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INDICATIVE BIOTECH FINISHING SCHOOLS (BTFS)

STRUCTURE OF THE COURSE

BIOTECH FINISHING SCHOOL (BTFS)

Sr. No. NAME OF THE MODULE

MODULE 1 Bioprocess and Fermentation Technology

MODULE 2 Plant Tissue Culture and Micropropagation

MODULE 3 Genetic Engineering and Seed Marker Technology

MODULE 4 Quality Assurance, Quality Control, Regulatory and GLP

MODULE 5 Clinical Research, Data Management & Pharmacovigilance

MODULE 6 Biosimilars, Monoclonal Antibodies and Recombinant Technology

MODULE 7 Environmental Biotechnology

MODULE 8 Animal vaccine and Diagnostics

MODULE 9 Genomics and Bioinformatics

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FINISHING SCHOOL MODULES

Module-1: Bioprocess and Fermentation Technology Unit I: Fermentation Technology Primary and secondary metabolites; Biotechnologically important Products produced through fermentation; Intracellular and Extracellular products such as enzymes, exopolymers, antibiotics, etc.; Classification of antibiotics and their biochemistry; Production of antibiotics, vitamins, etc.; Some specific cases (few) of penicillin, streptomycin, tetracyclines, griseofulvin, cephalosporin, ampicillin, pyocyanase, cephalosporin, valinomycin, etc.; Vitamin-A, Riboflavin, carotenoids, Solvents - glycerol, butanol, etc.; Biopolymers- exopolysaccharides, alaganides xanthan, dextran, curdlan polyhydroxybutrate, etc.; microbial insecticides, bio-fertilizers, etc. Unit II: Design and Operational Modes of Bioreactors /fermentor Principles and Practices in Bioreactors/ Fermentors Design, Functions, construction, etc.; Media Formulation; Fluid properties and flow behaviour; mechanically-agitated bioreactors for liquid cultures; quantification of process variables and material properties (density, molecular weight, temperature, pressure, flow rate and mixture composition; ideal gas law); material balances for physical (separation and mixing) processes, chemical and biochemical reaction processes, and other natural and industrial processes; product yield in biological processes and oxygen balance in bioreactors; heat and enthalpy balances for physical and reactive processes, and bioreactor cooling and temperature control, etc. Unit III: Immobilization and its Industrial applications Immobilized systems: Adsorption, covalent bonding, entrapment, encapsulation, cross linking, types of reactors, diffusion characteristics, effective factors, instability factors, deactivation rates, relative length of half life, etc.

Unit IV: Bio-separation and Downstream processing Downstream processing: Bioseparation; filtration, membrane filtration, centrifugation, sedimentation, flocculation, purification, solvent extraction, counter current extraction, ion exchange, affinity techniques, concentration, crystallization, reverse osmosis, ultrafiltration, drying, storage, and packaging, etc. Unit V: Strain Improvement and Upstream processing Isolation of microbes from soil air and water; Microbial screening procedure; Preservation of Microorganisms: Stock culture maintenance; storage at low temperatures on agar slants and liquid nitrogen; Storage in dehydrated form-dried culture, etc. Kinetics of microbial growth and death: Batch, fed-batch and continuous cultures; media for industrial fermentation, media formulation; Control of various parameters: sterilization;

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temperature control; aeration and agitation (Newtonian & Non-Newtonian Rheology) in bioprocess; Air sterilization, etc. Strain improvement of industrial important microorganisms: Physical, chemical and Different DNA mutating agents like UV, NTG, Nitrous acid, intercalating agents; Application of genetic engineering and protoplast fusion techniques in strain improvement, etc. Indicative Practicals:

1. Fermenter - design, operation and control, Microbial production of different products, Whole cell immobilization, Comparative study on rate of product formation using immobilized & suspension culture, Mixing and agitation in fermenters, RTD studies, Fed batch bioreactor

2. Monitoring and maintenance of process condition (Agitation, aeration, temperature, pH, DO, etc.)

3. i. Isolation of industrially important microorganisms, their maintenance and improvement. ii. Production of industrial compounds such as alcohol, beer, citric acid, lactic acid and their recovery. iii. Study of bio-reactors and their operations. iv. Production of biofertilizers. v. Experiments on microbial fermentation process, harvesting purification and recovery of end products. vi. Immobilization of cells and enzymes, studies on its kinetic behavior, growth analysis and biomass estimation. vii. Determination mass transfer co-efficients.

4. i. Determination of oxygen transfer rate and volumetric oxygen mass transfer coefficient (KLa) under variety of operating conditions in shake flask and bioreactor. ii. Determination of mixing time and fluid flow behavior in bioreactor under variety of operating conditions. iii. Rheology of microbial cultures and biopolymers and determination of various rheological constants. iv. Production of microbial products in bioreactors. v. Studying the kinetics of enzymatic reaction by microorganisms. vi. Production and purification of various enzymes from microbes. vii. Comparative studies of Ethanol production using different substrates. viii. Microbial production and downstream processing of an enzyme, e.g. amylase. ix. Various immobilization techniques of cells/enzymes, use of alginate for cell immobilization.

