Medical Safety

Utpal Pandya, Ph.D.

*** ******** ******* **. **: 409-

***-**** (Cell)

League City, Texas 77573

Email: ***********@*****.***

USA Citizen

Summary: An experienced biochemist with expertise in the field of molecular

biology, microbiology, toxicology, parasitic diseases, genomics, proteomics

and next generation sequencing (NGS), looking for a Senior Scientist

position in research and development field.

Education:

June 1-29, 2013: Leadership Fundamentals Certificate Program with

following modules: Being a Leader, Interpersonal Mastery,

Negotiations and Conflict Management, Social Intelligence

and Ethics, The Power of "You in Action" (Capstone),

University of Houston, Texas.

1988 - 1993: Ph.D., Chemistry, Kanpur University, Kanpur, India.

Dissertation: "Nucleic Acid Structure and function as a

target for Antihelminthic Drug Action and Drug Design".

Advisor: Professor Dr. O.P. Shukla.

1985 - 1987: M.Sc., Chemistry, Lucknow University, Lucknow, India

1983 -1985: B.Sc., Chemistry, Botany and Zoology, Lucknow Christian

College, Lucknow University, Lucknow, India

Experience:

May 2009-present: (40hrs/week) Research Assistant Professor, Division of

Research, University of Houston, Texas. Currently, my role is to run and

mange Next Generation Sequencing Core facility at University of Houston. At

NGS core, I oversee the day-to-day operations and work-flow of laboratory

staff, planning and performing hands-on experiments on NGS platforms (Ion

PGM and NextSeq 500). Earlier at Center for Biomedical and Environmental

Genomics (CBMEG, which is now re-structured as NGS core), I participated in

various projects that range from environmental metagenomics to the analysis

of human DNA in disease and normal state:

. Presence of unknown and known pathogens in environmental samples

(soil, water or air) from complex backgrounds.

. Environment and disease mediated alteration in the host genome,

specifically, the copy number, methylation patterns or mitochondrial

heteroplasmy.

. Developing assay and protocols for special projects such as, changes

in the metagenome of environmental samples either due to man-made or

natural disasters, including the loss of microbial diversity or the

appearance of specific bacterial populations in Deep Water Horizon Oil

Spill case [Nature Precedings No. 713,

http://precedings.nature.com/documents/5733/version/1 (2011)].

. Microbial metagenomes involved in industrial applications such as,

biofilm analysis and bio corrosion of "Cooling Towers" water

contamination.

. Actively involved in trainings and development of professionals for

the analysis of NGS data including, training sessions on the use

technical details of sequencing including sample preparation, library

generation and actual sequencing.

March 2008-April 2009: (40hrs/week) Research Scientist, Department of

Microbiology & Immunology, University of Texas Medical Branch (UTMB),

Galveston, TX.

. Leading contributors in preparation, planning, and culmination of

two successful space flight mission (STS-118 and STS-123)

associated with SPEGIS project.

. Investigate molecular mechanism of bacterial pathogenesis using

proteomics and functional genomics approach on Streptococcus

pneumoniae as a pathogen of interest.

. Responsible for smoothly running the laboratory. Mentored

undergraduate, graduate students, summer trainees and have

supervised technicians.

. Developed 96 well plate based assays for bacterial enzymes such as,

neuraminidase, pneumolysin and beta galactosidase.

. Capsule estimation by colorimetric, ELISA and microscopic studies.

. Experience in working under GLP, BSL2, BSL3, ABSL2 and blood borne

pathogens.

. Involved in overall project management and project success.

March 2001-March 2008: (40hrs/week) Post-doctoral Fellow, Department of

Microbiology & Immunology, UTMB, Galveston, TX.

. Study Streptococcus pneumoniae Expression of Gene in Space (SPEGIS)

and ground environment.

. Instrumental in studying the role of growth temperature and

extended passage on the virulence potential of S. pneumoniae in

mice.

. Developing method for identification of Biomarker/Vaccine candidate

for Streptococcus pneumoniae by proteomics approach, such as, SELDI

and PF2D.

. Train and manage Hazard Communication Act (HCA), Laboratory Safety,

and Radioactive Safety Program.

