Dr. Santanu Raychaudhuri

Brief Biography:

BIOGRAPHICAL SKETCH:Santanu Raychaudhuri, Ph.D. Microbiology, Immunology and Molecular Genetics 615 Charles Young Drive, Room 254A Los Angeles, Biomedical Science Research Building University of California Los Angeles (UCLA)

Education:
Undergraduate Calcutta University Calcutta University, Calcutta Physics, Chemistry, Math, Biology Chemistry (Hons), H. S (Sc) B. Sc (Hons)
Graduate Calcutta University, Biochemistry M. Sc. Jadavpur University & University of Connecticut Life Science & Molecular Biology Yeast Genetics, DNA Replication Ph. D., Awarded, 2001 Certificate Courses in UC San Diego Drug Development and Ongoing-2012 Clinical Trial Management Postdoctoral University of California, RNA Viruses transcription,
2002 – 2005: Los Angeles; MIMG Translation & replication
2009-onwards HCV-HIV Drug Development Mechanisms, Host-virus Interactions; Global Cellular Gene expressions University of California, Basic Sciences in Metabolic Diseases
2005 - 2009: Los Angeles, Pediatrics Epigenetics, Micro-RNA, Global aspects of Gene Expressions Sloan-Kettering Institute Yeast and mammalian DNA replication
1999-2002 New York City, NY mechanisms; Global aspects of Cell Cycle

Academic positions:

Postdoctoral: Sloan-Kettering Institute and UCLA Assistant Research Professor: UCLA

