2011-2012

KVS.BHARADWAJ M.Sc.Integrated Biotechnology Syllabus VI Semester

VIKRAMA SIMHAPURI UNIVERSITY :: NELLORE MSc INTEGRATED BIOTECHNOLOGY (Choice-Based SEMESTER SYSTEM) (Effective from 2011-2012 onwards) VI SEMESTER BT 601: Eukaryotic Molecular Biology

Unit I DNA Replication: DNA polymerases in eukaryotes. Origins and initiation of replication. Replication fork in eukaryotes. Mechanism of DNA replication Dissociation of chromatin, initiation, elongation and termination of DNA replication. Reassociation of chromatin. Fidelity of DNA replication. Telomerase: Maintaining the ends of chromosomes. Unit II RNA biosynthesis and processing, Eukaryotic RNA Polymerases. General transcription factors. Promoters and Enhancers. Transcription factor-binding sites. Eukaryotic repressors. Initiation of transcription by RNA Polymerase II. Transcription by RNA Polymerases I and III. Relationship of chromatin structure to transcription. Regulation of transcription by noncoding RNAs. RNA Processing and turnover. Post-transcriptional processing of hnRNA Capping, methylation, polyadenylation and RNA splicing mechanisms. Splicing of group I and group II introns. Processing of tRNA and rRNA primary transcripts in eukaryotes. Alternative splicing, RNA editing, RNA degradation. Inhibitors of eukaryotic transcription. Unit III Transport of mRNAs into cytoplams. Initiation, elongation and termination of protein biosynthesis. Regulation of translation. Chaperones and protein-folding. Enzymes that catalyze protein-folding. Glycosylation. Attachment of lipids. Regulation of protein function. Regulation by small molecules. Protein phosphorylation. Proteinprotein interactions. Protein degradation Ubiquitin-Proteasome pathway. Lysosomal proteolysis. Unit IV Selective transport of proteins to and from the nucleus. Regulation of nuclear protein import. Transport of RNAs. Ribosome assembly; Protein sorting and transport: Endoplasmic reticulum and protein secretion. Targeting proteins to endoplasmic reticulum. Insertion of proteins into ER membrane. Export of proteins and lipids from ER. Protein sorting and export from the Golgi apparatus. Eukaryotic gene controls: Homeotic genes , Gene knockout, Sex chromosome Genes. Regulation of gene expression in eukaryotes: gal operon in yeast. Gene silencing technologies: antisenceRNA, siRNA, RNAcagin, microRNA. Terminator gene technology in cotton.

VIKRAMA SIMHAPURI UNIVERSITY NELLORE

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2011-2012

KVS.BHARADWAJ M.Sc.Integrated Biotechnology Syllabus VI Semester

BT 602: Animal Physiology

Unit I Introduction - Scope and fields of Physiology; Food requirements - Carbohydrates, proteins, fats, minerals, water and vitamins. Digestion Intracellular and extracellular. Digestive enzymes and their role in digestion. Absorption. Respiration - External and internal (tissue) respiration; Respiratory pigments Disibution, composition, properties and functions. Transport of oxygen and carbon dioxide Anaerobiosis. Circulation Types, composition, properties and functions of blood. Types of heart. Human Cardiac cycle Cardiac rhythm, origin of heart beat, regulation of heart beat, ECG and blood pressure. Elements of aviation and space physiology. Unit II Excretion Organs of excretion in animals. Kinds of excretory products Ornithine cycle, mechanisms of urine formation in mammals, hormonal regulation of excretion. Homeostasis Regulatory mechanisms: osmoconformers, osmoregulators, organs concerned with osmo-ionic regulation, osmoionic regulation in aquatic and terrestrial vertebrates. Thermoregulation Acclimation and acclimatization. Heat death, cold death. Poikilotherms, heterotherms, homeotherms. Temperature regulation in poikilotherms and homeotherms. Physiology of hibernation and aestivation. Biorhythms Definition, types and examples and adaptive significance. Unit III Nervous tissue Neuron: structure, types of neurons and their distribution. Giant nerve fibres Myelinated nerve fibres. Nerve impulse Definition, conduction of impulse, saltatory conduction, synapse and synaptic transmission of impulses. Neurotransmitters. Autonomic nervous systern. Muscle proteins Mechanism of contraction, Con cycle. Theories of muscle contraction, Muscle twitch. Muscle fatigue. Isotonic and isometric contraction. Aerobic and isometric exercises. Bioluminescence Definition, types, chemistry and adaptive significance. Chromatophores. Unit IV Endocrine glands Structure, secretions and functions of endocrine glands in vertebrates: Pituitary, hypothalamus, thyroid, parathyroid, adrenal, thymus, islets of Langerhans, sex organs. Gastrointestinal hormones. Hormones of insects and Crustaceans. Receptors Classification. Chemoreceptors Touch receptors, equilibrium receptors. Photoreceptor Vertebrate mammalian eye, structure of retina and visual pigments. Physiology of vision Binocular vision, adaptation to darkness, Compound eyes and Mosaic vision. Phonoreceptors Mammalian ear, organ of corti, working mechanism. Phono reception .

