Department of Biotechnology

Syllabus for

M. Sc. Biotechnology

Effective from academic session 2016-2017

Central University of Rajasthan

NH-8, Bandarsindri, Kishangarh-305817

Distt Ajmer

M.Sc. Biotechnology Course Structure

Semester I

Course Code Course Name Course Type

Credits

MSBT- 101 Biochemistry T 3

MSBT- 102 General Microbiology T 3

MSBT- 103 Enzymology & Enzyme Technology T 3

MSBT- 104 Biophysics & Structural Biology T 3

MSBT- 105 Computers, Mathamatics and Statistics for Biologists T 3

MSBT- 106 Elective I

A. Human Physiology B. Plant Physiology

T 3

MSBT- 107 Analytical and Biochemical Techniques Laboratory L 3

MSB- 108 Microbiology Laboratory L 3

Total credits 24

Semester II

Course Code Course Name Course Type

Credits

MSBT- 201 Genetic Engineering & Molecular Biotechnology T 3

MSBT- 202 Immunology T 3

MSBT- 203 Molecular Genetics T 3

MSBT- 204 Cell Biology and Stem Cell Biology T 3

MSBT- 205 Laboratory safety, Biosafety and IPR T 3

MSBT- 206

Elective I

A. Ecology and Evolution B. Eukaryotic and Human Genetics

T 3

MSBT- 207 Genetic Engineering Laboratory L 3

MSBT- 208 Immunology & Cell Biology Laboratory L 3

Total credits 24

Semester III

Course Code Course Name Course Type Credits

MSBT- 301 Fermentation & Bioprocess Technology T 3

MSBT- 302 Plant Molecular Biology & Plant Biotechnology T 3

MSBT- 303 Developmental Biology and Animal Biotechnology T 3

MSBT- 304 Bioinformatics and Genome informatics T 3

MSBT- 305

Elective I A. Applied Environmental Biotechnology B. Nanobiotechnology C. Among the elective courses offered by Biochemistry

and Microbiology departments

T 3

MSBT- 306

Elective II A. Molecular basis of drug design & development B. Genomics and Proteomics C. Among the elective courses offered by Department of

Microbiology and Biochemistry

T 3

MSBT- 307 Animal and Plant cell culture Laboratory L 3

MSBT- 308 Bioinformatics and Genome informatics laboratory L 3

Total credits 24

Semester IV

Course Code Course Name Course Type Credits

MSBT- 401 Journal Club Presentation Tu/ P 3

MSBT- 402 Review of Literature for Major Project Tu 3

MSBT- 403 Major Project (Research Dissertation) Tu/L 15

MSBT- 404 Research Dissertation Presentation Tu/ P 3

Total credits 24

Total Credits 96 T: Teaching Classes, L: Laboratory Classes, Tu: Tutorial Classes, P: Presentation.

MSBT- 101 Biochemistry Credit 3

Unit - I Carbohydrates: Sugars:- mono-, di-, and poly-saccharides; Metabolism:- basic concepts, central role of ATP in metabolism, anabolic and catabolic pathways; Bioenergetics– basic principles, equilibrium and concept of free energy. Pentose Phosphate Pathway (PPP) and its role in biosynthetic reactions; Glycogen synthesis, breakdown and its regulation, Modified carbohydrates: glycosaminoglycans, cardioglycosides and bacterial cell wall polysaccharides, glycoproteins, lectins. Unit - II Lipids: Lipids: Classification, Brief account of the chemical properties and Structure of lipids (Storage and Membrane lipids); Fatty acid biosynthesis and degradation; Synthesis and degradation of steroids; Biological role of the following: Fatty acids, Acyl glycerols, Phospholipids, Plasmalogens, Sphingolipids, Lycolipids, Steroids, Eicosanoids–Prostaglandins, Thromboxanes, & Leukotrienes, Leptin and Visfatin; Lipoproteins; Biomembrane organization. Unit - III Amino acids and proteins: Amino acids, structure and functional group properties; Non– standard, non–protein and biologically active amino acids; Amino acid metabolism, Urea cycle, one carbon reaction; Amines and their roles in cell function; Co-factors: vitamins and coenzymes; Nucleosides and nucleotides: structure and characteristics; Properties of nucleic acids in solution; Nucleotide biosynthesis and metabolism; Salvage pathways, its regulation and diseases. Books recommended

❖ Biochemistry by Voet D., Voet J.G.; John Wiley and Sons. ❖ Lehninger Principles of Biochemistry by Nelson, D. C. and Cox, M.M.; W. H. Freeman. ❖ Biochemistry by Berg J.M., Tymoczko J.L. and Stryer L.; W.H. Freeman and Co. ❖ Principles and Techniques of Biochemistry and Molecular Biology by Wilson/Walker,

Cambridge University Press

MSBT- 102 General Microbiology Credit 3

Unit - I Methods in microbiology: Pure culture techniques, theory and practices of sterilization, Principles of microbial nutrition; Formulation of cultural media, Enrichment culture techniques for isolation of Chemoautotrophs, Chemoheterotrophs and Photosynthetic microorganism.

Microbial diversity & systematics: Classification of bacterial and archaeal systematics: Conventional and modern methods of Bacterial taxonomy; Classification of bacteria according to Bergey’s manual, polyphasic approach of bacterial identification, 16S rRNA, genomic similarity - content of guanine (G) + cytosine (C) (%GC), DNA-DNA homology, fatty acid analysis; General characteristics of Archaea as the earliest life forms, Archaea v/s Eubacteria, Acellular microbes, Metagenomics, Meta-transcriptomics and Microbiome.

Unit - II Microbial Growth: Definition of growth, mathematical expression of growth, growth curve, diauxic & synchronous growth, continuous culture; Effect of environmental factors like temperature, acidity, alkalinity, water availability & oxygen on bacterial growth.

Microbial Physiology: Metabolic pathways of glucose dissimilation in aerobic and anaerobic microbes, Fermentation (alcoholic and acidic), Nitrate and Sulfate reduction, Methanogenesis and Acetogenesis, Nitrogen metabolism, nitrogen fixation, glycolysis, Krebs cycle, Glyoxylate cycle, Entner Duodoroff (ED) pathway, HMP shunt, ATP synthesis, microbial photosynthesis. Unit - III Introduction to mycology and phycology: General characteristics of Fungi and Algae, and their cultivation, Cultural characteristics, Microscopic morphology, Importance of Fungi and Algae in industry and food production; Fungi as pathogens of men, animals and plants.

Introduction to virology: Discovery and structure of viruses; Classification of viruses; Replication of Viruses: Lytic and Lysogenic cycles, Cultivation of viruses, Detection and enumeration of viruses – viral assay.

Introduction to antimicrobial agents: Antibiotics, Chemotherapeutic agents: Major classes and mechanism of action, Minimal inhibitory concentration (MIC), Microbial Drug resistance.

