Grou p-A Group -B Group -C Group -D · Waste water treatment – primary waste water treatment:...

Ph.D in Biotechnology Course Work Syllabus

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VISVESVARAYA TECHNOLOGICAL UNIVERSITY, BELGAUM

SCHEME AND SYLLABUS FOR Ph.D. /M.Sc(Engg) Course work (BIOTECHNOLOGY)

Note: • M.Tech degree holders have to select one subject from each group • M.Sc degree holders have to select six subjects by choosing atleast one subject from each group. • Subjects studied in earlier degrees are not permitted to select for Ph.D./M.Sc Engg course work

Subject Code Groups Marks

10Res.BT11X Group-A 100

10 Res.BT12X Group-B 100 10 Res.BT13X Group-C 100 10 Res.BT14X Group-D 100

Group-A Group-B Group-C Group-D 10Res.BT111 - Biomolecules and Molecular Biology

10 Res.BT121 -Thermodynamics 10 Res.BT131 - Applied Bioinformatics 10 Res.BT141 -Tissue Engineering

10Res.BT112 - Plant and Animal Biotechnology

10 Res.BT122 -Bioprocess control and Instrumentation

10 Res.BT132 - Computer Programming and Biostatistics

10 Res.BT142 -Bioethics, biosafety and IPR

10Res.BT113 - Microbial Biotechnology

10 Res.BT123 -Advanced Downstream Processing

10 Res.BT133 - Genomics, Proteomics and Microarray

10 Res.BT143 -Management, Entrepreneurship and Biobusiness

10Res.BT114 - Environmental Biotechnology

10 Res.BT124 -Reaction Engineering 10 Res.BT134 -Data warehousing and Data mining

10 Res.BT144 -Clinical Biotechnology

10Res.BT115 - Food Biotechnology

10 Res.BT125 -Heat and Mass transfer 10 Res.BT135 -Java for Bioinformatics & Biomedical Application

10 Res.BT145 -Renewable Energy Sources

10Res.BT116 Pharmaceutical Biotechnology

10 Res.BT126 -Bioreactor Design and Economics

10 Res.BT136 -Molecular Modeling and Simulation

10 Res.BT146 -Nanobiotechnology

10Res.BT117 -Agriculture Biotechnology

10 Res.BT127 -Biosensors: Design and Applications

10 Res.BT137 - Metabolic Engineering 10 Res.BT147 -Research Methodology


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GROUP – A

10Res.BT111 Biomolecules and Molecular Biology

Introduction to Macromolecules: Introduction to Biomolecules; Macromolecules; Carbon chemistry; Nucleic acids: storage and transfer of genetic information; Proteins: structure, folding and catalysis; Lipids: membranes, energy transactions; Carbohydrates: energy transactions, building blocks. Nucleic Acids: Structure of DNA-A, B, Z and triplex DNA. Measurement of properties-Spectrophotometric, CD, and AFM. Electron microscope analysis of DNA structure: Geometries, Glycosidic bond, Rotational isomers, preferred torsion angles and Ribose puckering. Primary, secondary and tertiary structure of DNA. Melting of DNA double helix (Hyperchromicity). Structure of RNA: Structural aspects of mRNA, tRNA and rRNA; importance of siRNA; RNA-Protein interactions during transcription and translation. Proteins: Composition and primary structure of proteins; Conformational analysis and forces that determine protein structures and geometries; potential energy calculations, phi, psi, omega angles, Ramachandran or steric contour diagram, chi angles of side chains in proteins; hydrogen bonding; disulphide bonds; hydrophobic interactions; alpha helices; beta sheets; helix to coil transition, general features and thermodynamic aspects of protein folding and folding kinetics, protein-ligand interactions, Scatchard plot, co-operative interactions. Hemoglobin Hill constant. Relationship between the primary, secondary, and tertiary structure of proteins. Fibrous proteins; Quaternary structures: dimers, homo and hetero dimers, trimers, tetramers; Domain structures of proteins. Replication, Repair and Recombination: Replication initiation, elongation and termination in prokaryotes and eukaryotes; Enzymes and accessory proteins; Fidelity; Replication of single stranded circular DNA; Gene stability and DNA repair- enzymes; Photoreactivation; Nucleotide excision repair; Mismatch correction; SOS repair; Recombination: Homologous and non-homologous; Site specific recombination; Chi sequences in prokaryotes; Gene targeting; Gene disruption; FLP/FRT and Cre/ Lox recombination. Prokaryotic and Eukaryotic Transcription: Prokaryotic Transcription; Transcription unit; Promoters: Constitutive and Inducible; Operators and Regulatory elements; Initiation; Attenuation; Termination: Rho-dependent and independent; Antitermination; Transcriptional regulation: Positive and negative; Operon concept: lac, trp, ara, his, and gal operons; Transcriptional control in lambda phage; Transcript processing; Processing of tRNA and rRNA Eukaryotic transcription and regulation; RNA