Total Credit (T-P-P): 9-9-11 :

Course Division (list of all divisions) :

Track Courses (3-6-0)

1. Computational Biology 1-2-0
2. Genetic Engineering and its applications 1-2-0
3. Genetics and Genomics 1-2-0

Practice Courses (0-9-0)

1. Molecular Genomics 0-3-0
2. Plant Tissue Culture Technologies 0-3-0
3. Techniques in Molecular Biology 0-3-0

Project (0-0-11)

1. Exploration of available various sequences from different crops.
2.In vitro micro-propagation of banana and hardening.
3.Commercial production of horticultural crops.
4.Standardization of protocol for in vitro micro-propagation of horticulture crops.
5.DNA isolation, amplification and gel electrophoresis of plant sample.
6.Phenotyping and genotyping of rice varieties for abiotic stress tolerance.
7.Genome editing techniques towards crop improvement.

8. The RNA secondary structure variation in viruses and the possible implication in pathogenicity

9. Understanding RNA Protein interactions in viruses

Syllabus:

1. Computational Biology
   Theory:

Biological databases: Overview of biological databases, nucleic acid & protein databases, primary, secondary, functional, composite, structural classification of databases. Alignment using BLAST and CLUSTAL W.

RNA and DNA folding: Introduction to RNA and DNA folding, Softwares and webservers used for DNA or RNA folding: Mfold, RNAfold, RNA structure

Insilico Drug Design: Basic Concepts, importance and application. Molecular Docking

Python Tools for Computational Molecular Biology: Introduction to Biopython

Practice in Project Mode: NCBI GenBank resources - Overview, Access, Data Usage, Confidentiality, International Nucleotide Sequence Database Collaboration, Data Type, European Nucleotide Archive - sequence assembly information and functional annotation, DNA Data Bank of Japan (DDBJ). Kyoto Encyclopedia of Genes and Genomes (KEGG), Retrieval of sequence/structure from databases, Visualization of structures, Docking of ligand receptors, BLAST exercises, Molecular models, drug design, Python based computational biology - Biopython.

Suggested Readings:
• Attwood TK & Parry-Smith DJ. 2003. Introduction to Bioinformatics. Pearson  Education.
• Rastogi SC, Mendiratta N & Rastogi P. 2004. Bioinformatics: Concepts, Skills and Applications. CBS.

2. Genetic Engineering and its applications
Theory:

Plant Tissue culture: Cell culture media and sterilization techniques, Callus culture, nodal and tip culture, Protoplast and Embryo culture, Embryo culture and embryo rescue, protoplast isolation, culture and plant regeneration Somatic embryogenesis, Somaclonal variation and crop improvement, Germplasm conservation.

Recombinant DNA technology: Introduction to genetic engineering, restriction endonucleases and methylases; DNA ligase, T4 DNA polymerase, polynucleotide kinase, alkaline phosphatase. Gene cloning vectors: Plasmids; Bacteriophages; phagemids; Lambda vectors; Cosmids; Artificial chromosome vectors (YACs; BACs).Construction of recombinant DNA and expression cassettes, Transformation (mobilization of vectors into competent bacteria), selection and analysis of recombinant clones, Isolation of mRNA and total RNA; reverse transcriptase and cDNA synthesis; Genomic DNA & plasmid DNA isolation and purification, genomic DNA and cDNA libraries, screening of libraries.

Gene transfer in Plants: Vector mediated Gene transfer, Molecular basis of crown gall and hairy root diseases, features of Ti and Ri plasmids, mechanism of T-DNA transfer, role of virulence genes, vectors based on PTi & PRi, binary and co-integrate vectors, physical and chemical methods of gene transfer. Introduction to gene editing, ZFNs & TALENs, CRISPR/Cas System, Case studies of gene editing for crop improvement.

Practice in Project Mode: DNA isolation and purification, Callus induction, Agrobacterium mediated gene transfer in plants, vector construction, cloning and transformation.

Suggested Readings:
Glick, B. R. and Pasternak (2003). Molecular Biotechnology: Principles and Applications of Recombinant DNA. ASM Press, Washington, D. C., USA.
Kyte, L. and Kleyn, J. (1996). Plants from Test Tube to: an Introduction to Micro propagation, 3rd Ed. Timber press, Port land, USA.
Reference Book
Pollard, W. J. and Walker (1990).Plant Cell and Tissue Culture Vol VI. Humana press Clifton, USA.

3. Genetics and Genomics

Theory:

Basic of genetics: Mendel’s Laws, concept of dominance, segregation, independent assortment; Chromosome theory of inheritance.

Genome Mapping and Sequencing: Genetic and physical mapping, Markers for genetic mapping, Human Genome Project, Genome sequencing projects for microbes, Genome sequencing projects for plants and animals, Accessing and retrieving genome project information from the web. Genome sequencing: assembly, alignment and annotation. DNA sequencing strategies,  Next generation sequencing strategies.

Functional genomics and proteomics: Introduction to genomics, transcriptome analysis for identification and functional annotation of gene, forward and reverse genetic approaches. Introduction to proteomics, proteomics technologies: 2D-PAGE, isoelectric focusing, Mass spectrometry.
Practice in Project mode:  Demonstration of web tools for genome analysis. Effect of abiotic stress on field crops (Phenotyping), Effect of growth regulators on field crops (Phenotyping), Salinity/Cold/High Temperature stress tolerance genes and their responsiveness (Genotyping), Molecular markers (RAPD, SSR, AFLP etc) and their analysis.

Suggested Readings:
•Practical Applications of Plant Molecular Biology By Robert J. Henry.
• Biochemistry and Molecular Biology of Plants edited by Bob B. Buchanan, Wilhelm Gruissem, Russell L. Jones.