1 M.Sc. Biotechnology (Two Year Programme with Practicals) Scheme

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M.Sc. Biotechnology (Two year programme with practicals) Scheme of instruction and examination (For students admitted from 2017-2018 and onwards)

Hrs of instruct- Scheme of Examination tions /

Subject Name of Paper / week Part

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ofExam Duration Duration First Semester I 17MBTC01 Biochemical Concepts for Biotechnology 4 – 3 40 60 100 3 I 17MBTC02 Cell Biology and Microbiology 4 – 3 40 60 100 3 I 17MBTC03 Molecular Biology 4 – 3 40 60 100 3 I 17MBTC04 Biophysical Techniques 4 – 3 40 60 100 3 I 17MBTC05 Practicals I – Analytical Techniques in – 6 6 40 60 100 4 Biotechnology I 17MBTC06 Practicals II – Cell Biology and Microbial – 5 6 40 60 100 3 Techniques Library 1 – – – – – – II CSS 2 – – – – – – Second Semester I 17MBTC07 Genetics 4 – 3 40 60 100 3 I 17MBTC08 Animal Biotechnology 3 – 3 40 60 100 3 I 17MBTC09 Bioinformatics 3 – 3 40 60 100 3 I 17MBTC10 Recombinant DNA technology 3 – 3 40 60 100 3 I 17MBTC11 Practicals III – Animal Biotechnology and – 4 6 40 60 100 3 Bioinformatics I 17MBTC12 Practicals IV – Recombinant DNA – 6 6 40 60 100 3 Technology I 17MBTC13 Mini Project 1 – – 100 – 100 2 I Interdisciplinary Course 4 – 3 40 60 100 4 II CSS 2 – 3 1 II Professional Certification – – – – – – 2 Internship during summer vacation for one month

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instruct- Scheme of Examination tions /

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ofExam Duration Duration Third Semester I 17MBTC14 Immunology and Immunotechnology 4 – 3 40 60 100 3 I 17MBTC15 Plant Biotechnology 4 – 3 40 60 100 3 I 17MBTC16 Enzymes and Bioprocess Technology 4 – 3 40 60 100 3 I 17MBTC17 Pharmaceutical Biotechnology 4 – 3 40 60 100 3 I 17MBTC18 Practicals V – Immunotechnology and Plant – 5 6 40 60 100 3 Biotechnology I 17MBTC19 Practicals VI – Enzymes and Bioprocess – 6 6 40 60 100 4 Technology I 17MBTC20 Environmental Biotechnology (Self Study) 1 – 3 40 60 100 4 I Multidisciplinary Course 2 – 3 100 – 100 2 II 17MBTC21 Internship – – – 100 100 2 Fourth Semester I 17MBTC22 Food Biotechnology and 3 – 3 40 60 100 3 Nanobiotechnology I 17MBTC23 Biostatistics and Research Methodology 4 – 3 100 – 100 3 (Open Book Test) I 17MBTC24 Thesis 23 – – 100 100 200 6 Total 2700 85 Other courses to be undergone by the students: MOOC course – 2 credits Note: Minimum 85 credits to earn the degree

Other courses offered by the department IDC offered by the Department of Biotechnology  IDC – 17MBTI 01 Prospects of Biotechnology

MDC offered by the Department of Biotechnology  MDC – 17MBTM01 Scientific and Technical Writing

Biochemical Concepts for Biotechnology

Semester I Hours of Instruction / week : 4 17MBTC01 No. of credits : 3

Objectives : 1. To understand the basic biological concepts involved in Biotechnology 2. To understand the chemical principles in the biological systems 3. To study the properties and the importance of the major small molecules and macromolecules in the biological system.

Unit I – Introduction 12 hrs Properties of water – its effect on dissolved molecules – weak interactions – ionization of water – weak acids and weak bases – pH and its importance – biological buffers Concepts of bioenergetics, thermodynamics in biological system – Electron transport chain – oxidative phosphorylation Introduction to metabolism – anabolism and catabolism

Self study : Chemical bonds – physical interactions – viscosity, diffusion, osmotic pressure, surface tension

Unit II – Carbohydrates 12 hrs Structure and functions of biologically important mono-, di-, oligo- and polysaccharides – metabolism of carbohydrates – glycolysis, TCA cycle, glycogenesis, glycogenolysis and pentose phosphate pathway.

Self study : Gluconeogenesis

Unit III – Amino acids and Proteins 12 hrs Amino acids – classification and structure – peptide bond formation – biologically important peptides – insulin, oxytocin, vasopressin, glutathione Proteins – Orders of protein structure – primary, secondary, supersecondary, tertiary and quaternary – Ramachandran plot – conformation of proteins Protein catabolism – urea cycle. Metabolism of one carbon compounds, deamination, decarboxylation, transamination, transmethylation – denaturation of proteins

Self study : Positive and negative nitrogen balance; Protein Energy Malnutrition (PEM)

Unit IV – Lipids 12 hrs Classification and chemistry of lipids, structure and metabolism of fatty acids – fatty acid interconversion – outline of triacylglycerol and lipoprotein metabolism – cholesterol metabolism.

Self study : Interrelationship between carbohydrate, protein and lipid metabolism.

Unit V – Nucleic acids and Vitamins 12 hrs Structure and functions of DNA – nitrogenous bases, nucleosides, nucleotides – biologically important nucleotides – Watson and Crick model of DNA structure – A, B and Z forms of DNA – triple and quadruple structures of DNA – supercoiling of DNA – Properties of DNA – buoyant density, viscosity, denaturation, Cot curves Major and minor classes of RNA – structure and function of RNA types Chemistry of vitamins and coenzymes – NAD+, NADP+, FMN, FAD, CoASH, TPP, PLP, Biotin, Tetrahydrofolate and coenzyme B12.

Self study : Disorders linked to disturbances in nucleic acid metabolism – gout

Total 60 hrs

References:

1. Berg, J., Tymoezko, J.L. and Stryer, L. (2008) Biochemistry, 6th Edition, W.H. Freeman Publishing Company, New York. 2. Boyer, R. (2006) Concepts in Biochemistry, 3rd Edition, John Wiley and Sons Inc. 3. Devlin, T.M. (2010) Textbook of Biochemistry with clinical correlations, 7th Edition, John Wiley and Sons Inc. Publications. 4. Mathews, C.K., VanHolde, K.E. and Ahem, K.G. (2000) Biochemistry, 3rd Edition, Benjamin Cummings Publishing Co., Inc., U.K. 5. Mckee, T. and Mckee, J.M. (2003) Biochemistry – The Molecular Basis of Life, 4th Edition, Oxford University Press. 6. Murray, R.K, Bender, D.A, Botham, K.M., Kennelly, P.J., Rodwell, V.W. and Weil, P.A. (2009) Harper’s Illustrated Biochemistry, 28th Edition, The McGr.w-Hill Companies. 7. Nelson, D.L and Cox, M.M. (2008) Lehninger’s Principles of Biochemistry, 5th Edition W.H. Freeman Publishers, New York. 8. Voet, D. and Voet, J.G. (2010) Biochemistry, 4th Edition, John Wiley and Sons, New York.

Cell Biology and Microbiology

Semester I Hours of Instruction / Week : 4 17MBTC02 No. of credits : 3

Objectives : 1. To understand the basis of cell organization and how eukaryotic cells work at the molecular level 2. To provide an overview of cell structure and function, including the flow of information from genes to proteins, and regulation of cellular processes, signalling and proliferation of cells 3. To describe how antibiotics work by interfering with cellular processes 4. To discuss the importance of microbes in ecological and industrial processes and to explain the basis of microbial pathogenesis and the host response to microbial infection

Unit I –Cell Organization 12 hrs Structural differences between prokaryotic and eukaryotic cells – structure and functions of sub-cellular organelles – mitochondria, endoplasmic reticulum, Golgi complex, ribosomes, lysosomes, peroxisomes, glyoxysomes, chloroplasts, cytoskeletal elements – cytoplasm – ultrastructure of nucleus – nuclear envelope, chromatin, nucleolus

Self study : From molecules to the first cell – prokaryotic and eukaryotic cell organization

Unit II - Membrane structure and function 12 hrs Prokaryotic and eukaryotic cell envelopes – plasma membrane – lipid bilayer – fluid mosaic model – rafts (elementary concepts only) – types of cell junctions – CAMs, ECM – transport across membranes – pinocytosis, phagocytosis, permeability of water and salts, salt antagonism, co-transport and active transport – ATPase, ABC transporters, ion channels, ionophores, aquaporins.