. Responsible for mentoring the undergraduate, graduate students,

summer trainees, supervising technician.

. Presentation at meetings/conferences.

September 1997-February 2001: (40hrs/week) Post-Doctoral Fellow, Department

of Biochemistry and Molecular Biology, UTMB, TX.

. Worked on the molecular pathogenesis of cancer, focusing on the

expression, structure and function, and characterization of

glutathione S-transferases and its transporter DNP-SG ATPase/

RLIP76 in human tissues and human cell lines.

. First time documented cataractogenesis is accompanied and preceded

by apoptosis in the rat lens epithelial cells model, which can be

prevented with daily supplement of curcumin, an active ingredient

of medicinal herb turmeric.

. Developed HPLC/MS based methods to detect curcumin-glutathione

interactions.

September 1993-August 1997: (40hrs/week) Research Associate, Council of

Scientific & Industrial Research (CSIR), Central Drug Research Institute,

(CDRI) Lucknow, UP, India.

. Responsible for executing independent projects on molecular targets

for chemotherapy of parasitic infections.

. Developed DNA topoisomerases and polymerases based assay for

screening anti-filarial compounds.

. Developed UV-Spectrophotometer method to study polyamine-DNA

interactions.

. Responsible for coordinating several collaborative projects in the

lab and training summer students.

March 1990-August 1993: (40hrs/week) Senior Research Fellow, Council of

Scientific & Industrial Research (ICMR), CDRI, Lucknow, UP, India.

. Developed methods to study the role of DNA-drug interaction,

polyamines and enzymes of oxidative metabolism from filarial

parasites.

. Hands on experience of working with several pathogens, such as,

Acanthamoeba culbertsoni, Mycobacterium habana, Micrococcus luteus,

Escherichia coli, Brugia malai, Setaria cervi, Hymenolepis nana and

H. diminuta.

March 1988-February 1990: (40hrs/week) Junior Research Fellow, Council of

Scientific & Industrial Research (ICMR), CDRI, Lucknow, UP, India.

. Developed simple and effective DNA isolation method form from

helminthes parasites as well from bacterial cells.

. Developed method to estimate GC content of DNA from several

pathogens by thermal denaturation study.

Professional Skills:

. Exceptional communication and inter-personal skills.

. Ability to meet tough dead lines.

. Exceptional ability for teamwork and executing independent projects.

. Excellent data management and analytical skills.

. Excellent troubleshooting and problem-solving abilities

Technical Skills:

. Next Generation Sequencing: Sample preparation, library generation,

sequencing and analysis on Ion Torrent PGM and Illumina's NextSeq500

and GAIIx platform.

. Genomics/Proteomics: Differential gene expression analysis using micro

arrays and protein chip arrays.

. Molecular Biology: Cloning and expression of eukaryotic proteins, DNA,

RNA extractions from bacterial cells, tissue and tissue culture cells,

quantitative PCR, RT-PCR, Real time RT-PCR, Southern and Northern

hybridizations, radio-labeling of oligo-nucleotides.

. Microbiology/Cell Biology and Protein Chemistry: Maintenance of

bacterial and mammalian cell culture, cell apoptosis study, protein

and enzyme purification, SDS-PAGE, western blotting, immuno-

precipitation.

. Spectrophotometry: UV-visible and fluorescence analysis, HPLC, MALDI-

TOP, SELDI-TOF, LC -MS/MS.

. Biochemical/Enzymatic Assays: Enzymatic assays for bacterial enzymes

such as neuraminidase, peumolysin, beta-galactosidase, capsule

estimation by colorimetric and microscopic studies, ATP determination

in cells, ATPase assay of proteins, ELISA, radioimmuno assay,

mammalian enzymes such as GSTs, DNPG-ATPASe, glutathione reductase

etc.

. Animal work: Worked with mice (virulence and immunization), rat

(toxicity study) and rabbits (immunization).

Computer Skills:

. Microsoft Office (Word, Excel, PowerPoint, and Outlook).

. Experience using internet applications and databases like NCBI, BLAST,

UCSC and IGV Genome Browser etc.

. Data analysis using Sigma Stat and Graphpad Prism.