Books recommended

❖ Prescott’s Microbiology by Willey, Sherwood & Woolverton; McGraw-Hill Education.

❖ Brock Biology of Microorganism by Madigan & Martinko; Pearson. ❖ Microbiology: an introduction by Tortora, Funke & Case; Pearson. ❖ Microbiology: application based approach by Pelczar & Chan; Tata McGraw Hill

Education. ❖ Ananthanarayan and Paniker's Textbook of Microbiology

MSBT- 103 Enzymology & Enzyme technology Credit 3

Unit - I Definition, nomenclature and classification of enzymes, Isozymes, characteristic features of enzymes, Enzyme cofactors, Catalytic power, Catalytic strategies and Substrate specificity, Lock and key model, Induced fit hypothesis, Active site- structure, substrate binding, role of catalytic amino acid residues, Catalytic mechanisms of enzymes with representative examples, Types of enzyme inhibition, regulation of enzymes, kinetics of enzyme-catalyzed reactions, effect of pH and temperature on enzyme activity, Thermodynamics of enzyme-catalyzed reactions, Enzyme pathways and regulatory networks. Unit - II Strategies for the discovery of improved and novel enzymes for industrial applications (homology and structure based approaches, screening methods, use of mutants). Optimization of industrial enzymes by mutagenesis; Protein engineering strategies to improve enzyme stability, specificity and activity; Enzyme immobilization - types, advantages, drawbacks and applications; Artificial enzymes; Isolation and purification of industrially important enzymes. Unit – III Enzymes used in different industries, Enzyme catalysis in organic solvents, enzyme replacement therapy – definition, modes of administration, enzyme deficiency disorders and enzyme therapy; Application of enzymes: Cosmetic benefits, Enzyme-based biosensors; Enzymes in clinical diagnosis: primary and secondary serum enzymes, considerations for Reliable serum enzyme assays, Intracellular distribution of diagnostic enzymes, Enzyme markers of Xenobiotic toxicity - Pharmacogenomics related to polymorphism of drug metabolizing enzymes, , KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway. Books recommended

❖ Fundamentals of Enzyme Kinetics by Athel Cornish-Bowden; Portland Press. ❖ Fundamentals of Enzymology by Nicholas Price and Lewis Stevens; Oxford

University Press. ❖ Enzyme Assays and Enzyme Profiling: High Throughput Screening, Genetic

Selection and Fingerprinting by Jean-Louis Reymond (Editor); Wiley VCH. ❖ Enzyme Technology by Martin Chaplin and Christopher Bucke; Cambridge

University Press. ❖ Methods in Enzymology, Volume 1, 1955. ❖ Biochemistry by Donald Voet and Judith G. Voet; John Wiley and Sons ❖ Artificial Enzymes by Ronald Breslow (Editor), Wiley VCH.

MSBT- 104 Biophysics & Structural Biology Credit 3

Unit - I Introduction to the physical chemistry of proteins, Nucleic acids and other biomolecules. Principles of biomolecular structure.

Forces determining bimolecular structures and interactions: Van der Waal’s and Electrostatic interactions, Hydrogen bonding, Hydrophobic interactions and role of water in bimolecular structure; Disulphide bonds.

Techniques for structure determination: Circular Dichroism (CD), Electron microscopy TEM & SEM, X-Ray Diffraction and Nuclear Magnetic Resonance (NMR). Unit - II Proteins: Definition and examples of primary, secondary, tertiary and quaternary structures of Proteins; Concept of Ф and Ψ angles and the Ramachandran plot, Structural aspects of α- helix, β-sheet and turns in proteins, Concepts of Super-secondary structures and domains in Proteins. Unit - III Nucleic Acid: Structure of Nucleosides, Nucleotides and Oligonucleotides; Structure of DNA, Watson and Crick model– Base pairing and base stacking, Variation in DNA structure polymorphism: A, B and Z DNA; Structure of RNA and tRNA; DNA-protein interaction: motifs, histones. Books recommended

❖ Introduction to Protein structure by C. Branden, J. Tooze; Garland Publishing Inc. ❖ Biochemistry by L. Stryer; WH Freeman and Co. ❖ Biophyscial chemistry Part I & III by Cantor and Schimmel; WH Freeman &

Company. ❖ Nucleic acid structure by S.Neidle (ed); VCH Publishing, Weinheim. ❖ The structure and action of proteins by Dickerson and Geis; Benjamin/ Cummings

Publishing.

MSBT- 105 Computer, Math and Statistics for Biologists Credit 3

Unit - I Basic Computing: Computers: Definition and their anatomy; Software, hardware and firmware; Data and its processing; Database Management System (DBMS); Programming language Perl, Windows/Linux; Basics of computer networking. Unit - II Biostatistics: Mean, Mode, Median, Mean deviation, Standard deviation and Standard error of the mean, Confidence intervals, Hypothesis testing, P values, Methods of sampling of biological data and analysis using common hypothesis tests (‘t’, ‘z’ and ‘F’ and �2 tests) of significance for small and large samples, Tukey’s and Scheffe's test, Non-parametric tests: Wilcoxon-Mann-Whitney rank sum test, Fisher's exact test, Permutation tests, Regression and ANOVA, Clustering, Principal Component Analysis (PCA), Coefficient of variation, Correlation (Karl Pearsons, Co-efficient of correlation, Rank correlation) and Regression analysis, Regression equations taking suitable examples from biological data, Spread sheet (including informatics applications). Unit - III Mathematics: Probability: Theorems on probability, Binomial and Normal distribution; Permutation, combinations and Binomial theorem; Rates and topics from differential calculus such as max/min functions of one variable differentials and approximations; Partial derivatives, max/min function of more than one variable and method of least squares; Antiderivatives, Indefinite and definite integrals; Logarithms and exponential functions; Differential equations and their applications in biology. Books recommended

❖ Maths from scratch for biologists by Alan J. Cann; Wiley-Blackwell. ❖ Easy Mathematics for Biologists by Peter C. Foster; Hardwood Academic Publisher. ❖ Statistics at the Bench: A Step-by-Step Handbook for Biologists by Martina Bremer

and Rebecca W. Doerge; Cold Spring Harbor Laboratory Press. ❖ Developing Bioinformatics Computer Skill by Cynthia Gibas and Per Jambeck;

O’Reilly Publication. ❖ Database Management Systems by Raghu Ramakrishnan, Johannes Gehrke;

McGraw-Hill Education. ❖ Beginning Perl for Bioinformatics by James D. Tisdall; O’Reilly Publication. ❖ The Art of R Programming by Nornam Matloff; No Starch Press.