Self study : Characteristics of ribosomes in eukaryotic cytoplasm, mitochondria and in prokaryotic cells

Unit III – Cell division, differentiation, cell cycle and cell death 12 hrs Cell division – amitosis, mitosis, meiosis – Cell differentiation – stem cells (elementary concepts only) – Cell cycle – phases, regulation, checkpoints – Cell death – necrosis, apoptosis, autophagy

Self study : Types of cell death other than necrosis, apoptosis and autophagy

Unit IV – Microbial taxonomy 12 hrs Classification of microorganisms – Characteristics of bacteria, fungi, algae, lichens and protozoa. Growth, culture and maintenance of microorganisms – Nutritional requirements – Uptake of nutrients – Microbial growth and measurement – Kinetics of growth

Self study : Discovery and origin of microbial world

Unit V – Culture media and types 12 hrs Techniques of pure culture isolation – Control of microorganisms – Sterilization and disinfection. Microbial pathology– identifying features of pathogenic bacteria, fungi and viruses,mechanism of microbial pathogenicity, etiology and pathology of common microbial diseases and currently recommended therapies for common bacterial, fungal & viral infections

Self study : Types of microbial nutrition – phototrophs, chemotrophs, lithotrophs, organotrophs

Total – 60hrs

References

1. Gupta, H.L and Jangir, H.L. (2010) Cell biology: Fundamentals and Applications, Agrobios, Jodhpur, India. 2. Plopper, G., Sharp,D. and Sikorski, E. (2015) Lewin’s cells, 3rd edition, Jones & Bartlett Publishers, Massachusetts 3. Cooper, G.M and Robert (2007) The Cell: a Molecular Approach, 4th Edition, ASM Press. 4. Gupta, P.K. (2005) Cell and Molecular Biology, 1st Edition, Rastogi Publications, Meerut. 5. Karp, G. (2010) Cell Biology, 3rd Edition, John Wiley&Sons, New Jersey, United States 6. Tortora, G.J., Funke, B.R. and Case, C.L. (2009) Microbiology, 2nd edition, Pearson Education, Inc. 7. Pelczar, M.J., Chan, E.C. and Krieg, N.R. (2006) Microbiology, 6th Edition, Tata McGraw Hill Publishing Company Ltd, New Delhi. 8. Prescott (2008), Microbiology, 7th edition, McGraw Hill International Edition, New York. 9. Talaro, K.P. and Talaro, A. (2008) Foundations in Microbiology, Tata McGraw Hill Publishers, New York. 10. Casida., J.R. (2006) Industrial Microbiology, 4th Edition, Wiley Eastern Ltd, New Delhi. 11. Gupta, P.K (2006) Biotechnology and Genomics, 1st Edition, Rastogi Publications, Meerut.

Molecular Biology Semester I Hours of Instruction / Week : 4 17MBTC03 No. of credits : 3

Objectives: 1. To understand the basis of genome organization and how eukaryotic cells work at the molecular level 2. To provide an overview of central dogma, including the flow of information from genes to proteins 3. To learn about gene expression and its regulation.

Unit I – Central dogma of molecular biology 12 hrs Outline of genetic information flow – organization of viral, prokaryotic and eukaryotic genomes – components of eukaryotic chromatin and chromosome structure – nucleosome, 30nm fiber and higher order structure – genome complexity – unique sequences and repetitive DNA (satellite, minisatellite and microsatellite). Split genes.

Self study : Importance of coding and non-coding regions of the genome

Unit II – DNA replication 12 hrs Basic features of replication - prokaryotic and eukaryotic DNA replication – unique aspects of eukaryotic chromosome replication, mechanism of replication. Enzymes and proteins involved in DNA replication. Telomeres and telomerase in replication – regulation of DNA synthesis. DNA damage and repair – excision, MMR, SOS response.

Self study : Effect of mutations in DNA

Unit III – Transcription and RNA processing 12 hrs Transcription in prokaryotes and eukaryotes – RNA polymerases – general and specific transcription factors – regulatory elements – mechanism of transcription regulation. Post transcriptional processes in eukaryotes – processing of mRNA (splicing and RNA editing), tRNA and rRNA – reverse transcription.

Self study : Deciphering of the codon; variations of the genetic code

Unit IV – Protein 12 hrs Genetic code: The salient features of genetic code; wobble hypothesis. Mutations – point, frameshift.Translation in prokaryotes and eukaryotes – translational machinery – Mechanism of initiation – elongation and termination– regulation of translation. Inhibitors of protein synthesis and post translational modifications – protein degradation – ubiquitin pathway

Self study : Signal peptidases and protein sorting

Unit V – Gene Expression 12 hrs Levels of regulation of gene expression – positive and negative control of gene expression in prokaryotes – operon models (lac and trp). Regulation of gene expression in eukaryotes – transcriptional (steroid hormones), post-transcriptional (alternative splicing). RNA interference. Epigenetic regulation (methylation, acetylation) – CRISPR-Cas 9-mediated genome editing

Self study : Environmental regulation of gene expression Total 60 hrs

References : 1. Ajoy, P. (2009) Textbook of Cell and Molecular Biology, Second edition, Books and Allied Publication, Mumbai. 2. Ramamurthi, K.S. (2009) Gene Flow and Molecular Biology, Alfa Publications, New Delhi. 3. Jeyanthi, G.P. (2009) Molecular Biology, MJP Publishers, Chennai. 4. Gupta, P.K. (2005) Cell and Molecular Biology, 1st Edition, Rastogi Publications, Meerut. 5. Karp, G. (2002) Cell and Molecular Biology – Concepts and Experiments, 3rd Edition, Garland Science Publication, New York 6. Lodish, H., Baltimore, D., Berk, A., Zipursky, L., Matsudaira, P. and Darnell, D.M. (2007) Molecular Cell Biology, 3rd Edition, Scientific American Books, W.H.Freeman and Co., New York. 7. Purohit, S.S. (2008) Cell and Molecular Biology: Fundamentals and Applications, Agrobios, Jodhpur, India. 8. Freifelder. D. (2007) Essentials of Molecular Biology, 2nd Edition, Narosa Publishing House, New Delhi. 9. Malacinski,G.M. (2015) Freifelder's Essentials Of Molecular Biology, 4th Edition, Narosa Publishing House, New Delhi. 10. Karp. G (2008) Cell And Molecular Biology : Concepts And Experiments, 5th edition John Wiley and Sons 5th Edition.

Biophysical Techniques Semester I Hours of Instruction / Week : 4 17MBTC04 No. of credits : 3

Objectives : 1. To become familiar with all the major biophysical techniques used in biotechnology research and industry for analyzing the structure and function of biomolecules. 2. To give an introduction to the methods used in the study of the structures, dynamics and interactions of biomolecules 3. To give an overview of how these techniques are used in practice in biotechnology research

Unit I – Microscopy techniques 12hrs Microscopy – Principle, instrumentation, sample preparation for optical, phase contrast, interference, polarization, inverted fluorescence, confocal and electron microscopes (SEM and TEM) and their applications. X-ray absorption and diffraction, X-ray fluorescence, detection and applications – super resolution microscopy (elementary concepts only)

Self study : Production and properties of X-rays

Unit II – Centrifugation and electrophoresis 12hrs Centrifugation – principle, types and applications of preparative and analytical ultracentrifuges. Chromatography – principle, methodology and applications of paper, thin layer, column (gel filtration, ion exchange, affinity), gas and HPLC. Electrophoresis – principles, types and their applications for proteins, nucleic acids, including gradient gel and pulse-field gel electrophoresis – agarose gel electrophoresis, PAGE, 2D-PAGE – capillary electrophoresis and immune electrophoresis – EMSA

Self study : Partition co-efficient of substances and its importance

Unit III – Spectroscopy 12 hrs Spectroscopy – principles, types of spectra – absorbance, emission and fluorescence. Types of spectroscopy – principle, instrumentation and applications of UVvisible spectroscopy, atomic absorption spectroscopy, Nuclear Magnetic Resonance spectroscopy and Electron Spin Resonance.

Self study : Nature of electromagnetic radiation

Unit IV – Spectroscopy and sequencing 12hrs Mass Spectroscopy – principles, method and applications, MALDI TOF, emission spectroscopy – principle, instrumentation and applications of Flame Photometry and Fluorimetry. Infrared Spectroscopy and Raman spectroscopy, GC-MS,LC-MS, Next generation sequencing (NGS)

Self study: Applications of IR and Raman spectroscopy

Unit V – Radioactivity and Scattering 12hrs Radiation biology – nature of radioactivity, measurement of radioactivity – Applications of radioactive and stable isotopes in biological research. Circular dichroism and optical rotatory dispersion, Polarography and Manometry – principles and applications. Biosensors – Concepts and applications. Neutron diffraction and Electron diffraction – principle and applications.