5. Upstream processing i . Media Preparation and autoclaving, Shake flask optimization (medium/pH/volume/inoculum percentage, etc.) ii. Experimental design and optimization: Plackett–Burman designs.

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6. Downstream processing i. Centrifugation, Filtration: TFF – principles and function, Membrane selection criteria, Cleaning and sterilization ii. Chromatography: Affinity Chromatography, Hydrophobic Interaction, Ion Exchange, Gel Filtration.

Suggested readings: 1. El-Mansi, EMT, Bryce, CFA, Arnold L., Allman, AR (2012). Fermentation Microbiology and

Biotechnology. CRC Press, Taylor & Francis. 2. Hui, YH, and Jytte J. (2003). Handbook of Food and Beverage Fermentation Technology. CRC

Press, Taylor & Francis. 3. Vogel, HC, Todaro, CL. (2005). Fermentation and Biochemical Engineering Handbook:

Principles, Process Design, and Equipment; Noyes Data Corporation/ Noyes Publications. 4. Walsh, G, Wiley, J. (1994) Biochemistry and Biotechnology. WILEY Blackwell. 5. Scragg AH. (1991). Bioreactors in Biotechnology. Ellis Horwood Limited, England. 6. Mukhopadhyay SN. (2004). Process Biotechnology Fundamentals. Viva Books Private

Limited, New Delhi.

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Module-2: Plant Tissue Culture and Micropropagation

Unit I: Introduction to cell culture Principles and Practices in Plant Tissue Culture, Totipotency, various techniques to produce novel plants and hybrids, preparation and composition of tissue culture media, etc.; Callus initiation and maintenance, suspension culture: single cell clones, etc.; Principles and Practices in Cyto-differentiation, etc.

Unit II: Somatic embryogenesis and Micro propagation Embryogenesis - induction, development and maturation, factors, applications and synthetic seeds, molecular biology of somatic embryogenesis – induction, development, synchronizing somatic embryo development, hormonal regulation, late embryogenesis abundant (LEA); Proliferation of axillary buds, induction of adventitious buds and bulbs, callus regeneration, somatic embryogenesis, continuous culture, immobilized cultures, estimation of growth and artificial seeds, etc.

Unit III: Tissue Culture & Cryopreservation Cloning: Isolation of single cells, culturing of single cell- different methods, culture cell viability test, Cryopreservation and slow growth cultures, freezing and storage, thawing, reculture; application of plant tissue culture production of secondary metabolites and industrial products, etc. Unit IV: Transgenic Technologies and Biotechnology Production of alkaloids and other secondary metabolites; Protoplast isolation and purification; Protoplast culture; Protoplast fusion; Somatic hybrids; Cybrids; Direct transformation of protoplasts using PEG; electroporation; Transformation by particle bombardment/ ‘Gene-gun’; Chloroplast transformation, Ti plasmid-based transformation; Ti and Ri plasmids, T-DNA genes, etc. Unit IV: Plant Transformation Plant Transformation applications for productivity and performance, production of transgenic plants resistant to herbicides, pathogens (Virus, fungi and bacteria), insect pests (Bt. Toxin gene) and abiotic stresses (drought, salt, chilling), etc.

Indicative Practicals: Basic techniques

a) Media preparation: Preparation of stocks, storage, documentation of media preparation, precaution and common trouble shooting while media preparation; Large-scale media preparation and automation in media preparation. b) Explant preparation: Surface sterilization protocols for leaf, buds, rhizomes, flower buds, tubers and bulbs; Documentation to identify or optimize sterilization protocols. c) Inoculation: Aseptic techniques, dissections, inoculation of axillary buds, terminal buds, leaves, roots, anthers, rhizomes, meristem, seeds and embryos.

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d) Maintenance of cultures: Maintaining the cultures in growth room; Clean room operations. e) Transfer of Plants to Green house: Conditioning and Maintenance of Plants in Green house.

Micropropagation technique: Optimization of various protocols of all stages. Development of technical know-how. Documentation and assessment of multiplication rate. Micropropagation of Commercially important Crop (Banana / Vanilla), etc. Somatic embryogenesis: Optimization of initiation, synchronization, maturation and germination techniques. Artificial seed technology, etc. Haploid production: Techniques involved in anther culture, pollen culture, ovary culture, ovule culture, Optimization of procedures for haploid plant production, Diploidization of haploids, etc. Protoplast culture: Techniques of isolation of protoplasts from leaves and callus, Culture of protoplasts by hanging drop technique and plating technique. Screening and studying the viability of protoplasts, etc.

