M.Sc. Biotechnology · M.Sc. Biotechnology S.No. Course Title Credits (Minimum credits required per...
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M.Sc. Biotechnology S.No. Course Title Credits (Minimum credits required per semester =24) Semester I 1 Biochemistry 4 2 Cell Biology and Molecular Biology 4 3 Immune Biology 4 4 Laboratory Course-I (Biochemical Analysis and Immunology) 4 5 Electives 8 Total 24 Semester II 1 Genetic Engineering 4 2 Advanced Molecular Biology 4 3 Developmental Biology 4 4 Laboratory Course-II (Molecular Biology and Genetic Engineering) 4 5 Electives 8 Total 24 Semester III 1 Genetics 4 2 Plant and Animal Biotechnology 4 3 Bioprocess engineering and Fermentation Technology 4 4 Laboratory Course-III (Plant and Animal Biotechnology, Bioprocess engineering and technology) 4 5 Electives 8 Total 24 Semester IV 1 Dissertation Critical Analysis of Research articles, Proposal writing 2 Research based Project 14 Seminar and Journal Club 2 Project presentation 2 Project viva 2 2 Electives 2 Total 24
Transcript of M.Sc. Biotechnology · M.Sc. Biotechnology S.No. Course Title Credits (Minimum credits required per...
M.Sc. Biotechnology
S.No. Course Title Credits (Minimum credits
required per semester =24)
Semester I
1 Biochemistry 4
2 Cell Biology and Molecular Biology 4
3 Immune Biology 4
4 Laboratory Course-I (Biochemical Analysis and Immunology) 4
5 Electives 8
Total 24
Semester II
1 Genetic Engineering 4
2 Advanced Molecular Biology 4
3 Developmental Biology 4
4 Laboratory Course-II (Molecular Biology and Genetic Engineering) 4
5 Electives 8
Total 24
Semester III
1 Genetics 4
2 Plant and Animal Biotechnology 4
3 Bioprocess engineering and Fermentation Technology 4
4 Laboratory Course-III (Plant and Animal Biotechnology, Bioprocess engineering and technology)
4
5 Electives 8
Total 24
Semester IV
1 Dissertation Critical Analysis of Research articles, Proposal writing 2
Research based Project 14
Seminar and Journal Club 2
Project presentation 2
Project viva 2
2 Electives 2
Total 24
Recommended Electives
1 Bio techniques 3
2 CRISPR-CAS 1
3 Microbiology 3
4 Biostatistics 2
5 Human and Medical Genetics 2
6 Spectroscopy and microscopy 2
7 Epigenetics-1 (gene organization and expression) 3
8 Introduction to Systems Biology: Network and Noise 3
9 Epigenetics-2 (Noncoding RNA and Stem cells) 2
10 Cancer Immunology 2
11 Oxidant signaling 2
12 Genomics and Proteomics 3
13 Bio-entrepreneurship 3
14 Intellectual Property rights 2
15 Biosafety 2
16 Bioethics 2
17 Drug discovery and Development 2
18 Nano-Biotechnology 2
19 Environmental Biotechnology 3
20 Advances in Microbial technology 2
21 Protein Engineering 3
22 Bioinformatics and Computational biology 4
23 Stem cell and Regenerative biology 2
24 Advanced Enzymology 4
Biochemistry
Unit I: Protein structure-function relationships: amino acids – structure and functional group properties, peptides and covalent structure of proteins, elucidation of primary and higher order structures, Ramachandran plot, evolution of protein structure, protein degradation and introduction to molecular pathways controlling protein degradation, structure-function relationships in model proteins like ribonuclease A, myoglobin, hemoglobin, chymotrypsin etc.; basic principles of protein purification; tools to characterize expressed proteins; Protein folding: Anfinsen’s Dogma, Levinthal paradox, cooperativity in protein folding, free energy landscape of protein folding and pathways of protein folding, molten globule state, chaperons, diseases associated with protein folding, introduction to molecular dynamic simulation.
Unit II: Enzyme catalysis – general principles of catalysis; quantitation of enzyme activity and efficiency; enzyme characterisation. relevance of enzymes in metabolic regulation, activation, inhibition and covalent modification; single substrate enzymes; concept of catalytic antibodies; catalytic strategies with specific examples of proteases, carbonic anhydrases, restriction enzymes and nucleoside monophosphate kinase; regulatory strategies; isozymes; role of covalent modification in enzymatic activity; zymogens. Enzyme kinetics: Michaelis-Menten equation and determination of Kinetic constants.
Unit III: Structure and functions of Carbohydrates, lipids, Nucleic Acids: Sugars - mono, di, and polysaccharides with specific reference to glycogen, amylose and cellulose, glycosylation of other biomolecules - glycoproteins and glycolipids; lipids - structure and properties of important members of storage and membrane lipids; lipoproteins. Structure and functions of DNA, RNA, and Lipids: Self-assembly of lipids, micelle, biomembrane organization - sidedness and function; membrane bound proteins - structure, properties and function; transport phenomena; nucleosides, nucleotides, nucleic acids - structure, a historical perspective leading up to the proposition of DNA double helical structure; difference in RNA and DNA structure and their importance in evolution of DNA as the genetic material.
Unit IV: Bioenergitics: Bioenergetics-basic principles; equilibria and concept of free energy; coupled interconnecting reactions in metabolism; oxidation of carbon fuels; recurring motifs in metabolism; Introduction to GPCR, Inositol/DAG//PKC and Ca++
signaling pathways; glycolysis and gluconeogenesis; reciprocal regulations and non-carbohydrate sources of glucose; Citric acid cycle, entry to citric acid cycle, citric acid cycle as a source of biosynthetic precursors; Oxidative phosphorylation; importance of electron transfer in oxidative phosphorylation; F1-F0 ATP Synthase; shuttles across mitochondria; regulation of oxidative phosphorylation; Photosynthesis – chloroplasts and two photosystems; proton gradient across thylakoid membrane; Calvin cycle and pentose phosphate pathway; glycogen metabolism, reciprocal control of glycogen synthesis and breakdown, roles of epinephrine and glucagon and insulin in glycogen metabolism; Fatty acid metabolism; protein turnover and amino acid catabolism; nucleotide biosynthesis; biosynthesis of membrane lipids and sterols with specific emphasis on cholesterol metabolism and mevalonate pathway; elucidation of metabolic pathways; logic and integration of central metabolism; entry/ exit of various biomolecules from central pathways; principles of metabolic regulation; steps for regulation.
Books Recommended: 1. Stryer, L. (2015). Biochemistry. (8th ed.) New York: Freeman. 2. Lehninger, A. L. (2012). Principles of Biochemistry (6th ed.). New York, NY: Worth. 3. Voet, D., & Voet, J. G. (2016). Biochemistry (5th ed.). Hoboken, NJ: J. Wiley & Sons. 4. Dobson, C. M. (2003). Protein Folding and Misfolding. Nature, 426(6968), 884-890. 5. Richards, F. M. (1991). The Protein Folding Problem. Scientific American, 264(1), 54-63.
Cellular and Molecular Biology
Unit I: Dynamic organization of cell: Universal features of cells; cell chemistry and biosynthesis: chemical organization of cells; internal organization of the cell - cell membranes: s t ructure of cel l membranes and concepts related to compartmentalization in eukaryotic cells; intracellular organelles: endoplasmic reticulum and Golgi apparatus, lysosomes and peroxisomes, ribosomes, cellular cytoskeleton, mitochondria, chloroplasts and cell energetics; nuclear compartment: nucleus, nucleolus and chromosomes.
Unit II: Chromatin structure and dynamics: Chromatin organization - histone and DNA interactome: structure and assembly of eukaryotic and prokaryotic DNA polymerases, DNA-replication, repair and recombination; chromatin control: gene transcription and silencing by chromatin-Writers,-Readers and –Erasers; Transcriptional control: Structure and assembly of eukaryotic and prokaryotic RNA Polymerases, promoters and enhancers, transcription factors as activators and repressors, trancriptional initiation, elongation and termination; post-transcriptional control: splicing and addition of cap and tail, mRNA flow through nuclear envelope into cytoplasm, breakdown of selective and specific mRNAs through interference by small non-coding RNAs (miRNAs and siRNAs), protein translation machinery, ribosomes-composition and assembly; universal genetic codes, degeneracy of codons, Wobble hypothesis; Iso-accepting tRNA; mechanism of initiation, elongation and termination; co- and post-translational modifications, mitochondrial genetic code translation product cleavage, modification and activation.
Unit III: Cellular Processes: Signalling, transport and trafficking. Molecular mechanisms of membrane transport, nuclear transport, transport across mitochondria and chloroplasts; intracellular vesicular trafficking from endoplasmic reticulum through Golgi apparatus to lysosomes/cell exterior. Cellular processes: Cell cycle and its regulation; cell division: mitosis, meiosis and cytokinesis; cell differentiation: stem cells, their differentiation into different cell types and organization into specialized tissues; cell-ECM and cell-cell interactions; cell receptors and trans-membrane signalling; cell motility and migration; cell death: different modes of cell death and their regulation. Manipulating and studying cells: Isolation of cells and basics of cell culture; observing cells under a microscope, different types of microscopy; analyzing and manipulating DNA, RNA and proteins.
Unit IV: Genome instability and cell transformation. DNA Repair and Recombination: DNA damage and Mutation: Physical and chemical DNA damaging agents. Spontaneous hydrolysis and deamination of DNA bases. Alkylating agents and radiations. Base analogues and intercalating agents. DNA repair systems: Direct reversal repair system (examples from prokaryotes and eukaryotes). Excision Repair system: Base excision and nucleotide excision repair mechanisms (examples from prokaryotes and eukaryotes). Mismatch repair system. Double-strand DNA break repair system: Homologous recombination repair and non-homologous end-joining (NHEJ) repair systems. DNA damage by- pass systems: Error-prone bypass in prokaryotes. Molecular Recombination. Homologous recombination: General features: Alignment of homologous DNAs. Generation of double-stranded breaks. Strand invasion and hetro-duplex formation.Holliday junctions and Branch migration. Homologous recombination in Eukaryotes. Molecular mechanism of meiotic recombination and its significance. Role of transposons in genome; viral and cellular oncogenes; tumor suppressor genes; structure, function and mechanism of action; activation and suppression of tumor suppressor genes; oncogenes as transcriptional activators.