Self study : Use of radioisotopes in the diagnosis and treatment of diseases; radiation health hazards Total 60 hrs

References : 1. Allen, J.P. (2008) Biophysical Chemistry, 1st Edition, Markono Print Media Limited, Singapore 2. Parthasarathy, B. K. (2007) Challenges and Opportunities in Nanotechnology, Isha Books, New Delhi 3. Charles, R., Cantor, I. and Schimmel, P.R. (2004) Biophysical Chemistry, Part II, W.H.Freeman & Co., New York. 4. Daniel, M. (2007) Basic Biophysics for Biologist, Agrobios, India. 5. Wilson, K. and Walker, J. (2012) Practical Biochemistry – Principles and techniques of Biochemistry and Molecular Biology, 7th Edition, Cambridge University Press, India 6. Hunt, G and Mehta, M. (2007) Nanotechnology Risk, Ethics and Law, Earthscan, London 7. Nolting, B. (2006) Methods in Modern Biophysics, 2nd Edition, Springer Publications, New Jersey. 8. Roshan, J. K. (2008) Advanced Biophysics, Anmol Publications Pvt, Ltd, New Delhi 9. Sharma, P.K. (2008) Origin and Development of Nanotechnology, Vista International Publishing House, New Delhi 10. Sheehan, D. (2009) Physical Biochemistry – Principles and Applications, 2nd Edition, John Wiley and Sons, USA. 11. Serdyuk, I.N., Zaccai, N.R. and Zaccai, J. (2007) Methods in Molecular Biophysics – Structure, Dynamics and Function, Cambridge University Press, India 12. Upadhay, A., Upadhay, K. and Nath, N. (2002) Biophysical Chemistry – Principles and Techniques, Himalaya Publishing House, Mumbai 13. Campbell,I.D, Biophysical Techniques(2012) John Wiley and sons, USA

Practicals I – Analytical Techniques in Biotechnology

Semester I Hours of Instruction / Week : 6 17MBTC05 No. of credits : 4

Objectives : 1. To develop an understanding of the range and uses of analytical methods in Biotechnology. 2. To develop practical skills in the procedures and instrumental methods applied in analytical tasks 3. To practice a problem-solving approach in analyzing various parameters

Experiment

1. Spectrophotometry – Preparation of standard curves using linear regression and 5 hrs assessment of linear ranges and reliability in spectrophotometry 10 hrs 2. Measurement of absorption spectra using spectrophotometer and nanospectro- photometer (demo) 6 hrs 3. Paper chromatography 6 hrs 4. Thin layer chromatography 7 hrs 5. Column chromatography – ion-exchange, adsorption and molecular sieving, HPLC and HPTLC(group experiments / demo) 7 hrs 6. Agar and agarose gel electrophoresis and 7 hrs Polyacrylamide gel electrophoresis (group experiment / demo) 14 hrs 7. 2-D gel electrophoresis and flow cytometry (demo) 8 hrs 8. Methods of cell lysis – osmotic / chemical / enzymatic lysis of the cells – monitoring cell lysis by observing release of cellular material and change in light scattering – mechanical rupture of cells – ultrasonic rupture. 7 hrs 9. Extraction of cellular materials into saline, buffers, solvents – precipitation from extracts. 7 hrs 10. Separation of cell organelles by ultracentrifugation. 6 hrs 11. Visit to well-equipped laboratories with analytical instruments

Total 90 hrs

References: 1. Kaur, H. (2001) Instrumental Methods of Chemical Analysis, PragatiPrakashanPublications, Pune 2. Sheehan, D. (2009) Physical Biochemistry – Principles and Applications, 2ndEdition, John Wiley and Sons, USA. 3. Wilson, K. and Walker, J. (2006) Practical Biochemistry – Principles and techniques of Biochemistry and Molecular Biology, 6th Edition, CambridgeUniversity Press, India.

Practicals II – Cell Biology and Microbial Techniques

Semester I Hours of instruction / week : 5 17MBTC06 No. of credits : 3

Objectives : 1. To understand the basic techniques in cell biology, cell count determination and cell size determination 2. To understand the principles of sterility and the use of physical and chemical methods of sterilization 3. To perform routine microbiological analysis of samples and interpret the data from microbiological analysis

Experiments

CELL BIOLOGY 1. Use of simple, compound and phase-contrast microscopes 5 hrs 2. Squash stain – Observation of mitotic chromosomes in root tips and meiotic chromosomes in flower buds. 5 hrs 3. Cell counting methods – use of hemocytometer – calibration of the ocular micrometer and measurement of average cell size and chromosome length. 5 hrs 4. Chromosomal banding techniques. 5 hrs MICROBIOLOGY 5. Preparation and use of glassware-cleaning solution – Sterilization – physical methods (dry heat, moist heat, incineration, radiation) – chemical methods (phenol, alcohol, formaldehyde, hypochlorite). 5 hrs 6. Preparation and selection of simple culture media. 5 hrs 7. Identification and enumeration of microorganism from air, water, soil, tooth scum, skin and body fluids. 5 hrs 8. Isolation of pure and axenic cultures – serial dilution, pour plate, spread plate, streak plate methods and stab culture techniques for long time storage. 5 hrs 9. Staining techniques – Gram, simple, acid fast, flagella, capsule and spore. 5 hrs 10. Microscopy of different organisms – bacteria, cyanobacteria, microalgae and fungi 5 hrs 11. Antibiotic sensitivity of microbes 5 hrs 12. Estimation of microbial growth by turbidimetry 5 hrs 13. Identification of unknown bacteria by biochemical tests 5 hrs 14. Extracellular enzyme activity of microbes 5 hrs 15, Immobilization of Saccharomyces cerevisiae and alcohol production 5 hrs 16. Visit to well-equipped laboratories with cell biology and microbiology facilities

Total 75 hrs

References: 1. Purohit, S.S. (2008) Microbiology: Fundamentals and Applications, 7th Edition, Agrobios, India.

2. Watson, J.D., Baker,T. A., Bell, S.P., Gan, A., Levine, M. and Losick, R. (2009) Molecular Biology of the Gene, 5th Edition, Pearson Education Inc. 3. Krebs, J.E. Goldstein, E.S. and Kilpatric, S.T. (2011) Lewin’s Genes X - Jones and Barlett Publishers. 4. Griffiths, A.J. F., Gelbard, W.M., Miller, J.H., Lewontin, R. C. (2000) Modern Genetic Analysis, W.H. Freeman and Company. 5. Saikia, R, Bezbaruah, R.L and Bora, T.C (2008) Microbial Biotechnology, New India Publishing agencies, New Delhi. 6. Cappuccino,J and Sherman, N. (2013) Microbiology: A laboratory manual, Tenth edition, Benjamin Cummings Publishers,USA. 7. Dubey,R.C. and Maheswari,D.K. (2010) Microbiology, Third Edition, S.Chand and Company Publishers, NewDelhi. 8. Bharti Arora and D.R Arora. (2007) Practical Microbiology, second edition, CBS. 9. Manideepa Sen Gupta and Mallika Sen Gupta (2016) Practicals in Microbiology, First Edition, Jaypee Brothers Medical Publishers

Genetics

Semester II Hours of instruction / week : 4 17MBTC07 No. of credits : 3

Objectives : 1. To teach the central concepts, principles and analytical methods used in classical, population, quantative and evolutionary genetics. 2. To discuss basic concepts of genetics, including the cell cycle, trait inheritance, mitosis / meiosis and crossing over. 3. To understand the types and effects of mutations of the genetic material

Unit I – Mendelism & Non-Mendelism 12 hrs Basic principles of inheritance – Mendel’s study of heredity – Monohybrid and Dihybrid crosses – Mendelian principles in Human genetics – pedigrees, segregation and genetic counseling. Extension of Mendelism – Incomplete dominance, codominance, epistasis, pleiotropy

Self study : Nature of genetic material

Unit II – Sex chromosomes 12 hrs Sex linked genes – sex determination – dosage compensation of X-linked genes, Variations in the number and structure of chromosomes – cytological techniques – polyploidy and aneuploidy – rearrangements of chromosome structure – Banding patterns in chromosomes

Self study: Chromosome structure and organization

Unit III – Genetic Linkage 12 hrs Crossing over and chromosome mapping in eukaryotes. Transformation, transduction and conjugation – gene mapping – genetic recombination in bacteria – generalized and site specific recombination

Self study: Fine structure of gene and regulatory elements

Unit IV – Mutation and DNA repair 12 hrs Classification of mutations and mutagens – molecular mechanism of mutation – expression of mutagenesis – gene mutation, Chromosome alteration and sister chromatid exchanges, lethals, transformation. Detection of DNA damage at molecular level – Ames test – DNA repair

Self study: Oncogene and tumor suppressor genes

Unit V – Transposable genetic elements and extra chromosomal inheritance 12 hrs Transposable elements in bacteria and eukaryotes, Retrotransposons – Mechanism of transposition. The genetics of mitochondria and chloroplasts – The genetic control of animal development and behavior

Self study : Fundamentals of population genetics

Total 60 hrs

References : 1. Krebs,J.E., Goldstein, E.S. and Kilpatrick,S.T. (2011) Genes X, Jones &Bartlett Publications, Massachusetts 2. Pierce,B.A. (2014) Genetics-A conceptual approach, fifth edition, W.H. Freeman & Company, New York 3. Griffiths, A.J., Wessler, S.R., Lewontin, R.C., Gelbart, W.M., Suzuki, D.T. and Miller,J.H. (2007) Introduction to Genetic analysis, 8th edition, W.H. Freeman and Company, New York. 4. Hartwell, L.H., Hood, L., Goldbug, M.L., Reynolds, A.E., Silver, L.M. and Veses, R.C.(2006) Genetics – from genes to genomes, 3rd Edition, McGraw Hill Higher Education, Boston. 5. Jeyanthi, G.P. (2009) Molecular Biology, MJP Publishers, Chennai. 6. Karp, G. (2008) Cell and Molecular Biology, 5th edition, John Wiley & Sons Inc., NewYork. 7. Klug, W.S. and Cummings, M.R. (2005) 3rd reprint, Concepts of Genetics, 7th edition, Dorling Kindersley (India) Pvt Ltd., New Delhi and Pearson Education, New York. 8. Lewin, B. (2008) Genes IX, Jones and Bartlett Publishers, Massachusetts. 9. Russell, P.J. (2006) Genetics, 2nd Edition, Pearson Benjamin Cummings, New York. 10. Strickberker, M.W. (2006) Genetics, 3rd Edition, Pearson Prentice Hall, New Delhi. 11. Purohit, S.S. (2008) Cell and Molecular Biology: Fundamentals and Applications, Agrobios, Jodhpur, India.

