M Sc. Biotechnology and Bioinformatics

Bioinformatics

  1. Introduction to Bioinformatics & Computational Biology
  2. Statistical Genomics
  3. Genome Assembly and Annotation
  4. Biomolecular Modelling and Simulation
  5. Transcriptomics and Metagenomics
  6. Biological Data Management
  7. Biological network modelling and analysis
  8. Computer programming in bioinformatics
  9. Machine Learning Techniques in bioinformatics

Molecular Biology and Biotechnology

  1. Principles of Biotechnology
  2. Fundamentals of Molecular Biology
  3. Molecular Cell Biology
  4. Techniques in Molecular Biology I
  5. Omics and Systems Biology
  6. Plant Genetic Engineering
  7. Techniques in Molecular Biology II
  8. Introduction to Bioinformatics
  9. Plant Tissue culture
  10. Microbial and Industrial Biotechnology
  11. Molecular Plant Breeding
  12. IPR, Bio-safety and Bioethics
  13. Immunology and Molecular Diagnostics
  14. Nano Biotechnology
  15. Nano Biotechnology
  16. Bio-entrepreneurship
  17. Stress Biology and Genomics
  18. Stress Biology and Genomics

M.Sc. in Bioinformatics

  1. Introduction to Bioinformatics and Computational Biology

Content:  Overview of available genomic resources on the web; NCBI/ EBI/ EXPASY etc; Nucleic acid sequence databases; GenBank/EMBL/ DDBJ; Database search engines: Entrez, SRS. Overview/concepts in sequence analysis; Pairwise sequence alignment algorithms: Needleman and Wunsch, Smith and Waterman; BLAST, FASTA; Scoring matrices for Nucleic acids and proteins: PAM, BLOSUM, Multiple sequence alignment: PRAS, CLUSTALW. Sequence based gene prediction and its function identification. Preprocessing of gene expression data; Data Normalization techniques, Data quality control: Modelling of errors, Imputation etc; High-throughput screening. Optimization Techniques: concept and applications, Simulated Annealing, Genetic Algorithms: Ab initio methods for structure prediction; Information theory, entropy and relative entropy. Foundations for Machine learning Techniques: Unsupervised and Supervised Learning, Cross Validation Techniques, Markov Model, Bayesian Inference: concepts and applications, Hidden Markov Model and applications, Introduction to WEKA package.

Practicals: Database Similarity Searches, Multiple sequence alignment, Genome databases, Structural databases, Derived databases, Gene annotation, Gene prediction software. Analysis of DNA microarray experiments, Expression profiling by microarray/gene chip, Proteomics, Pattern recognition, Hidden Markov Models, Gibbs Sampling, Analysis of single and multiple DNA or protein sequences.

  1. Statistical Genomics

Content:  Fundamentals of Population genetics: Hardy –Weinberg law, Effect of systematic forces on changes in gene frequency; Principles of Quantitative genetics: Values, Means and Variances, Detection and Estimation of Linkage, Inbreeding, Selection, Genetic Parameter Estimation, Variance component estimation, BLUP, G x E interaction, Path Analysis. Molecular Marker based classification: similarity measures, clustering methods, bootstrapping; QTL mapping: Detection and Estimation of QTL, Single Marker Analysis, Interval Mapping and MQM; Design and Analysis of Expression Data; Genome Selection; Genome Prediction, Genetic Markers, Association Mapping; Genome Wide Association Analysis.

Practicals: Population genetics: Hardy-Weinberg law, Estimation of linkage, Inbreeding, Selection, Genetic parameter estimation, Variance component estimation, BLUP, Path analysis, Molecular marker based classification, Estimation of QTL, Single marker analysis, MQM, Analysis of gene expression data, Genome selection and Genome prediction.

  1. Genome Assembly and Annotation

Content:  Types and methods of genome sequence data generation; Shot gun sequencing method; Problems of genome assembly, Approaches of genome assembly: Comparative Assembly, DE novo Assembly; Read coverages; Sequencing errors, Sequence Quality Matrix, Assembly Evaluation; Challenges in Genome Assembly. Various tools and related methods of genome assembly: MIRA, Velvet, ABySS, ALLPATHS-LG, Bambus2, Celera Assembler, SGA, SOAPdenovo, etc. Basic concepts of genome annotation; Structural and Functional Annotation; Identification of open reading frame (ORF) and their regularization, Identification of gene structure, coding regions and location of regulatory motifs.

Practicals: Genome assembly methods for data from various sequencing platform, Sequencing error determination, Sequence quality matrix; Various tools for genome assembly: MIRA, Velvet, ABySS, ALLPATHS-LG, Bambus2, Celera Assembler, SGA, SOAP denovo, etc. Structural and functional Genome annotation.

