User:Chinmay Shukla

Contact Info

<html>Chinmay Shukla</html> <html> </html> 352 Godavari Hostel, Indian Institute of Technology, Madras, Tamilnadu, India. <html> Email:<a href="mailto:chinmay.shukla@biotech.iitm.ac.in">chinmay.shukla@biotech.iitm.ac.in</a></html> <html> Email:<a href="mailto:chinmay21191@gmail.com">chinmay21191@gmail.com</a> </html>

Education

<html> <ul> <li>Master of technology in Biotechnology, <a href="http://www.iitm.ac.in/">IIT Madras </a> (2013) Bachelor of technology in Biotechnology, <a href="http://www.iitm.ac.in/">IIT Madras </a> (2012)</li> Current GPA: 8.93/10 (Branch ranking – 1st) <li>Board of Higher Secondary Education (2008) School: St. Xaviers Loyola Hall </li> Graduated with 86.1% <li>Board of Secondary Education (2006) School: St. Xaviers Loyola Hall </li> Graduated with 93.6% </ul> </html>

Research Projects

<html> <ul> <li>Khorana Scholar 2012: Metabolic Networks and DNA Computing</li> [<a href="http://www.biochem.wisc.edu/faculty/ansari/"> Dr.Aseem Ansari </a>,<a href="http://www.ece.wisc.edu/~parmesh/"> Dr. Parmeswaran Ramanathan </a>, <a href="http://reedlab.che.wisc.edu/"> Dr. Jennifer Reed </a>; University of Wisconsin, Madison, May 2012 - July 2012] <ol type:"i"> <li>Metabolic Engineering of Escherichia Coli K-12 MG1665 to increase Valine Production using Transcription activator like effectors (TALEs)</li> Abstract: I worked on a novel way of directing and controlling metabolic networks. We Implemented a known deterministic Branched Chain Amino Acid (BCAA) biosynthesis model and identified key nodes (genes) which can be perturbed to increase the production of L-Valine by 400% in silico. Valine is a commercially important small molecule by itself and also useful in the biofuels industry. We are also coupling the deterministic model with whole genome reconstructions of Escherichia Coli K-12 MG1665 and using constraint based network analysis (COBRA) to predict important parameters like rate of cell growth (biomass) hence adding another dimension in the model. In order to implement the in silico perturbations in vivo, we are designing light sensitive(luxR promoter based) TALEs (Transcription activator like effectors) to modulate the activities of the key genes and control valine production in a light sensitive manner. Light controlled activation of TALEs provides us an easy control to switch TALEs on and off depending on the rate of growth of cell. Although metabolic engineering based on whole genome reconstructions is fairly well known, this work is novel in the way of finely controlling metabolic networks. <li>Constructing Clocks and NAND Gates and hence large scale circuits like memory, flip flops with simple DNA gate motifs which use toehold mediates strand displacement reactions</li> Abstract: It is very advantageous to program molecular systems to perform complex autonomous tasks and this has motivated research into the design of synthetic biochemical circuits. Of late, cell-free nucleic acid systems have evolved that exploit non-covalent hybridization of toeholds and subsequent strand displacement reactions to create cascades that implement digital and analogue circuits. Recently, a simple DNA gate architecture has been described for synthesizing large scale circuits like comparators, square root circuit and pulse generators. Infact, a small DNA brain implementing the Hopfield neural network (with pre determined weights) has also been made this way. AND and OR gates have been made but so far people have not been able to make the NOT gate and hence dual rail logic has to be used to convert all the gates in a circuit to AND/OR gates. Alongwith a graduate student in the <a href="http://www.biochem.wisc.edu/faculty/ansari/">Ansari Lab</a>, I tried to make NAND gate (a universal gate) using a combination of a clock and a AND gate. Although, we were not able to make this gate due to difficulties in designing DNA strands, the whole process of understanding such circuits and trying to simulate and design novel circuits was one of the best experiences of my life which taught me a lot. </ol> </ul> </html> <html> <ul> <li>Comparative Super-Resolution Imaging of the Primary Cilium</li> [<a href="http://cellbiology.yale.edu/people/derek_toomre.profile">Dr. Derek Toomre</a>, <a href="http://cellbiology.yale.edu/ccmi/cinema.aspx"> CINEMA Lab</a>, Yale University, May - July 2011] Abstract: Super Resolution microscopy is powerful technique to look at closely spaced objects. There are three major commercially available super resolution modalities – SIM, PALM and STED. There have been only a few studies giving a head to head comparison between various super resolution modalities. I directly compared these techniques to give more biological detail about a new and highly important organelle; the primary cilium. I showed that all the approaches can resolve changes in the axoneme ultra structure not visible by conventional confocal microscopy and that the cilium gets wider as we move from the tip to the base and hence it is more conical than cylindrical as traditionally thought of. Based on my novel findings, I am in the process of preparing the manuscript for a journal publication. I also used Total Internal Reflection Fluorescent Microscopy(TIRFM) to investigate the role of Rab8 in primary cilium biogenesis. </ul> </html> <html> <ul> <li>Functional studies of SNPs in the human renalase gene and their correlation with hypertension</li> [Dr. Nitish R Mahapatra, <a href="http://www.biotech.iitm.ac.in/faculty/nitish.htm"> Cardiovascular Genetics Lab </a> , IIT Madras, August 2012 - April 2013] Abstract:The renalase protein is a flavin adenine dinucleotide-dependent amine oxidase. Renalase is secreted by the kidney and it degrades catecholamines like norepinephrine and dopamine which are circulating in the blood. Since, catecholamines cause general physiological changes that prepare the body for physical activity they lead to increase in heart rate, blood pressure and blood glucose levels. Hence, renalase which is known to degrade these molecules is also thought to have an effect on blood pressure. In the last few years, Single Nucleotide Polymorphisms (SNPs) have been identified in the Northern Han Chinese population and European populations which have a strong correlation with hypertension. Since, SNPs can vary in different populations, the first part of my project aims at examining whether SNPs in the renalase gene have a correlation with hypertension in Indian population also. If there is a correlation between the SNPs and hypertension, I will try to determine the effects of the SNP on renalase expression and hence find the molecular reasons for the correlation of the SNPs with hypertension. </ul> </html> <html> Please feel free to <a href="mailto:chinmay21191@gmail.com">contact me</a> in case you want a more detailed report/poster for any of my research projects </html>