VIKRAMA SIMHAPURI UNIVERSITY NELLORE

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2011-2012

KVS.BHARADWAJ M.Sc.Integrated Biotechnology Syllabus VI Semester

BT 603: Plant Physiology

Unit I Introduction to plant physiology: Translocation of water and solutes. Plant cell water relations, Mechanism of water uptake and transport in plants; SPAC concept. Stomatal movements, Phloem transport of organic substances Phloem loading and unloading; passive and active solute transport; membrane transport proteins. Stress physiology: Plant responses and tolerance mechanism to abiotic stress such as water, salt, heavy metal and high temperature stresses. Changes associated with leaf senescence. Unit II Photosynthesis: General concepts and historical background; photosynthetic pigments; photosystems and light harvesting complexes. Photooxidation of water Oxygen evolving complex. Water oxidation clock. Mechanisms of photosynthetic electron and proton transport; Photophosphorylation ATPase; Regulation of PSI and PS II activities, Energy spillover mechanism; Rubisco activation and its mechanism of action; Light activation of photosynthetic enzymes; chloroplast protein phosphorylation and enzyme regulation of photosynthetic carbon assimilation; mechanism, regulation and significance of photorespiration. Carbon assimilation Calvin Cycle, C4 cycle and CAM pathway. Biosynthesis of starch and sucrose. Physiology of flowering : Photoperiodism and Photoinduction. Endogenous clockers and its regulation; Physiological signals of floral induction: Genetic and molecular analysis. Vernalization. Unit III Respiration and lipid metabolism: Overview of plant respiration, glycolysis, TCA cycle, electron transport and ATP synthesis, Pentose phosphate pathway, glyoxylate cycle. Structure and functions of lipids, fatty acid biosynthesis. Synthesis of membrane, structural and storage lipids; catabolism of lipids. Nitrogen and sulphur metabolism: Biological nitrogen fixation, mechanism of nitrate uptake and reduction, ammonia assimilation, sulphate uptake and assimilation. Unit IV Plant growth regulators and elicitors: Physiological effects and mechanism of action of auxins, gibberellins, cytokinins, ethylene, abscisic acid, brassinosteroids, polyaminers, Jasmonic acid and salicylic acid. Signal Transduction : Overview, receptors and G-Proteins, Phospholipid signalling, role of cyclic nucleotides. Calcium-calmodulin cascade, protein kinases and phosphatises. Specific signalling mechanisms two components sector. Regulator system in plants, sucrose, senescing mechanism. Hormone receptors signal transduction and gene expression.

VIKRAMA SIMHAPURI UNIVERSITY NELLORE

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2011-2012

KVS.BHARADWAJ M.Sc.Integrated Biotechnology Syllabus VI Semester

BT 604: Computational Biology Unit I Elementary Commands and Protocols, ftp, telnet, http, printer on information theory; BioinformaticsIntroduction, Scope of Bioinformatics and Applications. Strings, Edit Distance, String Similarity- methods; Alignment- local, Global Alignment; Gap- Gap penalty; Parametric Sequence Alignments- Sub Optimal Alignments; comparison of pair wise and Multiple Alignment. Unit II Biological Information on the web- Introduction to Databases; Database Search; Algorithms Issues in Database Search; Information Retrieval from Databases; Sequence Database search- FASTA, BLAST; Amino acid substitution matrices- PAM and BLOSUM; Data Mining and Visualization. Unit III Understanding evolutionary process; origins of molecular phylogennetics. Common multiple sequence alignment methods; method of phylogenetic analysis, tree evaluation, problems in phylogenetic analysis, automated tools for phylogenetic analysis; ultrametrics trees and distances; maximum parsimony. Unit IV DNA Sequencing Map assembl, cDNA sequencing, Genome Sequencing; Genome Mapping ; comparitive sequence analysis; basis of gene prediction, gene prediction- in microbial genomes, gene prediction methods, other gene pridiction tools, gene annotation; molecular prediction with DNA strings; human genome mapping (HGM.)