Animal Biotechnology

Semester II Hours of instruction / week : 3 17MBTC08 No. of credits : 3 Objectives : 1. To understand the principles and applications of animal cell culture 2. To understand the importance of stem cells and regenerative medicine 3. To know the methods involved in animal transgenesis 4. To understand the concept of xenotransplantation 5. To comprehend the beneficial effects of biotechnology on diagnosing and treating animal diseases

Unit I – Introduction 9 hrs Animal cell and tissue culture – history and scope. Qualitative and quantitative requirements of animal tissue culture. Role and importance of growth factors, types of culture media – natural and artificial media. Role of serum. Initiation of cell cultures – types – primary culture, cell lines, maintenance of cultures – monolayer and suspension cultures – preservation and authentication.

Self study : Layout of animal tissue culture laboratory and sterilization methods

Unit II–Modifications and applications of cultured cells 9 hrs Large-scale culture of cell lines – Scaling up of animal cell cultures, genetic modification – transfection of animal cells and markers to select transformants. Cellular senescence – measurement of cell death, cytotoxicity and viability assays.

Self study : Growth kinetics of cell culture; embryo and organ culture

Unit III – Stem cell culture 9 hrs Stem cell culture – Origin, types – adult, embryonic culture and applications, Adult stem cells in clinical trials – reprogramming somatic cells into induced pluripotent stem cells – direct reprogramming of cells. Stem cells in livestock, Three dimensional culture; tissue engineering – stages, support materials, cell sources, applications in regenerative medicine; cell fusion and its applications.

Self study : Ethical aspects in stem cell research; Tissue culture as screening system for cytotoxicity and diagnostics tests

Unit IV – Cloning and its applications 9 hrs Somatic cell nuclear transfer – Genetic engineering of animal cells – embryo technology, gene knockout technologies and mice model for human genetic disorder. Cloning of animals – principles. Human therapeutic cloning – the relationship between stem cells and cloning – xenotransplantation, Model organisms in Biotechnology and Biomedical sciences, developments in molecular markers in livestock – developments in livestock genomics and applications of molecular markers

Self study : The Dolly story – cloning of pets and endangered species; Ethical aspects of cloning; IVF and artificial insemination

Unit V – Animal transgenesis 9 hrs Animal transgenesis – principles and methods – biopharming in animal transgenesis, disease resistant transgenic animals and transgenesis in aquaculture. Pest management using juvenile hormone analogs, biocontrol agents, Pheromones, Biotechnology of silkworms, insect cell culture and its products.Marine Biotechnology – therapeutics from marine organism resources. Nutrigenomics,metabolomics and its role in animal production

Self study : Animal models for disease and injury Total 45 hrs

References: 1. Freshney, R.I. (2005) Culture of Animal Cells – A Manual of Basic Techniques, 5thEdition, John Wiley and Sons, New York. 2. Gupta, P.K. (2006) Biotechnology and Genomics, 1st Edition, Rastogi Publications,Meerut. 3. Masters, R.W. (2000) Animal cell culture – A practical Approach, 3rd Edition, UniversityPress, Oxford. 4. Purohit, S.S. (2006) Biotechnology: Fundamentals and Applications, Agriobios, India 5. Sathyanarayana, U. (2005), Biotechnology, 2nd Edition, Books and Allied Ltd., Calcutta 6. Davis, J.M. (Ed.) (2005) Basic Cell Culture, 2nd Edition, A Practical Approach,Oxford University, New York. 7. Portner, R. (2007) Animal Cell Biotechnology, Methods and Protocols, 2nd Edition,Humana Press, New Jersey. 8. Butler, M. (2004) Animal Cell Culture Technology – Basics, 1st Edition, AcademicPress, New York. 9. Ranga, M.M. (2007)Animal Biotechnology, 3rd Edition, Agrobios, India. 10. Potten, C.S. (2006) Stem cells - Academic Press, UK. 11. Srivastava, A.K., Singh, R.K., Yadav, M.P. (2009) Animal Biotechnology, Oxford andIBH Publishing Company. 12. Singh. B, Gautam, S.K and Chauhan M.S. (2015) Textbook of animal Biotechnology, The Energy Resource Institute,TERI press, New Delhi, India

Bioinformatics

Semester II Hours of instruction / week : 3 17MBTC09 No. of credits : 3

Objectives : 1. To build a strong background in bioinformatics 2. To introduce the students to the biological databases and the major bioinformatics tools 3. To master the computational techniques used biological sequence and structure analysis 4. To understand the potential applications of bioinformatics

Unit I – Introduction to bioinformatics 9 hrs Biological databases – features and layout – sequence databases, structure databases, specialized databases – primary and secondary databases – genome databases, microbial and cellular databanks, model organism databases – database search and retrieval tools – Entrez, SRS and other tools.

Self study : Structural classification of proteins (SCOP, CATH and other classifications)

Unit II – Sequence analysis 9 hrs Need and importance for sequence analysis – pairwise alignment – dot plot, dynamic programming – global (Needleman-Wunsch) and local (Smith-Waterman) alignment algorithms – scoring matrices – gap penalties – substitution matrices – need, types – PAM and BLOSUM – pairwise alignment tools – BLAST, FASTA. Multiple alignment – Clustal – NJ plot – phylogenetic trees – parts, types – construction and analysis of phylogenetic trees – PHYLIP.

Self study : Variations of BLAST – PSI-BLAST, PHI-BLAST, bl2seq

Unit III – Bioinformatic tools 9 hrs Analysis of nucleotide sequences – detecting ORFs, finding genes, constructing restriction maps, designing primers and probes, calculating Tm, theoretical translation of coding region – prediction of Secondary structure of RNA. Bioinformatic tools to analyze protein sequences – finding protein parameters – tools for peptide cleavage and mapping – prediction of secondary structure of proteins.

Self study : Programs used to analyze nucleotide and protein sequences

Unit IV – Genomics and Proteomics 9 hrs Structural, functional and comparative genomics – DNA microarrays – present status and future prospects. Proteomics – traditional proteomics vs modern proteomics – 2-D gel electrophoresis, mass spectroscopy, MALDI-TOF and other methods of analysis. Protein microarrays – present status and future prospects.

Self study : Modifications of DNA microarrays – transcriptomics

Unit V – 3-D structural analysis of biomolecules 9 hrs Molecular visualization tools – RasMol, Deep View.– homology modelling of proteins, Molecular modelling (elementary concepts of force field, stereodynamics and energy minimization) – prediction of ligand binding – design of best-fitting ligands – Computer-aided drug design – steps involved – lead compound identification, optimization, energy minimization, ADME studies, combinatorial chemistry and other approaches – QSAR – high throughput screening

Self study : Other visualization tools – Chime, WebLab Viewer, MolMol

Total 45 hrs

References : 1. Attwood, T. and Parry, D. (2002) Introduction to Bioinformatics – Pearson Publication, Asia 2. Claverie, J.M. and Notredame, C. (2003) Instant Notes in Bioinformatics, Wiley Publishing Inc., New York. 3. Claverie, J-M. and Notredame, C. (2003) Bioinformatics – A Beginner’s guide, 1st Edition –Wiley Publishing Inc, New York. 4. Gibas, C. and Jambeck, P. (2001) Developing Bioinformatics Computer Skills, Schroff. Publishers & Distributors Pvt. Ltd. 5. Krane, D.L. (2006) Fundamental Concept of Bioinformatics, Pearson Publication, Asia. 6. Lesk, A. (2007) Introduction to Bioinformatics, Oxford University Press, UK. 7. Mount, D. (2006) Bioinformatics, Sequence and Genome Analysis, CBS. 8. Simpson, R.J. (2003) Protein and Proteomics, Cold Spray Harbour Laboratory, New York. 9. Tisdall, J. (2003) Beginning Perl for Bioinformatics, Schroff Publishers & Distributors Pvt. Ltd. 10. Dubitzky, W. (2007) Fundamentals of Data mining in Genomics and Proteomics, Springer Publication, New Jersey. 11. Roy, D. (2009) Bioinformatics, Narosa publishing house, India. 12. Polanski, A. and Kimmel, M. (2010) Bioinformatics, Springer Pvt. Ltd. 13. Lacroix, Z. and Critchlow, T. (2009) Bioinformatics: Managing Scientific Data – Mayan Kaufmann Publishers, San Francisco. 14. Gromiha, M.M. (2010) Protein Bioinformatics: From Sequence to Function, Academic Press, New Delhi. 15. Ramsden, J.J. (2009) Bioinformatics: An introduction, Kluwer Academic Publishers.

