Formats for submission of projects

QUALIFICATIONS

B. Tech. Chemical Engineering, I. I. T. Madras (1989).

Ph. D. Chemical Engineering, Purdue University, USA (1993).
AREA OF SPECIALIZATION: Synthetic and Systems Biology; Biochemical Engineering

Quantification of Biological Networks

Analysis of Metabolic and Regulatory Networks

Optimization and Development of Biological and Food Processes

Recent Publications in 2008-2011 (total peer reviewed publications: 87)
1. Can Metabolic Plasticity be a Cause of Cancer? Warburg Waddington Legacy Revisited, Paike Jayadeva Bhat, Lalith Durante, KV Venkatesh, Jaswandi Dandekar and Abhay Kumar, Clinical Epigenetics, (2011).
2. Characterization of the Adaptive Response and Growth upon Hyperosmotic Shock in Saccharomyces Cerevisiae, Jignesh Parmar, Sharad Bhartiya and KV Venkatesh, Molecular Biosystems, 2011 (Article in press)
3. Phenotypic Characterization of Corynebacterium glutamicum Using Elementary Modes towards Synthesis of Amino Acids, Rajvanshi, M., K.V Venkatesh, Systems and Synthetic Biology, 2011 (Article in Press).
4. In silico quantification of optimal lysine synthesis during growth of Corynebacterium Glutamicum on Mixed Substrates (Glucose and Lactate), Kalyan gayen, Manish Kumar, Meghana Rajvanshi and KV Venkatesh, International Journal of Biotechnology and Biochemistry, 7 (1), 115-132, 2011.
5. Phenotypic characterization of Corynebacterium glutamicum under osmotic stress conditions using elementary mode analysis, Rajvanshi, M., K.V Venkatesh,. Journal of Industrial Microbiology and Biotechnology , pp. 1-13, 2010.
6. Experimental and Steady State analysis of the GAL regulatory system in Kluyveromyces lactis, Venkat R. Pannala, Sharad Bhartiya and K. V. Venkatesh, FEBS Journal, 277, 2987 – 3002, 2010.
7. Chemotaxis of Escherichia coli to L-serine, , Rajitha R. Vuppula, Mahesh. Tirumkudulu and K. V. Venkatesh, Physical Biology, 7 (2), art. no. 026007 2010.
8. Mathematical modeling and Experimental validation of chemotaxis under controlled gradients of methylaspartate in Escherichia coli, Molecular Biosystems, Rajitha R. Vuppula, Mahesh. Tirumkudulu and K. V. Venkatesh, 6, 1082 – 1092, 2010.
9. Stability analysis of the GAL regulatory network in Saccharomyces cerevisiae and Kluyveromyces lactis, BMC Bioinformatics, Vishwesh Kulkarni, K. V. Venkatesh, Pushkar Malakar, Lucy Y Pao, Michael Safonov and Ganesh Viswanathan, 11(S43) 2010.
10. Application of methylene blue dye reduction test (MBRT) to determine growth and death rates of microorganisms, Subir Nandy and K. V. Venkatesh, Journal of Microbiology Research, 4(2), 61-70, 2010.
11. Tomato Redness for assessing ozone treatment in extending shelf-life, Journal of Food Engineering, Suhas S. Zambre, K. V. Venkatesh and N. G. Shah, 96(3), 463-468, 2009.
12. Quantification of the effect of amino acids on an integrated mTOR and insulin signaling pathway, Molecular Biosystems, PK Vinod and KV Venkatesh, 5, 1163 - 1173, 2009.
13. A Model-based Study Delineating the Roles of the Two Signaling Branches of Saccharomyces cerevisiae, Sho1 and Sln1, during Adaptation to Osmotic Stress, Physical Biology, Jignesh Parmar, Sharad Bhartiya and KV Venkatesh, 6 (3), 2009.
14. Systems Biology – connecting Genotype to Phenotype, BioByte, KV Venkatesh, 2009.
15. Optimization of bioprocesses using metabolic engineering, Book Chapter:, Devesh Radhakrishnan, Meghna Rajvanshi, Kalyan Gayen & K. V. Venkatesh, Bioprocess and Bioproducts, Edited by Soumitra Biswas, Nirmala Kaushik and Ashok Pandey, AsiaTech Publishers, 2009.
16. Modeling and Experimental studies on Intermittent Starch feeding and citrate addition in Simultaneous Saccharification and Fermentation of Starch to Flavor Compounds, Journal of Industrial Microbiology & Biotechnology, Abhijit R Chavan, Anuradha Raghunathan and K.V.Venkatesh, 36(4), 509-519, 2009.

