Project Manager Research

SOMES KUMAR DAS, Ph.D.

**** **** *** **** ************ PA 19131 913-***-**** *********@*****.***

SUMMARY

A highly interdisciplinary scientist (chemistry/physics/biology) with four years of industrial experience in biotechnology beyond dissertation and post doctoral research, including new technology, method, assay and product development. Has broad working knowledge that spans into bio-, photo- and electro- chemistry specializing in single molecule fluorescence and nano-pore based detection. Experienced in the biochemistry/biophysics of DNA and proteins including mapping/sequence analysis of DNA in nano-channel arrays and protein biophysical and structural analysis. Deeply involved in the development of high throughput fluorescence microscope, nano-channel chip and biochemical assays for sample preparation and fluorophore labeling of long DNA molecules: all are in commercialization. Recently developed assays to detect genetic variations e.g., SVs, SNPs and CNVs by introducing new fluorophore labeling schemes, utilizing standard molecular biology techniques and multi-color high throughput fluorescence imaging at ultra-high sensitivity. Built fluorescence microscope/spectroscopy systems, gained extensive experience in synthesis of fluorescent dyes along with the labeling of biomolecules. A competent project manager, supervisor and lab coordinator; multi-tasking and excellent team player.

COMPETENCIES

Fluorescence/Bioanalytical detection

• Fluorescence, CD, UV-Vis spectroscopy

• Fluorescence microscopy, mul-ticolor imaging.

• Single molecule imaging, tracking and photobleaching

• Optical instrumentation development

• Fluorescent dye synthesis and labeling of bio-molecules.

• SPR, DSC, HPLC, SDS-PAGE, IEF, SEC.

• Surface modification, binding -immobilization of protein or DNA on surfaces.

Biochemistry/Biophysics

• Protein, DNA isolation and characterization

• PCR amplification, target enrichment, DNA hybridiza-tion, ligation, polymerization and restriction digestion

• DNA mapping by fluorescence imaging in nano-channel arrays, detection of SNP/SV /CNVs

• Kinetic and thermodynamic characterization of membrane proteins. Subunit counting in protein oligomers by single molecule photobleaching.

Electrophysiology/Nanopore detection

• Single channel electrophysiology of bacterial toxins and ion channel proteins.

• Electrochemical detection on electrode surface, Cyclic Voltammetry.

• Nano-pore based detection of DNA/proteins/peptides.

• Labview programming for signal detection and Matlab, Origin for data analysis.

• Experiences in lipid bilayer setups including suspended bilayer for simultaneous measurement of flu-orescence and electrophysiology.

INDUSTRIAL EXPERIENCE

Senior Scientist: BioNano Genomics, Inc. (privately held) (formerly Bionanomatrix Inc.), Philadelphia, PA.

07/08-05/12

• Strongly involved with the R&D team in method and assay development for the single molecule DNA structural analysis and mapping by fluorescence imaging in nano-fluidic channel arrays. Worked in optimizing and simplifying complex assays to achieve commercial levels of stability and performance by improving and troubleshooting the existing methods and assays (from 60% to > 90% fluorescence labeling of DNA).

• Took leading role in designing and developing new, highly efficient fluorescent labeling schemes compatible to the Company’s NanoAnalyzer and nanochannel chip for high content fluorescence imaging to extract the sequence information of DNA.

• Acted as the key person in the advanced technology group to explore and develop new technology, applications, assay and protocols by providing intellectual and creative solutions, and research support. Designed, implemented, and analyzed experiments to test the feasibility of new methods. Developed project plans collaboratively and assumed responsibility for timely project completion. Documented the work and research summaries, prepared SOP's and invention disclosures.

• Established and optimized new method and protocols starting from the sample preparation to nano-channel loading (achieved maximum resolvable occupancy from 3% to ~10%) and fluorescence imaging of long DNA molecules for mapping to detect genetic variations.

• Improved DNA polymer stretching efficiencies in nano-channel, assessed alternative high throughput DNA stretching strategies, and developed understanding of the fundamental physical principles relevant to DNA stretching and nano-fluidic device function.

• Developed new method for size and concentration determination of sub-kilobase oligonucleotides by fluorescence imaging in nano-channel arrays.

• Worked closely and iteratively with nano-fabrication, bioinformatics, instrumentation engineers and molecular biologists to optimize existing technologies; develop, optimize and validate new methods, applications and assay schemes for the purpose of product development.

• Managed a number of research grants (NIH, NIST, STTR) by conducting research and preparing progress reports. Led the collaborative projects with UCSF, UPENN, Drexel University and Complete Genomics Inc.

• Wrote one grant proposal, published/prepared peer-reviewed 4 articles and 2 patents.

• Managed people, projects and partnered with many cross functional teams.

