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I a I5 ;, -, (A bstract.l \1.I'hil tlio-Technologr (Semester pattenr) - Moditlcation of 51'llabus - Implemented from the academic rear 2008-09 onlvards - Orders Issued. GENERAL AND ACADEMIC BRANCH _ I 'J' SECTION \tr ( i i\1./J I r 42 I 9,/08 Read: l. 2. 3. Dared. Calicut University P.o, l6/01/2009. Minutes o1'the meeting of Board of Studies in Bio-Technology of 301612008 - Item No.3. ltem No.2(xiii) of the minutes of meeting of Faculty of Science of 29/812008. Item No.IIA (12) of the minutes of meeting of Academic Council of 7ll0/2008. ORDER l-he Board of Studies at its meeting held on 30/06,'2008, r,ide paper read (l) above, resolved to consider the rnodiflcation of the Sl,llabus fbr N4.Phil Bio-Technology course. The Faculty of Science hetd on 2910812008. vide paper read (2), endorsed the minutes of tloard of'studies and tlre Acadernic Council helcl on 0111012008 as per paper read (3) approved the \anle Sanction has therefbre been accorcieci to implcnterrt thc sy'llabus of M.Phil Bio-Technologl' (Semester pattern) tiorn the acadernic i'ear 2008-09 onwards. Orders are issued accordingly. Copy ot'the s1'llabus appended. sd/ASSISTANT REGISTRAR (G&A_D FOR REGISTRAR fo 1 . 2. Head of the Department of Bio-technology l'he Director. College Development Council. Copy to: Controller of Exarninationsi EGIiEnquiry/Ex.Sn./ AR & DR concerned/ Tabulation Sn./ GAI 'F' Sn./ SF/DF/FC. Forwarded./By Order ae-."a*_ SECTION OFFICER DTANILA\GAI\GA l-Jl a2'19 08 Or doc , I a I t .l UNIVERSITY OF CALICUT DEPARTMENT OF BIOTECHNOLOGY SYLLABUSFoRM.PhiIBIoTECHNoLoGYISEM.ESTERPATTERN., 2008-09) tf t"tn Academic Year EligibilitY for admission: CandidateswithmastersdegreeinBrotechnology/Bioinformaticsl Biochemistry/Microbiology/MolecularBiology/genetics/Agriculturel with Biotechnology specializatton sciences / Biological sctences Veterinary marks of animal biotechnology ) with 55% i culture tissue / (plant Biotechnology by University or foreign University recognized this University or any other lndian other regulations pertaining to course Phil M for apply to of C,alicut are eligible admission,course,schemeofevaluationshallbegovernedbytheexistingrules of the UniversitY' ,l 1 UNIVERSITY OF CALICUT DEPARTMENT OF BIOTECHNOLOGY SYLLABUS FOR M.PhiI BIOTECHNOLOGY SEMESTER PATTERN (From Academic year 200g_09i 1' lntroduction to research topic, literature coilection and review preparation of Bibilography, preparation of manuscripts, reports / dissertation. Experimentar designs, raboratory practices, Biosafety with respect rDI\jA Technology 2. Principres of Microscopy: simpre and compound mrcroscope, phase contrast, and inverted microscope, erectron microscope (TEM & sEM), Flouresence mrcroscope, confocal microscope 3' Histochemistry' lmmunohistochemistry, tissue preparation-wax embedding, processing of microtome and cryostat sections, rocalization of metobolite: proteins, nucleic acids, enzymes 4' Microbiological techniques. Pure culture techniques, enrichment techniques, replica plating' cultivation of anacrobic microorganoms, maintenance of microbial cultures' Establishment, maintenance and apprication of animal cell cultures. b L .a 5 Plant tissue culture methods: Tissue culture media and growth regulators. cell culture meristem culture, hairy root culture Protoplast isolation and fusion. Secondary metabol ite p rod uction, generation of tra nsgen ic.plants 6. Principles and application of various instruments and techniques: colorimetry U.V.