Name: Upasana Ray

CURRICULUM VITAE
NAME: Upasana Ray DESIGNATION: Ramanujan Fellow, School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal.
Email: [e-mail] [e-mail] Phone: [phone] Date of Birth: 11^th October 1982
EDUCATION/ TRAINING and EXPERIENCE
INSTITUTION/DEPARTMENT	DEGREE	MM/YY	FIELD OF STUDY
University of Delhi, India	B.Sc.(Hons.)	08/2004	Zoology
University of Delhi, India	M.Sc	08/2006	Zoology
Indian Institute of Science (IISc), Bangalore Department of Microbiology and Cell Biology Mentor: Prof. Saumitra Das	PhD	11/2011 (defense)	Molecular Virology
Indian Institute of Science (IISc), Bangalore Department of Microbiology and Cell Biology Mentor: Prof. Saumitra Das	Research Associate	08/2011-03/2012	Molecular Virology
National Institutes of Health (NIH), USA National Cancer Institute (NCI) Lab of Cellular Oncology, Tumor Virus Molecular Biology Section Mentor: Dr. Christopher B. Buck	Post- Doctoral Fellow	04/2012-07/2015	Molecular Virology/Vaccine Development
School of Medical Science and Technology Indian Institute of Technology Kharagpur West Bengal	Reported to avail Ramanujan Fellowship award (dated November, 2015)	February 2016	Molecular Virology/ Virus particle assembly and vaccine
Indian Institute of Science (IISc), Bangalore Molecular Biophysics Unit Mentor: Prof. Raghavan Varadarajan	Post- Doctoral Fellow/ Research Associate	April 2016	HIV vaccine
School of Medical Science and Technology Indian Institute of Technology Kharagpur West Bengal	Ramanujan Fellow	continuing	Molecular Virology/ Virus particle assembly and vaccine

Area of interest

Major: Virus/ virus-like particle assembly/ self-assembly, virus tropism, vaccine, anti-viral therapeutics

Additional and exploratory (future side interests):

a) Virome of human brain and physiological relevance/ possible role in viral evolution/ human brain functions/ aging.

b) High altitude biology, device design to support adverse environmental conditions

c) Relating exercise, sleep, recreation and food habits to human brain functions, individual personality, attitude, endurance and success. This area has special connection to betterment of students under study and work pressure and often experience acute depression.

d) Understanding the wild-life of IIT, Kharagpur campus.

Area of Research as a post-doctoral fellow at NIH

I) Major project: Understanding the tropism/biology of JC polyomavirus (JCV) antibody-escape mutants responsible for causing an ‘AIDS-defining’, fatal demyelinating brain disease, Progressive Multifocal Leukoencephalopathy (PML); establishing a screening strategy for at-risk individuals and development of virus like particle (VLP) based vaccine to fight against JCV-induced PML. JCV vaccine was tested for neutralizing antibodies in mice. The VLP based vaccine was also tested in a single human vaccine trial and showed promising neutralizing antibody response with a parallel decrease in serum viral load. (Ray et al, 2015; Science Translational Medicine).
II) Side projects:

1. BK Polyomavirus (BKV) serotypes and BKV VLP based vaccine: In this project BK polyomavirus variants/ serotypes were studied. BKV causes renal nephropathy in immune-suppressed people. It was shown that two amino acid mutations near the cellular glycan receptor binding site lead to generation of fully distinct serotypes. Further, BKV VLPs were engineered and when used as vaccine candidates showed very potent cross reactive neutralizing antibody response (Pastrana et al, 2013; Journal of Virology).

2. Characterization of serum amyloid P protein (SAP): As an off-shoot of the main project, it was found that one of the JC polyomavirus mutants was getting neutralized strangely by every tested human serum samples. The serum factor was found to be a non-antibody neutralizing factor and identified as the serum amyloid P protein (SAP) by serum fractionation using HPLC, neutralization assays and Mass spec analyses. It was also found that the binding of SAP with its virus substrate is calcium dependent.
3. Discovery of Torque-teno virus in PML patient’s cerebrospinal fluid: While hunting for the possibility of finding new JCV variants in PML patients’ body fluid samples it was found that cerebrospinal fluid had Torque teno viruses (non-circular single stranded DNA viruses). (Genome Announcement under preparation)
Area of Research as a PhD student and Research Associate at IISc
Investigating the molecular interplay of Hepatitis C Virus (HCV) non-structural protein, NS3 and human La protein with HCV RNA, their role in regulating the switch from translation to replication modes of the viral RNA and targeting the switch to design peptide based antiviral candidates.