17. Stochastic analysis of the GAL genetic switch in Saccharomyces cerevisiae: Modeling and experiments reveal hierarchy in glucose repression, Vinay Prasad, K V Venkatesh, BMC Systems Biology, 2:97, 2008

18. Effect of temperature on the cannibalistic behavior of Bacillus subtilis, Subir Kumar Nandy, Vinay Prasad and K. V. Venkatesh, Applied and Environmental Microbiology, 2008.
19. Quantification of cell size distribution as applied to the growth of Corynebacterium glutamicum, Kalyan Gayen and K. V. Venkatesh, Microbiological Research, 163, 586-593, 2008.
20. Quantification of Signaling Networks, P K Vinod and K V Venkatesh, Journal of the Indian Institute of Science, 88:1, Jan-Mar 2008.
21. Effect of Carbon and Nitrogen on the Cannibalistic Behavior of Bacillus subtilis, Subir Kumar Nandy and K. V. Venkatesh, Applied Biochemistry and Biotechnology, March, 2008 (Online first).
22. A Steady State Model for the Transcriptional Regulation of Filamentous Growth in Saccharomyces cerevisiae, P K Vinod and K V Venkatesh, In Silico Biology, 8, 0018, 2008.
23. Integration of global signaling pathways, cAMP-PKA, MAPK and TOR in the regulation of FLO11, P K Vinod, Neelanjan Sengupta, P J Bhat and K V Venkatesh, PLoS 0NE, 3(2):e1663, 2008.

AWARDS AND RECOGNITION
1. Associate Editor, BMC Systems Biology.

2. Member Editorial Board, International Journal of Systems and Synthetic Biology

3. International judge for international Genetically Engineered Machines (iGEM-2009), MIT USA

4. Invited to an International Workshop on “Physiological Modeling” organized by The Mathematical Biosciences

Institute, Ohio State University, USA, May 21-24, 2007.

5. Invited by Royal Society, London, UK to a workshop on Advances in Biosciences as relevant to Systems and

Synthetic Biology, September 2006.

6. Member of Organizing comittee, Indo-US Fronteirs of Engineering Meet, jointly hosted by National Academy of

Engineering, USA and Indian National Academy of Engineering, March 2-4, 2006.

7. Swaranjayanthi Fellowship from DST (2004).

8. Hindustan-Dorr-Oliver Award for Excellence in use of technology in Rural Development (2004)

9. Anil Kumar Bose award from Indian National Science Academy (INSA) for paper published in Journal of

Biological Chemistry (2004).

10. Visiting Research Fellow, School of Molecular and Biological Science, Oxford (Brookes) University, Oxford, UK

(May-June, 2002).

11. Visiting Research Professor, Department of Chemical Engineering, University of Delaware, Delaware, USA from

January 2001 to Deccember 2001.

12. INSA Young Scientist Award, 1999 from Indian National Science Academy for Research.

13. INAE Young Engineering Award, 1998 from Indian National Academy of Engineers.

14. Amar-Dye-Chem Award, 1999 from Indian Institute of Chemical Engineering for excellence in research.

PhD THESES GUIDED
1. Ms. Anuradha Raghunathan, Simultaneous Saccharification and Fermentation of starch, 1999.

2. Ms. Jyoti Bajpai Dikshit, Quantification of metabolic network of Lactobacillus rhamnosus, 2003.

3. Malkhey Verma, Protein production utilizing Recombinant Yeast in Bioreactors, 2005.

4. Vivek Mutalik, Quantification of signaling and regulatory networks, 2006.

5. Kalyan Gayan, In-silico analysis of Metabolic Networks, 2007.

6. Nikhil Chaudhary, Study of the regulatory design of Tryptophan system in Escherichia coli, 2007

7. Subodh Rawool, Steady state analysis of gene regulatory networks – simulation of micro-array data, 2008.

8. Manish Shakdwipee, Analysis of Renreable Hydrogen Options, 2008

9. Subir K Nandy, Effect of nutritional stress on the viability of B. subtilis and E. coli in mixed culture, 2009.

10. Vinod PK, Quantification of signalling networks in Yeast and Mammalian systems to nitrogen availability 2009.

11. Suhas Zambre, Application of ozone in enhancing shelf life of tomato and potato, 2009.

12. Abhijit Chauhan, Optimal operation of fermentation processes: Application to flavours production, 2010

13. Ms. Rajitha Vuppula, Chemotaxis of E. coli to controlled gradients of attractants, 2010

14. Venkat Pannala, Dynamic analysis and Characterization of the GAL system in Yeast, 2011.

15. Jignesh Parmar, System Level Analysis of Osmotic Effect on Yeast, 2011.

450. Details of Research Projects being implemented/completed/submitted by the Principal Investigator

1. Investigator(s) Name & Institute: Rajdip Bandyopadhyaya

Chemical Engg. Dept.

