skr Dr. Suvendra Kumar Ray
Associate Professor and Head
Department of Molecular Biology and Biotechnology
Tezpur University
Tezpur - 784 028
Assam, India
Office : +91 3712 275406
Mobile: +91 9954472151
Email: suven@tezu.ernet.in
suvendra1973@gmail.com
suvendraray@yahoo.com
Computational Biology and Bioinformatics
Research in Computational Biology and Bioinformatics of our group at TU



About Me

My home town is at Khardasahi, in Jagtsinghpur District of Odisha State in India. I like reading biography of scientists, knowing the events that lead to interesting scientific discoveries. Keep strong faith on basic understanding.

Academic

Teaching

I mainly teach genetics, evolutionary genetics, and molecular biology to students. I prefer emphasizing more on the philosophy of the topics rather than sharing lots of informations with students. In genetics I teach Mendelian, Non-mendelian inheritance, recombination and linkage, Hardy-Wienberg equilibrium, different aspects of bacterial genetics, bacterial genomes. In molecular biology I teach mainly DNA structure, DNA replication, mismatch repair in DNA, mechanisms of different recombinations in DNA. In evolutionary genetics I teach selection of recessive traits in organisms, selection, neutral theory of molecular evolution, evolution of genome composition, molecular phylogeny. I try to encourage students to ask questions and I teach for learning from students.

Research Interest

I developed interest to study virulence functions of phytopathogenic bacterium during my PhD. I studied the role of type II protein secretion system (T2SS) in the virulence of Xanthomonas oryzae pv. oryzae, the causal agent of bacterial leaf bight of rice. I learned molecular genetic tools during these days. The observation which I found surprising is that T2SS deficient mutant fails to co-migrate with wild type strain upon co-inoculation. I also studied the role of an adhesion function in this bacterium.

After joining Tezpur University, my research interest has been divided in two different areas: (i) Molecular plant microbe interactions (ii) Molecular evolution .

Molecular Plant Microbe Interactions

R. solanacearum is a plant pathogenic bacterium. The bacterium is soil borne and causes a lethal wilt disease in more than 200 plant species which includes important vegetables such as brinjal, potato, tomato etc. The bacterium is widely distributed on the globe as the disease is reported from tropical, subtropical and temperate countries. Because of its aggressiveness, large host range, broad geographical distribution, and long persistence in soil, the bacterium is regarded as the most important plant pathogen. In India, bacterial wilt is an important disease. We are addressing the following questions:

a. what is the role of hemagglutinin adhesion functions in this bacterium.
b. what is the role of other bacteria associated with Ralstonia solanacearum in wilted plant.
c. after inoculation, how do some susceptible plants among the population escape the lethal wilting caused by the bacterium.


Molecular Evolution

Though synonymous codons encode the same amino acid, they are used in different frequencies in genomes. This is known as codon usage bias which is observed in all genomes including viruses. It is now well known that selection mechanisms are operating at the translational level to shape codon usage bias in organisms. We are addressing the following questions:

a. how much tRNA gene number contributes towards the selection.
b. whether codon dictates anticodon or the vice versa.
c. how protein folding influences codon usage bias in organisms.


Computer Aided Drug Design

As an application part to our codon usage bias study, we realized that codon-anticodon interaction is important attribute to the selection of certain synonymous codons in high expression genes. Further the codon-anticodon interaction is also influenced by anticodon modification enzymes. It is interesting to learn from the literature that anticodon modification enzymes are not always same among the three kingdoms of life Eukarya, Bacteria and Archaea. We are trying to exploit this avenue to design novel antibiotics using computer aided drug design approach.