Suggested readings: 1. Razdan, MK (2003). An introduction to Plant Tissue culture. Oxford & IBH Publishing Co,

New Delhi. 2. Nigel, WS, Mark, RF. (2008). Plant Biotechnology: An Introduction to Genetic

Engineering. Adrian Slater, Oxford University Press. 3. George, EF. (1999). Plant Propagation by Tissue Culture. Exegetics Limited, 4. Slater, A. (2004). Plant Biotechnology: The genetic manipulation of plants. Oxford

University Press, New York. 5. Bhojwani, SS. (1990). Plant Tissue Culture. Elsevier Science Publisher, The Netherlands. 6. Galun, E, Breiman, A. (1997). Transgenic Plants. Imperial College Press, UK. 7. George, EF. (1996). Plant Propagation by Tissue Culture. Exegetics Ltd., UK. 8. Glick, BR, Pasternak, JJ. (2003). Molecular Biotechnology. ASM Press American Society

for Microbiology, USA. 9. Halford, N. (2006). Plant Biotechnology. John Wiley & Sons Ltd., Wiley-VCH Verlag

GmbH & Co., Germany.

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Module 3: Genetic Engineering and Seed Maker Technology `

Unit I: Plant Genetic Engineering Methods of gene transfer- Agrobacterium tumefaciens mediated, Agrobacterium rhizogenes mediated; Recovery of transformed plants, gene expression and applications; Selectable markers, reporter gene and promoter in plant vectors; Chloroplast engineering, etc. Unit II: Gene Transfer & Molecular Breeding Vectorless or direct DNA transfer- Physical gene transfer methods, particle bombardment or biolistic method, macroinjection, microinjection, liposome mediated transformation, silicon carbide fiber mediated transformation, ultrasound mediated gene transformation; chemical methods of gene transformation- PEG mediated gene transfer, Calcium phosphate co-precipitation, DEAE dextran procedure, etc. Development of sequence based molecular markers - SSRs and SNPs; QTL mapping using structured populations; AB-QTL analysis; Association mapping of QTL; Fine mapping of genes/QTL; Map based gene/QTL isolation and development of gene based markers; Allele mining by TILLING and Eco-TILLING; Use of markers in plant breeding, etc. Marker assisted selection (MAS) in backcross and heterosis breeding; Transgenic breeding; Foreground and background selection; MAS for gene introgression and pyramiding: MAS for specific traits with examples, etc. Unit III: Development of Transgenic Plants Selection, regeneration and reproduction of transgenic plants; Production of virus, bacteria, fungi, insect resistance plants. Transgenic crops for improved quality, herbicide tolerant, stress resistant plants, Transgenic plants for molecular farming: edible vaccines, plantibodies, plantigens, bioplastics, biofuels, biofarming for carbohydrates; Anti-sense RNA technology-iRNA and its application in crop improvement; mechanisms and applications in post harvesting improvement; Golden rice technology and biotransformation of high value metabolites through cell culture, etc. Unit IV: GM Crops concerns about GM crops, Public acceptance of genetically modified crops; Plant breeders rights, Farmers rights, Plant variety protection, convention on biodiversity; case studies on plant patents- patenting of Basmati rice in USA, Revocation of Turmeric patent and Neem patent. Transgenic plants: field containment, Bt and terminator – technology protecting systems. (GURTs); GM Foods: substantial equivalence, safety testing and labeling, etc. Unit V: Seed Technology Principles and practices of hybrid seed production: Selection of site for seed production; Compact area approach; Sowing, row spacing, fertilizer and irrigation; Isolation, planting ratio and seed rate; roguing and pollen shedders; Barstar and Barnase system for production of hybrid seeds; Terminator Technology; Artificial- Synthetic Seeds: Production of synthetic seed encapsulation,

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Production of normal and transgenic seeds; Steps of commercial and artificial seed production, Artificial seed propagation, Seed germplasm and storage in different conditions; Cryopreservation; Static conservation of seeds, Clonal seed orchards; Seed certification; seed banks; IPR and Plant breeders Rights, etc. Indicative Practicals:

1. Plant tissue culture: Instruments used in Tissue culture 2. Preparation of nutrient media; handling and sterilization of plant material; inoculation,

sub culturing and plant regeneration, etc. 3. Initiation and maintenance of callus cultures. 4. Initiation and maintenance of suspension cultures and secondary metabolite production. 5. Extraction and analysis of secondary metabolites of medicinal plants by TLC/HPLC 6. Agrobacterium mediated transformation of plants. 7. Biolistic transformation of callus cultures and analysis –GUS/PCR. 8. Cryopreservation techniques and germplasm conservation. 9. Genomic DNA isolation from plants and agarose gel analysis. 10. Genetic fingerprinting of plants by RAPD/ISSR 11. Detection of genetically modified commercial crops by PCR-Cotton. 12. Plasmid isolation and restriction digestion analysis. 13. Preparation of DNA insert by restriction digestion and gel purification. 14. Selection of recombinants and their analysis for inserts. 15. SDS-PAGE analysis of seed proteins. 16. Dot blot, Southern Blotting and Western blot of seed proteins. 17. Genomic library preparation in plasmid vector. 18. Virus indexing of mother plants and micropropagated plants by Dot blot and PCR. 19. Genetic fidelity testing of micropropagated crops-Banana. 20. Gene transfer using different methods, reporter gene expression, selection of

transformed tissues/ plants, molecular analysis, etc. 21. To provide hands on training on various molecular techniques used in molecular

breeding and genomics.