. Microarray gene expression analysis using Spotfire, SAM, SeqLab,

SeqWeb.

. Protein Array analysis using Ciphergen and Beckmann PF2D software.

. Basics, HTML, DHTML, UNIX.

Awards and Honors:

1. Biography selected in 2010, 2012 and 2013 edition of Marquis Who's Who

in America.

2. NASA Group Achievement Award (2008) for "The SPEGIS" project team, one

of the most prestigious awards a group can receive, and is presented

to groups who have distinguished themselves by making outstanding

contributions to the NASA mission.

3. Research Associate (1994-1997), CSIR, New Delhi, India

4. Research Associate (1993-1994), ICMR, New Delhi, India

5. Senior Research Fellowship (1991-1993), ICMR, New Delhi, India

6. Junior Research Fellowship (1988-1990), ICMR, New Delhi, India

Workshops and Trainings Conducted and Organized at University of Houston:

. UH-CBMEG Workshop on Next Generation of Sequencing Platforms: Provided

trainings on Ion Torrent and Illumina GAIIx to trainee from Columbia

University at University of Houston, Houston Texas September 3-8,

2012.

. Hands on Training on Next Generation Sequencing Platforms: Provided

training on Ion Torrent and Illumina GAIIx to trainee from Columbia

University, Johns Hopkins Applied Physics Lab, Tessarae, Sandia

National Lab and Edgewood Chemical Biological Center at University of

Houston, Houston Texas January 17-22, 2012.

. Hands on Training on Next Generation Sequencing Platforms: Ion Torrent

and Illumina GAIIx training provided to trainee from Johns Hopkins

Applied Physics Lab and Naval Research Lab at CBMEG, University of

Houston, Texas September 26-30, 2011.

Trainings and Certificate Courses:

1. Biological and Chemical Safety Program (BSL3 Training), offered by

Health and Safety Services/ Radiation Safety Certificate course, UTMB,

Galveston, Texas (4/2009)

2. Biological and Chemical Safety Program (BSL2 Refresher), offered by

Health and Safety Services/ Radiation Safety Certificate course, UTMB,

Galveston, Texas (2/2009)

3. Galveston County Community Emergency Response Team (CERT) Training,

Galveston County Emergency Response Center, League City, Texas (2009).

4. Euthanasia of Research Animals: AVMA Guidelines course conducted by the

AALAS Learning Library (8/ 2008)

5. Pain Recognition and Alleviation in Laboratory Animals course conducted

by the AALAS Learning Library (8/2008)

6. Good Laboratory Practices (GLPs) for Vaccine Laboratories with cGMPs and

21 CFR Part 11 certifying course at UTMB, Galveston, Texas (March 18th

2005)

7. HIPAA General Awareness certifying course at UTMB, Galveston, Texas

(March 31st 2003)

8. Diploma in Complete Pro, COMP-U-Learn, Houston, Texas (2000)

specializing in Basics, HTML, DHTML, UNIX, C, C++, Oracle 8i and VB.

9. Molecular Biology course at UTMB at Galveston, Texas (1999)

10. Biological and Chemical Safety Program, offered by Health and Safety

Services/ Radiation Safety Certificate course, UTMB, Galveston, Texas

(8/1999)

11. Basic Radiation Safety in the Laboratory, offered by Health and Safety

Services/ Radiation Safety Certificate course, UTMB, Galveston, Texas

(1/1998) and refresher every year

Teaching/Mentoring/Supervising Responsibilities:

. University of Houston: I have participated in the direct supervision

and mentoring of several summer undergraduate, graduate and work study

students in laboratory.

. Naila Naaz Federal work study student (July-Aug 2009)

. Alex Nunez Federal work study student (Sept- Dec 2011)

. Sana Basheer Federal work study student (Feb 2012-April

2012)

. University of Texas Medical Branch, Galveston:

o Summer undergraduate, graduate and work study students:

. Dr. John Kencht Federal work study student (June- July

2008)

. Nina Williams Technician and graduate student (2003-

2008)

. Mars Chafi Federal work study student (June-

July 2005)

. Vicki Mai Federal work study student (June- July

2004)

. Chris Allen Graduate rotation student (2003-

2004)

. Dang, Y. D MS student from Netherlands on rotation

(2002-2003)

. Marissa Gonzales Graduate student (2001-2002)

o Department of Microbiology and Immunology: Dr. Niesel's

laboratory

03/2001 - 4/2009: Train and manage Hazard Communication Act

(HCA), Laboratory Safety, and Radioactive Safety Program

Published Gene Bank Sequences:

1. Pandya, U., Watson, D.A. and Niesel, D.W (2002). AF533688

Streptococcus pneumoniae strain R6 Mga-like regulatory protein gene,

complete cds AF533688.1 GI:33329874.