Employment History (Past to present):
1. University of Connecticut Health Center Farmington, CT Department of Microbiology (Formerly) (Nov.1995 to Oct.1998)
2. Research Fellow Under the supervision of Prof. Shlomo Eisenberg, an associate of Prof Arthur Kornberg, Nobel Laureate: The delineation of a novel DNA replication origin of the yeast Sacharomyces cerevisiae: the initiation mechanisms of the eukaryotic chromosomal DNA replication in the budding yeast as a model system. The role of transcription factors specificities in the regulation of DNA replication origin firing. Memorial Sloan-Kettering Cancer Center (Nov. 1998 – Feb. 2001) Sloan-Kettering Institute Manhattan, NY Department of Molecular Biology (Nov. 1998 – Feb. 2001)
3. Research Technician Under the supervision of Prof. Jerard Hurwitz, a national academy member of USA: The initiation mechanisms of the eukaryotic DNA replications using fission yeast as a model system. Purifications of the major DNA replication origin binding protein complexes from yeast and baculovirus systems have been performed. Understanding of the various DNA replication commitment pathways and the cell-cycle regulation in the higher eukaryotes is the basis for the understanding of how the cancer cells divide sporadically. UCLA University of Los Angeles, California Department of Microbiology, Immunology and Molecular Genetics
4. Post-graduate Research Associate (June 2002 to July 2005) Under the supervision of Prof. Asim Dasgupta, an associate of Prof. David Baltimore, Nobel Laureate: Molecular virology in positive-strand RNA viruses and the mechanism of actions of It’s inhibitors. Translational control of gene expressions in mammals.
Research Topics:
(i). Mammalian positive strand RNA virus gene regulation in replication, transcription and translational control with the emphasis on HCV and Polio virus. Molecular targeting of the anti-virus therapeutics in HCV has been investigated.
(ii). Development of Hepatitis C NS5A inhibitors. The molecular etiology of hepatocellular carcinoma (HCC) caused by hepatitis C. Expression and purifications of all structural and non-structural HCV proteins in E. coli and Hepatic cell-lines. Structure-function analysis of Core and NS5A in-vitro and in-vivo. Signal transduction pathways modulated by these regulatory proteins of the host systems.
(iii). Mechanisms of IRES (Internal Ribosome Entry Sites) mediated RNA translation. Translational inhibitors for positive strand RNA viruses. Development of artificial small IRES element of high biological activity for functional analysis of translational regulation of protein synthesis: construction of HCV genome harboring artificial IRES and/or mutations directing high level of protein synthesis and thus high-titer virus.
(iv). Cellular IRES: VEGF and TFIID. Molecular chaperones in the cellular RNA translation in the event of stress conditions. Mechanism of actions of molecular chaperones in both viral and cellular RNA translations is being hypothesized. UCLA University of Los Angeles, California Department of Pediatrics, Developmental Biology
5. Assistant Research Professor (Aug.2005 to Feb. 2009)
Research Topics:
(i). The role of chaperone proteins in both yeast and mammalian systems in the control of the RNA translation. The cellular IRES-mediated translation (VEGF, TFIID and GLUT) contributes in the synthesis of the essential proteins under `stress conditions’ and that the `chaperones’ have immense roles in regulating the cellular translation processes.
(ii). The glucose transporter genes (Glut3, 4, 1) 5’-UTR ribosome-landing sequences (IRES) are active in the glucose and amino acids starved conditions. Mechanism of actions of these RNA structures in the translation of the glucose transporters in diabetic rodents and cell culture model systems, both Neuroblastoma (N2A) and skeletal muscles (C2C12).
(iii). Brain specific glucose transporter protein: Glut3 knock-out mice (both conditional and total knock-out) to elucidate the functional activities of the glucose transporter protein in brain functions. Conditional mice are presently being made.
(iv). Epigenetic control of gene expression in higher eukaryotes. Involvement of genetic and epigenetic events in normal and patho-physiological conditions in mammals has been studied. The control of the glucose transporter gene transcription by epigenetic mechanisms in diabetic, obese and insulin resistant animal models.
(V). The micro-RNA mediated gene silencing: Specific micro-RNA regulates the diabetic and insulin resistance/sensitivity in skeletal muscle through the interaction of the specific target genes. Mechanism of actions of micro-RNA in the inhibition of the specific cellular RNA translation under stress conditions has been investigated.
(Vi). The role of glucose transporter 3 in the adult neuronal and embryonic stem cells. Role of micro-RNA in the stem cells proliferation and differentiation has been aimed at. UCLA University of Los Angeles, California Microbiology, Immunology and Molecular Genetics
6. Research Assistant Professor (March. 2009 to Present)
(i). Focusing on HCV-mediated liver carcinogenesis. Hepatic Stem cells and how HCV affects this group of cells in normal and patho-physiological conditions.
(ii). Mechanism of actions of HCV-IRES inhibitors and the proposition of gene therapy in HCC patients.
(iii). The plant anti-oxidant Quercetin mediated inhibition of hepatitis C. Mechanism of actions of this group of inhibitor in the host-cell interaction. The role of Quercetin in HCV morphogenesis. The encapsidation signal for hepatitis C. The mechanism of action of HCV encapsidation.
(iv). The role of microRNA in HCV development and progression in host liver cells.
(v). The mechanism of HCV assembly/morphogenesis.
(vi). Viral mediated (HCV, HIV, and DNA viruses) Thymidine Kinase membrane upregulation:TK-1 mAb therapy as a anti-cancer drug. Collaborating with a pharmaceutical company.

Appointments:
1. University of California at Los Angeles, Assistant Research Professor, MIMG, 2009 April onwards.
2. University of California at Los Angeles, Assistant Research Professor in the Department of Pediatrics & Developmental Biology, 2005 Aug – 2009 March.
3. University of California at Los Angeles, Postdoctoral Research Associate, Department of MIMG, 2002 June to 2005 July
4. Memorial Sloan-Kettering Cancer Center, Senior Research Technician, New York City, USA, 1998-2001, under the supervision of Prof. Jerard Hurwitz.

