Structural Biology [https://www.DVasuLab.com]
Over the initial years, we have gained a certain sense of directionality with respect to our science. Details of our current focus areas can be seen below:
(1) Chromatin Structural Biology: Histone proteins package eukaryotic DNA into chromatin. The dynamic DNA-protein complex called nucleosomes forms the basic element of chromatin. All eukaryotic genomic processes, both natural and pathological, including transcription, replication, recombination, repair, chromosome segregation, carcinogenesis, and viral infection, can be fully understood only in the context of nucleosomes. The core of a nucleosome, called the nucleosome core particle (NCP), consists of fourteen turns of B-form DNA around an octamer of histone proteins.
A nucleosome is known to be the binding platform for several protein factors. In order for a protein to gain access to chromosomal DNA/histone proteins, it needs to interact and/or compete with the histone proteins/DNA of the nucleosome. Studies involving nucleosomes are of greater significance than isolated studies focusing on the interaction of protein factors with individual histone(s) or DNA. In this context, we work on some nucleosome-interacting proteins.
Around the theme of chromatin structural biology, another of our interests is histone chaperones. Histone chaperones are a group of proteins that bind histones and regulate nucleosome assembly. The mode of action of several histone chaperones is not well-understood. Also, it is not completely clear what decides the specificity of certain histone chaperones for H3/H4, H2A/H2B, or histone variants. In order to better understand these molecular machines, we work on a few projects dealing with the structural characterization of some important but poorly characterized histone chaperones. A major interest in this direction has been nucleoplasmins. Our endeavors with histone chaperones have gotten us to initiate structural characterization work on certain histone deacetylases (HDACs) as well!
(2) Structural Biology of Clp Machinery Proteins: The caseinolytic protease (Clp) machinery is present in bacteria, plants, and other eukaryotes. These proteases usually associate with Clp chaperone proteins that help in the ATP-dependent unfolding of substrates, which need to be taken in for proteolysis by the proteases. ClpD is a Clp-associated chaperone unique to plants. Plant ClpC and ClpD proteins both get localized into chloroplast stroma. However, our work from ILS has shown that the structure of ClpD is quite different from that of ClpC in its N-terminus. Our interest in plant Clp machinery proteins is to understand their distinct roles in protein homeostasis and stress response. In addition, we also work on mycobacterial Clp chaperones due to their importance as a target in anti-mycobacterial research.
(3) Infectious Disease Structural Biology: A couple of our chromatin structural biology and Clp machinery projects have infectious disease flavor. In addition, we also work on proteins from bacteria, fungi, viruses, and parasites that are infectious to humans. We have recently started working on candidate proteins from the pathogens that infect cultured shrimps.
Over and above these, additional structural biology projects are being taken up from time to time collaboratively.
Our collaborators @ ILS:
- Dr. Balachandran Ravindran (immunology)
- Dr. Narottam Acharya (yeast genome instability)
- Dr. Soma Chattopadhyay (virology)
- Dr. Tushar Kant Beuria (bacterial cell division)
- Dr. V. Arun Nagaraj (plasmodium biology)
Other major collaborators:
- Prof. Kim Lewis, North Eastern University, Boston, USA (antibacterials)
- Prof. Sheng Luan, University of California at Berkeley, USA (plant FKBPs)
- Prof. Klaas van Wijk, Cornell University, USA (plant protein homeostasis)
- Prof. Claudia Jonak, Austrian Inst. of Technology, Austria (plant stress factors)
- Prof. Aline V. Probst, CNRS, France (histone variants and chaperones)
- Prof. Anil Grover, University of Delhi-South Campus, India (plant stress tolerance)
- Prof. Jagneshwar Dandapat, Utkal University – Bhubaneswar, India (immunology)
- Prof. Rabindra Behera, NIT – Rourkela, India (ferritin nanocages)
- Prof. Meenu Kapoor, Indraprastha University – New Delhi, India (plant DNMTs)
- Dr. Devinder Sehgal, NII – New Delhi, India (bacterial virulence)
- Dr. Bhavani Shankar Sahu, NBRC – Manesar, India (vesicle biogenesis)
- Dr. Rahul Modak, KIIT University – Bhubaneswar, India (bacterial deacetylases)
- Dr. Subhendu K. Otta, CIBA – Chennai, India (shrimp pathogens)
- Dr. Insaf Ahmed Qureshi, University of Hyderabad, Hyderabad – India (Leishmania proteins)
As we have technical expertise in making nucleosome core particles and nucleosomal arrays, our group is open to collaborative projects dealing with nucleosome binding factors.