2. Pandya, U., Watson, D.A. and Niesel, D.W. (2002). AF533689

Streptococcus pneumoniae strain SPN 4 Mga-like regulatory protein

gene, complete cds AF533689.1 GI:33329876.

3. Pandya, U., Watson, D.A. and Niesel, D.W. (2002).

AF533687 Streptococcus pneumoniae strain D39 Mga-like regulatory

protein gene, complete cds AF533687.1 GI:33329872.

4. Pandya, U., Dang,Y., Watson, D.A. and Niesel, D.W. (2005) DQ201176

Streptococcus pneumoniae strain ATCC 6304 histidine kinase gene,

complete cds DQ201176.1 GI:77921680.

Publications:

1. Widger, W, Golovko, G, Martinez, A, Ballesteros, E, Howard, J, Xu, Z,

Pandya, U, Fofanov, V, Rojas, M, Bradburne, C, Hadfield, T, Olson, N,

Santarpia, J, and Fofanov, Y. Longitudinal Metagenomic Analysis of the

Water and Soil from Gulf of Mexico Beaches Affected by the Deep Water

Horizon Oil Spill. Nature Precedings (2011) No. 713

http://precedings.nature.com/documents/5733/version/1

2. Pandya, U., Sinha, M., Luxon, B. A., Watson, D. A., Niesel, D. W.

Global transcription profiling and virulence potential of

Streptococcus pneumoniae after serial passage. Gene. 443(1-2):22-31,

2009.

3. Sonnenfeld, G., Aviles, H., Butel, J., Shearer, W.T., Niesel, D.W.,

Allen, C., Pandya, U., Blanche, A., Abbal, M. Bed Rest and Immunity.

Acta Astronotica 60: 234-236, 2007.

4. Allen, C. A., Galindo, C. L., Pandya, U., Watson, D., Chopra, A. K.,

Niesel, D. W. Transcription Profile of Streptococcus pneumoniae grown

under different conditions of normal Gravitation. Acta Astronotica 60:

433-444, 2007.

5. Allen, C.A., Galindo, C.L, Williams, N., Pandya, U., Watson, D.A.,

Chopra, A.K., Niesel. D.W. A Global Transcriptional Analysis of

Streptococcus pneumoniae in Response to Low-Shear Modeled Microgravity.

Gravit. Space Biol. Bull. 19: 143-144, 2006.

6. Pandya, U., C. Allen, D. Watson, and D.W. Niesel. Temperature

Responsive Streptococcus pneumoniae Gene Expression. Gene 360: 45-54,

2005.

7. Yang, Y., Cheng, J., Singhal, S.S., Saini, M., Pandya, U., Awasthi, S.,

Awasthi, Y.C. Role of Glutathione S-Transferases in protection against

lipid peroxidation. I. Over expression of hGSTA2-2 in K562 cell protects

against hydrogen peroxide induced apoptosis and inhibit JNK and Caspase

3 activation. Journal of Biological Chemistry 276: 193***-*****, 2001.

8. Awasthi, S., Cheng, J. Z, Singhal, S.S., Pandya, U., Sharma, R., Singh,

S.V., Zimniak, P., and Awasthi, Y.C. Functional reassembly of xenobiotic

transport from the N-and C-terminal domains of RLIP76 and identification

of ATP binding sites. Biochemistry 40: 4159-4168, 2001.

9. Awasthi, S., Singhal, S. S., Cheng, J., Pandya, U., Zimniak, P.,

Awasthi, Y. C. RLIP76. A novel glutathione-conjugate and drug

transporter. Chemico-Biological Int. 133: 28-32, 2001.