polymerase structure and assembly; RNA polymerase I, II, III; Eukaryotic promoters and enhancers; General Transcription factors; TATA box binding protein (TBP) and TBP associated factors (TAF); Activators and repressors; Transcriptional and post-transcriptional gene silencing. Post Transcriptional Modifications: Processing of hnRNA, tRNA, rRNA; 5'-Cap formation; 3'-end processing and polyadenylation; Splicing; RNA editing; Nuclear export of mRNA; mRNA stability; Catalytic RNA. Translation and Transport machinery; Ribosomes; Composition and assembly; Genetic code; Degeneracy of codons; Termination codons; Isoaccepting tRNA; Wobble hypothesis; Mechanism of initiation, elongation and termination; Co- and post-translational modifications; Genetic codon variation in mitochondria; Transport of proteins and molecular chaperones; Protein stability; Protein turnover and degradation.

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10Res.BT112

Plant and Animal Biotechnology

Techniques and Applications of Plant Tissue Culture : Plant culture media. Growth regulators and adjuvants. Methods of plant regeneration in vitro: organogenesis and embryogenesis. Callus culture, Single cell and cell suspension culture. Micro propagation techniques. Somatic embryogenesis. Production of industrially important secondary metabolites from plants. Hairy root culture. Protoplast culture for the production of somatic hybrids and cybrids. Production of haploids through anther, microspore, Ovule culture role in Plant breeding. Cryopreservation of plant cell and tissues. Transformation Techniques in Plants: Plant vectors for genetic transformation, Agrobacterium mediated gene transfer in plants, Organization of Ti plasmids. Design of Ti plasmid based vectors. Plant viruses as tool to deliver foreign genes. Physical methods of gene transfer – Electroporation, microinjection, particle bombardment, PEG and liposome mediated. Screening of transgenics by marker genes. Transgene silencing and stability. Transplastomic transformation - Chloroplast transformation. Metabolic Engineering in Plants: Plant oil modifications by genetic engineering; Production of medium and longer chain fatty acids. Improvement of seed oil for health benefits (PUFA oil). Metabolic engineering of flavanoids vitamin E, and carotenoid pathway (golden rice) Transgenic Plants as Biofactories: Biopharming in plants for the production of industrial enzymes, edible vaccines, plant antibodies, therapeutic proteins a Plant metabolic engineering for the production of biodegradable plastics (Polyhydroxybutyrate and Polyhydroxyvalerate), Biopharming of carbohydrate Transgenic Plants for Crop Improvement: Manipulation of photosynthesis to increase crop yield. Engineering plant proteins, lipids and vitamins for improved nutrition. Post harvest protection of plants: antisense technique to increase shelf life of fruits and flowers, Herbicide tolerance, Biotic and abiotic stress. Plant responses to abiotic stress. Transgenic strategies for drought, cold and saline tolerance. Genetic manipulation of plants for biotic stress: pest resistance plants. Transgenic technology for the development. Viral, bacterial and fungal resistance plants. Animal Cell Culture Technology: Culturing of cells, primary and secondary cell lines, Animal cell growth characteristics and kinetics; Scaling up of animal cell culture; Various types of bio-reactors used for animal cell cultures; Cell lines and their applications. Specialized techniques in animal cell culture-Amniniocentesis, Oncofetal antigenes, 3D culture, cell immobilization. Genetic Manipulation in Animals: Strategies for gene transfer in animal cells; mechanisms of transfection, vectors used in transfection. Methods of production of transgenic animals, recent advances in gene targeting technology. Characterization and screening of transgenic animals. Applications of genetically modified animals and molecular Biopharming. Stem cell research - Hematopoietic and embryonic stems cells. Gene Therapy- Prospects and problems; Knock out mice and mice model for human genetic disorder. Hybridoma Technology and Healthcare: Production of Hybridomas- Antibodies, Immunotoxins, Vaccines, Toxoids, Inerferons and Antiviral substances. Tumour immunology, Immune diagnosis and therapy with monoclonal antibodies. Animal Breeding and Ethical Issuses: Artificial insemination and storage; In vitro fertilization and embryo transfer micro manipulation of embryos, advantages of cell manipulation techniques. Hazards of artificial breeding. Ethical issues in animal biotechnological products and techniques.