Indian Institute of Technology Kanpur

(previous affiliation of the PI)

Project Title: Engineering thin mesoporous films for development of sensor
Project Status: completed

Duration: 3 years

Date of start: 1. 4. 2005

Funding agency: MHRD

Total cost: Rs. 20 lakhs

Summary of the project:
Thin mesoporous (or nanoporous, in this case) silica films have been formed by spin coating a sol-gel reaction mixture from the liquid phase. The pores consist of hexagonal channels of controllable diameter of either 5 nm or 20 nm approximately. This has been verified by AFM, BET etc. Subsequently the pores have been functionalized with OTS or TMCS to make them hydrophobic, so as to make only benzene selectively adsorb in the pores, whereas water is not. As a result it can be used as a way of detecting and separating benzene at a very low concentration of tens of ppm in an aqueous mixture. The adsorption dynamics and equilibrium has been followed by UV-Visible absorbance of peak of benzene. This can be used as a sensor, which can detect very fast, and work reversibly on the basis of presence or absence of a response stimulus, like benzene.
2. Investigator(s) Name & Institute: Rajdip Bandyopadhyaya

Chemical Engg. Dept.

Indian Institute of Technology Kanpur

(previous affiliation of the PI)

Project Title: Scanning mobility particle sizer (SMPS) for gas-borne nanoparticulate systems
Project Status: Equipment installed and project completed

Duration: 1 year

Date of start: 10. 9. 2005.

Funding agency: IIT Kanpur

Total cost: Rs. 31.8 lakhs
Summary of the project:
Gas-borne nanoparticulate systems find an important place in both environmental processes and in various technologies of commercial interest. The former comes under the purview of aerosol science, which involves the study of solid and liquid particles present in the atmosphere, and has implications in air pollution and climatic patterns. On the other hand, nanoparticles of carbon, iron, silica, titania and other metal oxides are synthesized in gas based processes (like chemical vapour deposition, flame and laser ablation reactors) for applications as reinforcing fillers, catalysts, pigments etc. Data on particle size distribution is fundamental to the understanding of the mechanism of formation and properties or new applications of these nanoparticles. The proposed Scanning Mobility Particle Sizing (SMPS) system furnishes this data.
SMPS has been utilized for obtaining particle size distribution data for both outdoor ambient aerosols and common household smoke particles in an enclosed, indoor environment. In the first case, patterns of diurnal and seasonal variations of nanoparticulates and black carbon in the environment has been analyzed and correlated successfully. On the other hand, in the second application area using SMPS; size distribution and chemical composition measurement of indoor aerosols has led us to identify the more harmful aerosols, among common household sources of smoke.
3. Investigator(s) Name & Institute: Rajdip Bandyopadhyaya

Chemical Engg. Dept.

Indian Institute of Technology Bombay
Project Title: General Strategies for Nanoparticles of Controlled Size, Shape and Composition: Magnetite as a Case Study for MRI Applications
Project Status: Finished

Duration: 3 years

Date of start: 7. 5. 2008

Funding agency: DST

Total cost: Rs. 38.94 lakhs

Summary of the project (Up-to date Technical progress report for on-going projects):

• 
  Achieved stable aqueous dispersions of magnetic Fe₃O₄ nanoparticles of diameter < 20 nm, coated with different coating agents – like citric acid, dextran, PAA etc.
  

• 
  Required cytocompatibility levels were obtained for citric acid or dextran coated Fe₃O₄ nanoparticles by incubating them with HepG2 cells, for up to 24 hrs.
  

• 
  For achieving a stable dispersion, the minimum shell thickness of a coating agent
  

required for a given particle size was predicted by Monte Carlo simulation.

• 
  Through experiments and MC simulation, the states of aggregation of particles were found.
  
• 
  Achieved continuous, silica thin films containing iron oxide nanoparticles (with negligible aggregation) distributed uniformly within the film.
  

Details of Research Projects being implemented/completed/submitted by the Co -Investigator
Investigator(s) Name & Institute: K. V. Venkatesh

Chemical Engg. Dept.

Indian Institute of Technology Bombay
Project Title: Characterization of heterogeneity in the microbial population using elementary mode analysis
Project Status: Ongoing

Duration: 3 years

Date of start: March, 2010

Funding agency: DST

Total cost: Rs. 31 lakhs

500. Any other relevant matter: None