10. Awasthi, S., Cheng, J., Singhal, S.S., Zhao, T., Saini M.K., Pandya,

U., Wronski, J.C., Zimniak, P., Awasthi, Y.C. Physiological substrates

of glutathione S-transferases. Chemico-Biological Int. 133: 217-233,

2001.

11. Pandya, U., Awasthi, Y. C., Singhal, S. S., Cheng, J., Yang, Y., Hai,

T., Zhao, T., Zimniak, P., Awasthi, S. Glutathione S-transferases: Some

new functional roles. Pharmacology and Therapeutics in the New

Millennium, S.K. Gupta Edition, Narosa Publishing House, New Delhi,

India. 61: 676-687: 2001.

12. Awasthi, S., Cheng, J., Singhal, S.S., Pandya, U., Pikula, S.,

Banderowicz-Pikula, J., Ziminak, P. and Awasthi, Y.C. Identity of

RLIP76 with the ATP-Dependent transporter for glutathione conjugates and

doxorubicin human tissues. Pharmacology and Therapuetics in the New

Millennium, S.K. Gupta Edition, Narosa Publishing House, New Delhi,

India. 65:714-725, 2001.

13. Pandya, U., Chandra, A., Awasthi, S., Jin, G-F., Godley, B.F., Awasthi,

Y.C. Attenuation of galactose Cataract by low levels of Curcumin in

diet. Nutrition Research 20:515-526, 2000.

14. Pandya, U., Saini, M.K., Jin, G.F., Awasthi, S., Godley, B.F., Awasthi,

Y.C. Dietary curcumin prevents ocular toxicity of naphthalene in rats.

Toxicology Letters. 115: 195-204, 2000.

15. Awasthi, S., Pandya, U., Singhal, S.S., Lin, J.T., Thiviyanathan, V.,

Seifert, W. E., Ansari, G. A. S., Awasthi, Y.C. Curcumin-Glutathione

Interactions and the Role of Human Glutathione S-transferase P1-1.

Chemico-Bio. Int. 128: 19-38, 2000.

16. Awasthi, S., Cheng, J., Singhal, S.S., Saini M.K., Pandya, U., Pikula,

S., Pikula, J.B., Singh, S.V., Zimniak, P., Awasthi, Y.C. Novel Function

of Rlip76: ATP-dependent Transport of Glutathione-Conjugates and

Doxorubicin. Biochemistry. 39: 9327-34, 2000.

17. Pandya, U., Srivastava, S.K., Singhal, S.S., Awasthi, S., Guo, J.,

Zimniak, P., Awasthi,

Y.C and Singh, S.V. Activity of allelic variants of Pi class human

glutathione S-transferase

toward chlorambucil. Biochem. Biophys. Res. 278: 258-262, 2000.

18. Awasthi, S., Singhal, S. S., Pandya, U., Gopal, S., Zimniak, P., Singh,

S.V., Awasthi,Y.C. ATP- Dependent Colchicine transports by human

erythrocyte glutathione conjugate transporter. Toxicol. Appl.

Pharmacol. 155: 215-226, 1999.

19. Singhal, S. S., Awasthi, S., Pandya, U., Saini, M., Cheng, J., Awasthi,

Y.C. The effect of curcumin on glutathione-linked enzymes and

cytotoxicity of 4-hydroxynonenal in k562 human leukemia cells.

Toxicology Letters 109: 87-95, 1999.

20. Zhao, T., Singhal, S. S., Piper, J. T., Cheng, J., Pandya, U., Clark-

Wronski, J., Awasthi, S., Awasthi, Y.C. The role of human glutathione S-

transferases hGSTA1-1 and hGSTA2-2 in protection against oxidative

stress. Archives Biochem. Biophy. 367: 216-224, 1999.

21. Singhal, S. S., Godley, B.F., Chandra, A., Jin, G., Pandya, U., Saini,

M. K., Awasthi, S., Awasthi, Y.C. Induction of 4-hydroxynonenal

metabolizing Glutathione S-Transferase, hGST 5.8 is an early adaptive

response to oxidative stress in RPE cells. IOVS 40: 2652-2659, 1999.

