B., Wallace, S.S., Doublié, S. “Genome and Cancer SNPs of the Human NEIL1 DNA glycosylase: Activity, Structure, and the Effects on Genome Stability”. Gordon Research Conference: Mutagenesis, Girona, Spain, June 2014.
- Prakash, A., Natarajan, A., Marky, L. A., Ouellette, M. M. and Borgstahl, G. E. O. “Identification of the DNA binding domains of human Replication Protein A that recognize G-quadruplex DNA”. Maintenance of Genome Stability, Jolly Beach Resort, Antigua, March 2010.
- Prakash, A., Deng, X., Oakley G., and Borgstahl, G. E. O. “Human Replication Protein A, Rad52, ssDNA Complex:  Stoichiometry and Regulation of Strand Transfer by Phosphorylation." Meeting on DNA Repair and Mutagenesis, Whistler, BC, Canada. June 2009.

National Conferences
- Prakash, A., Eckenroth, B.E., Imamura, K., Averill, A.M., Wallace, S.S., Doublié, S. “Structural Investigation of Human NEIL1 and a Viral Ortholog of NEIL2/3." Gordon Research Conference: Mammalian DNA Repair, February 2013, Ventura, CA.
- Prakash, A., Eckenroth, B.E., Imamura, K., Averill, A.M., Wallace, S.S., Doublié, S. “Structural Investigation of Human NEIL1 and a Viral Ortholog of NEIL2/3." Vermont Cancer Center Symposium, November 2011, Burlington, VT.
- Prakash, A., Deng, X., Oakley G., and Borgstahl, G. E. O. “Human Replication Protein A, Rad52, ssDNA Complex:  Stoichiometry and Regulation of Strand Transfer by Phosphorylation." UNMC Structural Biology Workshop. July 2009.
- Prakash, A., Deng, X., Oakley G., and Borgstahl, G. E. O. “Human Replication Protein A, Rad52, ssDNA Complex:  Stoichiometry and Regulation of Strand Transfer by Phosphorylation." Nebraska Epscor, Lincoln, NE. October 2008.
- Prakash, A., Deng, X., Oakley G., and Borgstahl, G. E. O. “Human Replication Protein A, Rad52, ssDNA Complex:  Stoichiometry and Regulation of Strand Transfer by Phosphorylation." Keystone Symposium, Santa Fe, NM. February 2008.
- Prakash, A., Deng, X., Dhar, K., Kolar, C.H., Oakley G., and Borgstahl, G. E. O. “The Stoichiometry and Affinity of ssDNA Coated human RPA Complexes with Rad52 and the Effects of RPA Hyperphosphorylation." 51st Annual Biophysical Society Meeting, Baltimore, MD. March 2007.
- Prakash, A., Bronich, T. “Star Polymer Unicellular Micelles as a Novel Approach to Drug Delivery.” Summer Undergraduate Student Research Presentations, UNMC, August 2004.

Oral Presentations
- Prakash, A., Carroll, B.L., Galick, H., Sweasy, J.B., Wallace, S.S., Doublié, S. “Single Nucleotide Polymorphisms of the Human NEIL1 DNA Glycosylase: Structure, Function, and Effects of Genome Stability”. DNA Repair and Mutagenesis (DRAM), Massachusetts Institute of Technology, Boston, MA, January 2015.
- Prakash, A., Carroll, B.L., Galick, H., Sweasy, J.B., Wallace, S.S., Doublié, S. “The Human NEIL1 DNA Glycosylase: Polymorphisms and Role in Mitochondrial Genome Maintenance”. Eppley Institute Seminar Series, The University of Nebraska Medical Center, Omaha, NE, December 2014.
- Prakash, A., Eckenroth, B.E., Carroll, B.L., Imamura, K., Averill, A.M., Sweasy, J.B., Wallace, S.S., Doublié, S. “Biochemical investigation of Human NEIL1 and its polymorphic variants and structural investigation of a viral ortholog of NEIL2/3”. Presented annually at the Program Project Grant monthly meeting, December 2011, February 2013, University of Vermont, Burlington, VT.
- Prakash, A., Borgstahl, G.E.O. “DNA Binding Specificity of RPA and Stoichiometry of RPA-DNA Complexes”. Presented annually at the Eppley Institute for Research in Cancer, UNMC, Graduate Student Seminar, May 2009, April 2008, August 2007, December 2006.
- Prakash, A., Deng, X., Oakley G., and Borgstahl, G. E. O. “Sequence specificity of the primary DNA binding domains of Replication Protein A”. Midwest Student Biomedical Research Forum, February 2007 and 2008, Omaha, Nebraska.
- Prakash, A. Majmudar, G. “Effect of PVP on Moisturization and Tightening of Skin”. Summer Undergraduate Research, Mary Kay Corp., Dallas, Texas, August 2002.

Other Activities and Societies:
- Post-doctoral association, UVM. Active member – 2011 - 2015
- Associate Faculty Member, Faculty of 1000 – 2011 - present
- American Cancer Society – Hope Lodge – Volunteer, 2011 – present
- American Cancer Society – Relay for Life – Team Captain, 2007-10
- Student Senate – Graduate College Senator 2006-07, 2007-08, 2008-10
- Student Representative - Eppley Cancer Institute UNMC 2007-08
- Graduate Studies Association – Member of the Executive Committee (Social Chair and PR Representative) 2010.

 

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