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10Res.BT113

Microbial Biotechnology

Introduction to Microbial Biotechnology: Scope and techniques. Cultivation and growth of microorganism – Physical conditions for cultivation of microorganisms, reproduction and growth of microorganisms. Structure and function of components of the bacterial cell envelope. Protein secretion with a special emphasis on its various roles in pathogenesis. Microbial Genetics and Strain Improvement: Transformation, conjugation and transduction. Development of industrial microorganisms – Mutation, mutant detection, mutant selection. Microbes and genetic engineering – Introduction to genetic engineering, producing genetically engineered microorganisms – Escherichia coli and Saccharomyces cerevisiae. Interaction between bacteria and bacteriophages. Microorganisms for insect and pathogen control – Bioinsecticides (Bt proteins, Chitinase). Fermentation and Downstream Processing: Types of fermenter, process of fermentation, Microbial culture system – batch culture, fed batch culture, continuous culture, measurement and control of bioprocess parameters, scale-up. Downstream processing – Solids removal, primary separation, purification and isolation of products. Microbial Production of Enzymes: Genetic and metabolic regulation of enzyme action and enzyme formation. Hydrolyses (Glycosidases, cellulase, proteolytic enzymes), Recombinant DNA technology for enzyme production. Immobilization of enzymes and cells – methods of immobilization, applications. Microbial Production of Organic Compounds: Solvents - Alcohol, Glycerol. Organic acids – Citric acid, acetic acid, L-ascorbic acid, lactic acid. Antibiotics – Penicillins (Penicillin), Cephalosporins (cephalosporin), Aminoglycosides (streptomycin), Tetracyclines (chlortetracycline), Macrolides (erythromycin A). Amino acids – L-glutamic acid, L-lysine, L-tryptophan. Vitamins – Vitamin B12, Riboflavin, Beta-carotene. Foods and beverages – Cheese, single cell protein (yeast), beer, wine. Polysaccharides (Xanthan) and polyhydroxyalkanoates (polyhydroxybutyrate). Microbes in Energy & Environment: Alcohol and methane from biomass, photo-biological hydrogen production, Electricity from biofuel cells. Microbial mining and metal biotechnology – Bioleaching and biosorption.

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10Res.BT114 Environmental Biotechnology