Recombinant DNA Technology

Semester II Hours of instruction / week : 3 17MBTC10 No. of credits : 3

Objectives : 1. To understand the concept of recombinant DNA technology for gene manipulation 2. To understand the gene manipulation methods and their applications 3. To explain the general principles of generating transgenic organisms 4. To analyze the ethical, legal and social issues involved in gene manipulation

Unit I Tools for gene manipulation 9 hrs General introduction. Basic steps in gene cloning: Isolation and characterization of DNA fragments; DNA manipulative enzy2mes and their applications – restriction mapping. Vectors in gene cloning – Multipurpose cloning vectors, broad host range vectors (plasmids, bacteriophages, cosmids); expression vectors (Lambda gt 11, Lambda ZAP, EMBL); plant transformation vectors (Ti plasmids); vectors for cloning large fragments (YAC, BAC), Methods of ligating – cohesive and blunt-end ligation, homopolymer tailing, linkers and adaptors for ligation. Methods of gene transfer – calcium phosphate co- precipitation, lipofection, viral mediated transfer, microinjection. Self study : Isolation of DNA from plant and animal tissues, electrophoretic analysis

Unit II Gene cloning 9 hrs Libraries – Construction of Genomic, cDNA, subtractive and EST libraries. Identification and characterization of insert DNA fragments, transformation, selection and screening strategies for recombinants and transformants – antibiotic resistance, blue-white selection, PCR, blotting, probe preparation, hybridization and autoradiography, immunological screening. Vector construction – transformation – selection – agrobacterium mediated gene transfer and selection using GFP Self study : Southern and Northern blotting; Using DNA fingerprinting in forensics – case studies in paternity suits, rape convicts, identification of mutilated dead bodies, etc.

Unit III Genome projects 9 hrs Genome Sequencing - Sangers sequencing, next generation sequencing Bioprojects – Human Genome Project and Rice Genome Project, mapping of the genome, sequencing approaches, annotation and applications (C4Rice). Self study : Personal genomes, Ethical, legal and social issues of genome projects

Unit IV Application of genetic engineering technology for human welfare 9 hrs Producing useful molecules (recombinant proteins in bacteria, yeast, plants, insects and mammals, cell cultures – production of withanolides) Improving agronomic traits (development of biotic and abiotic resistant crops, improving keeping quality and value added crops). To prevent and cure disease – gene therapy, DNA vaccines. Self study : Steps involved in the development of golden rice; Bt Cotton; Flavr Savr tomato (as case studies of transgenesis)

Unit V Biosafety and IPR 9 hrs Biosafety regulation, norms of releasing genetically engineered organisms. National and International regulatory bodies. Intellectual Property Rights and types, Patenting. Self study : Patenting laws prevalent in India in relation to the other countries Total 45 hrs References: 1. Brown, T.A. (2006) Gene cloning – An Introduction, 5th Edition, Blackwell Publishing Company, USA. 2. Dale,J.W and Schantz, M.V. (2007) From Genes to Genomes: Concepts and Applicationsof DNA technology, 2nd edition, John Wiley and Sons, UK 3. Glick, B.R. and Pasternak, J.J. (2003) Molecular Biotechnology, 3rd Edition, AmericanSociety for Microbiology, USA. 4. Mandoiu, I and Zelikousky A. (2016) Computational methods for Next Generation Sequencing Data Analysis, 1st Edition, John Wiley & Sons. UK. 5. Primrose, S.B., Twyman, R.M. and Old, R.W. (2006) Principles of Gene Manipulation, 7th edition, Blackwell Publishing Company, USA. 6. Kreuzer, H. and Mausey, A. (2001) Recombinant DNA and Biotechnology – A guide for student, 2nd edition, ASM Press, Washington.

Practicals III – Animal Biotechnology and Bioinformatics

Semester II Hours of instruction / week : 4 17MBTC11 No. of credits : 3

Objectives : 1. To learn the basic principles of animal tissue culture 2. To understand the methods of handling primary cultures and cell lines 3. To work with basic bioinformatics tools for biological sequence analysis 4. To familiarize with the use of bioinformatics tools for biological structure analysis

Experiment ANIMAL BIOTECHNOLOGY 1. Understanding the layout of the Animal Cell Culture Laboratory – maintenance of aseptic conditions 2 hrs 2. Sterilization techniques – preparation of media – filter sterilization – media storage – thermal inactivation of serum 2 hrs 3. Sterility tests – Testing for bacteria, mycoplasma, viruses 4 hrs 4. Cell counting – determining cell number using hemocytometer – dilution of cell suspension to obtain desired cell number 4 hrs 5. Determination of cell survival – trypan blue exclusion method 2 hrs 6. Primary culture – establishment of chick embryo fibroblast culture 4 hrs 7. Establishment of organ culture 4 hrs 8. Establishment of lymphocyte culture – inducing mitosis in suspension culture 9. Maintenance of cell lines 4 hrs 10. Staining of cell cultures and observation under microscope 2 hrs 11. Visit to well-equipped Animal facility 2 hrs

BIOINFORMATICS 11. Introduction to biological databases 2 hrs 12. Use of database search tools – Entrez, SRS 2 hrs 13. Pairwise alignment of sequences – BLAST and FASTA – near and far relative sequence identification using BLAST 2 hrs 14. Multiple alignment – Clustal – NJ plot 2 hrs 15. PHYLIP – construction of phylogenetic trees – rooted and unrooted trees 2 hrs 16. Molecular visualization – downloading atom coordinate file from pdb – using the coordinate file to view the molecules using molecular visualization tools – RasMol, Deep View (Spdbv) 4 hrs 17. Protein analysis tools – ExPASy 4 hrs 18. EMBOSS tools for sequence analysis 4 hrs 19. Gene finding programs – GeneMark, GeneScan 20. Biology Workbench – retrieval of sequences, alignment of sequences, 1 hr phylogenetic tree building – rooted and unrooted trees – alignment presentation method – secondary structure prediction of proteins 21. Computer-aided drug design and analysis – demonstration of the modules of 3 hrs Schrödinger Drug Design Suite 4 hrs

Total 60 hrs

References: 1. Ye, S.Q. (2010) Bioinformatics: A Practical Approach - CRC press, Taylor & Francis Group, UK. 2. Davis, J.M. (2002) Basic Cell Culture, 2nd Ed. - Oxford University press, New York. 3. Bourne, P.E. and Weissig, H. (2003) Structural bioinformatics, 2nd Ed. – Wiley Publications, U.S.A. 4. Periera – Raja, F (2005) Animal Biotechnology - Dominant Publishers and Distributors, New Delhi. 7. Butterworth-Heinemann (2004) In vitro cultivation of animal cells, Elsevier India Private Limited. 8. Gangal, G. (2007) Principles and Practice of Animal Tissue Culture, University Press (India) Private Limited.

Practicals IV – Recombinant DNA Technology

Semester II Hours of instruction / week : 6 17MBTC12 No. of credits : 3

Objectives : 1. To become proficient in isolating the DNA, RNA and protein components of cells 2. To understand the basic techniques in recombinant DNA technology 3. To learn to amplify the DNA using PCR and to study the polymorphisms 4. To learn the blotting techniques

Experiment 1. Isolation and estimation of DNA, RNA and protein 5 hrs 2. Isolation and purification of plasmid DNA i. Mini preparation ii. Purification by LMP agarose 5 hrs 3. Preparation and transformation of competent E.coli 5 hrs 4. Restriction enzyme analysis – restriction mapping 5 hrs 5. Agarose gel electrophoresis and PAGE of DNA and RNA 10 hrs 6. Southern blotting – RFLP analysis 5 hrs 7. Gene cloning – cloning a DNA fragment in Bluescript vector – Blue-White selection of transformed colonies – Characterization of transformants – Insertional inactivation 10 hrs 8. Isolation of DNA from bacteriophage 10 hrs 9. Isolation, estimation and restriction analysis of phage DNA. 10 hrs 10. Preparation of helper phage and its titration 10 hrs 11. Extraction, Purification and analysis of RNA i. Isolation of total RNA ii. Isolation of cytoplasmic RNA iii. Electrophoresis of RNA on denaturing gels 15 hrs 12. PCR and RAPD 13. Visit to well-equipped laboratories dealing with rDNA technology Total 90 hrs

References: 1. Agarwal,S.(2008) Techniques in Molecular Biology,1st edition, international distributing co,Lucknow, India. 2. Debnath,M (2008) Tools and techniques of biotechnology, 2nd edition, Pointer publishers, Jaipur, India.

Immunology and Immunotechnology

Semester III Hours of instruction / week : 4 17MBTC14 No. of credits : 3

Objectives 1. To have a key understanding of the components of the immune system, their functions and interactions. 2. To understand the immune mechanisms involved in disease conditions. 3. To impart knowledge on the latest techniques in immunology.

Unit 1 – The Immune System 12 hrs History of immunology - Cells and Organs of the immune system-structure and functions of the cells of the lymphoid and myeloid lineages and primary and secondary lymphoid organs. Differentiation and Generation of T-cells and B-cells from bone marrow. B-cell receptors and T-cell receptors. Stem cells - sources, types, properties & applications. Antigens – types and characteristic features, antigenicity & immunogenicity, epitopes, cross reactions. Haptens and mitogens. Antibodies – basic structure, types of immunoglobulins- structure, properties and functions, immunoglobulin super family. Complement cascades - components, mechanism of Classical, Alternative and other pathways, biological consequences of complement cascades and their fragments.