-visible spectrophotometry, HPLC, FPLC, centrifuges, transilluminator, Thermalcycler, sonicator, vacum concenirator, MS, NMR, COz incubator. Elisa reader, DNA Sequencer 7 Chromatography techniques: paper chromatography, TLC, column chromotography-molecular sieving and lon exchange, affinity chromatography, gas-chromatography, and HPLC B. Electrophoretic techniques: Polyacrylamide and agarose gel electrophoresis, capil.l,?ry electrophoresis, 2D electrophoresis, paper, Disc gel dectrophoresis. Pulse field electrophoresis, Rocket gel, RlD, isoelectric focusing 9. Radioactivity: Decay and measurement of radio activity, Geiger -Muller counter, Liquid scintillation counter, autoradiography radioimmunoassay. Application of isotope techniques in Biological systems. 10. Extraction of DNA, RNA, analysis of nucleic acids, spectrophotometry, colorimetry, electrophoresis, hybridization techniques - northern, in situ hybridization, FISH, colony hybridization, southern, western, PCR amplification, sequencing, cloning methods, RAPD, STS, RFLP, DNA, RNA Finger printing, micro affay. 11. Protein isolation, purification, amino acid sequencing: antibody generation, polyclonal and monoclonal 12 Application of Bioinformatics in prcteomics and genornics e g sequence data and genome data analysis , References Text Books 1' Modern Experimentar Biochemistry - Rodney Boyer third edn. 2' Principles and techniques of practical Biochemistry K.wilson and J.walker 3' An introduction to practical Biochemistry - D.T.plummer third Edn. 4' Molecular cloning - A-Laboratory manual vol.l, ll & lll. sanbrook and Russel 2001 5. Short protocols in Molecular Biology _ Ausbel et al. 6' Prant rissue curture - Theory and practice - s.s.Bhojwani and M.K.Razdan Elesevuer pull. 7' Biochemistry - Donard.Voet and Judith G.voet John wirey and sons rnc a Paper-ll Advances in Biotechnoloq,v 1) Recent development in microbiology: Microbial pathogenicity; Mechanism of of virulence, toxins, genetics of virulence, plasmids and virulence; Mechanism produced by drug resistance. Antibiotics: suipha drugs, pencillin; Types of toxins bacteria Exo, Endo and Entero toxins, mode of action, virulence and pathogenesis bacteria, 2) Fermentations: Methanogenesis and acetogenesis; nitrate oxidizing nitrate and sulPhate reduction 3) Degradation of xenobiotic compounds - pesticide degradation Bioplastics and its aPPlication industry Microbial delignification of wood in pulp and paper 4) Viruses of DNA and General properties of viruses, viral enzymes, Reproduction of DNA and RNA RNA phages including Hlv; Replication and transcription viruses; Viruses and cancer. of DNA' 5) Biosynthesis of DNA, Chemical Synthesis and purification 6) Enzyme catalysis and energy of activation' lsolation of of enzyme activity enzymes, expression of enzyme activity; Regulation Zymogens, covalent modification' allosterism, Positive and negative modulation, techniques of enzyme phosphorylations; Enzyme inductions and repression, immobilization' membrahes, purification of Recent development in protein purification using Lysozymes -) Applicatron of enzyme technology e g.pharmaceutics. pulp, leather and detergents industry. 7) A brief overview of Membrane structure and membrane systems comparlmentalization; Protein sorting and trafficking Mitochond ria and chloroplasts, Cytoskeleton, Cell Junctions, extracellular Matrix, Cell Nucleus, Cell signaling, Cell Cycle, Cancer and Apoptosrs 8) DNA replication, DNA repair ahd Recombination of DNA; Transcription and its reg ulation ; Translation References Text Books Environmental Microbiology - Methods and Protocols Ed:John.F.T.Spencer, Alicia & Ragout de sepncer,2004. Humana Press Microbiology - Mc.Kane, Kandell Micrgbial life - Perry, Stanley and Lory Microbiology - Prescott Foundations in Microbiology Talaro et.ai Molecular Biology of the Cell - Bruce