Suggested Readings

1. Bhojwani, SS. (1983). Plant Tissue Culture: Theory and Practice. Elsevier. 2. Christou, P, Klee H. (2004). Handbook of Plant Biotechnology. John Wiley & Sons. 3. Dixon, RA. (2003). Plant Cell Culture. IRL Press. 4. George, EF, Hall, MA, De Klerk GJ. (2008). Plant Propagation by Tissue Culture.

Springer. 5. Gupta, PK. (2004). Biotechnology and Genomics. Rastogi Publications. 6. Herman, EB. (2008). Media and Techniques for Growth, Regeneration and Storage.

Agritech Publications. 7. Pena, L. (2004). Transgenic Plants: Methods and Protocols. Humana Press. 8. Pierik, RLM. (1997). In vitro Culture of Higher Plants. Kluwer. 9. Chittaranjan, K. (2007). Genome Mapping and Molecular Breeding in Plants. Springer

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Module-4: Quality Assurance, Quality Control, Regulatory and GLP

Unit I: Good Manufacturing Practice Concepts GMP and cGMP; Legal requirements pertaining to GMP: GMP Guidelines, Standards, Regulatory agencies; Components of GMP: Organization & Personnel, Premises, Equipment, Raw Materials, Control on Manufacturing of dosage forms, Packaging and labeling control, Laboratory controls, Finished product release, Warehousing, Distribution and distribution records, waste and scrap disposal, Complaints and recalls, Specifications, Self inspection; GMP for ayurvedic formulations (Sch. T of D & C act), etc. Unit II: Good Laboratory Practice (GLP) GLP – an overview and basic information, Scope; Principles of GLP: Test Facility Organization and Personnel, Quality Assurance Programme, Facilities, Apparatus, Material, and Reagents, Test Systems, Test and Reference Items, Standard Operating Procedures, Performance of the Study, Reporting of Study Result, Storage and Retention of Records and Materials; Responsibilities in GLP; Implementing of GLP in non GLP analytical laboratory, etc. Unit III: Inspections, Quality Audit SOPs & protocols for various operations, production and process, packaging and labeling, warehousing, IPQC, Finished product release, Quality review, Quality audit, Audits of quality control facilities, Batch release documents, Distribution and distribution records, Recovered materials and reprocessing, retention samples handling of returned goods, Complaints and recalls, evaluation of complaints, recall procedures, related records and documents, Waste disposal, scrap disposal producers and records, Loan license (contract manufacture) audits, etc. Unit IV: Drug Regulatory Affairs Harmonization of regulatory requirements including ICH guidelines, regulatory requirements of different regions applicable to pharmaceutical developments, bulk manufacturing, quality control on finished products. Filing of INDA, NDA and ANDA for approval and registration. Review and comparison of each guidelines such as OECD, MHRA, WHO, FDA, ICH, etc. Unit V: Quality Assurance & Quality Management Quality assurance and control - Quality planning, QA program, QA aspect, Quality in material management, Vendor selection & development, etc.

Quality systems: US FDA Guidelines for GLP in non-clinical testing laboratories (only salient features will be covered); Organization & Functioning of Accreditation bodies- ISO-9000, ISO-14000, NABL and OSHA (ISO 18000); pharmaceutical industry Quality systems inspection technique (QSIT); Drug manufacturing inspections, etc.

Total Quality Management (TQM): Quality survey: inspection methods, Quality budget, Vendor Quality Rating. Total Quality Management: Definition, Models of TQM, Elements of TQM,

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Principles of TQM. Deming’s approach, PDCA cycle, Juran’s approach, JIT, Total Productive Maintenance (TPM), etc.

Indicative Practicals:

1. Case study. 2. Document preparation. 3. Auditing and document/ report writing and evaluation of reports. 4. Documentation for in process and finished products Quality control tests for Solid,

Semisolid and Sterile preparations. 5. Protocol preparation for purchase of manufacturing equipments and raw materials. 6. Protocol preparation for documentation of various types of records (BFR, MFR, DR, etc.) 7. Labeling comparison between brand & generics. (Review of Promotion Materials)

Suggested readings:

1. Wilson, K. Walker, J. (1995). Principles and techniques of practical Biochemistry. Cambridge University Press.

2. Chirikjian, JP. (1995). Biotechnology Theory and Technique for undergraduate laboratories. Jones and Barlett Publications.