Recommended Books: 1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P.. Molecular Biology of the Cell. New York: Garland Science. 2. Lodish, H. F. Molecular Cell Biology. New York: W.H. Freeman. 3. Krebs, J. E., Lewin, B., Kilpatrick, S. T., & Goldstein, E. S. (2014). Lewin's Genes XI. Burlington, MA: Jones & Bartlett Learning. 4. Cooper, G. M., & Hausman, R. E.. The Cell: a Molecular Approach ASM ; Sunderland. 5. Watson, J. D. (2008). Molecular Biology of the Gene (5th ed.). Menlo Park, CA: Benjamin/Cummings.
Immune Biology
Unit I: Overview of the Immune system: Historical perspective, Types of Immunity – Innate and Adaptive Immunity –Cell and Humoral immunity– Haematopoiesis – Cells of Immune System (B cell, T cell, APC, NK Cells) Lymphoid organs – Primary (Thymus, Bone marrow, Bursa of Fabricus), Secondary Lymphoid Organs – Lymph node, Spleen, Payer’s patches (GALT), Tonsils (MALT) – Development and maturation of Lymphocytes, Cytokines and their role in immune regulation. Immunological tolerance Cell mediated cytotoxicity, Mechanism of T-cell & NK- cell mediated lysis.
Unit II: Antigens and Antigen recognition Molecules – Antigen Characteristics and Antibody Diversity (IgG, IgM, IgA, IgD and IgE) – Structure, properties – Antigen processing and presentation, Detection of antigen – antibody intereaction – precipitation, agglutination, cytolysis, complement fixation, flocculation, opsonisation, immunofluorescence, ELISA – Monoclonal antibody
Unit III: Immune system in Health and Disease: Immunization and Immunization schedule – vaccines (attenuated, heat killed vaccines) – Types of Vaccine, Transplantation, Types of grafts, Graft rejection, Graft versus Host Disease, Clinical Transplantation
UNIT IV: Hypersensitivity reaction – Type I to V – Tumour immune response – immune diagnosis of tumour, immunotherapy of tumour – Immunodeficiency disorders – primary, secondary – Autoimmunity – localized and systemic autoimmunity, Hybridoma technology
Books recommended 1) Kuby, J. 2006. Immunology 4th Edition, Goldsby R.A., Kindt T.J., Osborne B.A., W.H. Freeman and Company 2) Roitt, I.M, 2006. Essential of Immunology 12th edition, ELBS, Blackwell Scientific Publication 3) Abul K. Abbas, Andrew H.L, Shiv Pillai, Cellular and Molecular Immunology 7/e Saunders Publications
Laboratory Course-I (Biochemical Analysis and Immunology)
1. To determine an unknown protein concentration by plotting a standard graph of BSA using UV-Vis Spectrophotometer and validating the Beer- Lambert’s Law.
2. Titration of Amino Acids and separation of aliphatic, aromatic and polar amino acids by thin layer chromatography.
3. Purification and characterisation of an enzyme from a recombinant source (such as Alkaline Phosphatase or Lactate Dehydrogenase or any enzyme of the institution’s choice)
4. Ion-exchange Chromatography/Gel Filtration/Affinity Chromatography 5. Antibody titre by ELISA method. 6. Complement fixation test. 7. Isolation and purification of IgG from serum or IgY from chicken egg 8. SDS-PAGE, Immunoblotting, Dot blot assays. 9. Demonstration of FACS.
Genetic Engineering
Unit I: Recombinant DNA Technology Tools: Restriction endonucleases: Historical perspective. Nomenclature. Different types of restriction-modification systems and their characteristic features. Blunt end and cohesive end cutters with examples. Four, six and eight cutter restriction enzymes. Restriction enzymes that create 5` and 3` overhangs. Isochizomers and isocaudemers. Restriction modification enzymes and their importance in DNA recombinant technology (Dam, DCM methylases). DNA ligases: E.coli and T4 DNA ligases. Chemistry of T4 DNA ligase reaction. DNA Phosphatases and their role in recombinant DNA technology. DNA Pol I and Klenow fragment and their role in recombinant DNA technology. Vectors: Plasmids: General features of plasmid vectors. Molecular regulation of high and low copy number plasmids. Characteristics features of pBR322, pUC series of plasmid vectors. General scheme of cloning in plasmid vectors. Selectable marker genes used in plasmid vectors and their mechanism of action. Molecular details of blue-white selection. Expression plasmid vectors: transcriptional and translation regulatory elements in expression plasmids. Characteristics feature of inducible plasmid expression vectors. yeast plasmid vectors: General features and mode of selection. Transformation of plasmid DNA in bacterial cells (Physical and chemical methods). Bacteriophages as cloning vectors: lambda- phage vectors: General characteristics features. Insertional lambda phage vectors (λ-gt10, λ-gt11). Replacement lambda phage vectors (λEMBL series). General scheme of cloning in lambda phage vectors and the criteria for recombinant vector selection. In-vitro packaging and its importance. M13 vectors: General features and scheme of cloning in M13 phage. Phagemid vectors: General features and their importance. Cosmid vectors: General characteristics and scheme of cloning in cosmid vectors. YACs: General characteristic features and scheme of cloning in YACs. BACs: General characteristic features and their importance.
Unit II: Genetic engineering techniques. Polymerase chain reaction: Principle and methodology. Setting of PCR reaction. source of template DNA (genomic DNA, RNA, etc). Features of an ideal primer. Primer design with restriction sites at the ends. Primer design for fusion protein constructs. Degenerate primers and their importance. DNA polymerase for PCR: characteristic features of error prone (Taq) and high fidelity DNA polymerases. different types of PCR (nested, asymmetric, multiplex). Applications of PCR. Reverse Transcription PCR (RT- PCR): Principle and methodology. Different methods of first strand and second strand cDNA synthesis. Characteristic features of different reverse transcriptases (RT) used in RT-PCR. Real-Time PCR: Principle and methodology. Ct value and its importance. Different
methods of fluorescent detection and probes (SYBER green, Taqman probe, Molecular beacon probes). Melting curves and their importance. Quantification and normalization of raw data. Applications of Real-Time PCR. DNA microarray: Principle and methodology. Different types of DNA arrays (Spotted microarrays and oligonucleotide arrays) and their characteristic features. Differential gene expression using fluorescent dyes. Application of microarrays. Proteomics: Protein separation by 2D Gel electrophoresis. Protein separation by multi-dimensional chromatography. Mass spectrometry: Electrospray Ionization (ESI), Matrix assisted Laser Desprption Ionization (MALDI), Mass analyzers, MS/MS. Different methods of protein identification. Protein arrays and their applications.
Unit III: Genomic and cDNA library construction. Different methods of screening. Site-Directed mutageneis: M13 vector based methods, plasmid vector based methods (single primer and double primer methods), PCR based methods. Protein engineering: Different methods and application of protein engineering. Hetrologous expression systems Expression in bacterial systems: Promoters and translation elements used in expression vectors. Inducible promoter systems. Expression and purification of GST fusion proteins. Expression in yeast: Various promoters elements used in expression vectors. Inducible expression systems in yeast (Gal and CUP1 system). Pichia pastroris as yeast expression systems. Expression in Insect cell line (Sf9/21): Baculovirus expression vectors. structure and construction of Basmid vectors. Expression of protein in baculoviral vectors. Expression in mammalian cells. Mammalian expression vectors. Viral and cellular promoter used in expression vectors. Importnace of kozak in expression vectors. Selectable marker genes. Tet-Off/On Inducible systems . Expression of proteins with fusion tags (HA, His, Myc, Flag, GFP) and their significance. In-vitro Transcription and translation and its application
Unit IV: Studying protein-protein interaction. Yeast Hybrid systems: Two hybrids based on split transcriptional activation, Split ubiquitin system, SOS recruitment system. Reverse two hybrid. Yeast three hybrid systems for proteinprotein, protein-RNA interactions. Transfections: Transient and stable transfection in animal cell. Physical, chemical and biological transfection agents. Repoter assays: Repoter genes and applications (Chlorophenicol acety transferase (CAT), Luciferase (Firefly and Renilla), living colours (Green fluorescent, yellow fluorescent and their application in colocalization studies). Dual luciferase assay and its application. Gene knock-downs: Antisence RNA technology with examples from animal and plant systems. RNA interference: Methodology and applications. Transgenics: Gene knock-in: Various methods of making transgenics (animals). Applications of transgenics with reference
to animals. Gene knock outs: Methodology based on Cre-LoXp system. Conditional and specific knock-outs. Gene targetting. Insertional mutagenesis: Transposon tagging: Different methods . Use of Plasmid rescue vectors, gene-trap vector, enhance trap vectors. Activation tagging. Different type of transposons used in gene tagging. Tagging with T-DNA (Brief account). Gene Therapy: Different types of gene therapies. Viral vectors and their role in gene therapy. Gene therapy and clinical trials. Success and failure stories.
Books Recommended: 1. Principles of Gene Manipulation and Genomics by Sandy B. Primrose, Richard Twyman: Blackwell PublishingProfessional. 2. Analysis of Genes and Genomes by Richard J. Reece: Wiley. 3. Molecular Biotechnology - Principles and Applications of Recombinant DNA by Glick, Bernard R.; Pasternak, Jack J.; Patten, Cheryl L: ASM Press.