Introduction: Concept and scope of environmental biotechnology. Elements of life and biodistribution of elements. Microbiology of air, water & soil, interactions among soil microorganisms. Role of environmental biotechnology in sustainable development. Waste Water Biotechnology: Nature and components of Waste water, Eutrophication – causes: detergents, effects and control. Waste water treatment – primary waste water treatment: unit operations, secondary waste water treatment: design and modeling of activated sludge process - aerobic and anaerobic, and tertiary waste water treatment - reverse osmosis and ultra filtration, microbial removal of phosphorous and nitrogen. Wastewater composition and treatment strategies in food processing & pharmaceutical industries - sugar factories, vegetable oil industries, potato processing industries, dairy industries, beverages industries distilleries & pharmaceuticals. Solid Waste Management: General composition of urban solid wastes, treatment: aerobic treatment, anaerobic treatment, biogass generation, solid waste management through biotechnological processes involving - hazardous wastes, Biomedical wastes, Dairy wastes, Pulp industry wastes, Textile industry wastes, leather industry wastes and pharmaceutical industry wastes, petroleum wastes treatment. Integrated waste management, super critical water oxidation of wastes. Energy and Environment: Renewable and non-renewable resources. Conventional fuels and their environmental impacts. Modern fuels and their environmental impacts. Biotechnological inputs in producing good quality natural fibers. Plant sources like Jetropha, Pongamia etc. Waste as an energy core, energy recovery systems for urban waste, technology evaluation, concept of gasification of wastes with molten salt to produce low-BTU gas; pipeline gas from solid wastes by syngas recycling process; conversion of feedlot wastes into pipeline gas; fuels and chemicals from crops, production of oil from wood waste, fuels from wood waste, methanol production from organic wastes. Gasohol, Dye-pigments, sensitized solar cells. Xenobiotics: Characteristics of Xenobiotics, dose response relationship, effects of xenobiotics, Relationship of Bioaccumulation with Chemical Structures, Eco-physiology of Bioaccumulation - Process of toxicants uptake, Factors affecting bioaccumulation, measurement of bioaccumulation. Degradation of Xenobiotics in the Environment. Biodegradable alternatives for xenobiotics. Biomonitors of environment, Bioremediation using microbes, Phytoremediation. Bioleaching & Biomining: Biometallurgy, Microbes in Bioleaching and Metal Recovery: Microbial recovery of phosphate, microbial extraction of petroleum and microbial production of fuels. Green Technology and Environmental Protection: Principles of green technology, enzyme based detergents, alternative pesticides, alternative fuels, bio polymers, techniques and directions in practicing green technology, super critical liquid carbon dioxide solvent, polylactic acid polymers, use of hydrogen peroxide as a benign bleaching agent in paper industry, enzymatic production of cotton textiles, biodegradable builders in detergents, replacement of wood preservatives and synthesis of specialty compounds. Biodiversity Conservation: Significance of biodiversity, threats to biodiversity, Biosphere reserves and Ecosystem Conservation, Approaches to Bioresource conservation programme, Biotechnological processes for bioresource assessment, BT in ex situ conservation of Biodiversity, BT and its role in utilization of Biodiversity, International initiatives for biodiversity management. Biotechnology & Climate Change: GHG & Carbon foot printing, Biotechnology- a sink for GHGs, reduction in GHG emission, alternatives for GHG, carbon credit & trading through BT. Environmental Management in Biotech Industries: Environmental issues of biotech industries, environmental management & ISO 14000, Lean manufacturing - waste minimization, Green solvents & solvent recovery, Excellence modules – 5S, Kaizen, six sigma. Future Strategies to Reduce Pollution and Conserve a Natural & Healthy Environment