RESEARCH & PROFESSIONAL EXPERIENCE

• Research Assistant Professor: Department of Chemistry & Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH. 12/06 to 06/08

Worked as laboratory head to setup a research laboratory to study membrane proteins utilizing single molecule fluorescence and single channel electrophysiology techniques. Built setups for TIRF, FRET and patch clamp experiments. Designed and executed experiments and analyzed data. Drafted scientific proposals, managed research projects, and prepared scientific reports. Attended scientific meetings and gave talks. Supervised and trained graduate and under-graduates.

Achievements: (i) Developed a unique lipid bilayer setup to record the fluorescence and electrical signals originated from the structural fluctuations of single membrane protein molecule interacting with the bilayer. (ii) Correlated the voltage dependent structural dynamics of channel protein Colicin-Ia with the fluorescence and electrical signals. Both of these high-tech methods were unique to the scientific community.

Research Associate: Department of Biochemistry and Molecular Biology, University of Kansas Medical Center. (Dr. Alexey Ladokhin Group), Kansas City, KS. 08/05 to 11/06

Research on the thermodynamics of membrane protein (bacterial toxins) binding to lipid membranes at different pH in presence of fluorinated surfactants using various spectroscopy tools including single molecule fluorescence correlation spectroscopy (FCS, autocorrelation and cross correlation), fluorescence resonance energy transfer (FRET) and fluorescence lifetime imaging (FLIM) combined with steady state (emission and excitation, polarization) and time resolved fluorescence spectroscopy (TCSPC). Did experiments, analyzed data, prepared project reports and manuscripts for publications. Presented the research findings in scientific conferences.

Achievements: (i) Was the first to show the application of fluorinated surfactants (non-invasive to membranes, solubilize and protect membrane proteins from aggregation or denaturation) in membrane protein research. (ii) Supervised a project on the determination of free energy change involved in binding of diphtheria toxin T-Domain to lipid membrane at different pH.

• Research Scientist: Department of Medical Biochemistry and Genetics, Texas A&M University. (Prof. Hagan Bayley Group), College Station, TX. 09/02 to 08/05

Established single molecule imaging laboratory. Prepared a lipid bilayer setup to study oligomerization of pore forming toxins on lipid membrane using single molecule fluorescence microscopy (single molecule photobleaching, single particle tracking) and single channel electrophysiology. Designed and optimized experimental protocols, did experiments, analyzed experimental data, prepared project reports and manuscripts for publication. Trained and helped graduate and under-graduate students.

Achievements: (i) Established a new and quick method for counting the subunits of membrane protein oligomers by single molecule photobleaching. (ii) Did spectroscopic screening of a large number of fluorescent dyes to find the suitable ones for specific single molecule fluorescence experiments. (iii) Designed and established several methods of making lipid bilayer for the study of membrane proteins by using fluorescence and electrophysiology detections separately or simultaneously. (iv) Designed and developed PDMS/photolithography based microchannel devices for single molecule studies.

• Post Doctoral Associate: Department of Chemistry, University of Connecticut. (Prof. Harry A. Frank Group), Storrs, CT. 05/99 to 08/02

Took part in laboratory research to study the structure and function of the molecular components of light harvesting proteins and reaction centers using biochemical, spectroscopic and electrochemical tools (fluorescence spectroscopy, HPLC, ultracentrifuge, SDS-Page, IEF, cyclic voltammetry etc.). Did experiments, analyzed data, prepared project reports and manuscripts for publications.

Achievements: (i) Established and scaled up protocols for isolation and purification of photosynthetic membrane proteins from plants/photosynthetic bacteria. (ii) Established a computational method to de-convolute the composite UV-Vis absorption spectral trace of light harvesting complex (LHCII) to those of its molecular components. (iii) Experimentally first to show direct and reversible electron transfer between electrodes and spinach Photosystem I reaction center (PS I) in lipid films by thin film voltammetry.

• Graduate Researcher: Indian Institute of Technology Kanpur, India. 06/94 to 03/99

Synthesized and characterized a number of fluorescent probe molecules. Studied the microenvironments of biomimetic sytems e.g., liposomes, micelles using those molecules as probes. Primary techniques used are steady state and time resolved fluorescence spectroscopy.

EDUCATION

• PH.D. in Biophysical Chemistry: 1999, Indian Institute of Technology Kanpur, India.

• M.S. Chemistry: 1994, University of Kalyani, West Bengal, India.

PUBLICATIONS

1. Single nucleotide identification in DNA by single molecule fluorescence imaging in nano-channel array. S. K. Das, M. Xiao, H. Cao. (Submitted)

2. Nano-mapping of the major histocompatibility complex: a model for structural variation analysis and sequence assembly. E. T. Lam, A. Hastie, C. Lin, D. Ehrlich, S. K. Das, M. D. Austin, P. Deshpande, H. Cao, N. Nagarajan, M. Xiao, and Pui-Yan Kwok. Nat. Biotech. (In press).

