User:Sonia Chothani: Difference between revisions
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<a href="http://2011.igem.org/Team:IIT_Madras/Dry_lab/Modelling">Click here to see more details on the modelling.</a> <br> | <a href="http://2011.igem.org/Team:IIT_Madras/Dry_lab/Modelling">Click here to see more details on the modelling.</a> <br> | ||
</ol> <br> | </ol> <br> | ||
[[Image: | [[Image: Jamboree11_Poster.jpg|center|800 px|Presented at the International Genetically Engineered Machines (iGEM) conference 2010]] | ||
<li><b>International Genetically Engineered Machines (iGEM) 2010 </b></li> | <li><b>International Genetically Engineered Machines (iGEM) 2010 </b></li> | ||
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[[Image: Jamboree_Poster.jpg|center|1050 px|Presented at the International Genetically Engineered Machines (iGEM) conference 2010]] | [[Image: Jamboree_Poster.jpg|center|1050 px|Presented at the International Genetically Engineered Machines (iGEM) conference 2010]] | ||
These were student initiated and organized project where we brainstorm towards a feasible, novel and socially significant idea. We also handled the Sponsorship, Finance and the laboratory equipment management. We generated a sponsorship of INR 8,00,000 to fund the projects and managed the laboratory requirements.<br><br> | These were student initiated and organized project where we brainstorm towards a feasible, novel and socially significant idea. We also handled the Sponsorship, Finance and the laboratory equipment management. We generated a sponsorship of INR 8,00,000 to fund the projects and managed the laboratory requirements.<br><br> | ||
[[Image: Research_Expo.jpg|center|800 px|Presented at the International Genetically Engineered Machines (iGEM) conference 2010]] | |||
==Industrial Experience== | ==Industrial Experience== | ||
Revision as of 04:28, 15 February 2012
About Me
<html> <body> <p> A senior student in the Department of Biotechnology, IIT Madras, I will graduate as a B.Tech (Biotechnology) in spring 2012.<br> Currently working in the Protein Bioinformatics Laboratory under the guidance of <a href = "http://www.biotech.iitm.ac.in/Gromiha">Dr. Michael Gromiha ( IIT Madras )</a> <br>
</body> </html>
Contact Info
<html> <body> <p> 129, Sharavathi Hostel<br> Indian Institute of Technology Madras<br> Adyar, Chennai 600036<br> Tamil Nadu,India<br> </body> </html>
- Email me through OpenWetWare
- Alternative Email-ID: schothani.iitm@gmail.com
- Contact Number: +919003214815
Education
- 2012, B.Tech, Biotechnology, Indian Institute of Technology Madras
Research Projects
Areas of Interest: Systems Biology, Bioinformatics and Synthetic Biology
- Organism Specific Protein-RNA interactions [Guide : Dr. M. M. Gromiha, IIT Madras Duration : Dec’11-Ongoing ] Understanding the recognition mechanism of Protein-RNA complexes has been a challenging task in molecular and computational biology. Computational biologists have studied non-redundant sets of these complexes and have formulated interesting facts. We would like to study whether a Protein-RNA recognition mechanism studied in only one organism can be generalized for all others or not. Expecting a varied behavior we would like to study how this change has evolved and observe a pattern over evolution.
- Reconstruction and Modelling of human specific Mitogen Activated Protein Kinase signalling pathways [Guide : Dr. Ramrup Sarkar, Mathematical Modeling and Computational Biology Laboratory, Centre for Cellular and Molecular Biology, Hyderabad, India Duration : May-July 2010] The initial phase of the work required a meticulous and patient reconstruction of a comprehensive MAPK signaling pathway (297 ‘species’ and 160 ‘reactions’) from various databases and literature. We used the Logical Steady State Analysis (LSSA) approach for modeling and analysis using the software CellNetAnalyzer (CNA). Further, a systematic perturbation study analysis to identify alternative pathways and optimal intervention points (targets) was carried out.
- Monsanto Research Centre [Bangalore, India May-Jul’11]
- Molecular Cloning [Dr. Thillai Chidambaram, Dept: Molecular Cloning, Vector Technology and Protein Analytics (MVP), 7 weeks]
- Gained experience in numerous sophisticated Molecular Biology Techniques for E.coli and Agrobacterium
- Submitted 3 successful clones which were forwarded to the next vertical (Transformation, MRC, Bangalore)
- Quality check time for transformants was reduced from 1 day to 4 hrs by optimizing cell growth
- Optimized a new cloning technique which uses Overlap Extension fusion. It helps to clone more than 1 inserts at a time. This is being continued at MRC to reduce the cost and time
- Experimentally calculated optimum insert concentration for a successful ligation hence optimized time for PCR amplification of the insert. The time was reduced from 3.5 hrs to 1 hr
- Bioinformatics [Dr. Subodh Rawool, Computational Biology Function , 2 weeks]
- Learnt Perl, a scripting language-within 4 days and developed scripts to overcome the shortcomings of currently available methods for dynamic visualization of metabolic networks.