Elective I

MSBT- 106

A. Human Physiology Credit 3

Unit - I Digestive system: Gastrointestinal anatomy and functions, motility, Nervous control and Blood circulation; Food intake and regulation, Digestive processes, Enzymes and secretions in the oral cavity and their functions, Stomach and intestine, Digestive glands and their regulation, Gastrointestinal disorders.

Cardiovascular system: Heart, Function of heart valves; Cardiac cycle- origin, conduction and regulation of Heart beat, ECG, Blood circulation, Regulation of Blood circulation, Micro-circulation and Lymphatic system, Blood cells, Blood plasma, Blood groups, Hemostasis and Blood coagulation, Cardiac disorders. Unit - II Respiratory system: Pulmonary ventilation, Mechanics of Pulmonary ventilation, Volumes and capacities, Principles of Gaseous exchange, Transport of gases, control and regulation of respiration, Respiratory disorders.

Nervous system: Components of the nervous system, Neuron and glial cells - different types, structure, function; Synapse: Nerve impulse transmission, Neurotransmitters. Organization of nervous system- CNS and PNS; Somatic nervous system, Autonomic nervous system-Sympathetic and Parasympathetic system, enteric nervous system, special senses, vision, hearing, taste and smell. Unit - III Uro-genital system: Body fluids and kidney, Mechanism of urine formation and regulation, Haemodialysis and Homeostatic imbalances in excretion, Kidney diseases and diuretics, Reproductive and hormonal function of the male, Female hormones and reproductive cycle, Pregnancy and lactation, Growth and development of foetus.

Skeletal system: Components of skeletal system, Axial and appendicular system, Skeletal muscles, Mechanism of muscle contraction, Excitation of skeletal muscles, Neuromuscular junction, Bone structure and function. Books recommended

❖ Guyton and Hall Textbook of Medical Physiology by John E. Hall; Saunders. ❖ Ganong’s Review of Medical Physiology by Kimm E. Barrett, Susan M. Burman,

Scott Biotano, Hedwen Brooks; Mcgraw Hill. ❖ Human Physiology: The Mechanisms of Body Function by Arthur J. Vander, James

Sherman & Dorothy S. Luciano; McGraw-Hill Higher Education.

Elective I

MSBT- 106

B. Plant Physiology Credit 3 Unit - I Photosynthesis, Light harvesting complexes, Mechanisms of electron transport, Photo protective mechanisms, CO2 fixation, C3, C4 and CAM pathways; Respiration and photorespiration, Citric acid cycle, Plant mitochondrial electron transport and ATP synthesis, Alternate oxidase, Photo respiratory pathway, Nitrogen metabolism, Nitrate and Ammonium assimilation, Amino acid biosynthesis.

Unit - II Plant hormones, biosynthesis, storage, breakdown and transport, physiological effects and mechanisms of action; Sensory photobiology, structure, function and mechanisms of action of Phytochromes, Cryptochromes and Phototropins. Stomatal movement; Photoperiodism and Biological clocks.

Unit - III Solute transport and photo assimilate translocation, uptake, transport and translocation of water, ions, solutes and macromolecules from soil, through cells, across membranes, through xylem and phloem; Mechanism of transpiration and guttation; Secondary metabolites, biosynthesis of terpenes, phenols and nitrogenous compounds and their roles; Stress physiology, responses of plants to biotic (pathogen and insects) and abiotic (water, temperature and salt) stresses.

Books recommended

❖ Physicochemical and Environmental Plant Physiology by P. Nobel; Academic Press. ❖ A Textbook of Plant Physiology, Biochemistry and Biotechnology by Verma, and

Verma; S. Chand Publishing. ❖ Fundamentals of Plant Physiology by V.K. Jain, S. Chand Publishing.

MSBT- 107 Analytical and Biochemical Techniques Laboratory Credit 3

➢ Preparation of an acetate buffer system and validate the Henderson-Hasselbach equation

➢ Estimation of sugars, iron, phosphate, vitamin C and organic acids

➢ Separation of amino acids and sugars by TLC, colorimetric determination of pK of amino acids

➢ Validation of Beer-Lambert’s law

➢ Estimation of an unknown protein concentration; Lowry/ BCA/ Bradford methods.

➢ Nucleic acid estimation

➢ Protein purification and separation by different chromatography techniques

➢ SDS-PAGE and Western blotting

➢ Automated biochemical tests (digital/diagnostic lab visit)

MSBT- 108 Microbiology Laboratory Credit 3

➢ Sterilization, disinfection, safety in microbiology laboratory

➢ Preparation of media for growth of various microorganisms

➢ Identification and culturing of various microorganisms

➢ Staining and enumeration of microorganisms

➢ Growth curve, measure of bacterial population by turbidometry and studying the effect of temperature, pH, carbon and nitrogen sources

➢ Isolation of enzyme producing microorganisms

➢ UV mutagenesis and Isolation of drug resistant mutants, transposon mutagenesis; Bacterial conjugation

MSBT- 201 Genetic Engineering and Molecular Biotechnology Credit 3 Unit - I Enzymes used in recombinant DNA Technology: Restriction enzymes, DNA polymerases DNA ligase, Reverse transcriptase, Polynucleotide kinase, Alkaline phosphatase.

Cloning Vectors: Plasmids and cloning vectors; High capacity cloning vectors – YACs, BACs and PACs; Shuttle vectors; Prokaryotic and eukaryotic expression vectors; Plant based vectors.

Techniques: Nick translation, Primer extension, Radioactive and non-radioactive probes; Blotting methods (Northern, Southern, Western and South Western); DNA-protein interactions– Mobility shift assay; DNase I foot printing; Methyl interference assay; Protein purification methods; Principles of maximizing protein expression. Unit - II Cloning Methodologies: Methods for construction of genomic and cDNA libraries; Lambda in vitro packaging; Identification and analyses of recombinant DNA clones; Protein-protein interaction and Yeast two hybrid system; Phage display; Ligation free cloning.

PCR: Primer design; DNA polymerases; Different types of PCR – Multiplex, Nested, Reverse transcriptase, Real time PCR, Colony PCR, Isothermal PCR; Application of PCR technology; Site-directed mutagenesis. Unit - III Gene Synthesis: Methods and applications; Methods for DNA Sequencing – classical sequencing, automated DNA sequencing, next generation sequencing, RNA sequencing. Gene silencing techniques: Introduction to siRNA, siRNA technology, microRNA, construction of siRNA vectors, principle and application of gene silencing; Gene knockouts.

Gene Therapy: Basic concepts, vectors used in the therapy. Books recommended

❖ Gene Cloning and DNA Analysis: An Introduction by T.A. Brown; Wiley-Blackwell. ❖ Principles of Gene Manipulation by S.B. Primrose, R.M. Twyman and R.W.Old;

Wiley-Blackwell. ❖ Molecular Cloning: A Laboratory Manual by J. Sambrook and D.W. Russel; Cold

Spring Harbor Laboratory Press. ❖ An introduction to genetic engineering by Desmond S. T. Nicholl; Cambridge

University Press.