  1. Bio-molecular Modelling and Simulation

Content:  Methods for 3D Structure Prediction: Homology modeling of protein 3D structures – approaches to loop building, energy considerations and evaluation of the accuracy of the model. ab initio approach to 3D structure prediction; Threading approach to 3D structure prediction. A Comparison of protein structure prediction methods: CASP. Basic principles of modeling, modeling by energy minimization technique, concept of rotation about bonds, energy minimization by basic technique for small molecules, Ramachandran plot, torsional space minimization, energy minimization in Cartesian space, molecular mechanics-basic principle. Basic concepts of Simulation Modelling: Units and derivatives, Force field and energy landscape, Truncation of non-bonded interactions, Introduction to solvation, Periodic boundary condition, Wald summation, implicit solvent model and continuum electrostatics, Monte Carlo simulation on parallel computers. Replica-exchange simulations, Restraint potentials, Free energy calculations, Membrane simulations. Energy Minimization: Concept of energy minimization - hypersurface, local and global energy minima, statement of problem. Derivative minimization methods - first derivative methods: the steepest descents method, line search in one dimension, arbitrary step approach, conjugate gradients minimization. Second derivative method – the Newton-Raphson method. Applications of energy minimization.

Practicals: Protein structure databases: PDB, MODBASE, Structure visualization – Rasmol and PyMol, Structural analysis- classification, CATH, SCOP, Protein geometry – bond length, bond angle, torsion angle, calculation of surface area, volume and radii: Swiss PDB Viewer. Small molecule generation - peptides and nucleic acids: ISIS draw / ChemSketch, Selection of query sequence, template selection: pdbBLAST, Comparative 3D structure prediction – SWISSMODEL, Model generation - building side chains and loops using Modeller, Threading, ab initio modeling, Structure validation - generation and analysis of Ramachandran plot using PROCHECK, WHATCHECK via SAVS server, Force field calculation and energy minimization, Structure refinement - loop building, removing non-bonded contacts, adding missing side chains via WhatIf interface, Scoring structural similarity - 3D structure alignment - RMS superimposition – VMD, Molecular dynamics simulation using Tinker. Simulation dynamics, Monte carlo simulation on parallel computers. Replica exchange simulation, free energy calculation. Docking.

  1. Transcriptomics and Metagenomics 

Content:  Microarrays, RNA-seq, Chip-Seq, EST-clustering, differential expression analysis. Taxonomic and genetic annotation of high throughput sequence data, microbial diversity analyses, analyses of microbial community composition and change and metabolic reconstruction analyses. Comparison between Metagenomics and AL, EC, Comparison between LCS and Metagenomics, Symbiotic Evaluations: SANE, Comparison between SANE and Metagenomics, Horizontal Gene Transfer: Microbial GA. Metagenome Sequencing, Single Cell Analysis, Host-Pathogen Interaction; Shotgun metagenomics; High-throughput sequencing; Comparative metagenomics; Community metabolism; Metatranscriptomics.

Practicals: Meta genome annotation, Analyses of microbial community composition and change and metabolic reconstruction analyses; Metatranscriptomics; Comparative metagenomics. Microarray data analysis; RNA-seq, chip-seq, EST-clustering.

  1. Biological Data Management

Content:  Database Management System (DBMS): Need for DBMS - File system vs Database system, Advantages of DBMS - DBMS Architecture – DBMS services - Data abstraction - Overview of Data Models: Hierarchical Model - Network Model - Entity-Relationship (E-R) Model: Symbols - Components of E-R Model: Entities, Attributes, Relationships - Relational Model, Object-oriented Model. Overview of Relational Database Objects – Relation – Tuple - Cardinality – Attribute – Degree - Domain - Primary key – Foreign key - Relational data structure – Relational Data Integrity and Constraints: Domain constraints, Entity integrity, Referential Integrity, Operational constraints - Codd’s Rules – Normalization: 1NF, 2NF, 3NF, BCNF, 4NF and 5NF. Structured Query Language (SQL): Overview of SQL – SQL Data types and Literals – SQL Commands: Data Definition Language (DDL), Data Manipulation Language (DML), Data Querying Language (DQL), Data Control Language (DCL), Data Administration Statements (DAS), Transaction Control Statements (TCS), SQL Operators: Arithmetic, Comparison, Logical and Set Operators – SQL Query, Nested Query - SQL Aggregate functions. Curation of genomic, genetic, proteomic data, High-throughput screening, array, qPCR data sets; Quality management of data: tools and techniques. Biological data sources, Data granularity, Schema modelling, architecture, query design, extraction, transformation and loading, Long term data management, storage and security. Bio-chip information system, visualization and reporting, Risk factors for data quality management. Un-structured or noSQL database; AI and BIG data Analytics.

Practicals: Understanding the data sources, Data granularity, Data modeling and architecture, development of database, Storage, Security, Visualization and reporting.

  1. Biological Network Modelling and Analysis

Content:  Introduction to biological networks, Graph theoretic modelling and analysis of biological networks, Discrete Dynamic modelling (Boolean networks, Petri nets), Continuous dynamic modelling (ODEs, stochastic simulation, etc.). Probabilistic modelling (Probabilistic Boolean networks, Bayesian networks, Mutual Information), Network inference from experimental data, Genome-scale modelling and network integration. Evolution of molecular networks, Network-guided GWAS studies, FBA and epistasis detection, protein function prediction

Practicals: Biological networks, Graph theoretic modelling and analysis of biological networks, Discrete Dynamic modeling; Continuous dynamic modeling; Probabilistic modeling; Genome-scale modelling and network integration; Evolution of molecular networks, Network-guided GWAS studies, FBA and epistasis detection, protein function prediction.

