Sandeep Misra

Address:

438 Beauregard Cir
Oxford, MS 38655
USA

Research Interests:

Microbiology Drug resistance
Bacterial pathogenesis
Food-borne diseases Phosphoproteomics of bacteria

Biography:

Sandeep K Misra, Ph.D. Postdoctoral Research Associate University of Mississippi Oxford, MS, 38655 Email: [email protected] Phone: 662-304-7265
Education: 2005 Ph.D. Life Sciences, Central Drug Research Institute, Lucknow, India.
1999 M.S. Biochemistry, Dr. R.M.L. Avadh University, Faizabad, India.
1997 B.S. Biology, Dr. R.M.L. Avadh University, Faizabad, India. Postdoctoral Research Experiences: Department of Biomolecular Sciences, University of Mississippi (2015- present)  Developing and improving methods for hydroxyl radical protein footprinting via fast photochemical oxidation of proteins utilizing mass spectrometry.  Identification of binding site of Arixtra to gp120 of HIV virus. MD Anderson Cancer Center, Houston, Texas, USA (2013 - 2014)  Identified novel protein biomarkers for the early diagnosis of hepatocellular carcinoma. Institut National de la Recherche Agronomique, Jouy-en-Josas, France (2010-2012).  Identified and analyzed Serine/Threonine/Tyrosine phosphoproteome of a gram positive, food-borne pathogen Listeria monocytogenes.  Identified its proteins overexpressed in response to PrfA, a main virulence regulator protein, by stable isotope labeling in cell culture (SILAC) approach.  Identified the substrate targets of Serine/Threonine phosphatase of L. monocytogenes. National Institutes of Health, Bethesda, Maryland, USA (2005-2009)  Identified and quantified phosphoproteins involved in the signal transduction pathway of cystic fibrosis transmembrane conductance regulator activation, mediated by forskolin and adenosine.  Identification of interacting partners of sodium-hydrogen exchanger regulatory factor-1 by quantitative immunoprecipitation coupled with knockdown method.  Identification of protein interactions involved in homologous recombination during mouse meiosis and mechanisms of action of Hop2, Mnd1 and Dmc1. Ph.D. Dissertation: “Characterization of folding intermediates of methylenetetrahydrofolate reductase from Escherichia coli.” Research performed under the supervision of Dr. Vinod Bhakuni.  Characterized the effect of modulation of hydrophobic and ionic interactions on the structure and function of tetrameric methylenetetrahydrofolate reductase from E. coli.  Stabilized dimers of this enzyme and demonstrated that it can still be active.  Determined the role of N- and C-terminal domains of hyaluronate lyase enzyme from Streptococcus pneumoniae. Analyzed the interaction between these domains. Selected Skills & Expertise:  Proteomics:1D and 2D-gel electrophoresis, sample preparation by in-solution and in-gel digestion, Enrichment of phosphopeptides, nano-HPLC coupled with mass spectrometer, Identification of phosphopeptides, Quantitative proteomics (unlabeled, dimethyl, SILAC labeled), Protein preparation after subcellular fractionation. Fast photochemical oxidation of proteins, Hydroxyl radical protein footprinting.  Bioinformatics: Proteomics database search engines: MaxQuant, Sequest, Proteome discoverer, X!Tandem, Mass Matrix and Byonic. Other proteomics softwares: Skyline, Scaffold, Panther, Ingenuity pathway analysis, Cytoscape, String, Ascore, Phosphoscore. GproX, Perseus, R, Prism, Netphosbac, Peptide cutter, Oncomine, Basic knowledge of python.  Molecular Biology: DNA and RNA extraction from various sources, DNA cloning, RT-PCR, Primer extension overlap, Gene cloning, Site-directed mutagenesis, Heterologous expression of proteins in bacterial expression system. Southern and Western blotting, Co-immunoprecipitation.  Protein Chemistry: Protein purification using various techniques viz. Size exclusion, Hydrophobic, Ion exchange and Affinity chromatography, Enzyme assays, Chemical modification and Chemical cross linking of proteins, Preparation of soluble proteins from inclusion bodies. Isoelectric focusing, Peptide purification. Protein-protein pull-down assays. ELISA.  Cell Biology: Mammalian cell culture, Transfection in mammalian cells, Immunohistochemistry, Fluorescence microscopy, confocal microscopy, in vivo cross-linking of proteins, and characterization of glycosaminoglycans. Research Publications: T Duarte-Salles, S.K. Misra, et al., Circulating osteopontin and prediction of hepatocellular carcinoma development in a large European Population. Cancer Prevention Research, 9 (9), 758-765. 