MSBT- 202 Immunology Credit 3

Unit - I Introduction to immunology - History, Cells and organs of immune system, Principle of innate and adaptive immunity; Complement systems. Antigen and Antibody - Antigen recognition by B and T cell receptors, Nature of the antigen molecule, Antigenicity, Immunogenicity, Haptens and adjuvants; The antibody molecule on the B cell surface and its structure and function, Generation of diversity in immunoglobulin, Isotypes, Allotypes and Idiotypes, Isotype switch and Affinity maturation, Monoclonal antibodies, Engineering antibody molecules for better applications.

Unit - II MHC molecules - MHC molecules, their structure and role in antigen presentation to T cells, Antigen processing and presentation, Non-classical MHC molecules, MHC molecules and disease susceptibility, Superantigens, HLA typing and transplantation. Development of B and T cells - Generation of B and T cells in the bone marrow and thymus, Rearrangement of antigen specific receptor gene segments and control of lymphocyte development, B and T cells immunity. Soluble mediators - Chemokines, Cytokines, Lipid mediators. Unit - III Immune response in health- Allergens, types of hypersensitivity reactions and diseases arising out of them, Autoimmunity, and Cancer Immunology. Immune reaction to infectious diseases- Viral infections, bacterial infections, Parasite and fungal infections, Vaccines.

Books recommended

❖ Janeway’s Immuno Biology by Kenneth M. Murphy, Paul Travers and Mark Walport; Garland Science.

❖ Kuby Immunology by Kindt, T. J., Osborne, B. A. and Goldsby, R. A.; W. H. Freeman.

❖ Fundamental Immunology by Paul, W. E.; Lippincott Williams and Wilkins. ❖ Cellular and Molecular Immunology by Abbas, A. K., Lichtman, A. H. and Pillai, S.;

Saunders.

MSBT- 203 Molecular Genetics Credit 3 Unit - I Discovery of DNA and RNA as genetic material; Gene concept - fine structure of gene, Mitochondrial and Chloroplast inheritance; Mutations - types, causes and effects; Analyses of mutagenic agents; Structural and numerical alteration of chromosomes -Deletion, Insertion, Inversion, Translocation, Duplication, Aneuploidy, Polyploidy.

Unit - II Replication, transcription and translation: Complexity of DNA (Cot- curve analysis), Repetitive DNA sequences, Satellite DNA sequences, DNA replication, DNA polymerases transcription, RNA polymerases & Sigma factor, Promoter, Enhancers and gene function control regions, RNA processing, Translation (Genetic Code- Codon concept, Codon bias), Structure of ribosome, tRNA, Aminoacyl tRNA synthetase.

Unit - III Recombination, DNA damage and repair: Molecular mechanisms of recombination (Homologous and Non- Homologous End Joining), DNA damage and repair. Prokaryotic molecular genetics: Bacterial Conjugation, Transduction and Transformation, Transposable genetic elements (transposons, retro-transposons). Regulation of gene expression and Synthetic Biology Books recommended

❖ Principles of Genetics by Snustad & Simmons; John Wiley & Sons. ❖ Principles of Geneticsby Robert Tamarin; McGraw-Hill Education. ❖ Genetics: Analysis and Principles by Brooker; McGraw-Hill Education. ❖ Genetics: Principles and Analysis by Harlt & Jones; Jones & Bartlett. ❖ Molecular Cell Biology by Lodish; W.H. Freeman. ❖ Molecular Biology of The Cell by Bruce Alberts; Garland Science. ❖ Cell & Molecular Biology by Gerald Karp; John Wiley & Sons.

MSBT- 204 Cell Biology and Stem Cell Biology Credit 3 Unit – I Cellular organization: Membrane structure and function, Structure of model membrane, Lipid bilayer and membrane protein diffusion, Osmosis, Ion channels, Active transport, ion pumps, Electrical properties of membranes. Structural organization and function of intracellular organelles: Cell wall, nucleus, mitochondria, Golgi bodies, lysosomes, Endoplasmic reticulum, Peroxisomes, Plastids, Vacuoles, Chloroplast. Cytoskeleton: Microfilaments, intermediate filaments and microtubules– Structure and dynamics. Microtubules and mitosis; Cell movements. Intracellular transport and the role of Kinesin and Dynein. Unit – II Intracellular protein trafficking: Protein synthesis on free and bound polysomes, uptake into ER, membrane proteins, mechanism of sorting and regulation of intracellular transport, post- translational modifications. Cell signaling: Hormones and their receptors, cell surface receptor, signaling through G-protein coupled receptors, signal transduction pathways, second messengers, regulation of signaling pathways, bacterial and plant two-component signaling systems, bacterial chemotaxis and quorum sensing. Cell – cell communication: Regulation of hematopoiesis, general principles of cell communication, cell adhesion and roles of different adhesion molecules, gap junctions, extracellular matrix, integrins, neurotransmission and its regulation.

Unit – III Cell division and cell cycle: Mitosis, meiosis, cell cycle, role of cyclins and cyclin dependent kinases, regulation of Cdk – Cyclin activity, induction of cancer with respect to cell cycle. Programmed cell death, aging and senescence. Stem cell biology: Applications, types of stem cells, hematopoietic stem cells, maintenance and control of differentiation of stem cells, characterization and expansion, inducible pleuripotent stem cells; ES cell technologies, Concept of Cell replacement therapy and regenerative medicine. Cancer: Genetic rearrangements in progenitor cells, oncogenes, tumor suppressor genes, cancer and the cell cycle, virus-induced cancer, metastasis, interaction of cancer cells with normal cells, apoptosis, therapeutic interventions of uncontrolled cell growth.

Books recommended

❖ Cell Biology by Pollard, T. D., and Earnshaw, W. C.; Saunders. ❖ Cell and Molecular Biology, Concept and Experiment by Gerald K.; Wiley. ❖ Molecular Cell Biology by Lodish, H., Berk A., Kaiser C. A., Krieger M., Bretscher

A., Ploegh H., and Scott M.P.;, Freeman, W. H. and Co. ❖ Molecular Biology of the Cell by Alberts B., Walter P., Johnson A., Lewis J., Morgan

D., and Raff. M., RobertsK., Walter P.; Garland Publishing Inc.