Technical Skills:
1. Recombinant DNA technology, DNA, cDNA Cloning
2. Genomic DNA, RNA and Plasmid preparations, CsCl purification
3. DNA sequencing, Bisulfite sequencing
4. Genomic and cDNA libraries in HT assays (Plasmid and phages)
5. PCR, RT-PCR associated techniques, Real-time PCR. Multiplexed PCR.
6. Extensive primer design experiences for various molecular biological techniques
7. Various site directed and linker scanning mutagenesis
8. Molecular genetics of the prokaryotic, viral and the yeast systems
9. Yeast strain generations, knock-outs, Two-hybrid/one hybrid systems for genetic interactions
10. Classical Protein purification systems
11. Chromatography techniques: FPLC, HPLC
12. Protein expression systems: E. coli, Yeast, Insect Cells/ Baculovirus
13 Affinity chromatography: protein tagging with his-tag, flag, HA, GST, EGFP and quick-step protein purifications
14. Immunoprecipitation techniques
15. Immunohistochemistry
16. Chromatin Immunoprecipitation (CHIP) techniques
17. Epigenetic analysis for histone modifications (antibody-based)
18. Generation of polyclonal antibodies in rabbit; Purification of IgG
19. ELISA
20. Fluorescence-based assays
21. Spectrophotometric assays
22. Molecular reporter gene expression assays (Luciferases, CAT, ?-galactosidase and GFP)
23. Southern-Western-Northern
24. RNase protection assay
25. Primer extension analysis
26. Northwestern analyses
27. RNA-protein interaction assays
28. siRNA/shRNA mediated gene silencing, micro-RNA analysis by HT methods
29. Gel shift and the foot-printing analysis for DNA/RNA binding proteins
30. Enzyme kinetics, enzyme assay developments and biochemical analysis
31. FACS analysis, Flow Cytometry Instrumentation and data collection
32. All aspects of mammalian cell cultures, confocal microscopy and transfection experiments (transient and stable)
33. Various cell based assays (eg., cytotoxic assays, proliferation assays, cell cycle assays
34. In vitro virus infection in cell cultures.
35. Generation of stable cell lines
36. Transcription assay systems
37. Replication assay systems
38. Translation assay systems
39. Gene therapy approaches through viral vectors, including lentiviral
40. Transduction experiments, Virus purification, Assays and Neutralization
41. BSL2 plus, GLP practices and other scientific federal bio-safety regulation standards
42. In vivo mice experiments and Knock-out mice. Conditional Knock-out
43. Computer expertise: Microsoft word, Excel, PowerPoint, Photoshop and other software programs for statistical analyses (ANOVA, T-Test & others) of biological data and extensive molecular biological research. Bioinformatics analysis

Research interests:

Molecular mechanisms of viral drug candidates, RNA viruses life cycles, molecular mechanisms of carcinogenesis and metabolic syndromes.

Any other information:

Publications HCV Published Papers:
1. R Khachatoorian, Vaithilingaraja Arumugaswami, Santanu Raychaudhuri, Piotr Ruchala, Oscar Gonzalez, Edna Miao, Eden Maloney, Asim Dasgupta, Samuel W French (2011). A Surface Exposed Beta-Sheet Hairpin in NS5A Mediates IRES Activity and Hepatitis C Viral Infection. Accepted to Hepatology.
2. Vanessa Fontanas, Santanu Raychaudhuri and Asim Dasgupta (2009). A cell-permeable peptide inhibits hepatitis C virus replication by sequestering IRES transacting factors. Virology. 2009 Nov 10; 394(1):82-90. Epub 2009 Sep 8.
3. Gonzalez O., Fontanes V., Raychaudhuri S., Loo R., Loo J., Langevin T., Arumugaswami V., Sun R., Dasgupta A. and French S (2009). The Heat Shock Protein Inhibitor Quercetin Attenuates Hepatitis C Virus Production. Hepatology, 2009 Dec; 50(6):1756-64.
4. Raychaudhuri S, Fontanes V, Barat B, Dasgupta A (2009). Activation of Ribosomal RNA Transcription by Hepatitis C Virus Involves Upstream Binding Factor Phosphorylation Via Induction of Cyclin D1. Cancer Research. 69: (5). March 1, 2057-2063.
5. Raquel E. Izumi, Saumitra Das, Bhaswati Barat, Santanu Raychaudhuri, and Asim Dasgupta (2004), An eighteen amino acid peptide from a highly conserved N-terminal region of human autoantigen La blocks polio and hepatitis C virus cap-independent translation and reveals a single tyrosine critical for La RNA binding and translation stimulation. Journal of Virology, 78 (7): 3763-76.
6. Samuel Wheeler French, JR, Oscar Gonzalez, Santanu Raychaudhuri, Vanessa Fontanes, Rachel Loo, Joseph Loo, and Asim Dasgupta. (2008). Proteomic Analysis of the HCV Encoded Peptide NS5 A Cellular Protein Complex. The FASEB Journal. 22:898.13