3. Millar, T. (2000). Biochemistry explained: A practical guide to learning Biochemistry. Harwood Academic Publishers.

4. Seidman, LA, Moore, CJ. (2000). Basic laboratory methods for biotechnology. Benjamin Cummings.

5. Brown, MS. (2013) Next-generation DNA sequencing Informatics. Cold Spring Harbor Laboratory Press.

6. Sidney, WH. (1991). Good Manufacturing Practices for Pharmaceuticals: A Plan for Total Quality Control (Drugs and the Pharmaceutical Sciences). Marcel Dekker Inc.

7. Weinberg, S. (2007). Good Laboratory Practice Regulation. CRC Press. 8. Bunn, G, Nally, JD. (2006). Good Manufacturing-Practices for Pharmaceuticals. CRC

Press

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Module-5: Clinical Research, Data Management & Pharmacovigilance

Unit I: Clinical Trial Design and Data Management Principles in Clinical Research design; Types of study designs, Research objective/ Hypothesis, Clinical Epidemiology, Phases of Clinical Trials, Clinical Trials in Pharmaceuticals, Biologicals and Vaccines, Trial differences for Nutraceuticals, new drugs, medical devices, Bioequivalence studies for generics; CRF (Case report form) Design for Clinical Trial; Query Resolution; Database update, drug safety and database locking; Data Privacy: Implications for Clinical Operations; Data Management in Epidemiology; Data Management in Pharmacoeconomics, etc. Unit II: Data Management & Medical Writing Descriptive Statistics: Data Types; Collection; Sampling, Compilation; Tables & Graphs, Measures of Central Tendency, Measures of variation; hypothesis testing in CR; Clinical Data Management: Principles of CDM, Data Entry, Queries & Data Clarification, Softwares in CDM; Medical Writing: Literature Search & Medical Articles, Contract writing, Publication, Abstracts, Bibliography, Clinical Study Reports, etc.

Unit III: Biostatistics and Its role in clinical Research Role of Biostatics in clinical trial; Population & Sample, Parameter & Statistic, Types of variables, Measures of Central Tendency-Mean, different types of mean, Median, Mode, Histograms, Scatter Plots, Construction & Labeling of graphs, Normal & Binomial Distribution, Research Hypothesis testing, Sample size calculation & Power, p-value, Confidence Interval, Randomization methods, Blinding in Clinical research, etc. Parametric & Non-parametric tests and its applications: t-test, Z-test, chi-square test, ANOVA, Spearman’s correlation coefficient test, Wilcoxon Rank Sum Test, Kruskal-Wallis test, Rank correlation, linear regression & correlation, etc. Unit IV: Drug Safety & Pharmacovigilance Principles of Pharmacovigilance: Importance; National & International Programs; Principles of Pharmacovigilance: ADR; Assessment; Medication errors, Signal detection; Risk assessments; Drug Dictionaries: Coding & Tools; Regulatory Guidelines: ICH, EMEA, USFDA, Sch. 'Y'; Drug Safety: PSURs; Package inserts, etc. Unit V: Clinical trials, GCP & Intellectual Property Rights Concept and fundamentals of IPR, Need and economic importance of IPR, Detail description of various IP Properties, IPR with emphasis on patent regime, registration of patent in India, US and Europe, International registration of patents, factors affecting IP protection, Penalties for violation or infringement, Trade related aspects of IPR. Concepts behind GATT, WTO, TRIPS, TRIMS and GATS, etc.

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Indicative Practicals:

Preclinical and Data entry

1. Planning a clinical study in Oracle Clinical 2. Designing a study 3. Designing Case Report Forms (CRFs) in Oracle Clinical 4. Testing Data Entry Forms and performing Test Data Entry 5. Designing Validation and Derivation Procedures in Oracle Clinical 6. Production data entry in Oracle Clinical 7. Discrepancy management in Oracle Clinical 8. DCF Management, Printing and Maintenance in Oracle Clinical 9. Animal Handling 10. Routes of administration of Drugs

Medical writing

1. Introduction to effective medical writing 2. Technical writing for pharmaceutical, medical device and biotech industries 3. Writing effective standard operating procedures and other process documents 4. Electronic common technical document

Clinical Statistics

1. Introduction to SAS & CDISC standards 2. Running SAS programs 3. Descriptive information and statistics 4. An overview of statistical tests in SAS 5. Exploring data with graphics 6. Using where with SAS procedures 7. Missing values in SAS 8. Common SAS options 9. Overview of SAS syntax of SAS procedures 10. Common error messages in SAS 11. Inputting raw data into SAS 12. Reading dates into SAS and using date variables 13. Creating and recording variables 14. Using SAS functions for making/recording variables 15. Sub-setting variables and observations 16. Labeling data, variables and values 17. Using Proc Sort and the BY statement 18. SAS Functions

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Suggested Readings:

1. McFadden, E. (2007). Management of data in clinical trials. Wiley-Blackwell. 2. Good, PI. (2002). A manager's guide to the design and conduct of clinical trials. Wiley-

Blackwell. 3. Grant, GR, Ewens, WJ. (2005). Statistical Methods in Bioinformatics: An Introduction.

