Bio-sketch
Name: Krishnashish Bose
Specialization: Atomic Force Microscopy
I have chosen to be a biophysicist because of the great challenges a biological system offers to doing measurements and understanding it. One more reason is that we living beings are the best work of God.
Place of Birth: Calcutta, West Bengal
Country of origin: India
April 2012 - 28th June 2013
M.Sc Project in IIT Delhi: Characterization of Protein aggregates based on their elastic modulus.
Supervisors: Assoc Prof. Dr. Bishwajit Kundu and Prof. Dr. Bodh Raj Mehta
Other collaborators: Dr. Deepak Varandani (Senior scientist), Assoc Prof. Dr. Jitendra Pratap Singh
22nd July 2013 - 2017
Ph.D research in NTU Singapore:
During my PhD I have mainly focused on the development and application of Atomic Force Microscopy (AFM) in aqueous solution to visualize the structure of higher order DNA G-quadruplexes, RNA G-quadruplexes and the human telomere complex of TRF1/TRF2/Rap1. I have developed three new immobilization strategies to attach the molecules of interest to the Mica surface for visualization with AFM.
Project 1: DNA G-quadruplexes
It is now widely believed in the scientific community that DNA G-quadruplexes are highly dynamic and polymorphic; and are no less relevant than the double helix DNA. In fact, more than 100,000 potential G-quadruplex forming sequences have been identified in the human genome. This raises several questions about their role in biology and diseases, including those related to aging and cancer. Even though several structures of DNA G-quadruplexes have been reported, due to technical limitations of NMR and X-ray techniques, only short DNA sequences were chosen. And, no correlation has been found with the structure and length of DNA, except for the fact that the stability of DNA G-quadruplexes usually decline with sequence length. It is thus largely unclear if such long repetitive sequences form G-quadruplexes and if yes then what is the higher order structure of such DNA G-quadruplexes.
Using high resolution solution Atomic Force Microscopy and computational approaches, we have been able to obtain the structure of interlocked DNA G-quadruplexes formed by the Tetrahymena telomeric sequence d(G4T2G4). For the scientific community, it is for the first time that higher order DNA G-quadruplexes have been directly observed in aqueous solution. Our work could lay the foundation for understanding/manipulating the higher order assembly/organization of DNA G-quadruplexes in general.
Project 2: RNA G-quadruplexes
DNA is usually transcribed into RNA, which in turn is translated into proteins. Potential G-quadruplex forming DNA sequences are found in several genes, which upon transcription into RNA could lead to formation of RNA G-quadruplexes that can adversely affect its translation into the desired protein. Long repetitive G-rich DNA sequences in genes pose severe challenges for transcription and the resulting RNA transcripts could not only form RNA G-quadruplexes, but also pose a serious threat to the cellular machinery.
I am investigating two cases of long repeats of G-rich sequences: Telomeric Repeat Containing RNA (TERRA), and the hexanucleotide expansion of GGGGCC found in the brain of patients with ALS/FTD. We have obtained bacteria containing plasmids with long repeats of the sequence, from our research collaborators. PCR amplification of the desired section of the plasmid is done followed by transcription using suitable RNA polymerase. The DNA and RNA molecules are then visualized by AFM.
Project 3: Human telomere complex of TRF1/TRF2/Rap1
It is known that the mammalian telomeric sequence (TTAGGG)n can form DNA G-quadruplexes of several different secondary structures. However, the higher order structure formed by thousands of repeats of TTAGGG is unknown. It is known that the telomere is protected by the Shelterin complex, which comprises of several proteins including TRF1, TRF2 and Rap1. It has also been reported that the telomeric nucleosome complex formed by histones is not stable enough, and is thus unlikely to pack telomeric DNA. Thus, it is an unsolved mystery how thousands of repeat long DNA sequence at both ends of chromosomes are packed inside the nucleus of the cell. Researchers have reported observation of telomeric DNA complexes formed by TRF1, TRF2 and TRF2/Rap1 by AFM imaging in air; however, all such experiments were done by fixation with glutaraldehyde and observed in non-natural conditions.