Other RNA viruses:
1. Santanu Raychaudhuri, Vanessa Fontanes, Rajeeb Banerjee, Yana Bernavichute and Asim Dasgupta (2006). Zuotin, a ribosomal-associated DnaJ molecular chaperone, stimulates the cap- independent translation in yeast. Biochemical and Biophysical Research Communications, 350 (3), 788-95.
2. Pallab Kundu, Santanu Raychaudhuri, Weimin Tsai and Asim Dasgupta (2005), Shutoff of RNA polymerase II transcription by poliovirus involves 3C protease-mediated cleavage of the TATA-binding protein at an alternative site: incomplete shutoff of transcription interferes with efficient viral replication. Journal of Virology, 79(15):9702-13.
3. Sharma*, R., Raychaudhuri, S*. and Dasgupta, A (2004). The single nuclear localization signal (NLS) within the poliovirus 3D protein is required for nuclear entry of the viral protease precursor 3CD. Virology, 320, 195-205. *equal contribution 4. Mary K. Weidman, Rakhi Sharma, Santanu Raychaudhuri, Pallob Kundu, Weimin Tsai and Asim Dasgupta (2003). The interaction of small cytoplasmic RNA Viruses with the nucleus. Virus Research, 95, 75-85.

Metabolic Published Papers:
1. Santanu Raychaudhuri (2012). MicroRNAs Overexpressed in Growth-restricted Rat Skeletal Muscles Regulate the Glucose Transport in L6 Cell-culture System Targeting Central TGF-beta factor SMAD4. Accepted to PLOS One.
2. Nupur Raychaudhuri, Santanu Raychaudhuri, Manniksagar Thamotharan and Sherin U. Devaskar (2008), Histone code modifications repress glucose transporter 4 expression in the Intra-uterine growth restricted offspring. Journal of Biological Chemistry 16; 283(20): 13611-26. Epub 2008 Mar 7.
3. Sherin U. Devaskar and Santanu Raychaudhuri (2007). Epigenetics–A science of heritable biological adaptation. Review overview in the special issue of Pediatric Research, 61 (5), Pt. 2.
4. Amit Ganguly, Robert McKnight, Santanu Raychaudhuri, Bo-Chul Shin, Zhigui Ma, Kelle Moley and Sherin U. Devaskar (2007), Glucose Transporter Isoform 3 Mutations cause early pregnancy loss and fetal growth restriction. Am J Physiology Endocrinology Metabolism, 292:1241-1255.

DNA Replication Published Paper:
1. Fien K, Cho YS, Lee JK, Raychaudhuri S, Tappin I, Hurwitz J. (2004), Primer utilization by DNA polymerase alpha-primase is influenced by its interaction with Mcm10p. Journal of Biological Chemistry, 279(16):16144-16153.
2. Keong-Yeop Moon, Daochun Kong, Joon-Kyu Lee, Santanu Raychaudhuri and Jerard Hurwitz (1999), Proc. Natl. Acad. Sci. (USA), 96(22), 12367-72. Identification and reconstitution of the origin recognition complex from S. pombe.
3. Steven Wiltshire, Santanu Raychaudhuri and Shlomo Eisenberg (1997) Nucleic Acids Res. 25(21), 4250-4256. An Abf1 C-terminal region, lacking transcriptional activation potential, stimulates a yeast origin of replication.
4. Santanu Raychaudhuri, Randy Byers, Todd Upton and Shlomo Eisenberg (1997) Nucleic Acids Res. 25(24), 5057-5064. Functional analysis of a replication origin from S. cerevisiae: identification of a new replication enhancer.