  1. Biological Network Modelling and Analysis

Content:  BioJava- Packages, Data Import, Manipulation; Python- Basic Syntax, Loops, Functions; BioPython. Bioperl: Introduction, Modules: SeqIO, SearchIO, Seq Feature, Finding introns, Alignments, LiveSeq and Tree. Open MP: Clauses, Work sharing constructs, Synchronization constructs, Environment variables, Global Data, Runtime functions, Message Passing Interface (MPI): Introduction and programming, Point to point communications, Collective communications, Advanced MPI1 concepts, MPI2 introduction, Hybrid (openMP + MPI) programming. Compute Unified Device Architecture (CUDA): Introduction and Programming, GPU computing.

Practicals: BioPerl programing using bioperl modules such as SeqIO, SearchIO, LiveSeq and Tree; OpenMP programming on Work sharing and Synchronization constructs, Environment variables and global data; MPI programming on Point to point communications and Collective communications; Compilation of OpenMP and MPI programs; Execution of OpenMP and MPI programs; Use of high performance computing, computing resources and job scheduling.

  1. Machine Learning Techniques in Bioinformatics

Content: Introduction to statistical learning theory, Empirical Risk Minimization, Structural Risk Minimization; Classification: Decision tree, Bayesian, Rule based classification, ANN, SVM, KNN; Case based reasoning and Applications in Bioinformatics. Clustering: Partition Methods, Heirarchical methods, Density based methods, Grid based clustering, Model based clustering, clustering of high dimensional data, constraints based clustering, Analysis of MD trajectories, Protein Array data Analysis. Dimensional Reduction Techniques, Methods of Feature Selection, Resampling Techniques, Elements of Text Mining and Web Mining, Soft Computing and Fuzzy logic system and application in bioinformatics.

Practicals: Decision tree, classification techniques: ANN, SVM, KNN, Case based reasoning and its applications on biological data. Clustering techniques; Clustering of high dimensional data; Dimensional reduction techniques; Resampling techniques; Text mining and Web mining. Soft Computing and Fuzzy logic system & application in bioinformatics.

Molecular Biology and Biotechnology

  1. Principles of Biotechnology

Content:  History, scope and importance of Biotechnology; Specializations in Agricultural Biotechnology: Genomics, Genetic engineering, Tissue Culture, Bio-fuel, Microbial Biotechnology, Food Biotechnology etc. Basics of Biotechnology, Primary metabolic pathways, Enzymes and its activities. Structure of DNA, RNA and protein, their physical and chemical properties. DNA function: Expression, exchange of genetic material, mutation. DNA modifying enzymes and vectors; Methods of recombinant DNA technology; Nucleic acid hybridization; DNA/RNA libraries; Applications of gene cloning in basic and applied research, Plant transformation: Gene transfer methods and applications of GM crops. Molecular analysis of nucleic acids -PCR and its application in agriculture and industry, Introduction to Molecular markers: RFLP, RAPD, SSR, SNP etc, and their applications; DNA sequencing, different methods; Plant cell and tissue culture techniques and their applications.Introduction to genomics, transcriptomics, ionomics, metabolomics and proteomics. Plant cell and tissue culture techniques and their applications. Introduction to Emerging topics: Genome editing, gene silencing, Plant microbial interactions,Success stories in Biotechnology, Careers and employment in biotechnology. Public perception of biotechnology; Bio-safety and bioethics issues; Intellectual property rights in biotechnology.

  1. Fundamentals of Molecular Biology

Content:  Historical developments of molecular biology, Nucleic acids as genetic material, Chemistry and Nomenclature of nucleic acids; Structure of DNA: primary structure; secondary structure, Forms of DNA: A,B, Z and their function; Structure andTypes of RNA Genome organization in prokaryotes and eukaryotes; DNA Topology; DNA re-association kinetics, Types of repeat sequences. Central dogma of Molecular Biology; DNA replication- Classical experiments, Models of DNA replication; DNA replication, Origin and Steps in DNA replication - initiation, elongation and termination; Enzymes and accessory proteins and its mechanisms; Eukaryotic DNA replication in brief. Types of DNA damages and mutations; DNA repair mechanisms, Recombination: Homologous and non-homologous, Genetic consequences. Prokaryotic transcription, initiation, elongation and termination, promoters, Structure and function of eukaryotic RNAs and ribosomal proteins. Eukaryotic transcription – RNA polymerase I, II and III, Elongation and Termination, Eukaryotic promoters and enhancers, Transcription factors,Post transcriptional processing, Splicing: Catalytic RNAs, RNA stability and transport, RNA editing. Genetic code and its characteristics,Universal and modified genetic code and its characteristics,Wobble hypothesis; Translational machinery; Ribosomes in prokaryotes and Eukaryotes. Initiation complex formation, Cap dependent and Cap independent initiation in eukaryotes,Elongation: translocation,transpeptidation and termination of translation; Co- and Post-translational modifications of proteins; Translational control; Protein stability -Protein turnover and degradation. Gene regulation in prokaryotes, Constitutive and Inducible expression, small molecule regulators; Operon concept: lac and trp operons, attenuation, antitermination, stringent control.Gene regulation in eukaryotes– regulatory RNA and RNA interference mechanisms,Silencers, insulators, enhancers, mechanism of silencing and activation; Families of DNA binding transcription factors: Helixturn-helix, helix-loop-helix etc. Epigenetic regulations