3. Transition between two regimes describing internal fluctuation of DNA in a nanochannel. T. Su, S. K. Das, M Xiao, P. Purohit. PLoS One, 6(3): 2011, e16890.

4. Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes. S. K. Das, M. Austin, M. Akana, P. Deshpande, H. Cao, M. Xiao. Nucleic Acid Research, 38(18): 2010, e177.

5. FCS study of the thermodynamics of membrane protein insertion into the lipid bilayer chaperoned by fluorinated surfactants. Y.O. Posokhov, M.V.Rodnin, S. K. Das, B. Pucci, A.S.Ladokhin. Biophys J. 95(8): 2008, L54-56.

6. Membrane protein stoichiometry determined from the stepwise photobleaching of dye labeled subunits. S. K. Das, M. Darshi, S. Cheley, M. Wallace, H. Bayley. ChemBioChem, 8 (9), 2007, 994-999.

7. Isolation and characterization of carotenosomes from a bacteriochlorophyll c-less mutant of Chlorobium tepidum. N. U. Frigaard, H. Li, P. Martinsson, S. K. Das, H. A. Frank, T. J. Aartsma, D. A. Bryant. Photosynthesis Research. 86(1-2), 2005, 101-111.

8. Light harvesting by carotenoids incorporated into the B850 light-harvesting complex from Rhodobacter spheaeroides R-26.1: Excited-state relaxation, ultrafast triplet formation, and energy transfer to Bacteriochlorophyll. E. Papagiannakis, S. K. Das, A. Gall, I. M. H. van Stokkum, B. Robert, R. van Grondelle, H. A. Frank, J. T. M. Kennis, J. Phys. Chem. B. 107(23), 2003, 5642.

9. Electron Transfer Reactions of Redox Cofactors in Spinach Photosystem I Reaction Center Protein in Lipid Films on Electrodes. B. Munge, S. K. Das, R. Ilagan, Z. Pendon, J. Yang, H. A. Frank, J. F. Rusling, J. Am. Chem. Soc. 125 (41), 2003, 12457.

10. Inclusion Complexation of 2-(4 -N, N-Dimethylaminophenyl)-1H-naphth[2,3-d]imidazole by -Cyclodextrin: Effect on the Twisted Intramolecular Charge Transfer Emission. S. K. Das. Chem. Phys. Lett. 361, 2002, 21.

11. Pigment Compositions, Spectral Properties, and Energy Transfer Efficiencies between the Xanthophylls and Chlorophylls in the Major and Minor Pigment-Protein Complexes of Photosystem II. S. K. Das and H. A. Frank. Biochemistry-US: 41 (43), 2002, 13087.

12. The Photochemical Behavior of Xanthophylls in the Recombinant Photosystem II Antenna Complex, CP26. H. A Frank, S. K. Das, J. A. Bautista, D. Bruce, S. Vasil'ev, M Crimi, R. Croce, R. Bassi. Biochemistry-US: 40 (5), 2001, 1220.

13. Excited State Intramolecular proton transfer 2-(2 -Hydroxyphenyl)-1H-napth[2,3-dimidazole: Effects of Solvents and pH. S. K. Das, G. Krishnamoorthy and S. K. Dogra. Can. J. Chem. 78 (2): 2000, 191.

14. Intramolecular Excited State proton Transfer of 2-(2 -Hydroxyphenyl) benzimidazole in Non-ionic micelles Tweens. S. K. Das and S. K. Dogra. J. Coll. Interface Sci., 205, 1998, 443.

15. Ground and Excited State prototropic reactions in 2-(2 -Methoxyphenyl)-3H-imidazo [4, 5-b] pyridine. S. K. Das and S. K. Dogra. J. Chem. Soc Perkin Trans. 2, 1998, 2765.

16. Excited state Intramolecular Proton Transfer of 2-(2 -Hydroxyphenyl) benzimidazole in Non-ionic Micelles Brijs. S. K. Das and S. K. Dogra. J. Chem. Soc. Faraday Trans., 94, 1998 139.

17. Excited state intramolecular proton transfer reaction in 2-(2 -Hydroxyphenyl)benzimidazole in micellar solutions. S. K. Das, A. Bansal and S. K. Dogra. Bull. Chem. Soc. Jpn., 70, 1997, 307.

PATENTS

• Systems and methods for assessing biomolecule characteristics. P. Deshpande, A. G. Marlin, M. Kochersperger (jr), A. Sharaonov, W. Stedman, M. Xiao, H.B. Sadowski, S. K. Das, M Akana, D. Bozinov, M. Requa and H. Cao. Appl. No: 61/418,516. 01 December 2010.

• Methods and related devices for single molecule whole genome analysis. M. Xiao, S. K. Das, Appl. No. 61/253,639. 21 October, 2009.

WORK VISA STATUS

US Permanent Resident (Green Card)

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