Self study: History of immunology

Unit 2 – Immunity and Immune Response 12 hrs Types of immunities -Innate and Acquired. Immune response-Humoral and Cellular immune responses-their characteristics & effector mechanisms. Regulation of immune response.Immune response to infections-bacterial, viral, fungal and others. Immunodeficiency diseases-primary and secondary.

Self study: Immunodeficiency diseases

Unit 3 – Hypersensitivity and Autoimmunity 12 hrs Hypersensitivity – classification, causes, mechanism, clinical manifestations, diagnosis and treatment of Types I – IV hypersensitivities. Autoimmunity- classification, spectrum of autoimmune diseases, overlap, pathogenesis, diagnosis and treatment of autoimmune diseases.

Self study: Classification and spectrum of autoimmune diseases

Unit 4 – Immunogenetics and Transplantation Immunology 12 hrs Immunogenetics- antibody diversity- theories of antibody formation, organization of immunoglobulin genes and their expression, class switching. Major Histocompatibility Complex- organization, structure and functions of MHC and HLA genes and non-MHC molecules. Gene products. Role in antigen processing and presentation. Role of MHC in transplantation, disease susceptibility and resistance and genetic control of primary histocompatibility. Transplantation- types of grafts, principles involved and mechanism of transplantation of various organs, immunosuppressive therapy, graft rejection.

Self study: Organization of immunoglobulin genes and their expression, class switching

Unit 5 – Immunotechniques 12 hrs Principles of antigen-antibody interactions- characteristics features. Precipitation techniques-immunodiffusion and immuno electrophoresis. Agglutination techniques- haemagglutination, ABO blood grouping & Rh typing. Tagged assays- RIA, ELISA, immunofluorescence, immunoblotting, immunoelectron microscopy. Isolation of pure antibodies, Assays for complement, FACS, Flow cytometry. Antibody engineering - Hybridoma technology- polyclonal and monoclonal antibody production and their applications. Recombinant antibody production. Vaccine production- types of vaccines, principles of vaccine production, production of conventional and modern vaccines, new vaccine strategies and vaccines under development. Adjuvants- types and properties.Vaccination strategies, immunization schedules.

Self study: New vaccine strategies and vaccines under development.

Total – 60hrs

References 1. Peter J. Delves, Ivan Maurice Roitt, Seamus J.Martin and Deninis Burton (2016). Essential Immunology, 13 thedition ,Wiley Blackwell Scientific Publications, London. 2. Fathimunisa Begum (2014). Immunology, PHI Learning. 3. Judy Owen, Jenni Punt and Sharon Stanford, (2012), Kuby Immunology,7th edition, W.H.Freeman and Company, New York, USA. 4. Ian R.Tizard (2012), Veterinary Immunology, 9th edition, W.B.Saunders Co., Philadelphia. 5. Madhavee Latha P. (2012). Textbook of Immunology, 1st edition, S. Chand Publishers. 6. Basir Seemi Farhat (2012). Textbook of Immunology, 2nd edition, PHI Learning. 7. Talaro, K.P, Barry Chess and Talaro,A. (2011). Foundations in Microbiology, 8th edition, McGraw Hill Publishers , New York. 8. Hannigan, B.M. (2010). Immunology, 2nd edition, Viva Books 9. Kuby, J. Goldsby,R.A., Kindt,T.J. and Osborne, B.A. (2007). Immunology, 6th edition, W.H.Freeman and Company, NewYork, USA. 10. Rao, C.V. (2006). An Introduction to Immunology, 2th edition, Narosa Publishing House, Delhi, Chennai, Mumbai, Kolkata.

Plant Biotechnology

Semester III Hours of instruction / week : 4 17MBTC15 No. of credits : 3

Objectives : 1. To understand the principles and organization of plant genome 2. To know the techniques of analysis of plant genome 3. To understand the concepts of plant transgenesis and its applications 4. To understand the concepts and uses of plant tissue culture and plant Biotechnology

Unit 1– Plant genome organisation 12hrs Plant genome organization, Gene families in plants, RNA editing, Cytoplasmic male sterility, Photosynthesis - Light harvesting complexes, mechanism of electron transport, CO2 fixation –C3 and C4 pathway, CAM. Regulation of photosynthesis, photorespiration. Self study :Organisation of chloroplast genome and mitochondrial genome. Unit 2 – Nitrogen fixation and plant physiology 12hrs Nitrogen fixation- Basic concepts, nif genes and their regulation, potential scope in crop improvement nitrate and ammonia assimilation. Phloem transport, Plant hormones – Biosynthesis, storage, breakdown and transport - physiological effects and mechanism of action. Flower development – seed development and germination. Molecular biology of plant stress response – biotic and abiotic stresses. Self study:Phytochromes, cryptochromes and phototrophins. Unit 3 – Gene mapping 12hrs Gene mapping-Molecular markers and marker assisted selection – morphological,biochemical and molecular markers - Concept of physical and genetic maps, restriction maps, DNA fingerprinting, FISH, chromosome walking, chromosome jumping chromosome landing approach and map based cloning. Mapping and cloning of plant genes. Self study : Tagging - types – marker assisted and transposon tagging. Unit 4 – Genetic engineering of plants 12hrs Genetic engineering in plants - Strategies for cloning genes from plants, cloning methods based on DNA insertions,Plant transformation vectors – Ti plasmids, viral vectors. Selectable markers – reporter genes and promoters used in plant vectors.Direct transformation – by physical methods, Marker free transformation, Chloroplast transformation – Applications of plant transformation –Gene silencing in Transgenic plants – antisense technology (delayed ripening) – Terminator technology. Self study : Management aspects of genetic engineering – Ethical issues – IPR, TRIPS.

Unit 5 – Plant tissue culture 12hrs Plant tissue culture–In vitro culture of plants – Concept of totipotency– types of in vitro culture – meristem culture, organ culture, anther and pollen culture.Somatic embryogenesis – artificial seed –protoplast culture and protoplast fusion, embryo culture and embryo rescue. Embryogenesis and organogenesis. Production of secondary metabolites using cell culture – Biotransformations . Self study :Initiation, maintenance (callus, organ cultures) and applications of in vitro cultures.

Total – 60hrs

References: 1. Balbas.P&Lorence.A (2007), 2nd Edition, Methods in Molecular Biology, Recombinant Gene Expression, Reviews & Protocols, Human Press, New Jersey. 2. Buchanan, B.B., Gruissem,W. and Jones, R.L.,(2002), 1st Edition, Biochemistry and Molecular Biology of Plants, American Society of Plant Physiologists, Rockwille. 3. Gautam,N.C.(2006), Plant Biotechnology, Shree Publishers. 4. Heldt HW, (2005), 3rd Edition, Plant Biochemistry,Elseveir Academic Press Publication, USA. 5. Jeyanthi, G.P (2009), Molecular Biology, MJP Publishers, Chennai 6. Pareek, L.K, (2006), Trends in Plant Tissue Culture and Biotechnology,Agrobios,India. 7. Razdan, M.K. (2007), Introduction to Plant Tissue culture, II edition, Oxford and IBA Publications Co Pvt Ltd. 8. Srivastava, H.S. (2006), Plant Physiology, Biochemistry and Biotechnology,Rastogi Publications, Meerut. 9. Chawla,H.S. (2004) Introduction to plant Biotechnology, Science Publishers, Plymouth,U.K.

Enzymes and Bioprocess Technology

Semester III Hours of instruction / week : 4 17MBTC16 No. of credits : 3 Objectives : 1. To understand the mechanism of enzyme action, kinetics of enzyme and the applications in various fields 2. To know the enzyme extraction, purification and production 3. To understand the importance of principles of fermentation techniques 4. To know the large scale production of commercially important products

Unit 1 – Introduction to Enzymes, Nomenclature and kinetics 12 hrs Enzyme kinetics- Kinetics of single substrate and multisubstrate enzyme- catalyzed reaction Michaelis-Menten equation, Lineweaver Burk plot, Eadies- Hofstee plot and direct linear plots, kinetics of Enzyme inhibitions: competitive - noncompetitive and uncompetitive inhibition. Self study: Factors influencing the rate of enzyme reactions. Unit 2 – Mechanisms of enzyme catalysis 12 hrs Types of enzyme action- acid-base, electrostatic and covalent catalysis lysozyme, chymotrypsin, Role of metal ions in the activation of enzymes. Enzyme specificity - investigations of active site structure-evidence of ES complex, nucleophilic and electrophilic attack.