  1. Fundamentals of Molecular Biology

Content: Origin of life, History of cell biology, Evolution of the cell: endo-symbiotic theory, treeof life, General structure and differences between prokaryotic and eukaryotic cell; Similarities and distinction between plant and animal cells; different kinds of cells inplant and animal tissues. Cell wall, cell membrane, structure and composition of bio-membranes, Structure and function of major organelles: Endoplasmic reticulum Ribosomes, Golgi apparatus, Mitochondria, Chloroplasts, Lysosomes, Peroxisomes, Micro-bodies, Vacuoles, Nucleus, Cyto-skeletal elements. Membrane transport; Diffusion, osmosis, ion channels, active transport, mechanism of protein sorting and regulation of intracellular transport, transmembrane and vesicular transport - endocytosis and exocytosis; General principles of cell communication: hormones and their receptors,signaling through G-protein coupled receptors, enzyme linked receptors; signal transduction mechanisms and regulation, Cell junctions, Cell adhesion, Cell movement; Extracellular matrix. Chromatin structure, Cell division and regulation of cell cycle; Mechanisms of cell division, Molecular eventsat M phase, mitosis and cytokinesis, Ribosomes in relation to cell growth and division, Extracellular and intracellular Control of Cell Division; abnormal cell division: cancer- hall marks of cancer and role of oncogenes and tumor suppressor genes in cancer development - Programmed cell death (Apoptosis). Morphogenetic movements and the shaping of the body plan, Cell diversification, cellmemory, cell determination, and the concept of positional values; Differentiated cells and the maintenance of tissues and organ development; Stem cells: types and applications; Basics of Animal development in model organisms (C. elegans; Drosophila); Plant development.

  1. Techniques in Molecular Biology I

Practicals: Good lab practices, preparation of buffers and reagents. Principle of centrifugation and spectrophotometry. Growth of bacterial culture and preparation of growth curve, Isolation of Genomic DNA from bacteria. Isolation of plasmid DNA from bacteria. Growth of lambda phage and isolation of phage DNA.  Isolation and restriction of plant DNA (e.g. Rice / Moong / Mango / Merigold). Quantification of DNA by (a) Agarose Gel electrophoresis and (b) Spectrophotometry PCR using isolated DNA. PAGEGel electrophoresis. Restriction digestion of plasmid and phage DNA, ligation, Recombinant DNA construction. Transformation of E. coli and selection of transformants. Chromatographic techniques a. TLC b. Gel Filtration Chromatography, c. Ion exchange Chromatography, d. Affinity Chromatography; Dot blot analysis, Southern hybridization,Northern hybridization. Western blotting and ELISA. Radiation safety and non-radio isotopic procedure.

  1. Omics and Systems Biology

Content: Different methods of genome sequencing, principles of various sequencing chemistries, physical and genetic maps, Comparative and evolutionary genomics, Organelle genomics, applications in phylogenetics, case studies of completed genomes, preliminary genome data analysis, basics of ionomics analysis, different methods Protein-basics: primary-, secondary- and tertiary structure, Basics of X-ray crystallography and NMR, Principal and Applications of mass spectrometry, Proteomics: Gel based and gel free, Basics of software used in proteomics, MASCOT, PD-Quest, etc., Study of protein interactions, Prokaryotic and yeast-based expression system and purification Metabolomics and its applications, Use of 1D/2D NMR and MS in metabolome analysis, Multivariate analysis and identification of metabolite as biomarkers, Study of ionome using inductively coupled plasma – mass spectroscopy (ICP-MS), X-Ray Fluorescence (XRF), Neutron activation analysis (NAA), Data integration using genome, transcriptome, proteome, metabolome and ionome with phenome. Introductory systems Biology - The biochemical models, genetic models and systems model, Molecules to Pathway, Equilibrium binding and cooperatively – MichaelisMenten Kinetics, Biological oscillators, Genetic oscillators,Quorum Sensing, Cellcell communication, Drosophila Development, Pathways to Network, Gene regulation at a single cell level, transcription network, REGULATORY CIRCUITS, Negative and positive auto-regulation, Alternative Stable States, Bimodal Switches, Network building and analysis.

Practical: Isolation of HMW DNA and brief overview of sequencing, Primary information on genome data analysis.  BSA Standard curve preparation, Extraction of protein and estimation methods. Quantification of proteins from different plant tissues using spectrophotometry. 2-D Gel Electrophoresis, 2-D Image analysis. Experiments on protein-protein interaction (Yeast 2-hybrid, Split Ubiquitin system). Demonstration on MALDI-TOF. Demonstration on ICP-MS, AAS, Nitrogen estimation using various methods.