MSBT- 205 Laboratory Safety, Biosafety and IPR Credit 3

Unit - I Fundamental concepts of laboratory safety: Basic concepts of laboratory safety, Understanding, Organizing, Contain, Safe handling and Safe disposal of hazardous materials associated with biotechnology laboratory, Classification and sign labelling of hazardous laboratory chemicals (e.g. corrosives, inflammables, explosives, oxidizers, toxins, poisons, carcinogen, mutagen, environmental pollutant etc.); Quick assessment of chemical hazard via MSDS, NFPA diamond, Safe storage of hazardous chemical; Segregation and safe disposal of chemical waste; Fire safety and use of fire extinguishers, safety showers etc. Biotechnology laboratory specific safety concepts: Safe handling of scientific equipments (e.g. fume hood, centrifuges, autoclave, microwave oven, hot air oven, electrophoresis, ultra-sonicator, deep freezers, fluorescence microscope, radio- active material, laser enabled equipments etc. Good laboratory practices for safety in laboratories: Good laboratory practices, their role and importance, Personal hygiene, personal protective devices (lab coat, goggles, mask, gloves, boots etc.). Dos and Don’ts of a biotechnology laboratory, record keeping, accident reporting, first aid procedure.

Unit - II Biological safety: Historical background, introduction to biological safety cabinets, primary containment for biohazards, biosafety levels, biosafety levels of specific microorganisms and pathogens. Biological safety levels of common biological material used in biotechnology lab: Biosafety levels of cell line, primary cells, microbial cultures, viral samples, DNA vectors, recombinants generated etc.; Recommended biosafety levels for infectious agents and infected animals. Regulations and guidelines related to biosafety: Government of India, definition of GMOs & LMOs, roles of institutional biosafety committee, RCGM, GEAC etc. for GMO applications in food and agriculture; Environmental release of GMOs, risk analysis, risk assessment, risk management and communication; Overview of national regulations and relevant international agreements including Cartagena protocol Unit - III IPR issues: Types of IP: Patents, Trademarks, Copyright & related rights, Industrial design; Traditional knowledge, geographical indications, protection of new GMOs, IPs of relevance to biotechnology; Introduction to history of GATT, WTO, WIPO and TRIPS, provisional patents. Books recommended

❖ CRC Handbook of Laboratory Safety by Furr A.K.; CRC Press. ❖ Laboratory Health and Safety Handbook: Library and Archives Canada. ❖ Biological Safety: Principles And Practices by Fleming & Hunt; American Society

for Microbiology. ❖ Biosafety in Microbiological and Biomedical Laboratories: U.S. Department of

Health and Human Services.

❖ Recombinant DNA Safety Guidelines and Regulation: DBT, Govt. of India. ❖ Govt. of India guidelines related to Biosafety: (various links from

http://dbtbiosafety.nic.in/) ❖ Intellectual Property Rights: Legal and Economic Challenges for Development:

Cimoli. ❖ Indian Patent Laws: Kankanala KC, Narasani AK.

Elective I

MSBT- 206

A. Ecology and Evolution Credit 3

Unit – I Environment: Physical environment, biotic environment, biotic and abiotic interactions; Habitat and niche: Concept of habitat and niche, niche width and overlap, fundamental and realized niche, resource partitioning, character displacement; Population ecology: Characteristics of a population, population growth curves, population regulation, life history strategies (r and K selection), concept of metapopulation – demes and dispersal, interdemic extinctions, age structured populations. Unit – II Species interactions: Types of interactions, interspecific competition, herbivory, carnivory, pollination, symbiosis; Community ecology: Nature of communities, community structure and attributes, levels of species diversity and its measurement, edges and ecotones; Ecological succession: Types, mechanisms, changes involved in succession; Ecosystem: Structure and function, energy flow and mineral cycling (CNP), primary production and decomposition; Structure and function of some Indian ecosystems: terrestrial (forest, grassland) and aquatic (fresh water, marine,estuarine ). Unit – III Lamarck & Darwin - concepts of variation, adaptation, struggle, fitness and natural selection; Origin of cells and evolution of unicellular organisms: Origin of basic biological molecules, abiotic synthesis of organic monomers and polymers, concept of Oparin and Haldane, experiment of Miller (1953), the first cell, evolution of prokaryotes, origin and diversification of eukaryotes, multicellularity and development, diversification of plants and animals, generation of variation by mutation and recombination, random genetic drift, population structure, phenotypic evolution. Books recommended

❖ Ecology from Individuals to Ecosystems by Begon, M., Townsend, C. R., and Harper, J. L.; Wiley-Blackwell.

❖ Ecology: Principles and Applications by Chapman, J. L. and Reiss, M. J. Cambridge University Press.

❖ Environmental Science by Kemp, M. J. The McGraw-Hill Companies. ❖ Evolution by Barton, N.H., Briggs, D.E.G., Eisen, J.A., Goldstein, D.B., Patel, N.H.,.

Cold Spring Harbor Laboratory Press.

Elective I

MSBT- 206

B. Eukaryotic and Human Genetics Credit 3

Unit - I Introduction, History and scope of genetics, Mendelian principles of genetic inheritance and their applications (pedigree analyses, phylogenetic tree analyses), extension of Mendelian principles, chromosomal basis of genetic inheritance, mechanism of sex determination and sex linked inheritance; Chromosomal linkage, crossing over, chromosomal mapping, genetic and physical map distances, genetic markers; Eukaryotic chromosome, eukaryotic genome organization, ploidy, structural and numerical alteration of chromosomes (deletion, insertion, inversion, translocation, duplication, aneuploidy, polyploidy).

Unit - II Organization of human genome, pedigree analysis, monogenic and polygenic traits, gene mapping and linkage analysis, identifying recombinants and non-recombinants in pedigrees, two-point and multi-point mapping, homozygosity mapping, difficulties of mapping complex multifactorial traits, identifying human disease genes, allelic association, linkage disequilibrium, mutation detection, genetic counseling, prenatal diagnosis; cancer genetics, genetic disorders of metabolism (e.g. phenylketonuria neurogenetic disorders, muscular dystrophy, genetic disorders of hematopoietic systems: sickle cell anemia), multifactorial disorders: diabetes mellitus, mitochondrial syndromes, management of genetic disorders.

Unit - III Elements of population genetics, alleles and genetic variations, multi- allelic traits, calculation of allele frequency, Hardy–Weinberg equilibrium, molecular evolution - evolutionary changes of nucleotide sequences and DNA polymorphism, genetic drifts, neutral selection, genes in early development, maternal effect genes, pattern formation genes, homeotic genes. Books recommended:

❖ Principles of Genetics by Snustad & Simmons; Wiley & Sons.

❖ Genetics: Principles and Analysis by Harlt & Jones; Jones & Bartlett.

❖ Human Molecular Genetics by Strachan & Read; Garland Science.

❖ Human Molecular Genetics by Gerard Meurant; Academic Press.

❖ Human Evolutionary Genetics by Jobling, Hollox, Hurles & Kivisild; Garland Science.