Advanced Molecular Biology
Unit I: Prokaryotic and Eukaryotic transcription: Prokaryotic Transcription: Promoters: structure and function. RNA polymerases: Molecular composition, structure and function of each subunit. Role of sigma factor in promoter recognition and open promoter formation.Alternative sigma factors and their biological role. Single subunit RNA Polymerases (T3, T7 RNA Polymerases). Molecular events of transcription initiation. Transcription elongation. Elongation core complex: Structure and function. Proofreading during elongation. Transcription termination: Molecular mechanism of Rho dependent and independent Eukaryotic RNA polymerases: RNA Pol I, RNA Pol II and RNA pol III (structure and the genes they regulate). Promoters: Class II promoters: Structure and function (core promoter elements, upstreamelements, downstream elements, initiator elements). Class II general transcription factors: structure and function.Mechanism of transcription initiation at class II promoters. Pre-initiation complex. Recruitment and holoenzyme model of pre-initiation complex formation. Promoter clearence and RNA Pol II CTD phosphorylation. Class I promoters: Structure and function (core elements, upstream elements). Class I transcription factors. Class III promoters: Structure and function. Class III transcription factors. Transcription elogation: Molecular mechanism. Proofreading and RNA pol II pausing. Transcription termination. Termination signals and the molecular events.
Unit II: Eukaryotic Gene Regulation: Mechanism of Regulation. Regulatory Elements, Enhancers, Silencer Elements. Transcription Factors, Methods of Studying Transcription Factors. Domain Structure of Transcription factors, –DNA binding domains (Zinc Finger Domains, Leucine Zipper Domains, Homeodomains, Basic Domains). Transcription activation domains. Mechanism of Activator function. Transcriptional coactivators, Mediator Complex. Repressors and their role in Transcription. Chromatin Structure and Transcriptional Gene Regulation. Histones, Nucleosome, Nucleosomes as Transcription Barriers. Regulation of Nucleosome Dynamics. Histone Modifications and Transcription. Chromatin Remodeling and Histone Eviction in transcription. Transcription Memory and Maintenance of Genome Integrity. Structure & Epigenetics of Euchromatin versus Heterochromatin. Heterochromatin Gene Silencing. Regulation of Eukaryotic Gene Expression by Small RNAs. Gene Regulation During Development Transcription factor and developmentally regulated gene expression. Gene Regulation during Drosophila Development. Homeobox containing genes of Drosophila. Homeobox like genes in other organism
Unit III: Post-transcriptional RNA processing Heteronuclear RNA (hnRNA): Exons, introns, exon-intron junctions and splicing signals. RNA splicing: Molecular mechansim. Splicesome (structure, assembly and function). Alternative splicing. Regulation of splicing. Self-splicing RNAs with refrence to group-I introns and group-II introns. Ribosomal rRNA processing: Eukaryotic and prokaryotic rRNA processing. t-RNA processing and modifications. Trans-splicing. RNA editing and molecular mechanism. Post-transcriptional modifications of mRNA: Capping at 5`end. Structure and types of caps. Function of 5` end capping. Polyadenylation: Polyadenylation signals and mechansim of polyadenylation. Poly(A) polymerase. Functions of poly “A” tail.
Unit IV: Protein Translation. Translational machinery apparatus mRNA: Structural features of prokaryotic and eukaryotic mRNA Ribosomes: General structural features. Molecular components (prokaryotic and eukaryotic) t- RNA: Secondary and tertiary structure. Amino-acyl tRNA synthetases. Chemistry of tRNA charging with specific aminoacids Translational Initiation in prokaryotes: Molecular details. Formation of 30S and 70S initiation complex. Shine-Dalgarno sequence and its role in initiation complex formation. Translation initiation in eukaryotes: Initiation factors and their function. Role of eIF4E, eIF4G, eIF4A, eIF3, eIF2, eIF1, eIF5, eIF6. Scanning model of initiation. Formation of 48S and 80S initiation complex. Kozak sequence and its significance. Cap-dependent and Cap-independent translation. Role of Internal Ribosome Entry Sites (IRES). Cap-independent translation under stress conditions. Translational regulation: Prokaryotic regulation: Role of secondary structures, small RNAs and riboswithches. Eukaryotic regulation: Role of phosphorylations (stimulatory and inhibitory), Role of 4E-binding proteins in translation regulation. Secondary structures and translation regulation. microRNAs and their role in translation regulation Genetic code: General characteristic features. Breaking of genetic code. Whobble hypothesis and degeneracy. Translation elongation: Three-site ribosome model of tRNA binding. Role of EF-T. Proofreading during translation elongation. Peptidyl transferase reaction (chemistry and molecular components). Translocation and role of EF-G. Translation termination: termination codons. Release factors. Ribosome dissociation and the factors involved. Books Recommended: 1. Transcriptional Regulation in Eukaryotes: Concepts, Strategies, and Techniques by Michael F Carey, Stephen T Smale and Craig L Peterson. 2. Gene Regulation by David S. Latchman fifth edition. 3. Molecular Biology by Robert F Weaver: McGraw-Hill Higher Education. 4. Molecular Biology of the Gene by James D. Watson, et al: Pearson. 5. Lewins gene XI by Jocelyn E Krebs, et al: Jones and Bartlett Learning.
Developmental Biology
Unit I: Basic concepts of development: Potency, commitment, specification (autonomous, regulative and syncytial), induction, competence, determination and differentiation, morphogenetic gradients, cell fate and cell lineages, genomic equivalence and the cytoplasmic determinants, imprinting.
Unit II: Early development, morphogenesis and organogenesis of animals: Production and structure of gametes, cell surface molecules in sperm egg recognition in animals, acrosome reaction, fast and slow block to polyspermy, zygote formation. Lineage tracing. Patterns and molecular mechanism of cleavage, blastula formation, gastrulation patterns, concept and functions of primary organizer, neural induction, differential gene expression during formation of germ layers in Drosophila. Formation and differentiation of neural tube, differentiation of neurons, specification and regionalization of neural crest cells and their derivatives. Signaling pathways in embryonic development. Bone morphogenetic protein (BMP), fibroblast growth factor (FGF), Wnt signaling pathways, Notch/Delta, retinoic acid (RA), Hedgehog, and Endothelin signaling. Axes and pattern formation in Drosophila, amphibia and chick, derivatives of ectoderm, mesoderm and endoderm. Organogenesis- vulva formation in Caenorhabditis elegans; eye lens formation, formation of somite, limb development. Chromosomal sex determination- mammals and Drosophila. Environmental sex determination.
Unit III: Regulation of gene expression in Development: Transcriptional and Translational regulation Methylation Imprints Genes. RNA Polymerase asssociation with General Transcription factors. Regulatory Sequences in the endol6 Gene of Sea Urchin Embryos. Mechanisms of the Regulation of mRNA translation During Development Translation of mRNAs during Oogenesis, Nanos mRNA. Posttranslational regulation Posttranslational Modification of the Hedgehog Ligand, Esterification of Hedgehog, Diffusion of Sonic Hedgehog in vertebrate development. Implication of Vg1, a Localized Ligand in early Xenopus Development.
Unit IV: Developmental regulatory networks: Mechanisms used to establish Assymetric cell division in yeast, and C. elegans. Establishing the segments in Drosophila: Morphogens, Gap Genes Establish. Establishment of Axial Polarity in Drosophila, Pair-Rule Genes, Activated by Gap Genes, Regulation of the Gene eve, Segment Polarity Genes Intercellular Communication Involving Engrailed gene. Homeotic selector genes and parasegment identity: The Bithorax Complex, Other
Homeotic Genes. Cellular Interactions in Wing Development, Intercellular Signalingin Anteroposterior (A/P) Patterning Patterning of the Dorsoventral (D/V) Compartments. The Nieuwkoop Center, The Spemann Organizer, Morphogen: BMPs and Activin Homeotic Selector Genes in Vertebrates and Drosophila HOX Genes. Signaling in limb development: HOX Genes and Signaling Pathways
Books Recommended: 1. Gilbert S.F. Developmental Biology, 10th Edition, Sinauer Associates, Inc., Publishers Sunderland, Massachusetts, USA. 2. Slack J. M. W. Essential Developmental Biology, Wiley-Blackwell. 3. T. Subramonium (2013) Molecular Developmental Biology, ISBN.
Laboratory II: Molecular Biology and Genetic engineering
1. Total DNA isolation and cDNA synthesis. 2. Plasmid DNA isolation and DNA quantitation 3. Restriction Enzyme digestion of plasmid DNA 4. Agarose gel electrophoresis 5. Polymerase Chain Reaction and analysis by agarose gel electrophoresis 6. Vector and Insert Ligation 7. Preparation of competent cells 8. Transformation of E.coli with standard plasmids, Calculation of
transformation efficiency. Confirmation of the insert by Colony PCR and Restriction mapping
9. Expression of recombinant protein, concept of soluble proteins and inclusion body formation in E.coli, SDS-PAGE analysis
10. Purification of GST Tagged protein
Genetics
Unit I: Genetics of Bacteria and bacteriophages: Concept of a gene in pre-DNA era; mapping of genes in bacterial and phage chromosomes by classical genetic crosses; fine structure analysis of a gene; genetic complementation and other genetic crosses using phenotypic markers; phenotype to genotype connectivity prior to DNA-based understanding of gene.
Unit II: Drosophila and Yeast as genetic models: Monohybrid & dihybrid crosses, back-crosses, test-crosses, analyses of autosomal and sex linkages, screening of mutations based on phenotypes and mapping the same, hypomorphy, genetic mosaics, genetic epistasis in context of developmental mechanism. Yeast genetics Meiotic crosses, tetrad analyses, non-Mendelian and Mendelian ratios, gene conversion, models of genetic recombination, yeast mating type switch; dominant and recessive genes/mutations, suppressor or modifier screens, complementation groups, transposon mutagenesis, synthetic lethality, genetic epistasis.
Unit III: Population genetics and genetics of evolution: Introduction to the elements of population genetics: genetic variation, genetic drift, neutral evolution; mutation selection, balancing selection, Fishers theorem, Hardy-Weinberg equilibrium, linkage disequilibrium; in-breeding depression & mating systems; population bottlenecks, migrations, Bayesian statistics; adaptive landscape, spatial variation & genetic fitness. Quantitative genetics of complex traits (QTLs)
Unit VI: Quantitative genetics of complex traits (QTLs) Complex traits, mapping QTLs, yeast genomics to understand biology of QTLs. Laws of segregation in plant crosses, inbreeding, selfing, heterosis, maintenance of genetic purity, gene pyramiding.