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10Res.BT115

Food Biotechnology

Basic Constitutes of Food: Basic constituents of food, colloidal systems in food, molecular stability of colloidal systems, types of food starches, soluble fibers: pectin’s, mucilage & gums, protein rich foods, oils in foods. Food Microbiology: Microbial growth pattern, types of microorganisms associated with food: mold, yeast and bacteria. Contaminants of food stuff, milk and meat during handling and processing. Mechanism of food spoilage. Biochemical changes caused by microorganism. Determination of various types of food products. Food borne intoxicants and mycotoxins Food Preservation Technology: Food preservation by high and ultra high temperatures- canning, drying. Food dehydration: . Equipments for food dehydration: fixed tray dehydration, cabinet drying, tunnel drying. Freeze dehydration, controlled atmosphere, storage, Food preservation by irradiation treatment. Preservation by freezing and refrigeration. Frozen foods. Thermal properties of frozen foods. Food freezing equipments: Air blast freezers, plate freezers and immersion freezers. Preservation by Chemicals and Bacteriocins Food Production Technology: Importance of food industry, specific objectives of food processing, impact of food processing on food constituents. Production of single cell protein, Tailoring of milk proteins and milk fats, Production of fermented food products: yoghurt, pro-biotic cheese, nutritional value, labeling of constituents: Soya foods, organic foods, dietary foods, nutritional food supplements, Use of plant cell culture for the production of food additives (Vanillin, Capsaicin), microbial transformations, regulatory and social aspects of BT. Food packaging, edible films, Marketing of food and promotional strategies. Biotechnology for Improved Processing: Role of biotechnology in food industry, maintenance of nutritional quality, Enzymes in bakery and cereal products, utilization of hydrolases and lipases enzymes. Applications of immobilized enzymes in food industry, enzymes for enhanced flavor and aroma compounds, enzymes in fat and oil industries. Genetically modified plants for high nutritional food. Food Quality Assurance and Control: Importance and functions of quality assurance and control: Methods of quality, concept of rheology, assessment of food materials- fruits, vegetables, cereals, dairy products, meat and processed food products. Microbiological safety of food products, chemical safety of food products, contaminants by heavy metal, fungal toxins and pesticide residue. Food regulations, grades and standards, USFDA/ ISO 9000 Series. Food adulterations and safety, sensors and instrumental analysis in quality control food laws and standards.

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10Res.BT116

Pharmaceutical Biotechnology

Introduction: Introduction to pharmaceutical biotechnology, pharmacokinetic concepts, current research trends, new advances and approved biologicals for pharmaceutical use and manufacturing principles. Quality assurance and control; Concept of GMP, GLP.

Therapeutics based on biotechnology: Hematopoietic growth factor and coagulation factors, interferons and cytokines; Preparation and standardization of hormones-thyroid, insulin and growth hormones; Enzymes-Enzymatic therapy and monographs; antibiotics and their derivatives-penicillin, streptomycin, tetracycline, cephalosporins, macrolides, peptide antibiotics (any two); vaccines -BCG, DPT, Poliomyelitis, Typhus, toxoids-diptheria and tetanus; antitoxins-diptheria and gas-gangrene(any two); others-whole human blood, dried human plasma, gamma globulins, clinical dextran and absorbable haemostats, uses, and storage. Biotransformation: Introduction, methods used in biotransformation, steroid transformation, contraceptives, L- Dopa, chemical reactions and mechanisms (hydroxylation, aromatization, synthetic routes, epoxidation and others), production and application of monoclonal antibodies. Nutraceuticals: Antioxidants, flavanoids, carotenoids, cholesterol lowering chemicals, nutritional importance and their functions, deficiency diseases, nutritional status evaluation. Drug delivery systems: Introduction to drug delivery systems and methods, overview of barriers, calculation of drug metabolism and, pharmacodynamics. Recombinant Proteins and Proteomics in drug develop ment: Role of proteomics in drug development, Application of recombinant proteins in pharmaceutical industry, health care and future prospects.

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10Res.BT117

Agriculture Biotechnology

Applications of plant transformation technology for productivity and performance, disease resistance, genes and gene constructs used for viral resistance by coat protein mediated production, bacterial resistance by lysozyme gene and fungal resistance by chitinase and beta glucanase genes. Agrobacterium mediated tranformation. Crop improvement to resist adverse soil conditions. Salinity tolerance, drought resistance. Herbicide resistance in commercially important plants. Insecticide resistance through Bt-gene. Integrated pest management. current status of Bt crops in the world. Effect of transgenic crops on environment. Introduction to plant cell culture. Explant selection, sterilization and inoculation; Various media preparations; MS, B5, SH PC L-2; Callus and cell suspension culture; plant regeneration: organogenesis. Somatic embryogenesis; somaclonal variation, its genetic basis and application in crop improvement. Role of tissue culture in rapid clonal propagation, production of pathogen - free plants and "synthetic seeds"; haploid production: advantages and methods. Protoplast technology.

Antisense RNA technology (ACC synthase gene and polygalacturonase) Delay of softening and ripening of fleshy fruits by antisense RNA for ACC synthase gene in tomato, banana. Use of antisense RNA technology for extending shelf life of fruits and flowers. Protection of cereals, millets and pulses following harvest using biotechnology. Biotechnology for fortification of agricultural products- Golden rice, transgenic sweet potatoes.