Positions and Honors

1. 
   Ramanujan Fellowship award, (SERB-DST) (2015)
   
2. 
   INSA Medal for Young Scientists, Indian National Science Academy (INSA) (2015)
   
3. 
   Federal Technology Transfer Award, Center for Cancer research, National Institutes of Health (NIH) (2014)
   
4. 
   Fellows Award for Research Excellence, National Institutes of Health (NIH) (2013)
   
5. 
   Visiting Fellowship, National Cancer Institute (NCI), National Institutes of Health (NIH) (2012)
   
6. 
   Travel Award for the International Centre of Genetic Engineering and Biotechnology (ICGEB)-IUBMB workshop on ‘Human RNA Viruses’ held in New Delhi, India (2010).
   
7. 
   Best poster award in the “1st virology meeting” (IISc Centenary Symposium on Biology and Pathogenesis of viruses: Molecular Insights) at Indian Institute of Science, Bangalore (2009).
   
8. 
   Council of Scientific and Industrial Research (CSIR) Senior Research Fellowship (SRF) (2010).
   
9. 
   Council of Scientific and Industrial Research (CSIR) Junior Research Fellowship (JRF) (2006).
   
10. 
    Qualified for Finals of the QUEST (2003-2004) (Center for Science Education and Communication) and received certificate. Represented College in the Science Aptitude Contest organized for undergraduate students of the University of Delhi.
    
11. 
    Credit certificate received for International Competition for Schools (Mathematics) from The University of New South Wales (1996).
    

Technical Expertise
1. Working at biosafety level (BSL) 2 and 3 facilities
2. Handling human body fluids (blood and cerebrospinal fluid) (normal and infectious)
3. Virus/ VLP (virus-like particle)/ pseudovirus assembly, purification, titration, infection/transduction.
4. Serology: Virus-antibody neutralization assays, ELISA based techniques/ assays
5. Virus hunting/ discovery from human body fluids (blood and cerebrospinal fluid): Virus purification, Viral DNA isolation, enrichment and analysis by deep sequencing
6. Cell culture: Mammalian cell maintenance, freezing, revival, generation of cell lines, DNA and RNA transfection in mammalian cells, peptide transduction studies, Immuno-fluorescence assay (IFA).
7. Molecular Biology: Cloning and mutagenesis, protein purification, western blot, PCR and RT-PCR, RNA protein binding assays, Electrophoretic mobility shift assay (EMSA/ Gel retardation assay), Fractionation of human body fluids by HPLC (basic) (reverse phase and hydrophobic interaction chemistries), radioactive-isotope handling and nucleic acid/ protein labelling, reporter assay systems (luciferase and GFP), other basic molecular biology tools.
8. Analysis of virus particles by Transmission Electron Microscopy (TEM) (basic)
Additional courses undertaken at National Institutes of Health:

• 
  Translational research in clinical oncology (TRACO), Center for cancer research (CCR)
  
• 
  Stem Cells, Foundation for advanced education in the sciences (FAES)
  
• 
  Mouse Course 101, Center for cancer research (CCR)
  

Contributions

• 
  Lead Judge in 9th Annual Graduate Student Research Symposium, 2013 at NIH, Bethesda.
  
• 
  Chief Judge in FARE competition 2014 at NIH, Bethesda.
  
• 
  Editor, Fellows Editorial Board (FEB), NIH, Bethesda
  

Seminars/ Invited talk

1. 
   Virus-Host Interaction: Disease and Remedy, Indian Statistical Institute, Kolkata, West Bengal.
   
2. 
   Virus-Host Interaction, Saha Institute of Nuclear Physics, Kolkata, West Bengal.
   

Meetings Organized

1. 
   Indo-Taiwanese meeting, Indian Institute of Science, Bangalore, 2010.
   
2. 
   2^nd Virology meeting, Indian Institute of Science, Bangalore, 2011.
   

PUBLICATIONS

Publications in journals

First Author

1. 
   Ray, U. 2016. Virus like nanoparticles: Display matters Proceedings of Indian National Science Academy (Accepted) (Review)
   
2. 
   Ray, U., Cinque, P., Gerevini, S., Longo, V., Lazzarin, A., Schippling, S., Martin, R., Buck, C.B., and Pastrana, D.V. 2015. JC polyomavirus mutants escape antibody-mediated neutralization. Science Translational Medicine. 7(306):306ra151(PMID:26400912)
   
3. 
   Ray, U., Roy, C. L., Kumar, A. , Mani, P., Joseph, A. P., Sudha, G., Sarkar, D. P., Srinivasan, N., and Das, S. 2013. Inhibition of the interaction between NS3 protease and HCV IRES with a small peptide: A novel therapeutic strategy. Molecular Therapy (Nature Publishing Group). 21(1):57-67. (PMID:22910295)
   