Other Research interest

We also address some questions relating to plasmid transformation, recombination, bacterial growth in colony


External Collaborators

Research Area Collaborators NameCollaborators Address
Molecular Plant Microbe InteractionsDr. Ramesh V. Sonti CCMB, Hyderabad, India
Molecular Plant Microbe Interactions Dr. Gopaljee Jha NIPGR, New Delhi, India
Molecular Plant Microbe Interactions Dr. Stephane Genin LIPM, France
   
Molecular Evolution Prof. Tapash C. Ghosh Bose Institute, Kolkata, India
Molecular Evolution Dr. Rajat Banerjee Calcutta University, Kolkata , India
Molecular Evolution Dr. B. R. Powdel Dept. of Statistics, Darrang College, Tezpur, Assam , india
Molecular Evolution Dr. S. S. Satapathy Dept. Of CSE, Tezpur Universsity, Assam , India
Molecular Evolution Prof. Alak K. Buragohain Dept. of MBBT, Tezpur University , Assam, India. (Now VC at Dibrugarh University, Assam, India)
Molecular Evolution Prof. Malyananda Dutta Dept. of CSE, Tezpur University, Tezpur, Assam , India
Molecular Evolution Prof. M. Borah Dept. of Mathematics, Tezpur University, Tezpur, Assam , India
   
Computer Aided Drug Design Dr. N. Hoda Department of Chemistry, Jamia Millia Islamia University, New Delhi , India
Computer Aided Drug Design Dr. M. V. Satish Kumar Dept. of MBBT, Tezpur University, Tezpur, Assam , India
Computer Aided Drug Design Prof. R. C. Deka Dept. of Chemical Sciences, Tezpur University, Tezpur, Assam , India
Computer Aided Drug Design Prof. Alak K. Buragohain Dept. of MBBT, Tezpur University, Tezpur, Assam , India. (Now VC at Dibrugarh University, Assam, India)


Research Group


Dr. Rahul Kumar
Research Associate
Research Area : Studying the role of rpoN, the alternative sigma factor, in the pathogenicity of R. solanacearum, the causal agent of bacterial wilt in plants.
Email: rahultu@tezu.ernet.in ,   rahuls697@gmail.com
Contact: +91 9957769371

Dr. Niraj Agarwala 
Research Associate
Research Area : Sequencing genomes of some bacteria that invade/resides in tomato plant.
Email: btniraj@tezu.ernet.in ,   niru.niraj.s@gmail.com
Contact: +918486027249

Mr. Anjan Barman 
NET-JRF
PhD Student
Research Area : Characterization of hemagglutinin gene functions in Ralstonia solanacearum.
Email: abarman@tezu.ernet.in ,   anjbth@gmail.com
Contact: +91 9864334900

Ms. Tarinee Phukan
PhD Student
Research Area : Characterization of hemagglutinin gene functions in Ralstonia solanacearum.
Email: tarinee@tezu.ernet.in ,   tarineebiotech90@gmail.com
Contact: +91 9401121354

Mr. Niraj Singh 
DBT-JRF, ICAR(NET-LS)
PhD Student
Research Area : Studying rpoN regulon in Ralstonia solanacearum
Email: niraj12@tezu.ernet.in ,   neerajsingh710@gmail.com
Contact: +91 9678462554

Mr. Pankaj Losan Sharma
PhD Student
Research Area : Sequencing genome of Ralstonia solanacearum and other associated bacteria.
Email: pankaj1@tezu.ernet.in ,   pankajsarma88@gmail.com
Contact: +91 9613111679

Ms. Ruksana Aziz,
PhD Student
Research Area : Codon Usage Bias, Molecular evoluiton and protein folding.
Email: ruksana@tezu.ernet.in ,   rks.aziz786@gmail.com
Contact: +91 8399966064

Ms. Kristi Kabayshree,
PhD Student
Research Area : A study on the association of Ralstonia solanacearum to host plants.
Email: kristib@tezu.ernet.in ,   kkabyashree29@gmail.com
Contact: +91 8876754584



                                                                                      MIPPM 2014-15

                                                                                     LAB MEMBERS 2014-15




PhD Thesis Supervised

Dr. B. R. Powdel
Research Topic: Statistical study of nucleotide composition in bacterial genomes.
Dr. Powdel is a faculty member in the Dept. of Statistics, Darrang College, Tezpur.
Email: powdel@gmail.com

Dr. Siddhartha Sankar Satapathy
Research Topic: Computational analysis of genome sequences to find out factors influencing codon usage bias in bacteria.
Dr. Satapathy is a faculty member in the Dept. of Comp. Sc and Engg., Tezpur University, Tezpur.

Email: ssankar@tezu.ernet.in

Dr. Rahul Kumar

Research Topic:Studying virulance funcitons of Ralstonia solanacearum the causal agent of bacterial wilt in plants.