Alberts e/ al Molecular Cell Biology - Darn ell et al. Genes - Benjamin Lewin Cell and Molecular Biology - Karp Lehninger Principles of Biochemistry D.L.Nelson and M.M.Cox Freeman and Company Biochemistry - Mathews, Van Holde Fundamentals of Biochemistry - Voet ef a/ Science Journals Students are expected to keep track of the latesi reviews and articles on the above-mentioned topics from high impact journals such as Cell, Sceince, Nature, PNAS, Journal of Molecular Biology, Current Opinions in Cell Biology, Trends in Biotechnology, Genes and Development etc. 7 'a Paper-lll - Special Papers (Options) a. (1) Recombinant DNA Technology (2) Immunology and lmmunotechnology (3) Plant Biotechnology Recombinant DNA Overview of genomic DNA analysis; preparation, manipulation and mapping of HMW-DNA. Cloning systems-Plasmid / Bacteriophage based vectors / Cosmids, and aftificial chromosomes; Screening for recombinants PCR in genomic analysis - genetic engineering with PCR, RT-PCR, 5' & 3' RACE, MOPAC, Long PCR, lnverse PCR, Quantitative PCR and Differential Display-PCR. Site directed mutagenesis and its applications Detection of DNA variations. DNA sequencing , Gene expression systems and analysis Protein interactions- Two-hybrid and other interaction systems. Whole genome analysis and proteome analysis; DNA Microarrays References Text Books 1. Mblecular Cloning : A Laboratory manual Vol.l, ll & lll - Sambrook and Russel 2001. CSH, New York . Practical Approach Series - Glover and Hans. IRL Press 3. Genome Analysis : A Laboratory manual Vol.l, ll , lll & lV - Birren et al, 2000, 2. DNA cloning CSH, NY 4 Short Protocols in Molecular Biology - Ausbel et al '1998-John Wiley, USA. 6:, IMMUNOLOGY AND IMMUNOTECHNOLOGY 1. lntroduction: Phylogeny of lmmune system. lnnate and acquired/adaptive immunity, Clonal nature of lmmune response, memory cells 2. Organization and structure of lymphoid organs: primary and secondary 3. Nature and biology of antigens and superantigens 4. Antibody structure and function, immunoglobulin super family 5. Major histocompatibility complex: structure and function of class I and class molecules of human and mouse, regulation of MHC expresssion. ll 6. BCR & TCR generation of diversity:VDJ rearrangement mechanism of variable region, DNA rearrangement, isotype switching, expression of lg genes, secretion of immunoglobulins 7. Complaint system: activation of classical and alternative pathways, regulation of complement system. 8. Regulation of lmmune response: -Anllgen processing and presentation. generation of humoral and cell mediated rmmune responses -Activation and differentiation of B and T -lymphocytes 9 Cell -mediated cytotoxicity:Mechanism of T cell and NK cell mediated lysis, antibody-dependent cell mediated cytotoxicity, macrophage mediated cytotoxicity 10 Hypersensitivity (Type l. ll, lll & lV) l l.Autoimmunity: tolerance to self antigens, organ specific and systemic autoimmune disease, role of MHC in autoimmunity, mechanism for introduction of autoimmunity, treatment of auto imntune diseases. 12. Tumour immunology: Oncogenes and cancer introduction, tumour antigens effector mechanism to tumours, mechanism of tumour invasion and immunotherapy of tumours 13. Hybridoma technology and monoclonal antibodies. Myeloma Cell lines Fusion of myeloma cells with antibody - producing B-cells. Fusion methods selection and screening methods for positive hybrids - single cell cloning . q PLANT BIOTECHNOLOGY 1) lntroduction to Plant Biotechnology lntroduction preparation to cell and cell culture; Tissue culture techntques; and composition; Media Organogenesis; Somatic embryogenesis; Somaclonal variation and application; Shoot-tip