Bacterial Genetics Published Paper:
1. Santanu Raychaudhuri, Madhumita Basu and N. C. Mandal (1998) Microbiology, 144(8), 2131-40. Glutamate and cyclic AMP regulate the expression of galactokinase in Mycobacterium smegmatis.

Manuscript in Preparation:
1. Mysore S. Veena, Santanu Raychaudhuri, Huihong You, Saroj K. Basak, Kayvan Zainabadi, Gary Thomas, and Eri Srivatsan (2011), Phosphofurin-acidic cluster sorting protein 1 (PACS-1) plays a role in genome stability: Downregulation of PACS-1 by miRNA 449a leads to DNA damage and p53 activation. Prepared for Genes and Development.
2. Santanu Raychaudhuri and Asim Dasgupta (2011). Functional characterization of a small synthetic Internal Ribosome Entry Site (IRES) RNA element, PS3 and its inhibition on Hepatitis C virus. Prepared for Virology.
3. Santanu Raychaudhuri, Tingchao Chen, Taihra Ul-Hasan, Hangfei Qi, Vaithilingaraja Arumugaswami, Samuel W. French, Ren Sun and Asim Dasgupta (2011). Role of Hepatitis C 5’ Untranslated Region on the Viral Assembly and Morphogenesis. Prepared for PLoS Pathogen.

Presentations in Symposiums:
1. Santanu Raychaudhuri, Bhaswati Barat, Weimin Tsai and Asim Dasgupta (2005), Poster presentation in the IUMS (Microbes in the changing world) at San Francisco, California. (52-V-227, July 23-28) Hepatitis C Non-structural protein 5A stimulates the synthesis of ribosomal RNA from Pol-I specific promoter by CDK4/CyclinD1 mediated phosphorylation of Upstream Binding Factor-1 in Huh-7 cells.
2. Samuel French, Asim Dasgupta, Santanu Raychaudhuri (2008) Hepatitis C virus production is impaired by Heat Shock Protein Synthesis inhibitors (ID#503930). Abstract submitted in The Liver Meeting (AASLD) of 2008.
3. Santanu Raychaudhuri, Rakhi Sarma and Asim Dasgupta (2003), Oral presentation in 22nd American Society of Virology at University of California, Davis, (W28-4, July 12-16). Nuclear entry of Poliovirus protease-polymerase precursor 3CD: implications for host cell transcription shut-off.
4. Santanu Raychaudhuri, Vanessa Fontana, Bhaswati Barat and Asim Dasgupta (2008) Deregulation of Pol-I in HCV infected Liver cells. Presented @ International Symposium for Hepatitis C in Texas, Dallas.
5. Santanu Raychaudhuri and Asim Dasgupta (2011), The Mode of Action of a Small Peptide Inhibitor of Internal Ribosome Entry Site (IRES) for the Hepatitis C Virus Propagation in Human Hepatoma Cells. Accepted for presentation as a poster at the 18th International Symposium on Hepatitis C Virus and Related Viruses to be held in Seattle, Washington on 8- 12 September 2011.
6. Santanu Raychaudhuri, Kyeong-Yeop Moon, Daochun Kong, Joon-Kyu Lee and Jerard Hurwitz (1999), Abstract (108) in DNA replication meeting of Cold Spring Harbor Laboratory. The origin recognition complex of S. pombe: the importance of Orc3 and Orc6 subunits.
7. Keong-Yeop Moon, Daochun Kong, Joon-Kyu Lee, Santanu Raychaudhuri and Jerard Hurwitz (1999). Abstract and oral presentation in DNA replication meeting of Cold Spring Harbor Laboratory. Purification of the origin recognition complex from S. pombe.
8. Steven Wiltshire, Santanu Raychaudhuri, Randy Byers, Todd Upton and Shlomo Eisenberg (1998). Abstract, 340, in Yeast Genetics and Molecular Biology at College Park, Maryland. Analysis of the S. cerevisiae ARS121 and ARS1501 origins of replication indicate the presence of the origin-specific enhancers.
9. Nupur Raychaudhuri, Santanu Raychaudhuri, Manniksagar Thamotharan and Sherin Devaskar (2006), Presentation in Pediatric Academic Society, San Francisco, California. Modification of Histone-3 code regulates skeletal muscle insulin responsive glucose transporter 4 (Glut4) expression in the adult IUGR offspring.
10. Mysore S. Veena, Santanu Raychaudhuri, Huihong You, Saroj K. Basak, Kayvan Zainabadi, Gary Thomas, and Eri S. Srivatsan (2010), Increased expression of PACS-1 in cervical cancer is associated with loss of microRNA449a. Submitted in American Association of Cancer Research (AACR), will be published and presented in Washington D.C. meeting (Apr 17-21).
11. Santanu Raychaudhuri and Eri Srivatsan (2010), Mammalian glucose transport activity is regulated by nutrient-stress induced micro-RNA(s) through manipulation of essential signaling pathway in skeletal muscle. Submitted in Cambridge Healthcare Institute (CHI) conference. Will be published and presented in `MicroRNA in Development and Diseases’, Cambridge, MA, March 22-25.