 


Email: rahultu@tezu.ernet.in

Research Projects

ProjectPI and Co-PI Funding AgencyDuration Amount Status
Protein Folding Kinetics is a Selection Force on Shaping Codon Usage Bias in the High Expression Genes. (DoRD/MBBT/SKR/20-221) Dr.S. K. Ray, Dr. S. S. Satapathy, CSE, TU Dr. R. Banerjee, Kolkata University DBT, Twinning Under U-EXCEL-NER2 years(11/08/2014 – 10/08/2016)24.72 lakhs to TU(out of 42.32)lakhs
Sequencing genomes of some bacteria that invade/resides in tomato plant Dr.S. K. Ray, MBBT, TU DBT, Govt. of India Under U-EXCEL-NER3 years127.63 lakhsOngoing, Started Oct, 2013
Studying the role of rpoN, the alternative sigma factor, in the pathogenicity of R. solanacearum, the causal agent of bacterial wilt in plants Dr.S. K. Ray, MBBT, TU (India) and Dr. S. Genin, LIPM, CNRS-INRA, Castanet Tolosan, FRANCE IFCPAR/CEFIPRA, New Delhi, India3 YearsRs. 44.17 lakhs(Indian) and 45000.00 €(French) Ongoing, Started Dec, 2013
Characterization of a potential auto transporter adhesion function in Ralstonia solanacearum, the causal agent of bacterial wilt in plants Dr.S. K. Ray, MBBT, TU and
Dr. R. V. Sonti, CCMB, Hyderabad
DBT, Govt. of India (Twining)3 years 35.66 lakhs (out of 61.32) Ongoing, Started Nov, 2012
Understanding causes of codon usage bias in organisms Dr.S. K. Ray, MBBT,TU,                    Dr. S. S. Satapathy, CSE, TU and      Dr. T. C. Ghosh, Bose Institute, Kolkata DBT, Govt. of India (Twining) 2 years 15.50 lakhs (out of 26.36) Ongoing, Started Nov, 2012