Springer. 4. Jagota, A. (2000). Data Analysis and Classification for Bioinformatics. Bioinformatics By

the Bay.

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Module-6: Biosimilars, Monoclonal Antibodies and Recombinant Technology

Unit I: Recombinant DNA Technology: Expression vectors: Prokaryotic, Eukaryotic vectors—yeast, mammalian and insect cell systems. Viral vectors—retroviral, pox, rhabdo and adeno virus vectors. Fusion proteins—signals for protein secretion, purification of recombinant proteins, etc. Restriction and modification enzymes; Vectors; cDNA and genomic DNA library; Hybridoma technology; Gene isolation; Gene cloning; Transposons and gene targeting; DNA labeling; DNA sequencing; Polymerase chain reactions; DNA fingerprinting; Southern and northern blotting; In-situ hybridization; RAPD; RFLP; Site-directed mutagenesis; Gene transfer technologies; Gene therapy; Genetic engineering in animal cell culture; Animal cell preservation, etc. Unit II: Biosimilar Products: Regulation ; patent situation, First generation of biosimilar products; EPO, CSFs, bGH, insulin, hepatitis B vaccines, factor VIII, IFN; development of biosimilar and its requirements, etc. Unit III: Analysis of Recombinant Product: Protein based analysis: determination of protein concentration, amino acids sequencing, peptide mapping, electrophoresis (SDS-PAGE, native PAGE, electro-focusing, two-dimensional electrophoresis), Western blot, DNA based analysis, Sequencing, Hybridization, etc. Unit IV: Monoclonal Antibody Production: Production Mab in E,coli, second generation Mab, Advantages and disadvantages of Mab Application in disease diagnosis and therapeutic agent, Protein purification, Catalytic Mabs; Hybridoma technology and Recombinant technology to produce monoclonal antibody, monoclonal antibodies for therapeutic purpose and their mode of action, etc. Unit V: Recombinant vaccines: Subunit vaccines, Hepatitis B, FMD, HSV, TB, AIDS, RNA Vaccines, Edible vaccines, Attenuated vaccines, Cholera, Salmonella, Leishmania Vector recombinant vaccines - Vaccinia virus, Antigen delivery by bacteria, etc.

Indicative Practicals:

1. Isolation of Plasmid DNA from E.Coli by Alkaline lysis method 2. Gene Cloning: PCR Amplification, Restriction Digestion, Competent cell preparation, DNA

Ligation, Transformation, Screening of recombinant DNA 3. Induction of gene expression in E.coli, cell lysis and protein extraction 4. Visualization of proteins by SDS PAGE 5. Western blotting 6. ELISA

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7. Production of murine monoclonal antibody against antigens of infectious agents by hydridoma technique

8. Production of phage display library of scFv or camel nanobody 9. Selection of antigen-specific phage displayed antibody fragment by panning or other

technique Suggested Readings:

1. Rose, NR, Friedman, H, Fahey JL. (1986). Manual of Clinical Laboratory Immunology. American Society for Microbiology.

2. Chirikjian, J.P. (1995). Biotechnology Theory and Technique for undergraduate laboratories. Jones and Barlett Publications.

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Module-7: Environmental Biotechnology

Unit I: Bioremediation of Waste Water Detection and control of micro-organisms in environmental fresh water, in source and drinking water; Potable and nonpotable water; Methods of water sampling for pollution analysis; Biosensors - types and applications in environmental pollution detection and monitoring; Biological treatment: stabilization pond, aerated lagoon, activated sludge process, trickling filter anaerobic treatment, etc. Unit II: Bioremediation for Solid Waste & Air Pollution Management Treatment of solid wastes (Anaerobic digestion and composting): Biofertilizers, Bioplastics, Bioleaching, Biocontrol; Xenobiotic Compounds, Recalcitrance, Hazardous Wastes, Bioaugmentation, Biosorption of Heavy metals, Biodegradation of Xenobiotics, Biological Detoxification of oil spills, Bio applications to Hazardous Waste Management, Human health and xenobiotics, sources and treatment strategies for polychlorinated biphenyls, pesticides, toxic pollutants, polymers, Textile chemical residues ; Biomedical wastes, Types of biomedical wastes; Hazards caused by biomedical wastes; Treatment strategies for biomedical wastes; Air pollution and its control through Biotechnology (deodorization, reduction in CO2 emission, bioscrubbers, biobeds, biofilters, etc.). Unit III: Effluent treatment systems Sewage and waste water treatments systems; Primary, secondary and tertiary treatments; Measurement of treatment efficiencies; Biological treatments - aerobic versus anaerobic treatments; Environmental pollution control- Bioremediation, Bioaugmentation and Biostimulation; Biofilms in treatment of waste water; Biofilm development and biofilm Kinetics; Aerobic Biofilms; Bioreactors for waste water treatments; Reactors types and design; Reactors in series; Development and optimization of membrane bioreactor process for use in sanitary and industrial sewage treatment, etc. Unit IV: Biogas, Bio-Diesel & Bioenergy Energy conservation, energy development, alternative energy sources to reduce the impact of environmental pollution, Types and generations of bioenergy, Different production methods of bioenergy, Solar power - Solar cell & Solar heating, etc. Biogas technology, plant design, construction, operation, biogas form organic wastes, water weeds, landfills, microbiology of anaerobic fermentation, etc. Bio-diesels: Base materials used for production of Bio Diesel (Karanji oil, Neemoil, Sunflower oil, Soyabeen oil, Musturd oil, Palm oil, Jatropha seeds, Algae). Process of separation of Bio Diesel. Properties Diesel blended with vegetable oil, and difference in performance of Engine, etc. Unit V: Application of Technologies for Environment Types of separation technology, MBST and their cost effective application; Physico-chemical properties of membrane; Different membrane modules and their applications in Biotechnology and Food industries, etc.