Self study: Allosteric enzymes and isoenzymes. Unit 3 – Extraction and purification of enzymes 12 hrs Extraction of soluble enzymes and membrane bound enzymes. Purification and characterization of enzymes from natural sources. Immobilized enzymes- recombinant DNA technology in enzyme production- fusion proteins containing enzymes and their application- enzymes in bioconversions. Self study: Biotechnological applications of enzymes Unit 4 – Basic principles in Bioprocess 12 hrs Growth kinetics-Batch, Fed-batch and Continous culture. Screening of industrially important microbes- Isolation, preservation and improvement of strains for increased yield-primary metabolite and secondary metabolite.Media formulation and sterilization Bioreactors: dynamics and stability- ideal bioreactors, types of reactors: CSTR, Tower, Jet Loop, Air Lift, PFR, Bubble column, Packed bed Self study: Production of antibiotics- penicillin, streptomycin. Unit 5 – Aeration, Agitation, Bioprocess variable control and downstream processing 12 hrs Transport in cells, Transfer resistances and mass transfer coefficients-rate of oxygen transfer, Determination of oxygen transfers coefficients, heat transfer coefficients. Bioprocess control and monitoring variables : temperature agitation, pressure, and pH. Online measurement. ON/OFF control, PID control- computers in bioprocess control systems. Downstream processing- Steps involved in harvesting any product Self study: Chromatography techniques Total – 60hrs

References:

1. Palmer, T. (2004). Biochemistry and Molecular Biology by Understanding enzymes, Fourth edition. 2. Stanburry, P.F.,Whitaker, A.and Hall, S.J. (2013) Principles of Fermentation Technology. 3. Paulline M.Doran, (2005), Bioprocess Engineering Principles, Elsevier Publication, USA. 4. El-mansi, E.M.T., Bryce, C.F.A., Demain, A.L., Allman, A.R (2007), Fermentation Microbiology and Biotechnology, 2nd edition, Taylor and Francis. 5. Khan, M.Y. and Farha Khan (2014) Principles of Enzyme Technology , PHI learning, New Delhi.

Pharmaceutical Biotechnology

Semester III Hours of instruction / week : 4 17MBTC17 No. of credits : 3

Objectives: 1. To learn about biopharmaceuticals and its importance 2. To provide an overview on drug interactions and efficacy 3. To understand the process of drug development and validation

Unit I – Introduction 12 hrs Scope of pharmacology – sources, nature and classification of drugs – dosage forms and routes of drug administration – factors influencing dosage and drug action – absorption, distribution, metabolism and excretion of drugs – drug action – principles – protein targets – drug receptors – drug specificity. Drug receptor interactions – drug antagonism and adverse drug reactions.

Self study : Metabolism of drugs – phase I and phase II reactions

Unit II – Drug Development and Delivery 12 hrs Drug development – sources of biopharmaceuticals – impact of genomics, proteomics and related technologies on drug discovery and development – upstream processing – cell culture, plant, animal, microbial and other systems – pharmacogenetics – process validation Drug delivery system – concepts and advances – NDDS – oral, pulmonary, nasal, transmucosal amd transdermal.

Self study : Distribution of drugs and biological action

Unit III – Testing biopharmaceuticals 12 hrs Testing biopharmaceuticals – phases of preclinical and clinical studies – pharmacokinetics – drug absorption, distribution, biotransformation and excretion. Pharmacodynamics –drug receptor interactions and dose response relationship – Toxicity studies – acute and chronic exposures – factors influencing toxicity.

Self study : Quantitative pharmacokinetics

Unit IV– Product validation 12 hrs Product analysis and validation – protein based contaminants and its detection – immunological approaches to detect contaminants – endotoxins and other pyrogenic contaminants, validation of recovery and purification processes.

Self study : Factors affecting drug safety and efficacy

Unit V – Drug safety and IPR 12 hrs Drug safety and regulations – National authorities for drug regulations – FDA rules and regulatory issues and product approval for biopharmaceuticals. Intellectual Property Rights and patent – process patent and product patent.

Self study : Global Regulatory Guidelines

Total 60 hrs

References: 1. Satoskar, R.S and Bhandarkar, S.D. (2000) Pharmacology and Pharmacotherapeutics, 13th edition, Vol. I and II, Popular Prakeshan PVT Ltd, Mumbai. 2. Tripathi, K.D. (2003) Essentials of Medical Pharmacology, 5th edition, Jaypee brothers medical publishers, New Delhi. 3. Rang, H.P., Dale, M.M., Ritter, J. and Flower, R.J. (2007) Pharmacology, 6th edition, Churchill Living Stone Elsevier. 4. Barar, F.S.K. (2013) Text Book of Pharmacology, 1st edition, S.Chand and Company Pvt. Ltd. 5. Brenner, G.M. and Stevens, C.W. (2010) Pharmacology, Reed Elsevier India Pvt. Ltd. 6. Sharma, P.D. (2003) Toxicology, 2nd edition, Rastogi Publications, Meerut.

Practicals V – Immunotechnology and Plant Biotechnology

Semester III Hours of instruction / week : 5 17MBTC18 No. of credits : 3

Objectives: 1. To develop the skills of the students in the area of Immunotechnology 2. To learn various techniques like developing diagnostic tests, characterization of lymphocytes, purification of antigens, antibody engineering etc. 3. To learn about the several methods used in plant transgenesis, including protoplast culture. 4. To learn the use of Agrobacterium and the Ti plasmid as a gene vector

Immunotechnology 1. Purification and characterization of antibodies- Purification by 12 hrs ammonium sulphate precipitation, dialysis and chromatographic techniques. Characterization of T and B lymphocytes - lymphocyte subset identification and enumeration 2. Antigen – antibody reactions: Heamagglutination, hemolysis, precipitin 12 hrs ring test, Immunodiffusion - single radial, double radial 3. Immunoelectrophoresis - counter current, rocket, complement fixation 15 hrs test, ELISA, plaque forming cell assay

Plant Biotechnology 4. Plant Tissue culture: Media preparation, Surface sterilization, 12 Hrs Micropropagation, callus culture, organogenesis, Embryo culture 5. Protoplast preparation: Isolation and purification of protoplasts - 12Hrs Viability test for protoplasts - Protoplast culture - Direct transformation of protoplasts by electroporation 6. Tumor induction - in plants by Agrobacterium, introduction of binary 12 hrs vectors into Agrobacterium by triparental mating, Leaf disc transformation using Agrobacterium - Direct transformation of plant tissues by micro projectile bombardment. 8. Fiel7. Field visit to vaccine production units Total 75 hrs References: 1. Wilson, K. and Walker, J. (2006) Practical Biochemistry – Principles and techniques of Biochemistry and Molecular Biology, 6th Edition, CambridgeUniversity Press, India. 2. Kuby, J. Goldsby,R.A., Kindt,T.J. and Osborne, B.A. (2007). Immunology, 6th edition, W.H.Freeman and Company, NewYork, USA.

Practicals VI – Enzymes and Bioprocess technology

Semester III Hours of instruction / week : 6 17MBTC19 No. of credits : 4

Objectives :  To learn fermentation and its types and to isolate antibiotics from microbes  To get hands-on training in isolating the soil microbes and extraction of metabolites  To isolate and purify industrially important enzymes from the microbes  To increase enzyme efficiency by adopting immobilisation methods

Experiment 1. Components and Design of bioreactor (Demonstration) 6hrs 2. Production of biomass by batch fermentation 10hrs 3. Measurement of biomass 10hrs 4. Standardisation of culture conditions 10hrs 4. Production of antibiotics at labscale 8hrs 5. Enzyme immobilisation and checking enzyme efficiency 9hrs 6. Isolation of starch degrading microorganisms 9hrs 7. Isolation and assay of amylase and protease from soil bacterium and 9hrs fungus 8. Partial purification of enzymes by ammonium sulphate and acetone 9hrs precipitation methods – purification table construction 9. Enzyme kinetics – MM and LB plot – Inhibition by Dixon plot 10hrs 10. Visit to biotechnology product producing units Total – 90hrs

References :

1. Cappuccino and Sherman, (2005) Microbiology : a laboratory, Seventh Edition, Published by Pearson Education Inc. And Dorling Kindersley Publishing Inc. 2. Dubey, R.C. and Maheshwari, D.K. (2007) Practical Microbiology, Published by S. Chand Publications. 3. Palmer, T. (2004). Biochemistry and Molecular Biology by Understanding enzymes, Fourth edition.

Environmental Biotechnology (Self study)

Semester III Hours of instruction / week : 1 17MBTC20 No. of credits : 4

Objectives 1. To understand the basic concepts of ecosystem and waste management 2. To realize the importance of microbes as a source of food, biomass and fuel 3. To know the exploitation of microbes in remediation

Unit 1 Concept of Ecology and Ecosystem 3 hrs Environmental pollution-water, soil, air, noise and thermal. Biogeochemical cycles. Global environmental problems – Green house effect, reforestration through micropropagation, biodiversity, species conservation. Treatment of Waste water from distillery, dairy and tannery industries –parameters – BOD, COD, TSS, TDS - physical, chemical and biological wastewater treatment - primary, secondary and tertiary treatment - Solid waste management.

Unit II Biomass 3 hrs Plant biomass - Cellulose, starch, pectin, gum materials - Animal biomass - chitin, milk whey, Slaughterhouse wastes - Microbial biomass - algal blooms - in fresh and sea waters Fungal - Mushrooms, yeasts and bacterial fermentation biomass wastes . Concepts of single cell proteins - probiotics and their applications - Biomass feed stocks to fermentations.

Unit III Biofuels 3 hrs Microbial production of fuels: alcohols, hydrogen and methane. Microbial production of polymers (xanthan gums) Renewable and non-renewable energy sources - Green technology - Biofuels, biogas, bioethanol.

Unit IV Biodegradation of Xenobiotic compounds 3 hrs Organisms involved in degradation of chlorinated hydrocarbons - substituted simple aromatic compounds - polyaromatic hydrocarbons, pesticides, surfactants and microbial treatment of oil pollution. Concepts of bioremediation in-situ and ex-situ, Bioremediation of toxic metal ions – biosorption and bioaccumulation principles - Concepts of phytoremediation. Biomining - extraction and recovery of metals from ores and solutions using microbes; Biofertilizers.