I am trying to visualize the dynamics of the complex formed by telomeric duplex DNA with TRF1/TRF2/Rap1 complex, without any fixation and in physiologically relevant conditions.
Achievements:
2006
1. Scored 81% in class X CBSE Board Examination from Sainik School Purulia. My subjects were: Science, Mathematics, Social Science, Bengali and English. Scored highest in English followed by Social studies and Mathematics.
2008
1. Scored 75% in class XII CBSE Board Examination from Kendriya Vidyalaya 1, Salt Lake. My subjects were: Physics, Chemistry, Mathematics, Computer Science and English. Scored highest in English, followed by Chemistry and Computer science. Scored lowest in Physics but was determined to pursue a career in Physics only.
2. Got selected at Surendranath College. Spent a week there and then moved to Bidhannagar college which was very near to my home.
2011
1. Secured First class in B.Sc Physics (Hons.) from Bidhannagar Government College, Calcutta
2. Ranked 130 in the Joint Admission Test for M.Sc (JAM) organized by the Indian Institutes of Technology
3. Ranked 430 in the All India Joint Entrance Screening Test (JEST) for Ph.D/ Integrated Ph.D Programme in Physics organized by IMSC Chennai. [http://www.physicskerala.in/2011/03/jest-2011-results-published-at.html ]
4. Cleared the Entrance Test for Integrated Ph.D in Neurosciences organized by National Brain Research Centre
5. Got called for interview for M.Tech Nanotechnology in Delhi University.
6. Got called for interview for Int. Ph.D in Physics in SNBNCS, Kolkata. http://www.bose.res.in/bosetest2011/final_list.pdf
7. Took admission in Indian Institute of Technology Delhi for pursuing post graduation (M.Sc) in Physics. http://physics.iitd.ac.in/content/onroll-msc-students
2013
1. Cleared NET-JRF(Physics) held in Dec 2012.
2. Cleared GATE Physics held in Jan 2013.
3. Doing PhD in Physics at Nanyang Technological University Singapore.
Specialization: Atomic Force Microscopy
I have chosen to be a biophysicist because of the great challenges a biological system offers to doing measurements and understanding it. One more reason is that we living beings are the best work of God.
Place of Birth: Calcutta, West Bengal
Country of origin: India
April 2012 - 28th June 2013
M.Sc Project in IIT Delhi: Characterization of Protein aggregates based on their elastic modulus.
Supervisors: Assoc Prof. Dr. Bishwajit Kundu and Prof. Dr. Bodh Raj Mehta
Other collaborators: Dr. Deepak Varandani (Senior scientist), Assoc Prof. Dr. Jitendra Pratap Singh
22nd July 2013 - 2017
Ph.D research in NTU Singapore:
During my PhD I have mainly focused on the development and application of Atomic Force Microscopy (AFM) in aqueous solution to visualize the structure of higher order DNA G-quadruplexes, RNA G-quadruplexes and the human telomere complex of TRF1/TRF2/Rap1. I have developed three new immobilization strategies to attach the molecules of interest to the Mica surface for visualization with AFM.
Project 1: DNA G-quadruplexes
It is now widely believed in the scientific community that DNA G-quadruplexes are highly dynamic and polymorphic; and are no less relevant than the double helix DNA. In fact, more than 100,000 potential G-quadruplex forming sequences have been identified in the human genome. This raises several questions about their role in biology and diseases, including those related to aging and cancer. Even though several structures of DNA G-quadruplexes have been reported, due to technical limitations of NMR and X-ray techniques, only short DNA sequences were chosen. And, no correlation has been found with the structure and length of DNA, except for the fact that the stability of DNA G-quadruplexes usually decline with sequence length. It is thus largely unclear if such long repetitive sequences form G-quadruplexes and if yes then what is the higher order structure of such DNA G-quadruplexes.