2016. S.K. Misra, Francine Moussan Desiree Ake, Zongfu Wu, Eliane Milohanic, Thanh Nguyen, Cao, Pascale Cossart, Josef Deutscher, Veronique Monnet, Cristel Archambaud, Celine Henry. Quantitative proteome analyses identify PrfA-responsive proteins and phosphoproteins in Listeria monocytogenes. Journal of Proteome Research, 13, 6046-6057, 2014. S.K. Misra, E. Milohanic, F. Aké, I. Mijakovic, J. Deutscher, V. Monnet, and C. Henry. Analysis of the serine/threonine/tyrosine phosphoproteome of the pathogenic bacterium Listeria monocytogenes reveals phosphorylated proteins related to virulence. Proteomics, 11, 4155-4165, 2011. S.K. Misra and V. Bhakuni. Proteomics: identification of cancer biomarkers. In Current R&D Highlights, 32, 1-6, 2004. S.K. Misra and V. Bhakuni. Unique holoenzyme dimers of the tetrameric enzyme Escherichia coli methylenetetrahydrofolate reductase: characterization of structural features associated with modulation of the enzymes function. Biochemistry, 42, 3921-3928, 2003. Published Abstracts in Seminars/Conferences: S.K. Misra and J.S. Sharp. American society for mass spectrometry, Jun 5-9, 2016, San Antonio, Texas. Size-selective controlled heparin depolymerization to obtain heparin oligosaccharides. S. Misra and L. Beretta. The liver meeting, Nov 13-17, 2015, San Francisco, California. Circulating osteopontin and prediction of hepatocellular carcinoma development in a large European population. S.K. Misra, E. Milohanic, F. Aké, I. Mijakovic, J. Deutscher, V. Monnet and C. Henry. Human Proteome Organization, Sep, 4-7, 2011, Geneva, Switzerland. Analysis of the Serine/Threonine/ Tyrosine phosphoproteome of the pathogenic bacterium Listeria monocytogenes. S.K. Misra, E. Milohanic, F. Aké, I. Mijakovic, J. Deutscher, V. Monnet, and C. Henry. Société Française d'Electrophorèse et d'Analyse Protéomique, Sep, 3-7, 2010, Marseille, France. Identification of Serine/Threonine/Tyrosine phosphorylated proteins of Listeria monocytogenes. S.K. Misra, Y. Yang and V. Raghuram. NIH conference, April, 2-3, 2009, Annapolis, Maryland. Identification of interacting partners of human NHERF-1. S.K. Misra and V. Bhakuni. Centre for Cellular and Molecular Biology, Hyderabad, India. Nov, 24-29, 2002. Structural domains of Streptococcus pneumoniae and their interactions. Awards and Fellowships: ‘Postdoctoral Research’ award from Nationale Instutut de la Recherche Agronomique, France, 2010-2012. ‘Visiting scholar fellowship’ from National Institutes of Health, USA, 2005-2009. 'Senior Research Fellowship' from Council of Scientific and Industrial Research, India, 2002-2004. 'Junior Research Fellowship' from Council of Scientific and Industrial Research, India, 2001-2002. 'Research Scholar’s Fellowship' from Central Drug Research Institute, India, 1999-2001. Book Chapters: S.K. Misra. Chapter name: Natural Compounds: Cancer Preventive Agents Book name- Cancer Preventive and Therapeutic Compounds: Gifts from Mother Nature. Publisher: Bentham e-books (ISBN: 978-1-68108-492-3), 2017. Md.S. Akhtar, S.K. Misra, V. Bhakuni. Chapter name: Structural domains of Streptococcus pneumoniae hyaluronate lyase: their interactions and role in function and folding of the enzyme. Publisher: Alpha Science International. Book name: Deep Roots, Open Skies: New Biology in India, (ISBN-10: 8173196044), 2004. Articles Reviewed: 1- Assessment of microRNA-122 in Egyptian patients with HCV‐related liver cirrhosis: Is it a new serum prognostic marker. 2017. La Prensa Medica (Journal of Proteomics and Enzymology). 2- Rapid Identification of E. coli Bacteriophages using Mass Spectrometry. 2017. La Prensa Medica (Journal of Proteomics and Enzymology). 3- Optimization of biodegradation process for disperse textile dyes using brown rot fungi. 2017. La Prensa Medica (Journal of Proteomics and Enzymology). 4- Rectal adenocarcinoma with synchronous brain metastasis and prolonged overall survival (OS). 2017. Journal of Clinical and Medical Case Studies. 5- Isolation, Cloning, DNA sequencing and bioinformatics analysis of the parasporin1 gene of Bacillus thuringiensis. 2017. Journal of Proteomics & Bioinformatics. 6- In silico structure modeling and characterization of hypothetical protein YP_004590319.1 present in Enterobacter aerogenes. 2017. Journal of Proteomics & Bioinformatics. 7- Use of intravascular biopsy to diagnose a life-threatening giant primary anterior mediastinal yolk sac tumor. 2017. Journal of Clinical and Medical Case Studies. 8- The association between minerals and gastric cancer. 2017. “Advances in Oncology Research and Treatment”. 9- Long term survival with primary angiosarcoma: A case study of survival after simple resection. 2017. Journal of Clinical and Medical Case Studies.