To know more about our group, please have a look at https://DVasuLab.com
Our Group Members:
1. Ms. Archana Samal (UGC-SRF) – Ph.D. scholar
- BSc Honors (Botany) Honors, Shailabala Women’s College, Cuttack, 2016.
- MSc (Life Sciences), Central University of Punjab, Bathinda, 2018.
- Project JRF at Utkal University (Feb 2019 – Nov 2019).
- Joined our group at ILS as a Ph.D. scholar in March 2020.
- Current research interest: Chromatin structural biology
2. Mr. Surajit Gandhi (UGC-SRF) – Ph.D. scholar
- BSc (Zoology), Banwarilal Bhalotia College, Asansol, 2016.
- MSc (Zoology), University of Burdwan, Purba Bardhaman, 2018.
- Joined our group at ILS as a Ph.D. scholar in February 2020.
- Current research interest: Chromatin & infectious disease structural biology
3. Mr. Ketul Saharan (UGC-SRF) – Ph.D. scholar
- BSc (Biotechnology), Government National College, Sirsa, 2014.
- MSc (Botany), Kurukshetra University, Kurukshetra, 2016.
- JRF at School of Life Sciences, JNU, New Delhi, Aug 2017 – Feb 2019.
- Joined our group at ILS as a Ph.D. scholar in March 2019.
- His Ph.D. is registered with RCB, Faridabad.
- EMBO Scientific Exchange Grant (SEG) Fellow at NTU Singapore (Sept-Dec 2022)
- Current research interest: Chromatin & HDACs
4. Dr. Dharma Rao Tompa (Project-RA; Postdoctoral Fellow)
- BSc (Biochemistry), Andhra University, Visakhapatnam, 2009.
- MSc (Biochemistry & Molecular Biology), Central University of Kerala, Kasaragod, 2012.
- Ph.D. (Structural Biology and Molecular Biophysics), SASTRA University, Thanjavur, 2019.
- Post-doc at ICGEB, New Delhi, 2021-2022.
- Joined ILS as a post-doc in September 2022.
- Current research interest: Chromatin and infectious disease structural biology
5. Mr. Manoj Kumar Barik (Laboratory Technician)
- DMLT from JRN Rajasthan Vidyapeeth University (2019)
- Lab Technician in a private diagnostic laboratory in Bhubaneswar (2019-2021)
- Trainee Lab Technician from March to December 2021 in our group.
- Joined ILS as a Lab Technician in January 2022.
6. Mr. Vicky Kumar (XRD Facility In-Charge)
- BSc (Industrial Microbiology) Honors, Langat Singh College, Muzaffarpur, 2019.
- MSc (Biotechnology), DBT-RGCB, Thiruvananthapuram, 2022.
- Joined our group in ILS as the XRD Facility In-charge in February 2023.
7. Mr. Purushottam Patnaik (AUC Facility In-Charge)
- BSc (Zoology), Vikram Deb Autonomous College, Jeypore, Berhampur University, 2020.
- MSc (Microbiology), College of Pharmaceutical Sciences, Berhampur, 2022.
- Joined our group in ILS as the AUC Facility In-charge in February 2023.