culture; Protoplast isolation culture and function; Selection of hybrid cells and regeneratton of hybrid plants; Anther, pollen and ovary culture for the production of haploid plants and homozygous lines 2) lntroduction to Secondary metabolites Alkaloides, biological function of alkaloids; Plant amines; Non protein amino acids; Quinones; Resins: Steriods: Phenyl propanoids; Polusoprenes; Phe-polics: lnsecticids of plant origin 3) Production of lmmunomodulatory and antitumor compounds Mechanism of action; Alkylating agents; Antimetabolites; DNA intercalating agents; Production in culture eg. Ellipticines, vinblastine 4) Production of Food additives Colour; Anthocyanins; Crocin and crocetlns; Flavours; Vanilla; Garlic and onions; Sweeteners; Steriods 5) Production of lnsecticides phytoecdystero nes : Azad i rachti n ; Rotenoid s; O Pyreth rins ; Quasin 6) Production of secondary metabolltes through cultures production, purifleation and characten zation of monoclonal antibodies Application of monoclonal in biomedical research in clinical diagnosis and treatment 14. Antibody structure, antibody fold, CDR confirmation, Human monoclonal antibodies from VJD-gene Repertoires: expression of .anybody fragments in Bacteria, Generation of antibody genes using pcR, expression of Ab fragments on the surface of bacteriophage, vectors for phage display of Ab fragments, phage dispray instead of conventionar hybridoma. l5 Technology to produce antibodies; phage display to make antibodies without lmmunization to increase antibody affinity methods and protocols. 16 Strategies for Humanising antibodies; Humanised antibodies cloning and sequencing of murine rmmunuogroburin region segments, cDR grafting, expression of Humanised antibodies/reshaping technologies. lT Expressing antibodies in E.Coti. and overview, vector for antibody secretion, expression by secretion and detection using FLAG Tag 1' Kuby lmmunology, 4th edition, R.A.Goldsby, Thomas J.Kindt, i \!rrv\' su, Barbara A. Osbome (Freeman). 2. lmmunology, A short course, 4th ecjition Eli Benjamin, Rcchard coico, Geoffrey Sunshine (Wiley_Liss) 3. Fundamentals of lmmunology, William paul 4. lmmunology, Roit et al 5. lmmnuobiology, CA Janeway et al, Current Biology Ltd. 6. current protocols in lmmunology, JE coligna et ai, John wiley & Sons lnc 7. cellular and Molecurar lmmunology, A K Abbak et al., saunders company. 8. Antibodiy Engineering cAK Borrebaeck, oxford University press 9. Protein Engineering: principles and practice, JL cleland, cs crait, Wiley and Sons 10'Animal cell culture, J R w Master, oxford University press. John ll I ' Growth requirements (manipulation of media): Culture initiation. Time course study and metabolite production: Optimisation, Screening and selection of cells / clones for increasing the yield 7) Bioconversion of secondary metabolites General principles of bioconversion; Methods of Bioconversion: lmmobilization of plant cells: Enzyme preparation 8) Production of secondary metabolites through genetic transformation Development of transformed organ cultures; Agrobacterium and transformation process; Production of transformed hairy roots in plants; Antibody production through plants; Edible vaccines; Production of secondary metabolite In large scale References Text Books Plant Biochemistry & Molecular Biology - Peter J.Lea, Richard C.Leegod Plant Biochemistry & Molecular Biology - Hans, Walter Heldt Plant Cell Tissue and Organ culture - Bahaj et.al - Bhojwani et al Plant Cell and Tissue Culture - Narayanaswamy Biotechnology Secondary metabolites - Ramawat et'al Plant Cell Biotechnology - Endre.B Plant Biotechnology - Slater,scott and Fowler Plant Tissue Culture a I i ,