  1. Plant Genetic Engineering

Content:  Historical background, Restriction Enzymes; DNA Modifying enzymes, ligase, T4 DNA polymerase, Polynucleotide kinaseetc, Cohesive and blunt end ligation; Labeling of DNA: Nick translation, Random priming, Radioactive and non-radioactive probes, Hybridization techniques: Northern, Southern and Colony hybridization, Fluorescence in situ hybridization; Chromatin Immunoprecipitation; DNA-Protein Interactions: Electromobility shift assay. Plasmids; Bacteriophages; M13, Phagemids; Lambda vectors; Insertion and Replacement vectors; Cosmids; Artificial chromosome vectors (YACs; BACs); Animal Virus derived vectors-SV-40; Expression vectors; pMal,pET-based vectors; Protein purification; His-tag; GST-tag; MBP-tag, etc.; Baculovirus vectors system, Plant based vectors, Ti and Ri plasmids as vectors, Yeast vectors, Shuttle vectors. Transformation; Construction of libraries; Isolation of mRNA and total RNA; cDNA and genomic libraries; cDNA and genomic cloning, Jumping and hopping libraries, Protein-protein interactive cloning and Yeast two hybrid system; Phage display; Principles in maximizing gene expression; Codon optimization for heterologous expression. Introduction of DNA into mammalian cells; Transfection techniques. Principles of PCR, Primer design,DNApolymerases, Types of PCR – multiplex, nested, reverse transcriptase, real time PCR, touchdown PCR, hot start PCR, colony PCR, cloning of PCR products; T- vectors; Applications of PCR in gene recombination, Site specific mutagenesis, in molecular diagnostics; Viral and bacterial detection; Mutation detection: SSCP, DGGE, RFLP, Oligo Ligation Assay. Genetic transformation of plants: DNA delivery – Agrobacterium mediated method. Direct DNA delivery – chemical mediated electroporation and particle bombardment. Vectors and transgene design - Promoters and Marker genes. Chloroplast transformation. Development of marker-free plants. Analysis of transgenic plants – molecular and Biochemical assays, genetic analysis - Identification of gene integration site - Advance methods – cis genesis, intragenesis and targeted genome modification – ZFN, TALENS and CRISPR. Application of transgenic technology.

  1. Techniques in Molecular Biology II

Practicals: Construction of gene libraries (cDNA and Genomics). Synthesis and cloning of cDNA. Real time PCR and interpretation of data. Molecular markers i. RAPD. ii. SSR. iii. AFLP / ISSR and their analysis. Case study of SSR markers - construction of linkage map. QTL analysis using genotypic data based on SSR. SNP identification and analysis. Microarray studies and use of relevant software. Proteomics i. 2D gels, ii. Mass spectrometry; RNAi - designing of construct, phenotyping of the plant. Yeast 1 and 2-hybrid interaction. Generation and screening of mutants. Transposon mediated mutagenesis. Immunology and molecular diagnostics: Ouchterlony double diffusion, Immunoprecipitation, Radiation Immunodiffusion, Immunoelectrophoretic, Rocket Immunoelectrophoretic, Counter Current Immunoelectrophoretic,ELISA, Latex Agglutination, Immunohistochemistry.

  1. Introduction to Bioinformatics

Content:  Bioinformatics basics, scope and importance of bioinformatics; Biological databases for DNA and Protein sequences -PIR, SWISSPROT, GenBank, DDBJ, secondary database, structural databases –PDB,SCOP and CATH, Specialized genomic resources, Microarray database. Bioinformatics Tools Facilitate the Genome-Wide Identification of Protein-Coding Genes, Sequence analysis, Sequence submission and retrieval system-SEQUIN, BANKit, SAKURA, Webin, Sequence alignment, pair wise alignment techniques, multiple sequence alignment; Tools for Sequence alignment- BLAST and its variants; Phylogenetic analysis- CLUSTAL X, CLUSTAL W, Phylip, Tcoffee. Sequencing of protein; Protein secondary structure prediction- Chousfasman, GOR Method, Protein 3DStructure Prediction: Evaluation of models- Structure validation and refinement - Ramachandran plot, Force field calculations, SAVES. Protein function prediction- sequence and domain based, Primer designing- principles and methods.Drug discovery, Structure Based Drug Design- Rationale for computer aided drug designing, basic principles, docking, QSAR.

Practical: Usage of NCBI resources; Retrieval of sequence/structure from databases and submission; Different Databases, BLAST exercises.; Assembly of DNA and RNA Seq data; Annotation of assembled sequences, Phylogenetics and alignment; Visualization of structures, Docking of ligand receptors; Protein structure analysis and modeling.

  1. Plant Tissue Culture

Content: History of plant tissue culture, principle of Totipotency; Tissue culture media; Plant hormones and morphogenesis; Direct and indirect organogenesis; Direct and indirect somatic embryogenesis; Applications of planttissueculture; National certification and Quality management of TC plants; Genetic Fidelity testing and Virus indexing methods – PCR, ELISA. Micropropagation of field and ornamental crops; Virus elimination by meristem culture, meristemtip culture and micrografting; Androgenesis and gynogenesis - production of androgenic and gynogenic haploids - diploidization; Protoplast culture - isolation and purification; Protoplast culture; Protoplast fusion; Somatic hybridization - Production of Somatic hybrids and Cybrids;, Wide hybridization - embryo culture and embryo rescuetechniques; Ovule, ovary culture and endosperm culture. Large-scalecell suspension culture - Production of alkaloids and other secondary metabolites- techniques to enhance secondary metabolite production, Somaclonal and gametoclonal variations – causes and applications; Callus culture and in vitro screening for stress tolerance; Artificial seeds, In vitro germplasm storage and cryo-preservation. Commercial Tissue Culture: Case studies and success stories, Market assessment; project planning and preparation, economics, government policies Practical: Preparation of stocks - macronutrients, micronutrients, vitamins and hormones, filter sterilization of hormones and antibiotics. Preparation of Murashige and Skoog medium. Micro-propagation of plants by nodal and shoot tip culture. Embryo culture to overcome incompatibility, Anther culture for haploid production. Callus induction in tobacco leaf discs, regeneration of shoots, root induction, role of hormones in morphogenesis. Acclimatization of tissue culture plants and establishment in greenhouse. Virus indexing in tissue culture plants. (Using PCR and ELISA).  Plan of a commercial tissue culture unit.