❖ Human Population Genetics by Relethford; Wiley -Blackwell

❖ Genetics of Population by Hedrick; Jones & Bartlett. MSBT- 207 Genetic Engineering laboratory Credit 3

➢ Isolation of plasmid DNA

➢ Isolation of genomic DNA from bacteria/ yeast

➢ PCR amplification of a gene of interest and it’s analysis by agarose gel electrophoresis

➢ In vitro DNA ligation and bacterial transformation

➢ Confirmation of recombinant clones.

➢ Restriction map analysis.

➢ Purification of total RNA/poly A- RNA using oligo dT column

➢ Electrophoresis of RNA and DNA

➢ RT –PCR and Real-Time PCR

➢ Introduction to NGS

➢ Introduction to Microarray

MSBT- 208 Immunology and Cell Biology Lab Credit 3

➢ Double diffusion

➢ Radial-Immuno diffusion

➢ Immuno-electrophoresis

➢ ELISA: Dot ELISA, Sandwich ELISA, Competitive ELISA (Including DEMO)

➢ Isolation and purification of IgG from serum or IgY from chicken egg

➢ Immunohistochemistry

➢ Blood smear identification of leucocytes by Giemsa stain

➢ Separation of mononuclear cells by Ficoll-Hypaque

➢ Nucleus and cell organelles staining

➢ Chromosome preparations - mitotic and meiotic

MSBT- 301 Fermentation & Bioprocess Technology Credit 3

Unit – I Introduction to fermentation processes, types of fermentation processes, batch fermentation processes and its kinetics, plug flow fermentation process and its kinetics, continuous fermentation processes and its kinetics, fed batch fermentation processes and its kinetics, factors affecting fermentation processes. Unit – II Isolation, screening, characterization and preservation of industrially important microorganisms, optimization of media for industrial fermentation introduction(typical media and its components, medium formulation for growth and production, energy source, carbon source, nitrogen source, minerals, growth and production factors), assessment of oxygen requirement, antifoam, medium optimization, isolation & screening of mutants for industrial microorganisms, generation of recombinant microorganisms of industrial, application, their preservation and maintenance, quality control of preserved industrially applicable microorganisms. Unit – III Bioprocess development: down-stream processes: Recovery and purification of fermentation products, removal of microbial cells, microbial cell aggregation and flocculation, foam separation, precipitation, filtration, different types of filters and filter aids, industrial centrifugation and industrial centrifuges, basket centrifuge, tubular bowl centrifuge, solid bowl centrifuge, multi chamber centrifuge, disc bowl centrifuge, cell disruption (physical and chemical method), liquid-liquid extraction, aqueous two phase extraction, chromatography, membrane separation processes, drying and crystallization. Bioprocess development: Effluent treatment & process economics: Disposal, treatment processes, physical chemical and biological treatments, aerobic processes; Biological aerated filters (BAFs), rotating drums, fluidized bed system, activated sludge processes, anaerobic treatment, up flow anaerobic sludge blankets (UASB); By-products, fermentation economics & market potential; Introduction to fermentation process for products such as enzyme, biopharmaceuticals and monoclonal antibodies. Books recommended

❖ Principles of Fermentation Technology by Stanbury & Whitaker; Elsevier. ❖ Bioprocess Engineering Principles by Doran; Academic Press, Elsevier. ❖ Fermentation Microbiology and Biotechnology by El- Mansi & Bryce; CRC Press. ❖ Fermentation: A practical Approach by McNeil & Harvey; Oxford, IRL Press. ❖ Principles and Technology of Fermentation Engineering by Jian & Cheng; Chemical Industry

Press.

MSBT- 302 Plant Molecular Biology and Plant Biotechnology Credit 3 Unit - I

Plant genome organization, structural features of a representative plant mRNA- encoding gene, Matrix Attachment Region, RNA polymerases, rRNA genes, importance of introns, 5’UTR and 3’UTR, regulation of gene expression, CaMV 35S promoter.

Organization of chloroplast genome, nuclear-encoded and plastid-encoded genes for chloroplast proteins, ‘Endo symbiont’ theory of chloroplast evolution, targeting of proteins into chloroplast, plastid transformation; Organization of mitochondrial genome, coding capacity of mitochondrial genome, RNA editing in plant mitochondria, mitochondrial genome and cytoplasmic male sterility, cms cytoplasms and nuclear Rf genes, ‘Heterosis’ and three-line strategy for hybrid seed production. Unit - II Agrobacterium and crown gall tumours, mechanism of T-DNA transfer, comparison of conjugal transfer and T-DNA transfer, vir helper strains, Ti plasmid vectors for plant transformation, promoters, reporter genes and selectable marker genes in plant transformation vectors, strategies to eliminate selectable marker genes in transgenic plants. Unit - III Genetic engineering of plants for virus resistance, pest resistance, herbicide tolerance, fungal resistance and nematode resistance; Generation of male sterility for hybrid seed production; Delay of fruit ripening by genetic engineering; Improvement of seed storage proteins.

Production of antibodies in plants-secretory antibodies-scFv antibodies, production of pharmaceutically useful proteins in transgenic plants, engineering of useful traits by RNA silencing; Important bio-safety questions in transgenic plants, Intellectual Property Rights, Patents, Plant Breeders Rights, Convention of Biodiversity. Books recommended

❖ Plant Molecular Biology by Grierson, C., and S.N. Covey; Blackie, London. ❖ Plant Biotechnology: The genetic manipulation of plants by Slater, A., N. Scott and M.

Fowler; Oxford University Press. ❖ Biochemistry and Molecular Biology of Plants by Buchanan, B.B., W. Gruissen and R.L.

Jones;. American Society of Plant Biologists. Rockville, USA. ❖ Plant Biotechnology by Hammond, J.H., P. Mcgarvey and V. Yusibov;. Springer Verlag,

Heidelberg. ❖ Text Book of Biotechnology by Das, H.K.; Wiley India Pvt. Ltd., New Delhi.

MSBT- 303 Developmental Biology and Animal Biotechnology Credit 3 Unit - I Basic concepts of development: Potency, commitment, specification, induction, competence, determination and differentiation, morphogenetic gradients, cell fate and cell lineages, stem cells, genomic equivalence and the cytoplasmic determinants, imprinting, mutants and transgenics in the analysis of development. Gametogenesis, fertilization and early development: Production of gametes, cell surface molecules in sperm-egg recognition in animals, zygote formation, cleavage, blastula formation, embryonic fluids, gastrulation and formation of germ layers in animals; embryogenesis. Unit - II Morphogenesis and organogenesis in animals: Cell aggregation and differentiation in Dictyostelium; axes and pattern formation in Drosophila, amphibia and chick, organogenesis (vulva formation in Caenorhabditis elegans), eye lens induction, limb development and regeneration in vertebrates, differentiation of neurons, post embryonic development-larval formation, metamorphosis, environmental regulation of normal development, sex determination. Unit - III Basics of animal cell culture: Types of cell cultures, cell lines and primary cells (characteristics of finite, continuous and transformed cells in culture); Routine maintenance of cell cultures, microbial contamination of cell culture, cell culture media and culture vessels; Cell culture assays -cell viability and cytotoxicity tests, histological examination, CAM assay, filter well invasion, angiogenesis, tumorigenesis assays; Applications of animal cell culture, in vitro testing of drugs, production of human and animal viral vaccines and pharmaceutical proteins; Cryopreservation of cell lines, principle, methodology and applications; Induction of differentiation, physiological and non-physiological inducers.