Research Publications

  • Satapathy SS, Ray SK, Sahoo AK, Begum T, Ghosh TC (2015) Codon usage bias is not significantly different between the high and the low expression genes in human. Int J Mol Genet Gene Ther 1. Doi http://dx.doi.org/10.16966/ijmggt.103
  • Baruah VJ, Satapathy SS, Powdel BR, Konwarh R, Buragohain AK, Ray SK. (2015). Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins. J. Genet.
  • Ray S.K., Kumar R, Peeters N, Boucher C, Genin S. (2015). rpoN1, but not rpoN2, is required for twitching motility, natural competence, growth on nitrate and virulence of Ralstonia solanacearum. Front. Microbiol, 6, 229.
  • Satapathy, S.S., Ray S.K., Missed cites. Curr Sci, 107, 1633-1634.
  • Ray S.K., V.J. Baruah, S.S.Satapathy and R.Banarjee, 2014, Co-translational protein folding is revealing the selective use of synonymous codons along the coding sequence of a low expression gene.J. Genet. 93, 613–617.
  • Satapathy, S.S., Powdel, B.R., Dutta, M., Buragohain, A.K. and Ray S.K., 2014, Constraint on dinucleotides by codon usage bias in bacterial genomes. Gene, 536, 18.
  • Satapathy, S.S., Powdel, B.R., Dutta, M., Buragohain, A.K. and Ray S.K., 2014, Selection on GGU and CGU codons in the high expression genes in bacteria. J Mol Evol. 78, 13.
  • Kumar R, Barman A, Jha G, Ray S.K., 2013. Identification and establishment of genomic identity of Ralstonia solanacearum isolated from a wilted chilli plant at Tezpur, North East India. Current Sci. 105, 1571-1578.
  • Barman A, Kumar P, Kumar V, Doley R, and Ray S.K., 2013, Heat shock at 37°C with plasmid ligated at 37°C yields more number of Escherichia coli transformants than plasmid ligated at 16°C: a possible role of ligated plasmid conformation during heat shock. Current Sci. 104:747-751.
  • Pandey A, Ray S.K., Sonti R, Rajeshwari R. 2013. gltB/D mutants of Xanthomonas oryzae pv. oryzae are virulence deficient. Curr Microbiol. September 2013.
  • Khanppnavar B, Baruah S, and Ray S.K., 2013, TALE: an emerging tool for genome editing and genetic engineering. Current Sci. 104:576-578.
  • Powdel, B.R., Borah M and Ray S.K., 2010, Strand specific mutational bias influences codon usage of weakly expressed genes in Escherichia coli. Genes to Cells. 15:773-82
  • Satapathy S.S., Dutta M, Ray S.K. ,2010, Variable correlation of genome GC% with transfer RNA number as well as with transfer RNA diversity among different bacterial groups: αProteobacteria and Tenericutes exhibit strong positive correlation in both cases. Microbiological Res. 165:232-42
  • Powdel BR, Satapathy S.S., Kumar A, Jha PK, Buragohain AK, Borah M, Ray S.K., 2009, A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule). DNA Res.16:325-343
  • Ranjan A, Sinha AY, Dubey B, Saikia A, Buragohain AK, Ray S.K., 2008, Analysis of in-frame dinucleotides, encoded amino acids and synonymous codon choice in bacterial genomes reveals a common pattern. Curr Sci. 94:225-232
  • Das D, Satapathy S.S., Buragohain AK, Ray S.K., 2006, Occurrence of all nucleotide combinations at the third and the first positions of two adjacent codons in open reading frames of bacteria. Curr Sci. 90:22-24
  • Verma SK, Das D, Satapathy SS, Buragohain AK, Ray S.K., 2005, Compositional symmetry of DNA duplex in bacterial genomes. Curr Sci. 89:374-384
  • Das D, Verma SK, Ray S.K., 2005, An altered GC% region within potential hemagglutinin orfs of Ralstonia solanacearum. Curr Sci. 88:786-792
  • Ray S.K., 2004, Riboswitch: A new mechanism of gene regulation in bacteria. Curr Sci. 87:1168-1169.
  • Ray S.K., Rajeshwari R, Shrama Y, Sonti RV. 2002, A high-molecular-weight outer membrane protein of Xanthomonas oryzae pv. oryzae exhibits similarity to non-fimbrial adhesins of animal pathogenic bacteria and is required for optimal virulence. Mol Microbiol. 46:637-47
  • Ray S.K., Rajeshwari R, Sonti RV. 2000, Mutants of Xanthomonas oryzae pv. oryzae deficient in general secretory pathway are virulence deficient and unable to secrete xylanase. Mol Plant-Microbe Interact. 13:394-401


  • Other Publications



    LAB Alumni

    tr>
    Sl.No.NameYear
    1 Mr. Kulbhushan 2001-2003
    2 Dr. Ajeet Pratap Singh 2001-2003
    3 Dr. Debojyoti Das 2003-2005
    4 Dr. Sujit Kumar Verma 2003-2005
    5 Mr. Akhauri Yash Sinha 2004-2006
    7 Mr. Badri Nath Dubey 2004-2006
    8 Mr. Amit Ranjan 2004-2006
    9 Mr. Gaurav Kumar 2005-2007
    10 Mr. Aditya Kumar 2005-2007
    11Mr. Vinay Kumar 2005-2007
    12Mr. Anjan Barman 2007-2009
    13 Mr. V. J. Baruah 2007-2009
    14Mr. Rahul Kumar Rathour 2007-2009
    15Mr. Rupesh Kumar 2008-2010
    16Mr. Amit Kumar 2008-2010
    17Mr. Praveen Kumar 2010-2012
    18Ms. Shabiha Nudrat Hazarika 2011-2013
    19Mr. Sachin Sharma 2010-2012
    20Ms. Sangeeta Rani Sinha 2010-2012
    21 Ms.Kristi Kabyashree, (MSc) 2012-2014
    22 Mr.Yurembam Rojiv, (MSc) 2012-2014
    23Mr.Vinod Kumar Prajapati,(MSc)2012-2014
    24Ms.Priyanka Nath, (Int.MSc.)2009-2014
    25Ms.Anasuya Bhargab, (Int.MSc.)2010-2015
    26Mr.Madhurjya Borah, (Int.MSc.)2010-2015
    27Ms.Priyanka Koiri, (MSc.)2013-2015
    28Ms.Chandrika Burhagohain, (MSc.)2013-2015




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