Books Recommended: 1. Hartl, D. L., & Jones, E. W. (1998). Genetics: Principles and Analysis. Sudbury, MA: Jones and Bartlett. 2. Pierce, B. A. (2005). Genetics: a Conceptual Approach. New York: W.H. Freeman. 3. Tamarin, R. H., & Leavitt, R. W. (1991). Principles of Genetics. Dubuque, IA: Wm. C. Brown. 4. Smith, J. M. (1998). Evolutionary Genetics. Oxford: Oxford University Press.
Plant and Animal Biotechnology
Unit I: Plant tissue culture and animal cell culture: Plant tissue culture: historical perspective; totipotency; organogenesis; Somatic embryogenesis; establishment of cultures – callus culture, cell suspension culture, media preparation – nutrients and plant hormones; sterilization techniques; applications of tissue culture - micropropagation; somaclonal variation; androgenesis and its applications in genetics and plant breeding; germplasm conservation and cryopreservation; synthetic seed production; protoplast culture and somatic hybridization - protoplast isolation; culture and usage; somatic hybridization - methods and applications; cybrids and somatic cell genetics; plant cell cultures for secondary metabolite production. Animal cell culture: brief history of animal cell culture; cell culture media and reagents; culture of mammalian cells, tissues and organs; primary culture, secondary culture, continuous cell lines, suspension cultures; application of animal cell culture for virus isolation and in vitro testing of drugs, testing of toxicity of environmental pollutants in cell culture, application of cell culture technology in production of human and animal viral vaccines and pharmaceutical proteins.
Unit II: Plant genetic manipulation. Genetic engineering: Agrobacterium-plant interaction; virulence; Ti and Ri plasmids; opines and their significance; T-DNA transfer; disarmed Ti plasmid; Genetic transformation - Agrobacterium-mediated gene delivery; cointegrate and binary vectors and their utility; direct gene transfer - PEG-mediated, electroporation, particle bombardment and alternative methods; screenable and selectable markers; characterization of transgenics; chloroplast transformation; marker-free methodologies; advanced methodologies - cisgenesis, intragenesis and genome editing; molecular pharming - concept of plants as biofactories, production of industrial enzymes and pharmaceutically important compounds.
Unit III: Animal reproductive biotechnology and vaccinology : Animal reproductive biotechnology: structure of sperms and ovum; cryopreservation of sperms and ova of livestock; artificial insemination; super ovulation, embryo recovery and in vitro fertilization; culture of embryos; cryopreservation of embryos; embryo transfer technology; transgenic manipulation of animal embryos; applications of transgenic animal technology; animal cloning - basic concept, cloning for conservation for conservation endangered species; Vaccinology: history of development of vaccines, introduction to the concept of vaccines, conventional methods of animal vaccine production, recombinant approaches to vaccine production, modern vaccines.
Unit IV: Plant and animal genomics : Overview of genomics – definition, complexity and classification; need for genomics level analysis; methods of analyzing genome at various levels – DNA, RNA, protein, metabolites and phenotype; genome projects and bioinformatics resources for genome research – databases; overview of forward and reverse genetics for assigning function for genes. Molecular mapping and marker assisted selection Molecular markers - hybridization and PCR based markers RFLP, RAPD, STS, SSR, AFLP, SNP markers; DNA fingerprinting-principles and applications; introduction to mapping of genes/QTLs; marker-assisted selection - strategies for Introducing genes of biotic and abiotic stress resistance in plants: genetic basis for disease resistance in animals; molecular diagnostics of pathogens in plants and animals; detection of meat adulteration using DNA based methods.
Books Recommended: 1. Slater, A., Scott, N. W., & Fowler, M. R. (2008). Plant Biotechnology: an Introduction to Genetic Engineering. Oxford: Oxford University Press. 2. Buchanan, B. B., Gruissem, W., & Jones, R. L. (2015). Biochemistry & Molecular Biology of Plants. Chichester, West Sussex: John Wiley & Sons. 3. Glick, B. R., & Pasternak, J. J. (2010). Molecular Biotechnology: Principles and Applications of Recombinant DNA. Washington, D.C.: ASM Press. 4. Brown, T. A. (2006). Gene Cloning and DNA Analysis: an Introduction. Oxford: Blackwell Pub. 5. Primrose, S. B., & Twyman, R. M. (2006). Principles of Gene Manipulation and Genomics. Malden, MA: Blackwell Pub. 6. Slater, A., Scott, N. W., & Fowler, M. R. (2003). Plant Biotechnology: The Genetic Manipulation of Plants. Oxford: Oxford University Press.
Bioprocess Engineering and Fermentation technology
Unit-I: Basic concepts, Kinetics of Cell Growth: Kinetics of batch culture, Growth kinetics for continuous culture, Material balance for CSTR. Fundamentals of material and energy balance for processes with/without chemical reaction: Biomass Balances (Cells) in a Bioreactor, Material Balance in Terms of Substrate in a Chemostat, Modified Chemostat. Problems & Examples. Metabolic stoichiometry: Biomass and Product Yields, YX/S and YP/S. Overview of biosynthetic mechanisms.
Unit-II: Sterilization: Types of sterilization. Thermal death kinetics of microorganism. Heat sterilization of liquid medium, Batch mode, Continuous mode, Problems & Examples. Air sterilization. Fermentation overview: Inoculum development. Various types of Fermentation: submerged fermentation, aerobic and anaerobic fermentation. Bioreactor operations: Different types of bioreactors, Configuration of Bioreactors and their main components. Modes of bioreactor operation. Important bioreactor accessories.
Unit-III: Whole cell immobilization and their applications. Single cell protein. Cell disruption: mechanical, enzymatic,and chemical methods. Pre-treatment strategies. Solid-liquid separation: filtration, centrifugation, Adsorption,Problems/Examples. Liquid-liquid extraction, Solvent selection, Operating Conditions, Mode of Operation, Extractor Type Design Criteria. Membrane separation: ultrafiltration (Theory, Experimental set-up) reverse osmosis, dialysis, lyophilization. Precipitation of proteins by salting out, isoionic & semisynthetic polyelectrolyte methods.
Unit-IV: Applications of enzymes in food processing. Mechanism of enzyme function and reactions in process techniques; Enzymic bioconversions e.g. starch and sugar conversion processes; High-Fructose Corn Syrup; Interesterified fat; Hydrolyzed protein etc. and their downstream processing; baking by amylases, deoxygenation and desugaring by glucoses oxidase, beer mashing and chill proofing; cheese making by proteases and various other enzyme catalytic actions in food processing. Applications of Microbes in food process operations and production. Fermented foods and beverages; Food ingredients and additives prepared by fermentation and their purification; fermentation as a method of preparing and preserving foods; Microbes and their use in pickling, producing colours and flavours, alcoholic beverages and other products; Process wastes-whey, molasses, starch substrates and other food wastes for bioconversion to useful products; Bacteriocins from lactic acid bacteria – Production and applications in food preservation.
Books Recommended: 1. M.L.Shuler and F.Kargi, "Bioprocess Engineering--basic Concepts", 2nd Edn. Prentice-hall of India Pvt Ltd 2. P.M.Doran, "Bioprocess Engineering Calculations", Elsevier India Pvt Ltd 3. C. Ratledge & B. Kristiansen, "Basic Biotechnology" 3rd Edn. Cambridge University Press
Laboratory Course-III (Plant and Animal Biotechnology, Bioprocess engineering and technology)
1. Prepare culture media with various supplements for plant tissue culture. 2. Isolate plant protoplast by enzymatic and mechanical methods and attempt fusion by PEG 3. Animal cell culture demonstration 4. Basic Microbiology techniques a) Scale up from frozen vial to agar plate to shake flask culture. b) Instrumentation: Microplate reader, spectrophotometer, microscopy. c) Isolation of microorganisms from soil samples. 5. Analytical techniques like HPLC, FPLC, GC, GC-MS etc. for measurement of amounts of products/substrates.
Dissertation The objective of this semester is to expose students with broader needs of Research. Students will choose their project advisor upfront based on interest and their merit in the first two semesters. Proposal writing:The students in consultation with their faculty advisor will prepare a synopsis of the project to be pursued. In the following months, the synopsis should include the rationale, objectives, proposed methodology and significance of the study. The students shall make an open presentation of the synopsis during the fourth week of the semester. Research based Project :The project will be based upon research and actual bench work, carried under the guidance of faculty supervisor and in close collaboration with the research group. The students are expected to put in at least six working hours daily for a maximum of six months. The students will participate in Journal club and Lab meetings of the research group. Project report will be submitted and will be evaluated at the end of 4th semester. Part 1 of the project will be based upon introduction to the subject and a general review of the literature pertaining to the project. The students should be encouraged to write a review of the problem or on a related topic. Part 2 of the project will be based on the actual experimental work, presentation and analysis of the data generated. The project report should consist of Abstract, Rationale, Review of literature, Methodology, Results and discussion, and bibliography. Two examiners will evaluate the project reports of the students. The examiners will be nominated by the Head of the department from the panel of examiners proposed by the Project advisor, one of them will be the advisor. The examiners should be either from the department or from allied departments. Seminar and journal club :Each student under the supervision of a faculty advisor will deliver a seminar on a topic related to his/her Project work. The seminars will be conducted in 10th week of the semester. Two faculty members nominated by the Head of the department will evaluate the seminars. The journal club will consist of a research paper presentation to be assigned and evaluated by the Project advisor Project presentation: The students should make an open presentation defending their project work. One external expert and two faculty members nominated by the Head of the department will evaluate the presentation. The presentation will be open to all the students, scholars and teachers of the department and other allied departments. Project viva-voce : Project viva will be conducted by one expert and all the faculty members of the department
Electives Bio-techniques
Unit-I: Electrophoresis and Blotting Techniques: Basic principles & types of electrophoresis, Agarose gel electrophoresis, PAGE, SDS-PAGE and isoelectric focusing. Blotting techniques: Southern, Northern, Western, Farwestern, South-western and their applications. Determination of antigen antibody concentration by immunodiffusion, immunoelectrophoresis, ELISA.