VIKRAMA SIMHAPURI UNIVERSITY NELLORE

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2011-2012

KVS.BHARADWAJ M.Sc.Integrated Biotechnology Syllabus VI Semester

Recommended Books

BT 601: Eukaryotic Molecular Biology: 1. Molecular Cloning: a laboratory manual, Sambrook J., Fritsch EF. and Maniatis T, 2000. Cold Spring harbor Laboratory Press. 2. Introduction to Practical Molecular Biology, DEabre P, 1998. John Wiley & Sons Ltd. 3. Molecular Biology Labfax, T.A. Brown (Ed.), 1991. Bios Scientific Publishers Ltd. () 4. Molecular Biology of the Gene, Watson JD., Hopkins NH., Roberts JW., Steitz JA and Weiner AM, 1996. (The Benjamin/Cummings Publ.Co.). 5. Molecular Cell Biology, Darnell J, Lodish H and Baltimore D, 2000. Scientific American Books, USA. 6. Molecular Biology of the Cell, Alberts B., Bray D, Lewis J., Ralf M., Roberts K. and Watson J.D., 2001. Garland Publishing Inc. 7. Gene IX, Levin B, 2005. Oxford University Press. BT 602: Animal Physiology: 1. A textbook of Animal Physiology and Ecology, Sambasivaiah, Kamalakara Rao and Augustine Chellappa, 1990. S.Chand & Co. Ltd., New Delhi - 110 055, 480 pp. 2. Outlines of Aniimal Physiology, S. Viswanathan Parameswaran, Anantakrishnan and Ananta Subramanian, 1975. (Printers & Publishers) Pvt. Ltd., 329 pp. 3. General and Comparative Physiology, William S.Hoar, 1976. Prentice Hall of India Pvt. Ltd., New Delhi - 110 001, 848 pp. 4. Principles of Animal Physiology, 3rd Ed. Wood, D.W., 1983. 5. Comparative Animal Physiology, Prosser C.L., 1985. Satish Book Enterprise, Agra - 282 003, 966 pp. 6. Comparative Animal Physiology. C.L. Prosser. W.B. Saunders & Company 7. Mechanisms and Adaptation. R. Eckert. Animal Physiology. W. H. Freeman & Company 8. General and Comparative Animal Physiology. W.S. Hoar. 9. Animal Physiology. Adaptation and Environment. Schiemdt-Nielsen. Cambridge 10. Environment and Metabolic Physiology. C.L. Prosser. Wiley-Liss, New York. BT 603: Plant Physiology : 1. Biochemistry and Molecular Biology of Plants, Buchanan, B.B. Grussem, W. and Jones, R.L. 2000. American Society of Plant Physiologists, Maryland, USA. 2. Biochemistry and Physiology of plant Hormones (second edition). Moore, T.C. 1989. SpringerVerlag, New York, USA. 3. Biochemsitry and Molecular biology of plant Hormones. Hooykaas, P.J.J., Hall, M.A. and Libbeng, K.R. (eds) 1999. Elsevier, Amsterdam, The Netherlands. 4. Concepts in Photobiology: Photosynthesis and Photomorphogenesis. Singhal, G.S., Renger, G., Sopory, S.K. Irrgang, K.D. and Govindje 1999. Narosa Publishing House, New Delhi.

VIKRAMA SIMHAPURI UNIVERSITY NELLORE

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KVS.BHARADWAJ M.Sc.Integrated Biotechnology Syllabus VI Semester