22. Pandya, U., Saxena, J. K., Kaul, S.M., Murthi, P. K., Chatterjee, R.

K., Tripathi, R. P., Bhaduri, A. P., Shukla, O. P. DNA topoisomerases of

filarial parasites: Characterization and effect of antifilarial

compounds. Med. Sci. Res. 27: 103-106, 1999.

23. Pandya, U., Saxena, J. K., Shukla, O. P. Filarial DNA and its

interaction with polyamines and antifilarial drugs. J. Helminthol 71:

325-33, 1997.

24. Saxena, J. K and Pandya, U. Molecular targets for chemotherapy of

parasitic infections. Biol. Memoirs. 23: 23-31, 1997.

25. Saxena, J. K, Pandya, U., Gupta, D., Shukla, O. P. Antioxidant system

in adult and microfilariae of the bovine filarial parasite Setaria

cervi. J. Parasit. Dis. 20: 159-162, 1996.

26. Pandya U; Saxena JK; Shukla OP. Conformational dynamics of filarial DNA

and poly (dA. dT) poly (dA. dT) in the presence of suramin and spermine

J. Parasit. Dis. 20: 76, 1996.

27. Saxena, J. K., Pandya, U., Singh, R. P., Hussein, H., Kaushal, N. A.,

Shukla, O. P. Oxidative activities and electron transport in filarial

parasite Setaria cervi. J. Parasit. Dis. 19: 163-170, 1995.

28. Pandya, U., Shukla, O. P. Suramin destabilizes secondary structure of

filarial DNA. Med. Sci. Res. 22: 833-834, 1994.

29. Pandya, U., Saxena, J. K. Shukla, O.P. Effect of Ivermectin on thermal

denaturation of filarial DNA. Ind. J. Parasitol. 18: 121-126, 1994.

30. Mehlotra, R. K., Pandya, U., Saxena, J. K. Shukla, O. P. State of art

of in vitro cultivation of pathogenic amoebae. In "Proceedings of

Workshop on Cultivation of Parasites, 28 Nov.-10 Dec., 1994, C.D.R.I.,

Lucknow, pg. 132-137, 1994.

31. Pandya, U., Roy, U., Shukla, O. P. Isolation and characterization of

DNA from some helminth parasites. Med. Sci. Res. 19: 619-620, 1991.

32. Pandya, U., Shukla, O. P. Isolation of DNA from parasites using

guanidine hydrochloride. Ind. J. Parasitol. 14: 57- 62, 1990.

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Metrics

Citations 925

h-index 12

i10-index 13

References

David W. Niesel, Ph.D.

Chair & Professor

MRB, Route 1075

Department of Microbiology & Immunology

Member, Center for Tropical Medicine and Sealy Center for Structural

Biology

Senior Member, Sealy Center for Vaccine Development

Vice Dean, Graduate School of Biomedical Sciences

University of Texas Medical Branch Galveston, TX 77555

Phone: 409-***-****

Fax: 409-***-****

*******@****.***

Yogesh Awasthi Ph.D.

Professor

Address: 3500 Camp Bowie Blvd Fort Worth,

University of North Texas Health Science Center at Fort Worth, TX 76107

Department of Molecular Biology and Immunology

Office: RES 416G

Phone: 817-***-****

Email: ******.*******@****.******.***

Yuriy Fofanov, Ph.D

Professor

Department of Pharmacology & Toxicology

Campus Location: 5.426 Research Bldg 6 Mail Route: 0304

University of Texas Medical Branch Galveston, TX 77555

Phone: 409-***-****, 713-***-****

E-mail: ********@****.***

Zhenkang Xu, PhD

Research Scientist

Department of Pharmacology & Toxicology

Campus Location: 5.426 Research Bldg 6 Mail Route: 0304

University of Texas Medical Branch Galveston, TX 77555

Cell: 832-***-****

****@*****.***

Ashok Kumar Chopra, C.Sc., Ph.D.

Professor

MRB, Route 1070

Department of Microbiology & Immunology

University of Texas Medical Branch Galveston, TX 77555

Phone: 409-***-****

Lab: 409-***-****

Fax: 409-***-****

*******@****.***

Contact this candidate