Antibody production: Preparation of hybridomas, principle and selection of hybridomas, production of monoclonal antibodies and their applications in diagnostics and therapy, limitation of hybridoma technology, approaches to development of vaccines; Phage display technology for production of antibodies. Books recommended

❖ Animal Cell Biotechnology: Methods and Protocols by Pörtner, Ralf (Ed.); Springer protocols. ❖ Culture of Animal Cells: A Manual of Basic Technique by R. Ian Freshney; Wiley-Blackwell. ❖ Textbook of Animal Biotechnology by B Singh, S K Gautam, and M S Chauhan; TERI Press. ❖ Developmental Biology by S.F. Gilbert.; Sinauer Associates Inc. ❖ Principles of Development by Lewis Wolpert, Cheryll Tickle, Alfonso Martinez.; Oxford

University Press.

❖ An Introduction to Embryology by B. I. Balinsky; Thomas Asia Pvt.

MSBT- 304 Bioinformatics and Genome informatics Credit 3 Unit - I Data base concept, database management system, database browsing and data retrieval, sequence database and genome database, data structures and databases, databases such as GenBank, EMBL, DDBJ, Swissprot, PIR, Ensemble, UCSC genome browser, MIPS, TIGR, Hovergen, TAIR, PlasmoDB, ECDC, searching for sequence database using FASTA and BLAST algorithm; Phylogenetic studies, alignment of sequences, gene prediction and regulation, protein classification & structure prediction; Genome analysis methods; Computer programming. Unit - II Functional and structural genomics and their databases; Tools for obtaining genomics data, both functional and structural using microarrays and NGS; Data annotation, structure, mining, retrieval and security; Ethical aspects related genomic data collection. Unit - III Applications of genome informatics; Evolutionary relationship; Drug sensitivity and resistance; Synthetic biology and bioengineering; Platforms for genomic data analysis and methods for interpretation; 1000 Genomes project: first footstep to the vast genome informatics; Further scope in the field and future prospects. Books recommended

❖ Computational Methods in Mol.Biol./.Now Comprehensive Biochemistry Vol.32. S.L.Seizberg, DB Searls, S.Kasif; Elsevier. ❖ Bioinformatics: Databases and Algorithms by N. Gautham; Narosa Publications. ❖ Structural Bioinformatics by Bourne P.E. Ed Weissig; H. Wiley-Liss. ❖ Bioinformatics for dummies by Claverie Jean M. & Notredame C.; H. Wiley-Liss. ❖ Bioinformatics: Sequence and Genome analysis by David W. Mount; CBS Publishers

Elective I

MSBT- 305

A. Applied Environmental Biotechnology Credit 3

Unit - I Introduction and Basic Concepts: Introduction, basic concepts, environment & environmental processes, environmental resources; Atmosphere, characteristics of atmospheric gases, atmospheric circulations, hydrosphere. Unit - II Environmental Perturbations: Air, water and soil pollution, sources of pollution, point source pollution, non- point source pollution, air pollutants and their classification, green house factors and their effects, water pollution and type of water pollutants, water quality monitoring, ground water pollution, eutrophication, soil pollution, soil erosion, ozone depletion, acid rain (formation, measurement, effects and control of acid rain), global warming and climate change. Unit - III Application of Biotechnology in Environmental Management and Restoration: Structural and functional diversity of microbial communities, microbial populations in polluted environments, biodegradation and biotransformation of natural compounds (lignocellulose, petroleum products,), biodegradation and biotransformation of xenobiotic compounds (explosives, dyes, pesticides, insecticides, pharmaceuticals and personal care), microbial degradation mechanisms, chemical structure and properties influencing biodegradability, bio-adsorption of metal pollutants (by fungi, algae and moss), phytoremediation. Unit – IV Application of Biotechnology for sustainable environmental resources: Biofuel (Types: Bioethanol and Biodiesel), Biomethane (biochemistry and microbiology of microbial methane production), Biogas, Biofertilizers, Biopesticides, Composting, Bioleaching, Nanomaterials for environmental applications. Books recommended

❖ Environmental Biotechnology: Principles and Applications by Rittmann & McCarty; McGraw Hills.

❖ Environmental Biotechnology: Theory and Applications by Evans & Furlong; Wiley India Pvt. Ltd.

❖ Environmental Biotechnology by Alan Scragg; Oxford. ❖ Environmental Biotechnology, Basic Concepts and Application by Thakur I. S.; IKIPH Pvt.

Ltd. ❖ Environmental Biotechnology, New Approaches and prospective applications by Petre M;

InTech.

Elective I

MSBT- 305

B. Nanobiotechnology Credit 3

Unit - I Principles of Nanobiotechnology: Introduction to nanomaterials, from biotechnology to nanobiotechnology, top down and bottom up approaches for synthesis of nanomaterials, chemical transformation of biomaterials, machine-phase nanobiotechnology, molecular assemblers. Unit - II Protein and Peptide based Nanostructures- Chemistry and structure, assembly, recrystallization, diagnosis, methods of production, supported bilayers and membrane arrays, microbial nanoparticles production, magnetosomes, bacteriorhodopsins, nanoproteomics, DNA based nanostructures, DNA-protein nanostructures, self-assembled DNA nanostructures, nucleic acid nanoparticles. Unit - III Nanomaterials for Therapeutics: Fundamentals- Physicochemical principles of nanosized drug delivery systems, drug loaded nanoparticles- structure and preparation, liposomes, lipid based nanoparticles, solid lipid nanoparticles (SLP), biofunctionalisation of SLP, nanotubes, nanorods, nanofibers, and fullerenes for nanoscale drug delivery, carbon nanotubes, biocompatibility and drug delivery, toxicity of nanomaterials. Books recommended

❖ Nanobiotechnology, Concepts, Applications and perspectives by C.M. Niemeyer and C.A. Mirkin; WILEY-VCH, Verlag Gmb H&Co.

❖ Bionanotechnology, Lessons from Nature by S. David Goodsell; Wiley-Liss, Inc. ❖ Nanobiotechnology - II more concepts and applications by C.M. Niemeyer and C.A. Mirkin;,

WILEY-VCH, Verlag Gmb H&Co. ❖ Nanotechnology in Biology and Medicine: Methods, Devices, and Applications by Tuan Vo-

Dinh; CRDC press.