Unit-II: Chromatography: Theory of Chromatography; Migration. Dispersion. Chromatographic Resolution. Types: Gel filtration, Paper, thin-layer and partition c h r o m a t o g r a p h y . A f f i n i t y C h r o m a t o g r a p h y : I o n E x c h a n g e chromatography,Purification of specific groups of molecules (GST fusion proteins, Poly (His) fusion proteins, Tandem affinity purifications). Chromatin Immunoprecipitation Assay (ChIP assay), Chip Seq.
Unit-III: Centrifugation and Radioactivity: Basic principles of centrifugation. Types of centrifugation; differential centrifugation and density gradient centrifugation. Determination of Sedimentation Coefficient. Ultra centrifugation: Design and principles of an analytical ultracentrifugation. Isotopes, modes of radioactive disintegration, Radioactive decay, Radiation quantitation and units. Applications of radioactive isotopes in biochemical assays. Radiation hazards and its protection
Books Recommended: 1. Principles & Techniques Biochemistry & Molecular Biology. Wilson & Walker. Cambridge University Press. 2. Principles of Radioactive Techniques, Use & Handling. BARC 3. Biological Centrifugation (The Basics) by Dr John Graham 4. Chromatography: Basic Principles, Sample Preparations and Related Methods by Elsa Lundanes, Leon Reubsaet, Tyge Greibrokk . WILEY. 5. Basics of Centrifugation. ThermoFisher
CRISPR-CAS
Unit I: History of its discovery, Non-canonical models (type 1, type 2, type 3) of CRISPR-CAS system, Overview of CRISPR–Cas9. Comparing the CRISPR–Cas9 system with ZFNs and TALENs. Guide RNAs. Cell Culture for CRISPR–Cas Systems. Adeno Associated Virus mediated delivery system of CRISPR–Cas Systems. Unit II: CRISPR–Cas9 applications: CRISPR/Cas9 Genome Editing and functionalization. CRISPR–Cas9 Genome Engineering in Mouse and Saccharomyces cerevisiae genome. CRISPR–Cas9 editing in Human Pluripotent Stem Cells. CRISPR/Cas9 Screening.
Microbiology
Unit-I: Bacteria: Morphology of Bacterial cell, Classification of bacteria on various criteria’s, Structure & function Cell wall (Peptidoglycan), Outer membrane of Gram Negative bacteria; cell wall and cell membrane synthesis, Flagella and motility, cell inclusions like endospore (mechanism of endospore formation), Gas vesicles.etc Bacterial growth phase, Generation time, Kinetics of growth, Physical features influencing growth (temperature, pH).
Unit-II: Viruses: Discovery classification and structure of viruses, DNA Viruses, Positives strand, negative strand viruses, replication of retroviruses (HIV), structure & function of viroids and prions. Bacteriophage: General structure of phages, Life cycle of lambda phage, Regulation of gene expression in lambda phage (Lysogenic & lytic options).
Unit-III: Transformation: Plasmid- structure & properties (copy number, Incompatibility, Host range). Molecular mechanism of natural transformation. Transposition: Structure of transposons (Composite & non Composite) Mechanism of transposition. Conjugation: Mechanism of conjugation, Mechanism involved in the formation of F,HFr and F-prime. Transduction: Mechanism of specialized and generalized transduction. Toxins: Endo & Exotoxins and their mode of action. Antimicrobial agents: Anti-bacterial, Anti-Fungal antibiotics, Mode of action, Mechanism of drug resistance.
Books Recommended: 1. Molecular Genetics of Bacteria. Jeremy W. Dale, Simon F. Park: Wiley-Blackwell. 2. Microbiology by Prescott, Joanne M. Willey, Linda M. Sherwood, Christopher J. Woolverton: McGraw-Hill. 3. Fundamental Bacterial Genetics. Nancy Trun, Janine Trempy: Wiley- Blackwell.
Biostatistics
Unit I: General Introduction to Statistics, Basic Concepts. Scope of Statistical methods in Biotechnology. Sampling methods/strategies: Sample Selection. Simple Random Sampling, Convenience Sampling, Systematic Sampling, Stratified Random Sampling, Cluster Sampling, etc. Data; types & Uses. Medical/Biological Uncertainties: Surveys and Cross-Sectional Studies. Retrospective Studies, Prospective Studies, Experimental Studies and Quality Control Clinical Trials, Epidemiological Studies. Measurement of central tendencies: Arithmetic Mean, Median, Mode, Geometric Mean, Harmonic Mean. Measures of Dispersion: Range, Mean Absolute Deviation, Population Variance and Standard Deviation, Sample Variance and Standard Deviation, Calculating the Variance and Standard Deviation from Grouped Data, Coefficient of Variation (CV). Unit-II: Presentation of variation by figures; data representation: Histogram, Stem-&-Leaf Plot, Line Diagram, Frequency Polygon, Frequency Curve, Pie Diagram, Bar Diagrams, Scatter Diagram, Box-&-Whisker Plot, Bubble Plot, Growth chart, Dendrogram, Nomogram, Partogram, Pedigree Chart, Cartogram. Confidence Intervals: Confidence Intervals, Confidence Intervals for a Single Population Mean, Z and t Statistics for Two Independent Samples. Paired t Test. Principles of test of significance: One-Tailed Versus Two-Tailed Tests, p-Values, Type I and Type II Errors, The Power Function, Two-Sample t Test (Independent Samples with a Common Variance). Students t-test, ANOVA: Comparison of means in one or two groups (student’s t-test). Comparison of means in three or more groups (ANOVA), F-test. Unit III Practical: Introduction to MS EXCEL-Use of worksheet to enter data, edit data, copy data, move data. Use of in-built statistical functions for computations of Mean, S.D., Correlation, regression coefficients, t-test, ANOVA. Use of bar diagram, histogram, scatter plots, bubble plot, etc. graphical tools in EXCEL for presentation of data.
Books Recommended: 1. Introduction to Biostatistics and Research Methods by Sunder Rao and J Richards 2. Medical Statistics by David Machin, Michael J Campbell and Stephen J Walters, John Wiley and Sons
Human and Medical Genetics
Unit-I: Organization and distribution of the human genome: Overview. Human multigene families and repetitive coding DNA. Extragenic repeated DNA sequences and transposable elements. Genes in pedigrees: Genes in pedigree. Complications to the basic pedigree patterns. Factors affecting gene frequencies. Nonmendelian characters. Overview of mutation, polymorphism, and DNA repair. Pathogenic mutations. Nomenclature of mutations and databases of mutations.
Unit-II: Genomic revolution and Research in the post-genome (sequencing) era: History, organization, goals and value of the Human Genome Project. Modern molecular and cytogenetic methods (Modern PCR methods, FISH, MLPA, arrayCGH, Parent of Origin Effects, Prenatal Diagnosis, chorionic villus sampling (CVS), Preimplantation Genetic Diagnosis (PGD).
Books Recommended: 1. Thompsan and Thompsan: Genetics in Medicine, Elsevier publications. 2. Emery’s Elements of Medical Genetics. Elsevier
Spectroscopy and Microscopy
Unit-I: Principle and applications of Fluorescence spectroscopy; Jablonski diagram, steady-state fluorescence, timeresolved, Fluorescence resonance energy transfer (FRET), anisotropy. Circular dichroism (far-UV, near-UV). Infrared spectroscopy, Raman spectroscopy and dynamic light scattering.
Unit-II: Principle and applications of; bright-field, confocal (immunofluorescence), and super-resolution microscopy (STORM, STED, PALM), Electron microscopy, atomic force microscopy AFM (contact and tapping mode). Force spectroscopy: Principle and applications of AFM cantilevers, optical tweezers and magnetic tweezers in biological research.
Epigenetics-I (Gene organization and expression)
Unit I: Chromatin, Histones, Nucleosome, Nucleosome Structure, Histone Variants and complexes involved in their exchange, Modulation of Chromatin Structure, ATP dependent chromatin remodeling, Histone modifications Histone Code hypothesis, Interplay of DNA methylation and histone modifications.
Unit II: Epigenetics, Chromatin Boundaries: S. cerevisiae Silencing, S. pombe Centromeric Heterochromatin, RNAidirected Silencing. Epigenetic reprogramming in mammals, Epigenetic mechanisms regulating ES cell differentiation, Bivalent Chromatin Marks in maintaining stem cell pluripotency, Epigenetics and pathologies, Epigenetic therapies.
Recommended References: 1. Chromatin Structure and Function by Alan Wolffe. 2. Epigenetics by David Allis, Thomas Jenuwein, Danny Reinberg and Marie- Laure Caparros
Introduction to Systems Biology: Networks and Noise
Unit-I Introduction to systems biology, Networks-definition, properties of network, structure of biological networks, Cellular networks; genetic and molecular interaction networks-protein interaction networks, protein-DNA interaction networks, significance of cellular networks (combinatorial-out puts, multitasking), Synthetic networks. Systems biology and future medicine
Unit-II Noise-noise and robustness of cellular processes, Sources of noise; Intrinsic and Extrinsic noise, Noise in gene expression; stochastic gene expression, cell-to-cell variation in gene expression (cell-to-cell variation in number of RNA and protein molecules). Single cell measurements -Methods to study cell-to-cell variability of RNA and proteins. Noise and cellular decision-making (microbes to mammals). Non-genetic cellular heterogeneity and response.
Unit-III Proteomics; LC-MS/MS, identification of proteins in complex mixtures and its role in systems biology. Genome sequencing; library preparations, barcoding and sequencing methods (Mi-seq, Hi-seq), Transcriptomics; RNA-seq (method/analysis (determination of RPKM values) and applications. Chromosome conformation capture (3C, 4C, 5C and HiC). Chromatin-immuno precipitation coupled to sequencing (ChIP-seq)
Books Recommended: 1. An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon 2. A First Course in Systems Biology by Eberhard Voit
Epigenetics-2: Noncoding RNA and Stem cells
Unit-I: From central dogma to ncRNA and now functional RNA: Overview of ncRNA and their important role in current research. Biogenesis of Small (miRNA, piRNA, esiRNA) and long non-coding RNA (lnRNA) and their importance in gene regulation and disease pathogenesis. MicroRNA (miRNA) and lncRNA pathways in Neurodevelopmental and Neurodegerative disorders will be provided as an example.