  1. Microbial/ Industrial Biotechnology

Content: Introduction, scope and historical developments; Isolation, screening and genetic improvement (involving classical approaches) of industrially important organisms. Primary metabolites, production of industrial ethanol as a case study; Secondary metabolites, bacterial antibiotics and non-ribosomal peptide antibiotics as case study; Recombinant DNA technologies for microbial processes; Strategies for development of industrial microbial strains with scale up production capacities; Metabolic pathway engineering of microbes for production of novel product for industry. Microbial enzymes, role in various industrial processes, production of fine chemicals for pharmaceutical industries; Bio-transformations, Bio- augmentation with production of vitamin C as a case study; Bioreactors, their design and types; Immobilized enzymes-based bioreactors; Microencapsulation technologies for immobilization of microbial enzymes. Environmental Biotechnology, biotreatment for pollution control, treatment of industrial and other wastes, biomass production involving single cell protein; Bioremediation of soil; Production of eco-friendly agricultural chemicals, bio- pesticides, bio-herbicides, bio-fertilizers, bio-fuels, etc.

Practical: Isolation of industrially important microorganisms, their maintenance and improvement. Lab scale production of industrial compounds such as alcohol, beer, citric acid, lactic acid and their recovery. Study of bio-reactors and their operations. Production of bio-fertilizers. Experiments on microbial fermentation processofantibiotics, bio-pigments, dairy products, harvesting purification and recovery of end products.  Immobilization of cells and enzymes, studies on its kinetic behavior, growth analysis and biomassestimation.  Determination of mass transfer coefficient.

  1. Molecular Plant Breeding

Content: Inheritance of qualitative and quantitative traits. Heritability – its estimation, Population structure of self- and cross-pollinated species, Factors affecting selection efficiency. Development of different kinds of segregating populations – F2, F3, BC1F1, BC1F2, BC4F2, RIL (Recombinant Inbred Lines), AIL (Advanced Intercrossed Lines), DH (Di-haploid population), NIL (Near Isogenic lines), NAM (Nested Association Mapping), MAGIC (Multi-parent Advanced Generation Intercross population). Causes of sequence variation and its types, Types of molecular markers and development of sequence based molecular markers – RFLP, AFLP, SCARs, CAPS, SSRs, STMS, SNPsInDel and DARTseq; Inheritance of markers, Linkage analysis using test cross, F2, F3, BC1F1, RIL. Construction of genetic map, Mapping genes for qualitative traits; Genotyping by sequencing and high-density chip arrays. QTL mapping using structured populations; Association mapping using unstructured populations; Genome Wide Association Studies (GWAS),Principle of Association mapping– GWAS-SNP genotyping methods, DART array sequencing, Illumina’s Golden Gate Technology, Genotyping by sequencing methods- Fluidigm; GBS, Illumina Hi seq- Nano pore sequencing, Principles and methods of Genomic Selection, Fine mapping of genes/QTL; Development of gene based markers; Allele mining by TILLING and Eco-TILLING. Tagging and mapping of genes. Bulk segregant and co-segregation analysis, Marker assisted selection (MAS); Linked, unlinked, recombinant, flanking, peak markers. Foreground and background selection; MAS for gene introgression and pyramiding: MAS for specific traits with examples. Haplotype concept and Haplotype-based breeding; Genetic variability and DNA fingerprinting. Molecular markers in Plant variety protection, IPR issues, hybrid purity testing, clonal fidelity testing and transgenic testing.

Practical: Construction of linkage map. QTL analysis using the QTL cartographer and other software. SNP data analysis using TASEEL. Detection of haplotype block using SNP data - pLinksoftware. Genotyping by sequencing methods –Illumina genotyping platform.; Marker assisted breeding – MABB case studies quality traits in rice/maize.  Genome Assisted Breeding in model crops, Genomic Selection models usingthe morphological and SNP data.