Elective II

MSBT- 306

A. Molecular Basis of Drug Design & Development Credit 3 Unit - I Molecular Modelling – Concepts in molecular modelling, methods for modelling, homology modelling, threading and protein structure prediction, structure-structure comparison of macromolecules with reference to proteins, force fields, molecular energy minimization, Monte Carlo and molecular dynamics simulation, molecular modelling challenges.

Unit - II Molecular modelling in drug discovery: Computer representations of molecules, chemical databases and 3D database search, 3D pharmacophore, molecular similarity.

Molecular Docking: Rigid docking, flexible docking and docking based screening, preparation of ligand and receptor for docking, lead discovery, lead optimization, combinatorial library. Unit - III Pharmacokinetics, pharmacogenomics, chemoinformatics, chemogenomics, metabolism of drug: Quantitative Structure Activity Relationship (QSAR), ADMET studies; Adverse drug reactions, identification of drug targets, case studies of drug development. Books recommended

❖ Drug Action at the Molecular Level by Robert GCK, ed.; University Park Press Baltimore. ❖ Drug Discovery and Development by William H, Malick JB; Humana Press Clifton. ❖ The Basis of Medicinal Chemistry, Burer’s Medicinal Chemistry by Wolf ME, ed; John Wiley

& Sons, New York. ❖ Drugs from discovery to approval by Rick, N.G.; Wiley-Blackwell, USA. ❖ Molecular Modelling: Principles and applications by Leach AR; Prentice Hall, Pearson

Education Ltd.

Elective II

MSBT- 306

B. Genomics and Proteomics Credit 3

Unit - I Genome Sequencing: Genome sequencing projects, Next generation sequencing and understanding individual variation and diseases (technology of sequencing and assembly, bioinformatics of genome annotation, current status of genome sequencing projects), genomic browsers and databases, orthology prediction (comparative genomics), search for transcription factor binding sites (TFBS), computational prediction of miRNA target genes, de novo prediction of regulatory motifs in genome, single nucleotide polymorphisms (SNP) in medical genetics and basic research, application of genomics in personalized medicine, Nutrigenomics and Pharmacogenomics.

Unit - II Transcriptome analysis: Microarray analysis, types of microarrays and applications, EST, SAGE, Microarray data: normalization and analysis; Genevestigator and OncoMine – browsing microarray-derived gene expression profiles, tissue and stage-of-development-specific patterns of expression, co-expression of genes, pre-computed lists of differentially expressed genes; Standalone analysis of publicly available microarray expression data: GEO database, TM4 analysis suite; Assembly of EST: CAP3 program; Whole genome analysis of mRNA and protein expression.

Unit - III Proteomics: Protein analysis (measurement of concentration, amino-acid composition, N-terminal sequencing), 2-D electrophoresis of proteins, microscale solution iso-electricfocusing, peptide fingerprinting, LC/MS-MS, MALDI-TOF mass spectrometry for identification of proteins and modified proteins, SAGE and differential display proteomics; Protein-protein interactions: experimental and computational methods, databases, yeast two hybrid system; Metabolic pathways resources: KEGG, Biocarta; Nutrigenomics and metabolic health, analysis of microarray data, protein and peptide microarray-based technology. Books recommended

❖ Genomics, Proteomics and Metabolomics in Nutraceuticals and Functional Foods by Debasis Bagchi, Anand Swaroop, Manashi Bagchi; Wiley Publication.

❖ Biocode: The New Age of Genomics. by Dawn Field and Neil Davies, Oxford University Press.

❖ The Proteomics Protocols Handbook by John M. Walker (Editor), Humana Press.

❖ Introduction to Genomics by Arthur M. Lesk, Oxford University Press.

❖ Clinical Genomics by Shashikant Kulkarni and John Pfeifer, Academic Press.

❖ Clinical Proteomics: Methods and Protocols (Methods in Molecular Biology) by Antonia Vlahou, Manousos Makridakis, Humana Press.

❖ Proteomics: A Cold Spring Harbor Laboratory Course Manual by Andrew J Link, Cold Spring Harbor Laboratory Press.

MSBT- 307 Animal and Plant Molecular Biology Laboratory Credit 3

Plant tissue culture techniques

➢ Isolation of Genomic DNA and total RNA from plant tissues

➢ Cloning of selected genes into plant expression vectors

➢ Plant Transformation techniques: Agrobacterium mediated, Gene gun method

➢ Southern blotting and hybridization

➢ Introduction to plant tissue culture techniques

➢ Surface sterilization: Chemical and Physical

➢ Media preparation; Role of additives in different explant culture

➢ Organogenesis and Somatic embryogenesis

➢ Best Management Practices of Green house Animal Cell Culture Techniques

➢ Familiarization with animal cell culture laboratory and P1 to P4 facilities

➢ Sterilization techniques for animal cell culture laboratory

➢ Introduction to cell culture medium and the function of different components of the medium on cell growth

➢ Preparation of glassware and animal cell culture media

➢ Feeding and routine maintenance of animal cell culture

➢ Cell counting and viability

➢ Passaging of animal cell culture

➢ Cryopreservation of animal cells

➢ Revival of animal cells from cryopreserved cells

➢ Cell viability assays

Books recommended

❖ Cell culture and Somatic Cell Genetics of plants by Brown C. W and Thorpe T. A.; Academic Press Orlando .

❖ Plant Tissue Culture by Chu, C.; Peking Science Press, Peking. ❖ Plant Cell, Tissue culture and Organ culture Fundamental Methods by Gamborg O. L and

Phillips. G.G.; Narosa Publishing House, New Delhi. ❖ Plant Molecular Biology — A Laboratory Manual by Clark, Melody S. (Ed.); Springer Berlin.

MSBT- 308 Bioinformatics and Genome informatics laboratory Credit 3

➢ Databases: NCBI, Uniprot, PDB and PubMed

➢ Database, file, sequence formats and its conversion

➢ Database searching: BLAST, FASTA

➢ Genome database browsing: Ensemble, TIGR and PlasmoDB etc.

➢ Sequence annotation tools, for example: Expasy proteomics tools, EBI services, EMBOSS package

➢ Pair-wise sequence alignment: Needle, Water etc.

➢ Multiple sequence alignment: ClustalW, Muscle etc.

➢ Phylogenetic analysis: Phylip, MEGA

➢ Structure prediction: Modeller, I-TASSER etc.

➢ Structure visualization tools: Pymol, Chimera etc.

➢ Gene Prediction: Genscan, Glimmer etc.

➢ Genome alignment tools: VISTA, Blat etc.

➢ NGS sequence assembly and analysis: SEQanswers, NGSUtils

➢ Microarray sequence analysis: GenePublisher, ClustArray

➢ Chemoinformatics: ADMET studies