Using high resolution solution Atomic Force Microscopy and computational approaches, we have been able to obtain the structure of interlocked DNA G-quadruplexes formed by the Tetrahymena telomeric sequence d(G4T2G4). For the scientific community, it is for the first time that higher order DNA G-quadruplexes have been directly observed in aqueous solution. Our work could lay the foundation for understanding/manipulating the higher order assembly/organization of DNA G-quadruplexes in general.
Project 2: RNA G-quadruplexes
DNA is usually transcribed into RNA, which in turn is translated into proteins. Potential G-quadruplex forming DNA sequences are found in several genes, which upon transcription into RNA could lead to formation of RNA G-quadruplexes that can adversely affect its translation into the desired protein. Long repetitive G-rich DNA sequences in genes pose severe challenges for transcription and the resulting RNA transcripts could not only form RNA G-quadruplexes, but also pose a serious threat to the cellular machinery.
I am investigating two cases of long repeats of G-rich sequences: Telomeric Repeat Containing RNA (TERRA), and the hexanucleotide expansion of GGGGCC found in the brain of patients with ALS/FTD. We have obtained bacteria containing plasmids with long repeats of the sequence, from our research collaborators. PCR amplification of the desired section of the plasmid is done followed by transcription using suitable RNA polymerase. The DNA and RNA molecules are then visualized by AFM.
Project 3: Human telomere complex of TRF1/TRF2/Rap1
It is known that the mammalian telomeric sequence (TTAGGG)n can form DNA G-quadruplexes of several different secondary structures. However, the higher order structure formed by thousands of repeats of TTAGGG is unknown. It is known that the telomere is protected by the Shelterin complex, which comprises of several proteins including TRF1, TRF2 and Rap1. It has also been reported that the telomeric nucleosome complex formed by histones is not stable enough, and is thus unlikely to pack telomeric DNA. Thus, it is an unsolved mystery how thousands of repeat long DNA sequence at both ends of chromosomes are packed inside the nucleus of the cell. Researchers have reported observation of telomeric DNA complexes formed by TRF1, TRF2 and TRF2/Rap1 by AFM imaging in air; however, all such experiments were done by fixation with glutaraldehyde and observed in non-natural conditions.
I am trying to visualize the dynamics of the complex formed by telomeric duplex DNA with TRF1/TRF2/Rap1 complex, without any fixation and in physiologically relevant conditions.
Achievements:
2006
1. Scored 81% in class X CBSE Board Examination from Sainik School Purulia. My subjects were: Science, Mathematics, Social Science, Bengali and English. Scored highest in English followed by Social studies and Mathematics.
2008
1. Scored 75% in class XII CBSE Board Examination from Kendriya Vidyalaya 1, Salt Lake. My subjects were: Physics, Chemistry, Mathematics, Computer Science and English. Scored highest in English, followed by Chemistry and Computer science. Scored lowest in Physics but was determined to pursue a career in Physics only.
2. Got selected at Surendranath College. Spent a week there and then moved to Bidhannagar college which was very near to my home.
2011
1. Secured First class in B.Sc Physics (Hons.) from Bidhannagar Government College, Calcutta
2. Ranked 130 in the Joint Admission Test for M.Sc (JAM) organized by the Indian Institutes of Technology
3. Ranked 430 in the All India Joint Entrance Screening Test (JEST) for Ph.D/ Integrated Ph.D Programme in Physics organized by IMSC Chennai. [http://www.physicskerala.in/2011/03/jest-2011-results-published-at.html ]
4. Cleared the Entrance Test for Integrated Ph.D in Neurosciences organized by National Brain Research Centre
5. Got called for interview for M.Tech Nanotechnology in Delhi University.
6. Got called for interview for Int. Ph.D in Physics in SNBNCS, Kolkata. http://www.bose.res.in/bosetest2011/final_list.pdf
7. Took admission in Indian Institute of Technology Delhi for pursuing post graduation (M.Sc) in Physics. http://physics.iitd.ac.in/content/onroll-msc-students
2013
1. Cleared NET-JRF(Physics) held in Dec 2012.
2. Cleared GATE Physics held in Jan 2013.
3. Doing PhD in Physics at Nanyang Technological University Singapore.