5. Introduction to Plant Physiology. Hopkins, W.G. 1995. John Wiley & Sons, Inc., New York, USA. 6. Life Processes in Plants. Galston, A.W. 1989. Scientific American Library, Springer-Verlag. New York, USA. 7. Molecular Cell Biology (fourth edition). Lodish, H., Berk, A., Zipursky, S.L., Matsudaira, P., Baltimore, D.d and Darnell, J. 2000. W.H. Freeman and Company, New York, USA. 8. Molecular Plant Development: from Gene to Plant. Westhoff, P. (1998) Oxford University Press, Oxford, UK. 9. Photoperiodism in Plants (second edition). Thomas, B and Vince-Prue, D. (1997) Academic press, San Diego, USA 10. Physiochemical and Environmental Plant Hormones (Second edition). Nobel, P.S. 1999. Academic Press, San Diego, USA. 11. Plant Metabolism (second edition). Dennis, D.T. Turpin, D.H., Lefebvre, D.D. and Layzell, D.B. (eds) 1997. Longman, Essex, England. 12. Plant Physiology (2nd edition). Taiz, L. and Zeiger, E. 1998. Sinauer Associates, Inc., Publishers, Massachusetts, USSA. 13. Plant Physiology (4th edition). Salisbury, F.B. and Ross, C.W. 1992. Wadsworth Publishing Co., California, USA. BT 604: Computational Biology: 1. 2. 3. 4. 5. C++ by Balaguruswamy Principles of biochemistry Bioinformatics Lesk Introduction to Bioinformatics by Arthur M. Lesk, University of Cambridge. Learning the UNIX Operating System, Fifth Edition by Peek, Jerry; Todino- Gonguet, Grace; Strang, John. 6. Beginning Perl for Bioinformatics, 1st edition by O'Reilly & Associates, Inc. Sebastopol, CA, USA.

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2011-2012

KVS.BHARADWAJ M.Sc.Integrated Biotechnology Syllabus VI Semester

Practicals

BT - P601: Eukaryotic Molecular Biology and Animal Physiology 1. 2. 3. 4. 1. 2. 3. 4. 5. 6. Isolation of RNA from Yeast. Isolation of DNA from Plant Tissue Isolation of DNA from Animal Tissue Separation and purification of proteins by 2D Gel Electrophoresis.

Tissue somatic index and water content in selected tissues of frog. Gerentalogical dependence of cholesterol in selected tissues of frog Lipase activity in the selected tissues of frog. Insulin induced alterations in the active transport dynamics of glucose across the intestine of frog. Insulin and epinephrine impact on blood glucose and blood glycogen metabolism of frog. Oxygen consumption in crab Ozeoteliphosus anex anex as a function of size and calcium content in the blood and hemolymph of frog and crab. 7. Starvation-induced alterations in the blood glucose and tissue glycogen metabolism of frog. 8. Ammonia, urea and uric acid content in the selected tissues of crab. BT - P602: Plant Physiology and Computational Biology 1. Assay of chloroplast activity Hill reaction. 2. Demonstration of Kochs postulates citrus canker. 3. De-repression of dwarf characters of plants by gibberllins. 4. Determination of osmotic potential of plant cell sap. 5. Determination of plant tissue water potential. 6. Determination of the activity of succinate dehydrogenase and its sensitivity to inhibitors. 7. Determination of the rate of relative transpiration. 8. Effect of promoters and inhibitors on stomatal opening. 9. Effect of salt and water stress on the accumulation of proline. 10. Effect of solutes and temperature response of membrane permeability. 11. Estimation of chloride content and its accumulation ratio in aquatic plant. 12. Estimation of Rhizosphere, phyllospher, spermospher, microorganisms by serial dilution methods. 13. Estimation of titrable acidity of plant material. 14. Extraction and separation of soluble plant proteins by SDS PAGE. 15. Extraction, separation and determination of absorption spectra of chloroplast pigments. 16. Isolation of hyperparasites form plant fungal disease by serial dilution methods. 17. Isolation of pathogenic fungi and bacteria. 18. Measurement of photosynthetic CO2 assimilation rate using IRGA. 19. Preparation of standard curve of glucose and estimation of carbohydrate in the extracts of plant materials using anthrone reagent. 20. Preparation of standard curve of proteins and estimation of protein content in the extracts of plant materials using Lowrys or Brodfords method.

VIKRAMA SIMHAPURI UNIVERSITY NELLORE

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2011-2012

KVS.BHARADWAJ M.Sc.Integrated Biotechnology Syllabus VI Semester

21. Screening method of antagonists against pathogenic micro organisms. 22. Screening of antibiotics against pathogens by paper disc method. 23. Screening of botanical pesticides (plant extracts) against fungal pathogens by incoporating in the medium. 24. Seed viability test using tetrazolium chloride. 25. Separation of isozymes of peroxidase by native polyacrylamide gel electrophoresis. 26. Studies on hormonal regulation of senescence. 27. Submission of plant pathology Herbarium. 28. Substrate inducibility of the enzyme nitrate reductase. 29. Temperature, seed germination and acid phosphatase activity. 1. 2. 3. 4. 5. 6. Demonstration of BLAST, FASTA and other search engines. Clustering and contig assembly tool. Multiple sequence alignment and phylogenetic analysis. Gene finder (prediction) Restriction site analysis tools. Protein visualization tools.

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