Collaborators & Affiliations (Current):
(a) 1. Member: American Society of Virology (2003 onwards)
2. Member: Pediatric Association of Science (PAS)
3. Collaborator: Prof. Asim Dasgupta, UCLA, CA.
4. Collaborator: Prof. Eri Srivatsan, UCLA and VA Medical Center CA.
5. Collaborator: Dr. Samuel W. French, Assistant Professor, Department of Pathology, UCLA, CA.
(b) 1. Prof. Nitai C. Mandal, Bose Institute/Jadavpur University, Calcutta, India.
2. Prof. Shlomo Eisenberg, University of Connecticut Health Center, Farmington, CT
3. Prof. Jerard Hurwitz, Sloan-Kettering Institute, New York, NY, USA.
4. Prof. Asim Dasgupta, University of California Los Angeles, Los Angeles, CA
5. Dr. Saroj Basak, Assistant Professor, VA Medical Center, Los Angeles, CA
6. Dr. Rajan Singh, Associate Professor, Charles Drew University, Los Angeles, CA

(c) Does have graduate advisory experience with
1. Ms. Vanessa Fontana (Graduate student of Dr. Asim Dasgupta, MIMG, UCLA)
2. Mr. Jeremy Burton (Graduate rotation student of Dr. Asim Dasgupta, UCLA)
3. Ms. Yana Bernavichute (undergraduate student of Asim Dasgupta, presently Postdoctoral student in UCLA)
4. Neil Bachour (Master’s student of Asim Dasgupta at UCLA)
5. Ms. Analyne Schroeder (Graduate rotation student of Prof. Sherin Devaskar)
6. Ms. Nupur Raychaudhuri (Post-graduate researcher of Prof. Sherin Devaskar)
7. Ms Indu Michael (Research Tech), MIMG, UCLA
8. Mr. Kevin Shah (Undergraduate Student), UCLA
9. Mr. Shahil Shah (Graduated)
10. Ms. Taihra Ul-Hasan (Graduated)
11. Ms. Natalie Hardy (Undergrad)
12. Ms. Aiswaryaa Viswanath (Graduated)
13. Ms. Ann Quan (Graduated)
14. Rania Abolhossen (Undergrad)
15. Burdette Gebelein (Undergrad)
16. Vivian Lam (Undergrad)
17. Rina Nguyen (Undergrad)

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