  1. IPR, Bio-safety & Bioethics

Content: IPR: historical background in India; trade secret; patent, trademark, design& licensing; procedure for patent application in India; Patent Cooperation Treaty (PCT); Examples of patents in biotechnology-Case studies in India and abroad; copyright and PVP; Implications of IPR on the commercialization of biotechnology products, ecological implications; Trade agreements- The WTO and other international agreements, and Cross border movement of germplasms. Biosafety and bio-hazards; General principles for the laboratory and environmental bio-safety; Biosafety and risk assessment issues; handling and disposal of biohazards; Approved regulatory laboratory practice and principles,The Cartagen Protocol on biosafety; Biosafety regulations in India; national Biosafety Policy and Law; Regulations and Guidelines related to Biosafety in other countries. Potential concerns of transgenic plants – Environmental safety and food and feed safety. Principles of safety assessment of Transgenic plants – sequential steps in risk assessment. Concepts of familiarity and substantial equivalence. Risk - Environmental risk assessment – invasiveness, weediness, gene flow, horizontal gene transfer, impact on non-target organisms; food and feed safety assessment – toxicity and allergenicity.Monitoring strategies and methods for detecting transgenics. Field trails – Biosafety research trials – standard operating procedures, labeling of GM food and crop,Bio-ethics- Mankind and religion, social, spiritual & environmental ethics; Ethics in Biotechnology, labeling of GM food and crop; Biopiracy

  1. Immunology and Molecular Diagnostics

Content:  Immunity and its classification; Components of innate and acquired immunity; Lymphatic system; Hematopoiesis; Organs and cells of the immune system- primary, secondary and tertiary lymphoid organs Descriptions of Antigens - immunogens, hapten and adjuvants. Immunoglobulins-basic structure, classes & subclasses of immunoglobulins, antigenic determinants; Multigene organization of immunoglobulin genes; B-cell receptor; Immunoglobulin superfamily; Principles of cell signaling; Basis of self and nonselfdiscrimination; Kinetics of immune response, memory; B cell maturation, activation and differentiation; Generation of antibody diversity; T-cell maturation, activation and differentiation and T-cell receptors; Functional T Cell Subsets; Cellmediated immune responses, ADCC; Cluster of Differentiations (CDs), Cytokinesproperties, receptors and therapeutic uses. Phagocytosis; Complement and Inflammatory responses; Major Histocompatibility Complex - MHC genes, MHC and immune responsiveness and disease susceptibility, HLA typing; Antigen processing and presentation- endogenous antigens, exogenous antigens, non-peptide bacterial antigens and super-antigens; Cell-cell co-operation, Hapten-carrier system Precipitation, agglutination and complement mediated immune reactions; Advanced immunological techniques – RIA, ELISA, Western blotting, ELISPOT assay, immunofluorescence, flow cytometry and immunoelectron microscopy; Surface plasmon resonance, Biosenor assays for assessing ligand –receptor interaction, CMI techniques- lymphoproliferation assay, Mixed lymphocyte reaction, Cell Cytotoxicity assays, Apoptosis, Transgenic mice, Gene knock outs. Active and passive immunization; Live, killed, attenuated, sub unit vaccines; Vaccine technology- Role and properties of adjuvants, recombinant DNA and protein based vaccines, plant-based vaccines, Antibody genes and antibody engineering- chimeric and hybrid monoclonal antibodies, Immunity to Infection,Bacteria, viral, fungal and parasitic infections, Hypersensitivity – Type I-IV; Autoimmunity; Types of autoimmune diseases, MHC and TCR in autoimmunity; Transplantation, Immunological basis of graft rejection, immunosuppressive therapy; Tumor immunology – Tumor antigens.

  1. Nano Biotechnology

Content:  Introduction to Nanotechnology - Nanomaterials - Self-assembly to artificial assembly for creation of useful nanostructures – Bottoms up and Top down approach (Nano rods, nano cages, nanotubes, quantum dots, nanowires, metal/ polymer-based nanostructures) – Preparation and Characterization of nanoparticles (particle size analyzer, microscopy, viz. electron microscopy, atomic force microscopy, etc). Cell structure – Bio macromolecules: Types, Structure, Dynamics and interaction with water – Cellular nano machines – cellular transducers, membrane channels, membrane transporters, Membrane motors – Creation of bio-nanostructures (Nano liposomes, Nano micelles, Nanomotors, etc). Chemical, physical and biological properties of biomaterials and bio response: biomineralization, biosynthesis, and properties of natural materials (proteins, DNA, and polysaccharides), structure-property relationships in polymeric materials (synthetic polymers and structural proteins); Aerosol properties, application and dynamics; Statistical Mechanics in Biological Systems, Nanoparticular carrier systems; Micro- and Nano-fluidics; Drug and gene delivery system; Microfabrication, Biosensors, Chip technologies, Nano- imaging, Metabolic engineering and Gene therapy.

Practical: Isolation of enzymes and nucleic acids involved in biosynthesis of nanomaterials; Synthesis of Gold/silver Nanoparticles by biogenic methods, Synthesis of micelles and inverse micelles; Synthesis of Carbon Nano-materials by Chemical Vapor Deposition and Sputtering technique; Preparation ofthiolate silver nanoparticles, Purification and measurement of carbon nano materials; Zinc selenide quantum dot preparation, Synthesis of Iron Oxide Nanoparticle; Thin film preparation by spin coating technique, Synthesis of Nickel metal nanoparticle by urea decomposition method; Synthesis of Zinc Oxide nanoparticle.