4. 
   Ray, U., Ray, P. S. and Das, S. 2012 Ribosome-RNA interaction: A potential target for developing antiviral against hepatitis C virus. Current Science. Vol 102; No. 3. (Review)
   
5. 
   Ray, U., and Das, S. 2011. Interplay between NS3 protease and human La protein regulates translation-replication switch of Hepatitis C virus. Scientific Reports (Nature Publishing Group) 1:1. (PMID:22355520)
   
6. 
   *Mondal, T., *Ray, U., Manna, A. K., Gupta, R., Roy, S., and Das, S. 2008. Structural determinant of human La protein critical for internal initiation of translation of hepatitis C virus RNA. Journal of Virology 82:11927-38. (*joint first authors) (PMCID:18829760) (Cover page article)
   

Second Author

7. 
   Kumar, A., Manna, A. K., Ray, U., Mullick, R., Basu, G., Das, S. and Roy, S. 2014.Specific sequence of a beta-turn in human La protein may contribute to species specificity of Hepatitis C virus. Journal of Virology 88(8):4319-27 (PMID:24478427)
   
8. 
   Pastrana, D. V., Ray, U., Magaldi, T. G., Schowalter, R., M., Cuburu, N., and Buck, C. B. 2013. BK polyomavirus genotypes represent distinct serotypes with distinct entry tropism. Journal of Virology 87(18):10105-13 (PMID:23843634)
   
9. 
   Kumar, A., Ray, U. and Das, S. 2013. Human La protein Interaction with GCAC near the initiator AUG enhances HCV RNA replication by Promoting Linkage Between 5'-and 3'- untranslated regions. Journal of Virology 87(12):6713-26 (PMID:23552417)
   
10. 
    Manna, A. K., Kumar, A., Ray, U., Das, S., Basu, G. and Roy, S. 2013. A cyclic peptide mimic of an RNA recognition motif of human La protein is a potent inhibitor of hepatitis C virus. Antiviral Research 97(3):223-226. (PMID:23291201)
    
11. 
    Ravikumar, Y. S., Ray, U., Nandhitha, M., Perween, A., Raja Naika, H., Khanna, N. and Das, S. 2011. Inhibition of hepatitis C virus replication by herbal extract: Phyllanthus amarus as potent natural source. Virus Research 158:89-97. (PMID:21440018)
    

Patents

1. 
   Treating or Inhibiting JC polyomavirus infection and JC polyomavirus-associated progressive multifocal leukoencephalopathy. Christopher Buck, Upasana Ray, Diana Pastrana (US Application number: 61/919,043)
   
2. 
   Compositions, method and formulations for peptide based inhibitors of Hepatitis C virus replication. Saumitra Das, Upasana Ray, Debi P. Sarkar, Chaitrali Laha Roy, N. Srinivasan. (Application number: 4033/CHE/2011 A)
   
3. 
   Small antiviral peptides against Hepatitis C virus. Saumitra Das, Siddhartha Roy, Upasana Ray, Tanmoy Mondal, Asit Kumar Manna, Romi Gupta. (US Application number: 2009/0233868A1)
   

Book Chapters

1. 
   Upasana Ray, Saumitra Das (2009) Role of Human La protein in Translation and Replication of Hepatitis C Virus. Mechanisms of Microbial Pathogenesis. TATA McGraw-Hill publication.
   

2. 
   Upasana Ray, Chaitrali Laha Roy, Saumitra Das (2011) Viruses and our fight against them. UGC-sponsored national seminar on microbiology: development and challenges in basic and applied research (organized by department of microbiology, Ramakrishna Mission Vidyamandira, Belur Math in collaboration with Bose Institute, Kolkata)
   

Research Highlight/ Coverage

1. 
   Therapeutic opportunity knocks (2015): Science (Vol. 349; Issue: 6255; page-1501)
   
2. 
   Studies propose vaccination for troublemaking virus (2015): Multiple Sclerosis Discovery Forum
   
3. 
   Closing “blind spots” in patients’ immune response to lethal brain infection (2015): EurekaAlert
   
4. 
   Researchers work towards vaccination for PML (2015): MS UN Master Cylinder (Breaking News)
   
5. 
   Possible JC virus vaccination offers important implications for MS treatment (2015): Multiple Sclerosis News Today
   
6. 
   Hep C viral switch (2011): Nature India (doi:10.1038/nindia.2011.83)
   

Abstracts Published in Seminars/Conferences

1. 
   Upasana Ray, Paola Cinque, Valeria Longo, Christopher Buck, Diana V. Pastrana (2014) Neurovirulent JC polyomavirus mutants escape antibody mediated neutralization. DNA tumor virus meeting, Wisconsin, United States.
   