Unit-II: Non-Coding RNA (NcRNA) and neural stem cells (NSCs): miRNAs, and self-renewal and proliferation of NSCs. LncRNAs and proliferation of NSCs. NSC survival controlled by ncRNAs. NSC differentiation and cell fate determination mediated by ncRNA. NcRNA as a tool for stem cell based therapy.
Books recommended
1. The RNA world, CSHL press.
Cancer Immunology
Unit I: Oncogenes: Historical aspects, provirus, protovirus and oncogene hypothesis. Functional class of oncogenes(proto-oncogenes) Mechanism of carcinogenic transformation by oncogenes, viral oncogenes. Tumor suppressor genesproperties, mechanism of tumor suppressor genes in cancer induction with special reference to P53 gene. Inherited cancers.
Unit II: Tumor immunology and cancer diagnostics & therapy: Tumor immunology –Introduction, Mechanism of immune response to cancer, natural killer cells and cell mediated cytotoxicity. Biochemical, histological and radiological methods for cancer diagnosis Chemotherapy and radiotherapy strategies for cancer treatment. Cancer chemotherapeutic drugs. Types of radiation therapy. Immunotherapy of cancer – Rationale of immunotherapy, Tumor necrosis factor, interleukins, cytokines, interferons, vaccines, monoclonal antibodies.
Books Recommended: 1. Basic Immunology: Abul K. Abbas, Andrew H. Lichtman. 2. Janeway's Immunobiology, Garland Sciernce 3. Essential Immunology by Delvis, Martin , Burton and Roitt
Oxidant Signaling
Unit I: Reactive Oxygen Species. Origin, Production, Enzymatic and Non-enzymatic sources of reactive oxygen Species (ROS) production. Mitochondria as a source of ROS. Involvement of cytochrome complexes, Xanthine oxidase and NADPH oxidase. Effects on cell and biomolecules. Lipid peroxidation. Protein oxidation. Inactivation of different proteins. ROS as a secondary messenger. Regulation of signal transduction. Role in cancers. ROS detection in the cells.
Unit II: Antioxidants. Enzymatic antioxidants. Glutathione Peroxidase. Superoxide dismutase. Catalase. Nonenzymatic antioxidants. Mechanistic involvement of Vitamin C, Vitamin A. Vitamin E. Protective effects on the cell. Aging. Mechanistic players in aging. ROS in aging. Yeast as a model to study aging. C. elegans as a model to study aging. Pathways involved in aging. Role of ROS regulating protein in aging including p53 and p66shc.
Books Recommended: 1. Review Journals Like Antioxidant Redox Signaling. Internet Resources: Pubmed, Google, Google Scholar.
Genomics and Proteomics
Unit I: Genome mapping and sequencing projects, and Comparative Genomics: Genetic and physical maps; markers for genetic mapping; methods and techniques used for gene mapping, physical mapping, linkage analysis, cytogenetic techniques, FISH technique in gene mapping, somatic cell hybridization, radiation hybrid maps, in situ hybridization, comparative gene mapping.Human Genome Project, genome sequencing projects for microbes, plants and animals, accessing and retrieving genome project information from the web. Identification and classification of organisms using molecular markers- 16S rRNA typing/sequencing, SNPs; use of genomes to understand evolution of eukaryotes, track emerging diseases and design new drugs; determining gene location in genome sequence.
Unit II: Proteomics Aims, strategies and challenges in proteomics; proteomics technologies: 2D-PAGE, isoelectric focusing, mass spectrometry, MALDI-TOF, yeast 2-hybrid system, proteome databases.
Unit III: Functional genomics and proteomics Transcriptome analysis for identification and functional annotation of gene, Contig assembly, chromosome walking and characterization of chromosomes, mining functional genes in genome, gene function- forward and reverse genetics, gene ethics; protein-protein and protein-DNA interactions; protein chips and functional proteomics; clinical and biomedical applications of proteomics; introduction to metabolomics, lipidomics, metagenomics and systems biology.
Recommended Books: 1. Primrose, S. B., Twyman, R. M., Primrose, S. B., & Primrose, S. B. (2006). Principles of Gene Manipulation and Genomics. Malden, MA: Blackwell Pub. 2. Liebler, D. C. (2002). Introduction to Proteomics: Tools for the New Biology. Totowa, NJ: Humana Press. 3. Campbell, A. M., & Heyer, L. J. (2003). Discovering Genomics, Proteomics, and Bioinformatics. San Francisco: Benjamin Cummings.
Bio-entrepreneurship
Unit I: Innovation and entrepreneurship in bio-business Introduction and scope in Bio-entrepreneurship, Types of bio-industries and competitive dynamics between the sub-industries of the bio-sector (e.g. pharmaceuticals vs. Industrial biotech), Strategy and operations of bio-sector firms: Factors shaping opportunities for innovation and entrepreneurship in bio-sectors, and the business implications of those opportunities, Alternatives faced by emerging bio-firms and the relevant tools for strategic decision, Entrepreneurship development programs of public and private agencies (MSME, DBT, BIRAC, Make In India), strategic dimensions of patenting & commercialization strategies.
Unit II: Bio markets - business strategy and marketing Negotiating the road from lab to the market (strategies and processes of negotiation with financiers, government and regulatory authorities), Pricing strategy, Challenges in marketing in bio business (market conditions & segments; developing distribution channels, the nature, analysis and management of customer needs), Basic contract principles, different types of agreement and contract terms typically found in joint venture and development agreements, Dispute resolution skills.
Unit III: Finance, accounting and Technology management Business plan preparation including statutory and legal requirements, Business feasibility study, financial management issues of procurement of capital and management of costs, Collaborations & partnership, Information technology. Technology – assessment, development & upgradation, Managing technology transfer, Quality control & transfer of foreign technologies, Knowledge centers and Technology transfer agencies, Understanding of regulatory compliances and procedures (CDSCO, NBA, GCP, GLA, GMP).
Recommended Books
1. Adams, D. J., & Sparrow, J. C. (2008). Enterprise for Life Scientists: Developing Innovation and Entrepreneurship in the Biosciences. Bloxham: Scion. 2. Shimasaki, C. D. (2014). Biotechnology Entrepreneurship: Starting, Managing, and Leading Biotech Companies. Amsterdam: Elsevier. Academic Press is an imprint of Elsevier.
Intellectual Property Rights
Unit I: Introduction to IPR Introduction to intellectual property; types of IP: patents, trademarks, copyright & related rights, industrial design, traditional knowledge, geographical indications, protection of new GMOs; International framework for the protection of IP; IP as a factor in R&D; IPs of relevance to biotechnology and few case studies; introduction to history of GATT, WTO, WIPO and TRIPS; plant variety protection and farmers rights act; concept of ‘prior art’: invention in context of “prior art”; patent databases - country-wise patent searches (USPTO, EPO, India); analysis and report formation.
Unit II: Patenting Basics of patents: types of patents; Indian Patent Act 1970; recent amendments; WIPO Treaties; Budapest Treaty; Patent Cooperation Treaty (PCT) and implications; procedure for filing a PCT application; role of a Country Patent Office; filing of a patent application; precautions before patenting-disclosure/non-disclosure - patent application- forms and guidelines including those of National Bio-diversity Authority (NBA) and other regulatory bodies, fee structure, time frames; types of patent applications: provisional and complete specifications; PCT and conventional patent applications; international patenting-requirement, procedures and costs; financial assistance for patenting-introduction to existing schemes; publication of patents-gazette of India, status in Europe and US; patent infringement- meaning, scope, litigation, case studies and examples; commercialization of patented innovations; licensing – outright sale, licensing, royalty; patenting by research students and scientists-university/organizational rules in India and abroad, collaborative research - backward and forward IP; benefit/credit sharing among parties/community, commercial (financial) and non-commercial incentives.
Recommended Textbooks and References:
1. Ganguli, P. (2001). Intellectual Property Rights: Unleashing the Knowledge Economy. New Delhi: Tata McGraw-Hill Pub. 2. National IPR Policy, Department of Industrial Policy & Promotion, Ministry of Commerce, GoI 3. Complete Reference to Intellectual Property Rights Laws. (2007). Snow White Publication Oct. 4. Kuhse, H. (2010). Bioethics: an Anthology. Malden, MA: Blackwell.
Biosafety
Unit I: Biosafety and Biosecurity - introduction; historical background; introduction to biological safety cabinets; primary containment for biohazards; biosafety levels; GRAS organisms, biosafety levels of specific microorganisms; recommended biosafety levels for infectious agents and infected animals; definition of GMOs & LMOs; principles of safety assessment of transgenic plants – sequential steps in risk assessment; concepts of familiarity and substantial equivalence; risk – environmental risk assessment and food and feed safety assessment; problem formulation – protection goals, compilation of relevant information, risk characterization and development of analysis plan; risk assessment of transgenic crops vs cisgenic plants or products derived from RNAi, genome editing tools. Unit II: National and international regulations International regulations – Cartagena protocol, OECD consensus documents and Codex Alimentarius; Indian regulations – EPA act and rules, guidance documents, regulatory framework – RCGM, GEAC, IBSC and other regulatory bodies; Draft bill of Biotechnology Regulatory authority of India - containments – biosafety levels and category of rDNA experiments; field trails – biosafety research trials – standard operating procedures - guidelines of state governments; GM labeling – Food Safety and Standards Authority of India (FSSAI).