Group Alumni:
1. Dr. Ruchir Chandrakant Bobde
- BSc (Chemistry, Microbiology, Biotechnology), RTM Nagpur University, 2013.
- MSc (Biotechnology), RTM Nagpur University, 2016.
- Trainee at ACTREC, Navi Mumbai, Jan 2016 – Mar 2016.
- Project staff at ICAR-CICR, Nagpur, Oct 2016 – Jan 2017.
- Joined our group at ILS as a Ph.D. scholar in January 2017.
- PhD from ILS (RCB Faridabad) (Jan 2017 – Apr 2023).
- While with us, he worked on the theme of chromatin & HDACs
2. Dr. Manas Kumar Jagdev
- BSc (Biotechnology), Utkal University, Bhubaneswar, 2009.
- MSc (Industrial Biotechnology), Siksha ‘O’ Anusandhan University, 2011.
- Research trainee in Imgenex India Pvt. Ltd., Bhubaneswar, 2011-2012.
- Microbiologist in Sambit Aqua, Cuttack, 2012-2013.
- Chemist/Microbiologist in Spring Resources Pvt Ltd, Cuttack, 2013.
- Joined our group at ILS as a Lab Technician in September 2013.
- Upgraded to project SRF in December 2015.
- Registered for Ph.D. in Nov 2017.
- PhD from ILS (Utkal University) (Nov 2017 – Feb 2022).
- With us, he worked on plant & mycobacterial Clp chaperone machinery proteins.
- Current position: Postdoctoral researcher at the University of Texas, El Paso, USA.
3. Dr. Rajivgandhi Sundaram
- BSc (Biotechnology), Tiruvalluvar University, Vellore, 2010.
- MSc (Biotechnology), Periyar University, Salem, 2012.
- DMLT, Microtech Insitute of Paramedical Science and Research, Salem, 2011.
- Junior Executive in Biocon Research Limited, Bangalore, 2012-2013.
- JRF in School of Biological Sciences, NISER, Bhubaneswar, 2013-2014.
- Joined our group in ILS as a Ph.D. scholar in April 2014 with DBT-JRF.
- Ph.D. from ILS (Manipal Academy of Higher Education) (Apr 2014 – Aug 2021).
- With us, he worked on plant histone chaperones and PCNA.
- Current position: Postdoctoral researcher at Johns Hopkins University, Baltimore, USA.
4. Dr. Ajit Kumar Singh
- BSc (Biotechnology), Bangalore University, 2010.
- MSc (Biotechnology), Bangalore University, 2012.
- Trainee/Junior Executive in Biocon Research Limited, Bangalore, 2012-2013.
- JRF in Fermentation Technology Department, CFTRI, Mysore, 2013-2014.
- Joined our group in ILS as a Ph.D. scholar in April 2014 with DBT-JRF.
- Ph.D. from ILS (Manipal Academy of Higher Education) (Apr 2014 – Sept 2020).
- With us, he worked on plant FKBP-nucleoplasmins.
- Current position: Postdoctoral researcher at the University of Vermont, Burlington, USA.
5. Dr. Ashish Kumar
- BSc Honors (Biotechnology), Patna University, Patna, 2011.
- MSc (Biotechnology), Babasaheb Bhimrao Ambedkar University, Lucknow, 2013.
- Joined our group in ILS as a Ph.D. scholar in September 2013 with DBT-JRF.
- Ph.D. from ILS (Manipal Academy of Higher Education) (Sept 2013 – Sept 2020).
- With us, he worked on plant chromatin and histone chaperones.
- Current position: Postdoctoral researcher at Yale University, New Haven, USA.
6. Dr. Supriya Borah (co-supervisory)
- BSc (Agriculture), Assam Agricultural University, Jorhat, 2010.
- MSc (Agricultural Biotechnology), UAS, Dharwad, 2012.
- Ph.D. on co-supervisory from our group in ILS (Manipal Academy of Higher Education) (Feb 2013 – Oct 2019).