2. 
   Upasana Ray, Diana V. Pastrana, Paola Cinque, Christopher Buck (2014) JC polyomavirus antibody-escape mutants in progressive multifocal leukoencephalopathy. American Society for Virology (ASV) meeting, Colorado, United States.
   
3. 
   Upasana Ray, Diana V. Pastrana, Christopher Buck (2013) Antibody-Mediated neutralization of neurovirulent JC polyomaviruses. DNA tumor virus meeting, Birmingham, United Kingdom.
   
4. 
   Upasana Ray, Diana V. Pastrana, Christopher Buck (2013) Antibody-Mediated immunity against JC polyomaviruses causing progressive multifocal leukoencephalopathy. HIV/AIDS and cancer virology fall Think-Tank meeting, National Institutes of Health, Bethesda.
   
5. 
   Upasana Ray, Diana V. Pastrana, Christopher Buck (2012) Antibody-Mediated neutralization of neurovirulent JC polyomaviruses. HIV/AIDS and cancer virology fall Think-Tank meeting, National Institutes of Health, Bethesda.
   
6. 
   Upasana Ray, Saumitra Das. (2011) The translation replication switch in HCV. Indo-Singapore meeting, IISc, Bangalore, India.
   
7. 
   Upasana Ray, Chaitrali Laha Roy, Prashant Mani, Agnel Praveen Joseph, G. Sudha, Debi Sarkar, N. Srinivasan, Saumitra Das (2011) Targeting NS3 protease-HCV RNA interaction: A novel antiviral target. Poster presented at 2^nd Virology meeting at IISc. .
   
8. 
   Upasana Ray, Agnel Praveen Joseph, N. Srinivasan, Saumitra Das. (2010) Translation Replication switch of Hepatitis C Virus RNA. RNA 2010 organized by the department of biotechnology, University of Pune, India.
   
9. 
   Upasana Ray, Agnel Praveen Joseph, N. Srinivasan, Saumitra Das. (2010) Determinant within NS3 protease critical for RNA binding to mediate the switch from translation to replication of Hepatitis C Viral RNA. ICGEB-IUBMB workshop ‘Human RNA Viruses’, New Delhi, India.
   
10. 
    Upasana Ray, Saumitra Das (2010) Interplay between NS3 protease and human La protein regulates translation to replication in hepatitis C virus. 79^th Annual Meeting of the Society of Biological Chemists (Theme: Regulation of biochemical and cellular processes in diverse systems), IISc, Bangalore.
    
11. 
    Upasana Ray, Agnel Praveen Joseph, N. Srinivasan, Saumitra Das (2009) The interplay between NS3 protease and human La protein: Switch of translation to replication. IISc centenary symposium on biology and pathogenesis of viruses: Molecular insights (1st Virology meeting).
    
12. 
    Upasana Ray, Agnel Praveen Joseph, N. Srinivasan, Saumitra Das (2009). HCV NS3 protease interacts with HCV 5’UTR: Implications on multifunctional activities. IISc Centenary Symposium on ‘Mechanisms of microbial pathogenesis’, IISc, Bangalore.
    
13. 
    Upasana Ray, Agnel Praveen Joseph, N. Srinivasan, Saumitra Das (2008) Specific interaction of the protease domain of the NS3 protein with the HCV 5’UTR: possible implications. 15^th international symposium on Hepatitis C Virus and related viruses held at San Antonio, Texas.
    
14. 
    Upasana Ray, Agnel Praveen Joseph, N. Srinivasan, Saumitra Das (2008) The protease domain of Hepatitis C virus NS3 protein interacts with the 5’UTR: Implications on multifunctional activity. 77^th Annual Meeting of the Society of Biological Chemists (Theme: impact of basic and translational research on medicine, agriculture and industry), IIT Madras, Chennai.
    

Abstracts published in conferences/ seminars but presented by other authors

15. 
    Upasana Ray, Diana V. Pastrana, Christopher B. Buck (2013) Antibody-mediated neutralization of PML associated JCV mutants. Progressive Multifocal Leukoencephalopathy meeting, PML Consortium, New York Academy of Sciences.
    
16. 
    Parmjeet Randhawa, Diana V. Pastrana, Upasana Ray, Christopher B. Buck, Neil Christensen (2013) Characterization of the binding and neutralizing properties of monoclonal antibodies against the polyomavirus JC virion. Progressive Multifocal Leukoencephalopathy meeting, PML Consortium, New York Academy of Sciences.
    
17. 
    Diana V. Pastrana, Upasana Ray, Nicolas Cuburu, Christopher Buck (2012) Identification of multiple BKV serotypes. DNA Tumor virus meeting, Montreal, Canada. (attended)
    

Extracurricular activities
Semi-technical mountaineering/ hiking, bird and landscape photography, painting, Indian classical music