Recommended Textbooks and References: 1. Recombinant DNA Safety Guidelines, 1990 Department of Biotechnology, Ministry of Science and Technology, Govt. of India. Retrieved from http://www.envfor.nic.in/ divisions/csurv/geac/annex-5.pdf 2. Wolt, J. D., Keese, P., Raybould, A., Fitzpatrick, J. W., Burachik, M., Gray, A., Wu, F. (2009). Problem Formulation in the Environmental Risk Assessment for Genetically Modified Plants. Transgenic Research, 19(3), 425-436. doi:10.1007/s11248-009-9321-9 3. . Craig, W., Tepfer, M., Degrassi, G., & Ripandelli, D. (2008). An Overview of General Features of Risk Assessments of Genetically Modified Crops. Euphytica, 164(3), 853-880. doi:10.1007/s10681-007-9643-8
Bioethics Unit I Introduction to Bioethics. Ethics and Morality. Introduction to subject areas of Bioethics (Poverty, Birth control, ethics and religion, euthanasia, Environmental ethics). Bioethical Principles. Bioethics and boundaries of public and private. Bioethics and conflict of interest. Bioethics in Research.
Unit II Ethical issues concerning Embryonic Stem cells and Cloning. Animal cloning. Controversies regarding Designer babies. Gene therapy. Ethical controversies on Organ Transplantation. Surrogacy. Ethical regulations on Surrogacy. Genetically modified crops. Political and ethical issues involved in GMO,s. Advantages and Disadvantages. Ethical Limits of Animal use. Animal experiments in light of Bioethics.
Recommended Books 1. Title: Bioethics, an introduction for the biosciences Author: Ben Mepham Publisher: Oxford University, UK Year: 2013 Edition: 2nd 2. Title: Bioethics: An Anthology (Blackwell Philosophy Anthologies) Paperback. Authors: Helga Kuhse, Udo Schüklenk and Peter Singer Publisher: John Wiley & Sons; Year: 2015 Edition: 3rd Revised edition 3. Title: The Biological Foundations of Bioethics Author: Tim Lewens Publisher: OUP, Oxford Year: 2015 Edition: 1st
Drug Development
Unit I: Target identification, molecular modeling, and Optimization: Identification of target or drug leads associated with a particular disease by a number of different techniques including combinations of molecular modeling, combinatorial libraries and high-throughput screening (HTS); Conceptualizing the automation of the HTS process and the importance of bioinformatics and data processing in identification of lead compounds; Rational drug design, based on understanding the three-dimensional structures and physicochemical properties of drugs and receptors; Modelling drug/receptor interactions with the emphasis on molecular mechanisms, molecular dynamics simulations and homology modelling; Conformational sampling, macromolecular folding, structural bioinformatics, receptor-based and ligand-based design and docking methods, in silico screening of libraries, semi-empirical and ab-initio methods, QSAR methods, molecular diversity, design of combinatorial libraries of drug-like molecules, macromolecular and chemical databases. Identification of relevant groups on a molecule that interact with a receptor and are responsible for biological activity; Understanding structure activity relationship; Structure modification to increase potency and therapeutic index; Concept of quantitative drug design using Quantitative structure–activity relationship models (QSAR models) based on the fact that the biological properties of a compound are a function of its physicochemical parameters such as solubility, lipophilicity, electronic effects, ionization, stereochemistry, etc.; Bioanalytical assay development in support of in vitro and in vivo studies (LC/MS/MS, GC/MS and ELISA).
Unit II: Preclinical development Principles of drug absorption, drug metabolism and distribution - intestinal absorption, metabolic stability, drug-drug interactions, plasma protein binding assays, metabolite profile studies, Principles of toxicology, Experimental design for preclinical and clinical PK/PD/TK studies, Selection of animal model; Regulatory guidelines for preclinical PK/PD/TK studies; Scope of GLP, SOP for conduct of clinical & non clinical testing, control on animal house, report preparation and documentation Integration of non-clinical and preclinical data to aid design of clinical studies.
Unit III: Drug Manufacturing and Clinical trial design Requirements of GMP implementation, Documentation of GMP practices, CoA, Regulatory certification of GMP, Quality control and Quality assurance, concept and philosophy of TQM, ICH and ISO 9000; ICH guidelines for Manufacturing, Understanding Impurity
Qualification Data, Stability Studies. Objectives of Phase I, II, III and IV clinical studies, Clinical study design, enrollment, sites and documentation, Clinical safety studies: Adverse events and adverse drug reactions, Clinical PK, pharmacology, drug-drug interaction studies, Statistical analysis and documentation.
Recommended Textbooks and References: 1. Krogsgaard-Larsen et al. Textbook of Drug Design and Discovery. 4th Edition. CRC Press. 2. Kuhse, H. (2010). Bioethics: an Anthology. Malden, MA: Blackwell. 3. Nally, J. D. (2006) GMP for Pharmaceuticals. 6th edition. CRC Press 4. Brody, T. (2016) Clinical Trials: Study Design, Endpoints and Biomarkers, Drug Safety, and FDA and ICH Guidelines. Academic Press.
Nano Biotechnology
Unit I: Introduction to nanobiotechnology Introduction to Nanobiotechnology; Concepts, historical perspective; Different formats of nanomaterials and applications with example for specific cases; Cellular Nanostructures; Nanopores; Biomolecular motors; Bio-inspired Nanostructures, Synthesis and characterization of different nanomaterials.
Unit II: Nano Materials, Nano Films and Particles: Nanomaterials for catalysis, development and characterization of nanobiocatalysts, application of nanoscaffolds in sythesis, applications of nanobiocatalysis in the production of drugs and drug intermediates.Thin films; Colloidal nanostructures; Self Assembly, Nanovesicles; Nanospheres; Nanocapsules and their characterisation. Nanoparticles for drug delivery, concepts, optimization of nanoparticle properties for suitability of administration through various routes of delivery, advantages, strategies for cellular internalization and long circulation, strategies for enhanced permeation through various anatomical barriers.
Unit III: Aplications of Nanoparticles: Nanoparticles for diagnostics and imaging (theranostics); concepts of smart stimuli responsive nanoparticles, implications in cancer therapy, nanodevices for biosensor development.
Recommended Books:
1. GeroDecher, Joseph B. Schlenoff, (2003); Multilayer Thin Films: Sequential Assembly of Nanocomposite Materials, Wiley-VCH Verlag GmbH & Co. KGaA 2. David S. Goodsell, (2004); Bionanotechnology: Lessons from Nature; Wiley-Liss 3. Neelina H. Malsch (2005), Biomedical Nanotechnology, CRC Press 4. Greg T. Hermanson, (2013); Bioconjugate Techniques, (3rd Edition); Elsevier 5. Recent review papers in the area of Nanomedicine.
Environmental Biotechnology
Unit I: Bioremediation Introduction to environment; pollution and its control; pollution indicators; waste management: domestic, industrial, solid and hazardous wastes; strain improvement; Biodiversity and its conservation; Role of microorganisms in geochemical cycles; microbial energy metabolism, microbial growth kinetics and elementary chemostat theory, relevant microbiological processes, microbial ecology. Bioremediation: Fundamentals, methods and strategies of application (biostimulation, bioaugmentation) – examples, bioremediation of metals (Cr, As, Se, Hg), radionuclides (U, Te), organic pollutants (PAHs, PCBs, Pesticides, TNT etc.), technological aspects of bioremediation (in situ, ex situ). Application of bacteria and fungi in bioremediation: White rot fungi vs specialized degrading bacteria: examples, uses and advantages vs disadvantages; Phytoremediation: Fundamentals and description of major methods of application (phytoaccumulation, phytovolatilization, rhizofiltration phytostabilization).
Unit II: Biotechnology and agriculture Bioinsecticides: Bacillus thuringiensis, Baculoviruses, uses, genetic modifications and aspects of safety in their use; Biofungicides: Description of mode of actions and mechanisms (e.g. Trichoderma, Pseudomonas fluorescens); Biofertilizers: Symbiotic systems between plants – microorganisms (nitrogen fixing symbiosis, mycorrhiza fungi symbiosis), Plant growth promoting rhizobacteria (PGPR) – uses, practical aspects and problems in application.
Unit III: Biofuels Environmental Biotechnology and biofuels: biogas; bioethanol; biodiesel; biohydrogen; Description of the industrial processes involved, microorganisms and biotechnological interventions for optimization of production; Microbiologically enhanced oil recovery (MEOR); Bioleaching of metals; Production of bioplastics; Production of biosurfactants: bioemulsifiers; Paper production: use of xylanases and white rot fungi.
Recommended Books:
1. G. M. Evans and J. C. Furlong (2003), Environmental Biotechnology: Theory and Applications, Wiley Publishers. 2. B. Ritmann and P. L. McCarty, (2000), Environmental Biotechnology: Principle & Applications, 2nd Ed., McGraw Hill Science. 3. Scragg A., (2005) Environmental Biotechnology. Pearson Education Limited.
4. J. S. Devinny, M. A. Deshusses and T. S. Webster, (1998), Biofiltration for Air Pollution Control, CRC Press. 5. H. J. Rehm and G. Reed, (2001), Biotechnology – A Multi-volume Comprehensive Treatise, Vol. 11, 2nd Ed., VCH Publishers Inc.
Advances in Microbial Technology
Unit I: Environmental and food applications of microbial technology Environmental application of microbes; Ore leaching; Biodegradation - biomass recycle and removal; Bioremediation - toxic waste removal and soil remediation; Global Biogeochemical cycles; Environment sensing (sensor organisms/ biological sensors); International and National guidelines regarding use of genetically modified organisms in environment, food and pharmaceuticals. Application of microbes and microbial processes in food and healthcare industries - food processing and food preservation, antibiotics and enzymes production, microbes in targeted delivery application – drugs and vaccines (bacterial and viral vectors); Non-recombinant ways of introducing desirable properties in Generally recognized as safe (GRAS) microbes to be used in food (e.g., Yeast) - exploiting the existing natural diversity or the artificially introduced diversity through conventional acceptable techniques (mutagenesis, protoplast fusion, breeding, genome shuffling, directed evolution etc.).