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Indicative Practicals:

Enrichment, Isolation and Enumeration of Microorganisms from the Environment 1. Isolation and Enumeration of soil bacteria 2. Isolation and Enumeration of Green Algae by MPN Method 3. Isolation and Enumeration of Fungi 4. Enrichment of purple non sulphur bacteria.

Analysis of Waste Water 1. Collection, Processing and Storage of Effluent Sample 2. Determination of Biological Oxygen Demand (BOD) in Waste Water Sample 3. Determination of Chemical Oxygen Demand (COD) in Waste Water Sample 4. Determination of Dissolved Oxygen (DO) in Waste Water Sample 5. Determination of Total Dissolved Solids in Waste Water Sample 6. Analysis of Total Hardness of Waste Water Sample 7. Analysis of Temporary Hardness of Waste Water Sample 8. Analysis of Waste Water/Sludge for Heavy Metals 9. Determination of Sound Level by using Sound Level Meter 10. Organic nitrogen, Chloride, Sulfate, Ca-Mg Hardness, Phosphorus Phosphate Estimation Exp 11. Bacteriological analysis by MPN technique Exp. 12. Microbial degradation of textile dyes/pesticides/hydrocarbons and oils 13. Assay of enzymes involved in biotransformation. 14. Evaluation of toxicity of the product. 15. Bioremediation 16. Pollutant removal using microorganisms from industrial effluent. 17. Effect of heavy metals on microbial growth 18. Baseline Data Studies: EIA, REIA, etc.

Suggested Reading:

1. Davis, BD, Dulbecco, R, Eisen, HN, Ginsberg, HS. (1992). Microbiology. Harper and Row Publishers, Singapore.

2. Maier, RM, Pepper, IL, Gerba, CP. (2000) Environmental Microbiology. Academic press. 3. De, AK. (2000). Environmental Chemistry. New age International (P) Ltd., New Delhi, India. 4. Lave, LB, Upton, AC, (1987). Toxic Chemicals, health and the Environment. Baltimore: Johns

Hopkins University Press.

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Module-8: Animal vaccine and Diagnostics Unit I: Diseases Diagnostics Serodiagnostic: agglutination-reaction based tests, precipitation-reaction based tests, complement fixation test and enzyme immunoassays; Principles of molecular diagnostic tests: PCR, RT-PCR, Southern blotting, northern blotting, western blotting, dot-blot, DNA diagnostics versus serodiagnostics, Development and validation of diagnostic tests, etc. Unit II: Vaccines Classification, comparison of major types. Components of various types of vaccines: immunogens, adjuvants, stabilizers, preservatives, vehicles. Vaccine qualities: definitions and methods of testing. Vaccine development: cost-effectiveness of preventive immunization programmes, stages of development, clinical trials and regulatory requirements, etc. Unit III: Traditional vaccines Inactivated, attenuated and toxoid vaccines. Methods of construction of traditional vaccines: microbial cultures, embryonated eggs, cell culture. Seed-lots of vaccine organisms. Methods of inactivation and attenuation of pathogens, etc. Unit IV: Modern vaccines Nucleic acids, vector vaccines, recombinant expressed immunogens, synthetic peptides, marker vaccines, etc. Combination/multivalent vaccines; Novel immunomodulators and delivery systems; Modern methods of vaccine construction: methods based on synthetic chemistry and rDNA technology, etc. Unit V: Novel vaccines Nucleic acids, marker vaccines, mucosal vaccines, bacterial ghosts as vaccines, virus-like particles. Futuristic vaccines: anti-allergic, anti-autoimmune diseases, deaddiction vaccines, transplant survival/ prolonging vaccines; Immunization schedules of veterinary vaccines, logistic problems and vaccination failure; Strategies of disease control and eradication by vaccination, etc. Indicative Practicals: Serodiagnostic tests for infectious diseases

1. Bacterial slide and microtiter plate agglutination, agar gel immunodiffusion test 2. Passive hemagglutination, hemagglutination inhibition and latex agglutination tests,

complement fixation test, 3. Enzyme linked immunosorbent immunoassays, dot-ELISA, fluorescent antibody

technique, immuno-electron microscopy, virus neutralization test, etc.