- While with us, she worked on Clec14a protein that is involved in angiogenesis.
- Current position: DBT-RA at CDFD, Hyderabad
7. Dr. Shaikh Nausad Hossain (Postdoctoral Fellow)
- BSc (Biotechnology), Bangalore University, 2005.
- Diploma (Genetic Engineering), JIVAS, Bangalore, 2005.
- Project JRF at PGIMER, Chandigarh, 2005-2006.
- MSc (Molecular Biology), University of Queensland, Australia, 2008.
- Research Assistant, University of Queensland, Australia, 2008-2009.
- Ph.D. (Structural Biology), University of Queensland, Australia, 2013.
- Postdoctoral fellow at Okinawa Institute of Science and Technology (OIST), Japan, 2013-2016.
- Visiting postdoctoral fellow at NISER, Bhubaneswar, 2017-2018.
- Joined our group at ILS as an institutional postdoctoral fellow in July 2018.
- CSIR-SRA from December 2019 – December 2022.
- With us, he worked on the broad theme of infectious disease structural biology
8. Dr. Chinmayee Mohapatra (Postdoctoral Fellow)
- BSc Honors (Botany) Utkal University, Bhubaneswar, 2005.
- MSc (Biotechnology), Utkal University, Bhubaneswar, 2007.
- Ph.D. (Cell & Molecular Biology), Utkal University, Bhubaneswar, 2014.
- BCIL trainee in Imgenex India Pvt. Ltd., Bhubaneswar, 2007-2008.
- JRF/SRF in CIFA, Bhubaneswar, 2008-2014.
- Joined our group at ILS as a postdoctoral fellow in April 2014.
- Postdoc with our group in ILS under various schemes from Apr 2014 to Feb 2023.
- With us, she worked on Clp chaperone machinery proteins.
9. Dr. Aritreyee Datta (Postdoctoral Fellow)
- BSc (Biotechnology), Bangalore University, 2007.
- MSc (Biotechnology), KIIT University, 2010.
- Ph.D. (Biotechnology), University of Kolkata, 2017.
- SRF in Bose Institute, Kolkata, 2012-2017.
- Joined our group at ILS as a postdoctoral fellow in August 2017.
- Postdoc with our group in ILS from Aug 2017 to Oct 2022.
- While with us, she worked on chromatin and infectious disease thematic projects.
10. Dr. Sushil Kumar (Postdoctoral Fellow)
- BSc (Biology), University of Allahabad, 2001.
- MSc (Bioinformatics), University of Allahabad, 2005.
- MTech (Biotechnology), West Bengal University of Technology, Kolkata, 2007.
- Ph.D. (Structural Biology), JNU, New Delhi, 2015.
- JRF/SRF in CCMB, Hyderabad, 2008-2015.
- Postdoc with our group in ILS from May 2015 to May 2018.
- While with us, he worked in the broad area of chromatin & infectious disease structural biology.
- Current position: Scientist with Biocon, Chennai
11. Dr. Vipul Panchal (Project fellow)
- BSc (Chemistry – Honors), MS University, Baroda, 2008.
- MSc (Biochemistry), MS University, Baroda, 2010.
- Ph.D. from CSIR-IGIB, New Delhi, 2019.
- Project Fellow in our group at ILS from May 2018 to June 2019.
- While with us, he worked on certain viral enzymes involved in nucleotide synthesis.
- Current position: Postdoctoral researcher at the University of Bergen, Norway
12. Mr. Somanath Baral (Project-SRF)
- BSc Honors (Botany), Utkal University, Bhubaneswar, 2015.
- MSc (Botany), Berhampur University, Berhampur, 2017.
- MPhil (Botany), Berhampur University, Berhampur, 2019.
- Project JRF, IIT Kharagpur, May 2019 – December 2019.
- Project JRF with us from January 2020 to June 2022.
- While with us, he worked on the theme of chromatin & nucleoplasmins.