Unit II: Pharmaceutical applications of microbial technology Recombinant protein and pharmaceuticals production in microbes – common bottlenecks and issues (technical/operational, commercial and ethical); Attributes required in industrial microbes (Streptomyces sp., Yeast) to be used as efficient cloning and expression hosts (biologicals production); Generating diversity and introduction of desirable properties in industrially important microbes (Streptomyces/Yeast); Microbial cell factories; Downstream processing approaches used in industrial production process (Streptomyces sp., Yeast).
Unit III: Microbial genomics for discovery of novel enzymes, drugs/ antibiotics; Limits of microbial genomics with respect to use in human welfare; Metagenomics and metatranscriptomics – their potential, methods to study and applications/use (animal and plant health, environmental clean-up, global nutrient cycles & global sustainability, understanding evolution), Global metagenomics initiative - surveys/projects and outcome, metagenomic library construction and functional screening in suitable hosts – tools and techniques for discovery/identification of novel enzymes, drugs (e.g., protease, antibiotic) etc.
Recommended Books:
1. Lee, Y. K. (2013). Microbial Biotechnology: Principles and Applications. Hackensack, NJ: World Scientific. 2. Moo-Young, M. (2011). Comprehensive Biotechnology. Amsterdam: Elsevier.
3. Nelson, K. E. (2015). Encyclopedia of Metagenomics. Genes, Genomes and Metagenomes: Basics, Methods, Databases and Tools. Boston, MA: Springer US. 4. The New Science of Metagenomics Revealing the Secrets of Our Microbial Planet. (2007). Washington, D.C.: National Academies Press.
Protein Engineering
Unit I: Introduction to protein engineering Protein engineering – definition, applications; Features or characteristics of proteins that can be engineered (definition and methods of study) – affinity and specificity; Spectroscopic properties; Stability to changes in parameters as pH, temperature and amino acid sequence, aggregation propensities, etc. Protein engineering with unnatural amino acids and its applications. Methods of measuring stability of a protein; Spectroscopic methods to study physicochemical properties of proteins: far-UV and near-UV CD; Fluorescence; UV absorbance; ORD; Hydrodynamic properties–viscosity, hydrogen-deuterium exchange; Brief introduction to NMR spectroscopy – emphasis on parameters that can be measured/obtained from NMR and their interpretation.
Unit II: Applications of protein engineering. Forces stabilizing proteins – Vander-waals, electrostatic, hydrogen bonding and weakly polar interactions, hydrophobic effects; Entropy–enthalpy compensation; Experimental methods of protein engineering: directed evolution like gene site saturation mutagenesis; Module shuffling; Guided protein recombination, etc., Optimization and high throughput screening methodologies like GigaMetrix, High throughput microplate screens etc., Application to devices with bacteriorhodopsin as an example; Engineering antibody affinity by yeast surface display; Applications to vaccines, Peptidomimetics and its use in drug discovery.
Unit III: Computational approaches. Computational approaches to protein engineering: sequence and 3D structure analysis, Data mining, Ramachandran map, Mechanism of stabilization of proteins from psychrophiles and thermophiles v_i_s_-_à-_v_i_s_ _those from mesophiles; Protein design, Directed evolution for protein engineering and its potential.
Recommended Books:
1. Edited by T E Creighton, (1997), Protein Structure: a Practical Approach, 2nd Edition, Oxford university press. 2. Cleland and Craik, (2006), Protein Engineering, Principles and Practice, Vol 7, Springer Netherlands. 3. Mueller and Arndt, Protein Engineering Protocols, 1st Edition, Humana Press. 4. Ed. Robertson DE, Noel JP, (2004), Protein Engineering Methods in Enzymology, 388, Elsevier Academic Press. 5. J Kyte; (2006), Structure in Protein Chemistry, 2nd Edition, Garland publishers.
Bioinformatics and computational biology
UNIT-I: Introduction and Biological databases: Introduction: What Is Bioinformatics? Goal. Scope. Applications. Limitations. Introduction to Biological Databases : What Is a Database? Types of Databases. Biological Databases. Pitfalls of Biological Databases.
UNIT-II: Sequence Alignment: Pairwise Sequence Alignment and Multiple sequence analysis. Sequence Homology versus Sequence Similarity. Sequence Similarity versus Sequence Identity. Methods. Scoring Matrices. Statistical Significance of Sequence Alignment. Database Similarity Searching: Unique Requirements of Database Searching. Heuristic Database Searching. Basic Local Alignment Search Tool (BLAST). FASTA. Database Searching with the Smith–Waterman Method. Multiple sequence analysis; multiple sequence alignment; flexible sequence similarity searching with the FASTA3 program package; use of CLUSTALW and CLUSTALX for multiple sequence alignment; submitting DNA protein sequence to databases.
UNIT-III: Genome Sequencing Projects. The Cancer Genome Atlas (TCGA). Emergence of Next generation sequencing, 454 Pyro-sequencing, Illumina Genome Analyzer, Applied Biosystems Sequencing, Ion Torrent Sequencing, Polonator Technology, Nanopore Sequencing, Single Molecule Real Time DNA sequencing, Comparison of Next generation sequencing techniques, Drawbacks of NGS, NGS File formats, & applications. Post-Sequencing Workflows NGS: Integrated Genome Viewer (IGV), Data visualization, Cytoscape. Applications of NGS: Transcriptome (RNA) sequencing, Exome sequencing, Genome Annotation, Using NGS to detect sequence variants, ChIP-sequence, Biological theories on ChIP- sequence analysis, Understanding the non – coding genome, Disease gene identification, DNA fragment evaluation, Peak identification, Two condition comparison, Saturation analysis, Motif finding and related theories. NGSdatabases and analysis of ngs data NGS databases, Sequence Analysis: Pairwise and multiple sequence alignment methods.
Unit IV: Structure visualization Retrieving and drawing structures, Macromolecule viewing platforms, Structure validation and correction, Structure optimization, Analysis of ligand-protein interactions; Tools such as PyMol or VMD.
Books Recommended: 1. Developing Bioinformatics Computer Skills by Cynthia Gibas, Per Jambeck 2. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition by Andreas D. Baxevanis, B. F. Francis Ouellette
Stem cell and Regenerative biology
Unit-I: Stem Cells – Basics, Properties and Classification, Hematopoietic Stem Cells, Mesenchymal Stem Cells, Embryonic Stem Cells, Fetal Stem Cells, Stem cells from adult organs- Characteristics, Isolation, Culture and Characterization protocols. Stem Cells in regeneration: Gastrointestinal, Liver, Pancreas, Spinal cord injuries. Stem Cells in Neurological Disorders Unit II: Three-Dimensional Cell Culture, Organ Culture, Organotypic Culture Extra Cellular Matrices, Morphogenesis and Tissue Engineering, Principles of Tissue Culture, Bioreactor Design, Mechanochemical Regulation of Cell Behaviour, In Vitro and In Vivo Synthesis of Tissues and Organs, Micro-Scale Patterning of Cells and their Environment, Three-Dimensional Scaffolds, Tissue Engineering and Transplantation Techniques Regeneration of Bone and Cartilage, Bioprinting of Organs and Tissues
Books Recommended: R. Lanza, J. Gearhart et al (Eds), Essential of Stem Cell Biology. (2009), Elsevier Academic press. R. Lanza and I. Klimanskaya, Essential Stem Cells Methods. (2009), Academic Press
Advanced Enzymology
Unit-I: Properties of enzymes as catalytic power, specificity cofactors, brief nomenclature & classification of enzymes,isoenzymes, Monomeric and oligomeric enzymes, Enzyme localization, Enzyme assay, Direct and coupled assays.Review of uni-substrate enzyme kinetics and factors affecting the rate of enzymes catalyzed reactions. Derivation ofMichaelis Menten equation using steady state and equilibrium assumptions. Enzyme constants. Transformation of Michaelis-Menten plot to linear forms. Lineweaver-Burk plot, Eadie-Hofstee plots, Hanes plots, Eisenthal and Cornish-Bowden plot. Merits and demerits of linear plots. Haldane relationship for reversible reactions. King and Altman procedure for derivation of rate equation. Enzyme inhibition: types, Reversible and Irreversible inhibition. Kinetics of Enzymatic reactions in presence of reversible inhibitors. Determination of Kinetic and inhibitory constants, Primary and secondary plots.
Unit-II: Classification of multi substrate reactions with examples of each class. Ping-pong bi-bi mechanism, Randomorder mechanism, compulsory order mechanism, Kinetics of multi substrate reactions. General rate equation of Alberty.Derivation of rate expression for ping-pong & ordered Bi -Bi reaction mechanism. Primary and secondary plots fordetermination of kinetic constants for Multisubstrate reactions. Investigation of reaction mechanism using steady statemethods. Use of initial velocity, inhibition and exchange studies to differentiate between multi substrate reactionmechanism. Methods of examining enzymes-complex’s, trapping E-S Complex, Use of substrate analogs, chemical modifications and protease treatment, Site directed mutagenesis & effect of changing pH. Flexibility & conformational mobility of enzymes
Unit-III: Determination of rate constant for enzymes catalyzed reactions, Protein –Ligand binding includingmeasurement, analysis of binding isotherm. Cooperatively phenomenon . Hill and Scatchard plots Allosteric enzymes, sigmodial kinetics and their physiological significance. Symmetric and sequential models for action of allosteric enzymes and their significance
Unit-IV: Multi enzyme system: Occurrence, isolation and properties. Polygenic nature of multi enzyme system. Mechanism of catalysis of serine proteases, Ribonucleases and Triose phosphate isomerase. Enzyme regulation: general
mechanism of catalysis viz Acid-base, electrostatic, Covalent and enzymes Immobilized enzymes and their industrialapplication. Effects of partition on kinetics and performance with special emphasis on changes in pH and hydrophobicity.
Recommended Books: 1. Enzymes: Biochemistry, Biotechnology, Clinical Chemistry by Trevor Palmer, Horwood Publishing 2. Fundamentals of Enzyme kinetics by Athel Cornish-Bowden, Portland press 3. Fundamentals of Enzymology by Nicholas Price and Lewis Stevens, Oxford University Press 4. Enzyme Structure and Mechanism by Alan Fersht, W. H. Freeman 5. Enzymology by T. Devasena , Oxford University Press