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Molecular diagnostic techniques: 1. protein profiling of infectious agents by SDS-polyacrylamide gel electrophoresis 2. Antigen profiling of infectious agents by immunoblotting 3. Nucleic acids isolation from infectious agent 4. Detection of infectious agent nucleic acids by various formats of polymerase chain

reaction and reverse transcription-PCR, 5. Dot-blot technique, etc.

Suggested Readings:

1. Dodds WJ & Schulz R. (1999). Veterinary Vaccines and Diagnostics. Academic Press. 2. Levine MM, Kaper JB, Rappuoli R, Liu, MA, Good, MF. (2004). New Generation Vaccines.

Marcel-Dekker. 3. Pastoret, PP, Blancou, J, Vannier, C, Verschueren, C. (1997). Veterinary Vaccinology.

Elsevier. 4. Detrick, B, Hamilton, RG, Folds, JD. (2006). Manual of Molecular and Clinical Laboratory

Immunology. American Society for Microbiology. 5. Rose, NR, Friedman, H, Fahey, JL. (1986). Manual of Clinical Laboratory Immunology.

American Society for Microbiology. 6. Weir DM. (1986). Handbook of Experimental Immunology. Blackwell Scientific Publications.

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Module-9: Genomics and Bioinformatics

Unit I: Structural genomics Classical ways of genome analysis, large fragment genomic libraries; Physical mapping of genomes; Genome sequencing, sequence assembly and annotation; Comparative genomics, etc. Unit II: Functional genomics DNA chips and their use in transcriptome analysis; Mutants and RNAi in functional genomics; Metabolomics and ionomics for elucidating metabolic pathways, etc. Unit III: Bioinformatics Resources Biological databases – primary, secondary and structural, Protein and Gene Information Resources:

• Nucleic acid sequence databases: GenBank, EMBL, DDBJ • Protein sequence databases: SWISS-PROT, TrEMBL, PIR, PDB • Genome Databases at NCBI, EBI, TIGR, SANGER • Other Databases of Patterns/Motifs/System Biology

(Gene and protein network database and resources), etc. Unit IV: Sequencing: A tool with wide application

• Various file formats for bio-molecular sequences: genbank, fasta, gcg, msf, nbrf-pir etc. • Basic concepts of sequence similarity, identity and homology, definitions of homologues,

orthologues, paralogues. • Scoring matrices: basic concept of a scoring matrix, PAM and BLOSUM series. • Sequence-based Database Searches: what are sequence-based database searches, BLAST and

FASTA algorithms, various versions of basic BLAST and FASTA; DNA sequence analysis, cDNA libraries and EST, EST analysis, pairwise alignment techniques, database searching, multiple sequence alignment; Secondary database searching, building search protocol, computer aided drug design – basic principles, docking, QSAR, Analysis packages – commercial databases and packages, GPL software for Bioinformatics, web-based analysis tools, etc.

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Indicative Practicals:

1. Sequence retrieval from primary nucleotide and protein databases (GenBank) 2. Sequence retrieval from secondary nucleotide and protein databases (SWISSPROT, TREMBL) 3. Study of PDB format file. 4. Study of specialized databases (SGD, KEGG) 5. Bibliographic retrieval (PubMed, PubMed Central) 6. Database similarity (FASTA and BLAST) searches – Analysis of parameters affecting

alignment. 7. Pair wise comparison of sequences – Analysis of parameters affecting alignment. 8. Multiple alignments of sequences – Analysis of parameters affecting alignment. 9. Evolutionary studies / Phylogenetic analysis – Analysis of parameters affecting trees. 10. Identification of functional sites in Genes / Genomes. 11. Restriction mapping. 12. Primer Design. 13. Secondary structure prediction of proteins. 14. Protein structure visualization (RASMOL) 15. Pattern elucidation in Proteins (PROSITE). 16. Superposition of structures – Calculation of RMSD for main chain atoms. 17. Molecular Docking studies. 18. Genome databases of Plants, animals and pathogens 19. Metagenomics

Suggested Readings

1. Azuaje F, Dopazo J. (2005). Data Analysis and Visualization in Genomics and Proteomics. John Wiley & Sons.

2. Brown TA. (2007). Genome 3. Garland Science Publication. 3. Campbell, AM, Heyer, L. (2006). Discovering Genomics, Proteomics and Bioinformatics.

Pearson Education. 4. Attwood, TK, Parry-Smith, DJ. (1999). Introduction to Bioinformatics. Prentice Hall. 5. Rastogi, SC, Mendiratta, N, Rastogi, P. (2009). Bioinformatics: Concepts, Skills and

Applications. CBS.