Unit V Disaster management 3 hrs Types of environmental hazards and Disasters; Natural - volcanic eruption, earthquakes, landslides, cyclones, lightning, hailstorms; Man Induced Hazards - Soil erosion, chemical hazards, sedimentation problems, biological hazards. Disaster management - pre-disaster stage (preparedness), emergency stage, post disaster stage (rehabilitation); Integrated approach- role of Institutions and Media. Total – 15 hrs

References: 1. Ghosh, G.K.(2007), Disaster Management, 1st edition, Delhi 2. Edurado ,D (2008) Microbial Biodegradation: Genomics and Molecular Biology, Spain 3. Wang, L.K. (2010), Environmental Biotechnology, 1st edition, A Product of Humana Press. 4. Dubey,R.C. (2010) A textbook of Biotechnology, S.Chand and Company Ltd, New Delhi 5. Saikia,R., Bezbarrah,R.L.,Bora,T., (2008) Microbial Biotechnology, New India Publishing agency, New Delhi

Food biotechnology and nanobiotechnology

Semester IV Hours of instruction / week : 3 17MBTC22 No. of credits : 3

Objectives :  To introduce to the students, the various concepts and opportunities in the emerging field of nanobioscience.  To familiarise the students with the important concepts applicable to nanobiotechnology devices and applications.

Unit 1 Introduction to the nanoworld 9hrs. Biocompatibility – principles involved – Applications. Nanomaterials – Preparation of nanomaterials – top-down and bottom-up approaches, examples – Properties of nanoparticles Varieties of nanoparticles – quantum nanodots, Au, Ag, TiO2, SiO2, NiO, CO60, carbon nanotubes, polystyrene and lattices. DNA based nanostructures – topographic and electrostatic properties of DNA – Hybrid conjugates. Self study - DNA oligomers – use of DNA molecules in nanomechanics and Computing.

Unit II Characterization of nanoparticles and applications 9hrs. Absorption and light scattering properties, zeta potential, electron microscopy (TEM, SEM), atomic force microscopy (AFM), dynamic light scattering (DLS), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF), Agriculture, food and nutrition, cosmetics, environment and biology research. Solar power using nanotechnology – Nanotechnology in textile industry Self study - Successful products of nanobiotechnology in the market

Unit III Biomedical opportunities and applications 9hrs. Nanoparticles and nanosystems – nanodrugs, drug delivery systems, dendrimers, cantilevers, nanobots, lab-on-a-chip, nano surgical knives Nano analytical tools – imaging at nanoscale (scanning probes, optical tweezers) Nanotechnology in diagnostics – applications, materials used in Diagnostics and Therapeutic applications – Molecular Nanomechanics Nanoengineered cell environments and Nanosensors. Health and environmental impact of nanomaterials – nanotechnology risks and regulators – lab safety guidelines for handling nanomaterials Ethical aspects of nanotechnology – relation between science, technology and ethics

Self study - Current status of Nanobiotechnology, Future perspectives of Nanobiotechnology

Unit IV Food microbiology 9hrs. Basic principles of food fermentation -Fermented foods and enzymes in food industry – yoghurt, cheese, bread, sauerkraut – mushroom farming – Use of enzymes in food industry. Food spoilage and food preservation – Beverage technology and alternative sweeteners – Impact of biotechnology on food industries – Food additive synthesis – Food acidulants, flavours, thickeners and gelling agents. Self study : Regulatory aspects of the use of modern biotechnological methods in food industry

Unit V Production of metabolites 9 hrs Vitamins, organic acids, alcohols, alcoholic beverages, enzymes. Production of secondary metabolites – toxins Self study : Production of antibiotics – penicillin, streptomycin Total – 45hrs

References : 1. Schmid., Gethman and Wutscher (2006) Nanotechnology Assessment and Perspectives, Springer International edition. 2. Karkare, M (2008) Nanotechnology Fundamentals and Applications, I.K. International Publishing House Pvt. Ltd., New Delhi. 3. Mark Ratner and Daniel Ratner (2002), Nanotechnology: A Gentle Introduction to the Next Big Idea, Published by Pearson Education Inc. 4. Bandyopadhyay, A.K. (2010), Nanomaterials, Second Edition, New Age International (p) Limited. 5. Nanobiotechnology: Concepts, Applications and Perspectives. (2004) Edited by Niemeyer, C.M. and Mirkin, C.A. Published by Wiley-VCH, Weinheim. 6. Pradeep, T., (2007). Nano: The Essentials: Understanding Nanoscience and Nanotechnology, Published by the Tata McGraw-Hill Publishing Company Limited, 7 West Patel Nagar, New Delhi 110 008. 7. Challa, S.S.R. Kumar, Josef Hormes and Carola Leuschaer, (2005). Nanofabrication Towards Biomedical Applications, Techniques, Tools, Applications and Impact. Wiley-VCH, Weinheim. 8. Johnson-Green, P. (2002) Introduction to Food Biotechnology, CRC Press, London. 9. Ramesh, V.K. (2009) Food Microbiology, MJB Publishers. 10. Bielecki,S., Tramper, J. and Polak,J. (2014) Food Biotechnology, Elsevier Publishers

Biostatistics and Research Methodology (Open Book Test)

Semester IV Hours of instruction / week : 4 17MBTC23 No. of credits : 3 Objectives: 1. To understand the statistical tools commonly used in biological research 2. To assimilate the concepts of hypothesis testing and its importance in research 3. To know the aspects fundamental to research and to understand the methods of research 4. To know the nuances of technical writing of scientific documents like thesis and journal articles

Unit I Statistical survey and data collection 12 hrs Statistical survey – Organization of a statistical survey, methods of data collection, data representation, diagrammatical and graphical representation of data Sampling fundamentals – need for sampling, properties of an ideal sample, sampling procedures. Self study: Frequency distributions, sampling distributions, standard error

Unit II Measures of central tendency, deviation, correlation and regression 12 hrs Measures of central tendency – arithmetic mean, median, mode Measures of deviation – range, quartile deviation, variance, standard deviation Correlation and regression – correlation analysis and regression analysis Self study: Relationship between mean, median and mode; pros and cons of the measures of central tendency and deviation; applications of correlation and regression

Unit III Probability and hypothesis testing 12 hrs Probability and theoretical distributions – probability definition, types, binomial, Poisson and normal distributions, large and small samples, degrees of freedon Hypothesis testing – Formulation of null and alternate hypotheses, testing the hypothesis, Student’s t test, Chi square test and goodness of fit, Analysis of Variance (one way and twoway only), acceptance and rejection of hypothesis. Self study: Simple problems on probability, theoretical distributions, hypothesis testing; importance of hypothesis testing Unit IV Research methodology 12 hrs Research methodology – meaning of research, objectives of research, types of research, research methodology and research designs, single blind and double blind trials Inclusion and exclusion criteria – importance of inclusion and exclusion criteria in animal and human research with special reference to clinical research (elementary concepts only), examples and case studies. Self study: Random block design; importance of single blind and double blind studies

Unit VReport Writing 12hrs Writing a thesis – layout of the thesis, preparing the components of the thesis – hypothesis, abstract, introduction, review of literature, methodology, results, discussion, summary and conclusion, references Writing a journal article – format of an article – journal requirements – differences between the thesis components and article components; abstract preparation – concise presentation, outline of work presented; keywords – list of important technical terms; main article – introduction, materials and methods, results, discussion, presentation of tables, figures and graphs, conclusion, acknowledgement, references, conflicts of interest Avoiding plagiarism – definition of plagiarism, ethical issues, copyright issues. Self study: Different formats of thesis; plagiarism-detection software; ShobhGanga and ShobhGangotri Total - 60 hrs

References: 1. Gupta, S.P. (2010) Statistical methods, Sultan Chand and Sons, New Delhi. 2. Gurimani N (2008) An introduction to Biostatistics, M.J.P. Publishers, Chennai. 3. Banerjee, P.K. (2008) Introduction to Biostatistics, S. Chand and Co., New Delhi. 4. Kothari, C.R. (2004) Research Methodology, Methods and Techniques, II Edition, New Age International Publishers, New Delhi. 5. Day, R.A. (2006) How to write and publish a scientific paper, Cambridge University Press, UK. 6. Alred, G.J., Bursaw, C.T. and Oliu, W.E. (2003) The Handbook of Technical Writing, McGraw Hill Publishers, New Jersey. 7. Arumugam, N. (2016) Research Methodology: For Life Sciences, 1st Ed., Saras Publication, and New Delhi. 8. Holmes, D. and Moody, P. (2006) Research Methods For The Biosciences, Oxford University Press, UK. 9. Forthofer, R.N. and Lee, E.S. (2007) Biostatistics: A Guide To Design, Analysis And Discovery, Reed Elsevier India Private Limited, New Delhi. 10. Pagano, M. and Gauvreau, K. (2000) Principles Of Biostatistics, 2nd Ed, Duxbury/Thomson Learning, New York. 11. Kothari,C.R. and Garg, G. (2014) Research Methodology : Methods And Techniques, 3rd Ed., New Age International, New Delhi.