  1. Environmental Biotechnology

Content:  Basic concepts and environmental issues; types of environmental pollution; problems arising from high-input agriculture; methodology of environmental management; air and water pollution and its control; waste water treatment - physical, chemical and biological processes; need for water and natural resource management. Microbiology and use of micro-organisms in waste treatment; biodegradation; degradation of Xenobiotic, surfactants; bioremediation of soil & water contaminated with oils, pesticides and toxic chemicals,detergentsetc; aerobic processes (activated sludge, oxidation ditches, trickling filter, rotating drums, etc); anaerobic processes: digestion, filtration, etc. Renewable and non-Renewable resources of energy; energy from solid waste; conventional fuels and their environmental impact; biogas; microbial hydrogen production; conversion of sugar to alcohol; gasohol; biodegradation of lignin and cellulose; biopesticides; biofertilizers; composting; vermiculture etc. Treatment schemes of domestic waste and industrial effluents; food, feed and energy from solid waste; bioleaching; enrichment of ores by microorganisms; global environmental problems: ozone depletion, UV-B, greenhouse effects, and acid rain; biodiversity and its conservation; biotechnological approaches for the management environmental problems.

  1. Bio-entrepreneurship

Content: Scope in biotechnology; types of bio-industries – bio-pharma, bio-agri, bio-services and bio-industrial; Importance of entrepreneurship; introduction to bioentrepreneurship – biotechnology in a global scale; –skills for successful entrepreneur–creativity, leadership, managerial, team building, decision making; opportunities for bio-entrepreneurship- entrepreneurship development programs of public and private agencies (MSME, DBT, BIRAC, Startup & Make in India). Business plan preparation; business feasibility analysis by SWOT, socio-economic costs benefit analysis; funds/ support from various agencies; statutory and legal requirements for starting a company/ venture. Entry and exit strategy; identifying needs of customers; Market linkages, branding issues; developing distribution channels - franchising; policies, promotion, advertising; branding and market linkages for ‘virtual startup company’. Pricing strategy. Knowledge centers e.g., in universities, innovation centres, research institutions (public & private) and business incubators; R&D for technology development and upgradation; assessment of technology development; managing technology transfer;

  1. Stress Biology and Genomics

Content:  Different kinds of stresses (biotic and abiotic) and adaptation strategies: Plant cell as a sensor of environmental changes; role of cell membranes in signal perception; Ways of signal transduction in cells and whole plants as a response to external factors.Abiotic stresses affecting plant productivity – Drought, salinity, water logging, temperature stresses, light stress and nutrient stress; Drought stress – Effects on plant growth and development; Components of drought resistance; Physiological, biochemical and molecular basis of tolerance mechanisms; Biotic stress (insect and pathogen) resistance mechanism. Strategies to manipulate drought tolerance – Osmotic adjustment and Osmoprotectants - synthesis of proline, glycine betaine, poly amines and sugars; ROS and antioxidants; hormonal metabolism - ABA signaling; signaling components – transcription factors. Water logging stress – effects on plant growth and metabolism; adaptation to water logging,tolerance mechanisms -hormones and flooding tolerance. Strategies for improving submergence tolerance. Salinity stress – effects on physiology and metabolism of plants, SOS pathways and ion homeostasis,Strategies to improve salinity tolerance in plants. Water logging stress – effects on plant growth and metabolism; tolerance mechanisms. Physiological and biochemical changes – High & Low temperature tolerance mechanisms - molecular basis of thermo tolerance. Morphological and physiological changes in plants due to high and low light stresses - photo oxidation -plastid development. Characters of heliophytes and sciophytes – solar tracking – sieve effect and light channeling. Heavy metal stress – Al and Cd stress - effects on plant growth and development, biotech Strategies to overcome heavy metal stress Nutrient stresseffects on plant growth and development. Genetic manipulation strategies to overcome the stress effects. Genomics; transcriptomes, small RNAs and epigenomes; functional genomics; transfer of tolerance/resistant genes to model plants and validation of gene function. Different techniques for the functional validation of genes. Signaling pathway related to defense gene expression, R proteins, RNAi approach and genes from pathogens and other sources, coat protein genes, detoxification genes, transgenic and disease management. Bt proteins, resistance management strategies in transgenic crops, ecological impact of field release of transgenic crops. Bioinformatics approaches to determine gene function and network in model plants under stress.

  1. Gene Regulation

Content: Transcriptional regulation – Regulatory proteins, Activators and Repressors, Binding of RNA polymerase, Allosteric regulation, DNA looping, Cooperative binding, Antitermination, Combinatorial control – Regulation of lac, trp and ara Operons. Gene regulation in Lambda phage – lytic or lysogenic establishment. Regulatory sequences – Promoters, Enhancers, Silencers, Insulators, Locus Control Region. Activator proteins and their binding sites, DNA binding domain – Homeodomain, Zinc containing proteins, Leucine Zipper Motif, Helix-Loop-Helix, HMG proteins. Recruitment of RNA polymerase to promoter region, Nucleosomes and their modifiers. Signal integration. Signal transduction and transcriptional regulation. Gene Silencing. Epigenetic gene regulation. Regulation by RNA in prokaryotes and eukaryotes, RNA as defense agents. Riboswitches. Gene Silencing by RNA - siRNA & miRNA – synthesis and function. Noncoding RNAs their impact, categories and role in gene regulation, chromatin assembly etc. Negative auto-regulation, Positive auto-regulation, Bistable and Bimodal switch, Oscillating pattern of gene expression.