Giving a Biological side to it

 

Well, although I finished my B. Tech. in Chemical Engineering, IIT BOMBAY, I am more interested in allied biological fields of the same. Well, fascination to this field was gradual and strong. I have had enough exposure to this field during my B. Tech. years. So, I landed here in UIC, Chicago pursuing my PhD in Bioengineering. Well in the chronological order my exposures go as follows.

·        I first had some of the very basic knowledge to the vast field of biology and the genetics in the course “ Molecular Cell Biology ” in my sophomore year. This course formed the base for further build-up. It mainly looked into: organization of plants and animals, Biomolecules, Cellular processes, Information transfer in cells, Genetic engineering and Cell cultures.

 

·        Then I opted for the elective titled “ Introduction to Biochemical Engineering” which gave the basic insight into: characterization and classification of biological matter, kinetics of biological growth, Design and analysis of biological reactors, Transport phenomena in biological systems and Production, isolation and utilization of enzymes.   

 

·        Next I decided to do my internship in the same field and so headed for National Center For Biological Sciences (NCBS), Bangalore. This is biological the unit of Tata Institute of Fundamental Reaserch (TIFR). There I went on to develop a software called the Multi-Motif PHI-BLAST. This software is used to search the genomic database by aligning two sequences. The present version available at the NCBI site takes only one motif as the input. I had started from scratch and developed a parallel version of it for taking multiple motifs as the input. The one produced gave some excellent results. This software has now been put up on the web for people to use. The link is: http://www.ncbs.res.in/~faculty/mini/FMALIGN/home.html . We are soon going to submit a paper on this in "Bioinformatics Journal. This trip to NCBS gave me the best exposure to this field. I got an opportunity to acquaint myself with some of the softwares in this field BLAST, PHI-BLAST, PSI-BLAST, Gibb’s Motif Sampler, ClustalW, MEME, SPALSH and with all major Sequence Databases (GenBank/SWISSPROT/PDB/PDBAA).

 

 

·        I was also involved in a year-long project titled “ Effect of Shear on the cell cultures and their gene expressions” under Prof G. K. Suraishkumar along with one of my batchmates, Ravi. This project dealt not only with the effects of shear on the gene expression but we also tried to find out the reason as to why some particular genes are upregulated/downregulated in response to shear environment. We tried to find some sort of SSRE (shear stress responsive element) for the same. This further involved working with some of the related softwares in this field such as ClustalW and the databases such as SWISS-PROT. In the first stage we submitted a literary report on the topic. We then tried to find out the reason for the upregulation/downregulation.  

 

·        I also opted for a course entitled “Analysis of Biological and  Bioprocess Systems”. This course also gives insight into the following modules:

           Module 1  Bioinformatics

         Module 2  Metabolic engineering

         Module 3  Modeling and control of bioreactors

 

• Finally came the B. Tech Project (Senior Dissertation). I opted for a topic that relates to a technology that forms an important part of Biotechnology: Microarrays. This is titled “Gene Expression Analysis of E Coli. using the Microarray Results”. I worked on  the results (High  and Low Glucose Concentration) generated from the microarray experiments to find out what causes the upregulation/downregulation of some genes involved in the TCA cycle which in turn affects the metabolic rates of these genes.    

 

    Along with these courses/projects in biochemical field, I have had the regular courses as a part of my curriculum in Chemical Engineering. A few of the relevant courses are:

·        Transport phenomena,

·        Thermodynamics (I and II),

·        Fluid and fluid operations,

·        Heat transfer operations,

·        Kinetics,

·        Mass transfer (I and II),

·        Mathematics and Computational techniques for chemical engineers,

·        Process equipment design and economics,

·        Instrumentation and process control,

·        Reaction engineering,

·        Chemical process design,

·        Material technology, and

·        Chemical processes (I and II).