- Larsen & Toubro Infotech Ltd. [Powai, Mumbai, Jun-Jul’09]
<html> <a href="http://openwetware.org/images/1/17/Report_Sonia_Chothani.pdf">Click here to view the report.</a> <br> <a href="http://openwetware.org/images/b/ba/Reconstruction_%26_Modeling_Of_MAP_Kinase_Signaling_Pathway.ppt">Click here for the presentation</a><br> </ul> </html>
International Competitions/Conferences
<html> <ul> <b><li>International Genetically Engineered Machines (iGEM) 2011 </li></b> <i>Photonivorous bacteria for Resolution and Expression, IIT Madras, Jan-Nov’11 </i><br> <b>Won Gold, Asia's Best Natural Biobrick, Asia's Best Safety Commendation </b> <br> [Guide: Dr. Nitish Mahapatra, Dr. G.K Suraishkumar, Dr. Michael Gromiha]<br> [Asia Regionals, HKUST, Hong Kong (15th Oct’11)]<br> [World Championship, MIT, Boston (7th Nov’11)]<br><br>
<ol type="1"> <li> A light based technique to screen transformants using a positive control </li> An alternative to antibiotic screening technique for transformants. The screening plasmid here consists of a <a href="http://en.wikipedia.org/wiki/Proteorhodopsin">Proteorhodopsin(PR)</a> gene instead of the antibiotic resistance which in presence of light and <a href="http://en.wikipedia.org/wiki/Retinal">Retinal (A chromophore)</a> gives a proton gradient, this is used by ATP synthase to produce ATP. Hence giving an energy advantage allowing only the transformed cells to grow in a low carbon media. <li> A light based technique to improve protein productivity</li> Plasmid consisting of a Carbon Stress Promoter (pCSTA) and Proteorhodopsin, giving a survival advantage to the cells in low nutrient media. This would help improve the productivity of recomibnant proteins, biopolymers like Hyaluronic Acid and Curdlan. <br>
<li>Mathematical Modeling and computational tools </li> <ol type="1"> <li>Developed an open-source online tool for site directed mutagenesis primer design </li> <li>An extensive Reconstruction and Flux Balance Analysis study of metabolic pathways in E.coli at the genome scale, considering 1668 metabolites and 2383 reactions and their respective stoichiometry matrices was carried out using a Constraint Based approach. Upto 30% increase in growth rate was observed due to Proteorhodopsin at high carbon stress conditions</li> </ol> <a href="http://2011.igem.org/Team:IIT_Madras/Dry_lab/Modelling">Click here to see more details on the modelling.</a> <br> </ol> <br> [[Image: Jamboree11_Poster.jpg|center|800 px|Presented at the International Genetically Engineered Machines (iGEM) conference 2010]]
<li><b>International Genetically Engineered Machines (iGEM) 2010 </b></li> <i>Sweetening Pro-biotic Curd, Department of Biotechnology, IIT Madras, Jan-Nov’10</i><br> <b> Won Gold </b> <br> [Guide: Dr. Guhan Jayaraman]<br> [iGEM , MIT, Boston(7th Nov’10)]<br>
<ol type="1"> <li>Our innovations are two-fold: the idea of using a lactic acid bacteria (often used in the curdling of milk) to produce the sweetening protein(Monellin), and in using a regulatory mechanism that functions under a combination of constraints, like an AND gate</li> <li>Our regulatory mechanism combines the use of promoters that can be either induced or repressed by an external action, like providing Heat-shock, adding Niacin, or by the system falling below a certain pH </li> <a href="http://2010.igem.org/Team:IIT_Madras">Click here to go to our media wiki</a><br> <a href="http://openwetware.org/images/f/f5/11_02_10_Jamboree_presentation.pdf">Click here to view our presentation</a><br> </ol></html>
These were student initiated and organized project where we brainstorm towards a feasible, novel and socially significant idea. We also handled the Sponsorship, Finance and the laboratory equipment management. We generated a sponsorship of INR 8,00,000 to fund the projects and managed the laboratory requirements.
Industrial Experience
Offered a Research Consultant Position at Monsanto Research Centre, Bangalore
Understanding of Product Lifecycle Management and its Current Usage in Biotechnology Equipped the team with prospect maps and SWOT analysis of various clients
Academic projects/Presentations
Co-Curricular & Extracurricular activities
Useful links
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