AGP 441: Advances in Genomics and Proteomics          (60) 


UNIT I                 (15) 

ADVANCE NUCLEIC ACIDS TECHNIQUES                                     

Agarose gel electrophoresis, PFGE, Principles of PGFE, instrumentation, types and applications of PFGE. DGGE, Principles of DGGE, types and applications of DGGE, RT PCR, Real time PCR, principle of Real time PCR, types and application of Real time PCR,  (quantitative and qualitative), Designing Primers and probes for RT PCR, types of probes and their chemistries. RNA interference and gene silencing (si-RNA, mi-RNA) technology, Mi RNA. Various blotting techniques. 


UNIT II                         (15)


DNA sequencing technologies: Different chemistries in DNA sequencing, Next Generation sequencing (Sanger’s sequencing, SOLiD, Pyrosequencing), application of next generation sequencing (NGS), genomic library, EST library, cDNA library, Whole genome sequencing, Introduction to the concept of Transcriptomics and Metagenomics, Applications of Transcriptomics and Metagenomics.   


UNIT III                 (15) 


Evolution, elements of phylogeny, methods of phylogenetic analysis, Phylogenetic tree of life, comparison of genetic sequence of organisms. Identification of microbial isolates by 16S rDNA amplification and sequencing, methods of study of unculturable microbial flora from environmental sample,  16S rDNA library, 16S rRNA library, Ribosomal Database Project (RDP), Introduction to phylogenetic analysis tools, Concept of operational taxonomic unit (OTU)/ phylotypes, rarefaction curve, DOTUR, MOTHUR, MEGA, Phylip, PAUP, ClustalW. DNA based molecular markers technologies: RAPD, RFLP, AFLP, SCAR, SSR, ISSR, t-RFLP, The principles and applications of DNA based molecular markers. 


UNIT IV                (15) 


Concept of microarrays; spotted arrays, oligonucleotide arrays, designing the experiment, microarray design, microarray experimentation, Applications of microarray technology. Chromatography: gel permeation, adsorption (ion exchange, affinity), partition, HPLC, protein purification. 2-D analysis and Maldi-Tof in Proteomics, Mass spectroscopy for protein analysis, MALDI-TOF, Electrospray ionization, Tandem mass spectroscopy (MS/MS) analysis; tryptic digestion and peptide, fingerprinting (PMF), Protein Micro array in protein expression, profiling and Diagnostics. 


Suggested readings 1. Bernard R. Glick and Jack J. Pasternak, Molecular Biotechnology: Principles and Applications of Recombinant DNA.  2. Introduction to Bioinformatics, (Atwood, T. K. and Parry-Smith, D. J).  3. An introduction to Computational Biochemistry. (C. Stain Tsai, A JohnWiley and Sons, Inc., publications). 4. Developing Bioinformatics Computer Skills. (Cynthia Gibas and Per  Jambeck). 5. Bioinformatics Methods and Applications Genomics, Proteomics and Drug Discovery. (Rastogi S. C. Mendiratta, and Rastogi P.)  6. NCBI Web site: 7. Molecular Cloning by Sambruk and Russel (Maniatis)