Industrial Experience

<html> <ul> <li>Pre Clinical Trials of a Pancreatic Cancer Vaccine and DNA Fingerprinting to find signature sequences in medicinal herbs</li> [<a href="http://www.cadilapharma.com/">Cadila Pharmaceuticals</a>, Ahmedabad, May – July 2010] Abstract: </ul> </html>

Academic Projects

<html> <ul> <li>Transcriptional Regulation of Retinoblastoma gene</li> [<a href="http://www.biotech.iitm.ac.in/Mahalingam">Prof. S Mahalingam </a>, IIT Madras]

<li>Photosynthesis: A Mathematical Model <a href="http://www.biotech.iitm.ac.in/faculty/CFA%20exercises.htm">(CFA Project) </a> </li> [<a href="http://www.biotech.iitm.ac.in/faculty/gk.php">Prof. G K Suraishkumar </a>, IIT Madras]

<li> Analyzing the transport Phenomenon in Leeches <a href="http://www.biotech.iitm.ac.in/faculty/CFA%20exercises.htm">(CFA Project) </a> </li> [<a href="http://www.biotech.iitm.ac.in/faculty/gk.php">Prof. G K Suraishkumar </a>, IIT Madras] </ul> Please feel free to <a href="mailto:chinmay21191@gmail.com">contact me</a> in case you want a more detailed report for any of these projects. </html>

Scholastic Achievements

<html><ul> <li>Consistently risen and currently at Branch Position 1 in my class of 40 students.</li> <li>Khorana Scholar 2012: Received a scholarship of $ 4500 through the DBT-Govt. of India, IUSSTF and UW-Madison to be among the top 30 students in India to undertake research at University of Wisconsin, Madison during May-July 2012.</li> <li>Awarded the Dr. Anita Mehta-Damani Prize for the best academic record in the 5th and 6th semesters in Biotechnology</li> <li>Awarded the Sri S Vishwanathan Prize for securing the highest Cumulative Grade Point Average [CGPA] in Management minor of the B.Tech / Dual Degree / MA programme during 2010-2012 </li> <li>Secured a position in the top 1% students in JEE 2008 (Joint Entrance Examination for IITs) written by over 300,000 students.</li> </ul></html>

Co-curricular & Extracurricular Activities

--Chinmay Shukla 19:35, 7 July 2012 (EDT)

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User:Chinmay Shukla

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Contact Info

Education

Research Projects

Industrial Experience

Academic Projects

Scholastic Achievements

Co-curricular & Extracurricular Activities

--Chinmay Shukla 19:35, 7 July 2012 (EDT)

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