Importance of biofertlilizers in agriculture. (Rhizobium, azatobacter, Mycorrhiza, Frankia and Blue green algae) current practices and production of biofertilizers.

An overview of Legal and Socio-economic impact of Biotechnology. Biotechnology & hunger. Ethical issues associated with labeling and consumption of GM foods. Public perception of GM technology. Biosafety management. Cartagena protocol on biosafety. Ethical implication of BT products, public education, Biosafety regulations, experimental protocol approvals, guidelines for research, environmental aspects of BT applications.

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GROUP - B

10Res.BT121 Thermodynamics

Basic concepts in engineering thermodynamics: System, surrounding, open and closed systems. Properties, intensive and extensive properties. State and path functions, equilibrium state and phase rule, zeroth law of thermodynamics, reversible and irreversible processes. Laws of thermodynamics: First law of thermodynamics – General statement of first law of thermodynamics, first law of thermodynamics for cyclic and nonflow process, heat capacity. Second law of thermodynamics : General statement of second law , Principles of refrigeration, concept of entropy, Carnot principle, calculation of entropy changes, Clausius inequality, entropy and irreversibility, third law of thermodynamics. PVT behavior: PVT Behavior of pure fluids, equations of state and ideal gas law, processes involving ideal gas law: Constant volume, constant pressure, constant temperature, adiabatic and polytrophic processes. Estimation of thermodynamic property for real gases. Principles of corresponding states, generalized compressibility charts. Thermodynamics properties of fluids: Reference properties, energy properties, derived properties, work function, Gibbs free energy, relationships among thermodynamic properties: exact differential equations, fundamental property relations, Maxwell’s equations, Clapeyron equations, entropy heat capacity relations, modified equations for U and H, effect of temperature on U,H and S, relationship between Cp and Cv, Gibbs-Helmholz equation. Fugacity, fugacity coefficient, effect of temperature and pressure on fugacity, determination of fugacity of pure gases, solids and liquids, activity: effect of pressure and temperature on activity, thermodynamic diagrams. Properties of solutions: Partial molar properties, chemical potential, fugacity in solutions, Henry’s law and dilute solutions, activity coefficients, Gibbs-Duhem equation, property changes of mixing, excess properties. Phase equilibria: Criteria of phase equilibria, criterion of stability, duhems theorem, vapour liquid equilibria, VLE in ideal solutions, nonideal solutions, VLE at low pressure, VLE at high pressures, consistency test for VLE data, calculation of activity coefficient using Gibbs-Duhem equation, liquid –liquid equilibrium diagrams. Chemical reaction equilibirium: Reaction stoichiometry, criteria for chemical reaction equilibrium, equilibrium constant and standard free energy change, effect of temperature, pressure on equilibrium constants and other factors affecting equilibrium conversion, liquid phase reactions, heterogeneous reaction equilibria, phase rule for reacting systems.

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10Res.BT122

Bioprocess control and Instrumentation

Introduction to Process Control: Process control: flow, pressure, temperature and level measurements. Dynamic and steady state Processes. Automatic process control principles and Block diagram representation, open loop and closed loop system. Sensors: Physical, chemical and Biosensors. On-line sensors for cell properties. Off-line Analytical methods. Controllers: Introduction to Controllers, Classification of controller based on type of action: continuous and discontinuous, two position and floating controllers (discontinuous), Proportional, Proportional-Integral (PI), Proportional-Derivative (PD) & Proportional-Integral-Derivative (PID) controllers. Final Control Element: I/P Convert-pneumatic, electric and hydraulic actuators. Control valve-characteristics of control valve. Types of valve: Globe, Butterfly, Diaphragm and Ball. - Process Monitoring: Agitation and capacity coefficient in fermenters; Control of pH, dissolved oxygen, dissolved carbon dioxide, temperature, foam etc. Rheological measurement and control application of microcomputers in the study of microbial bioprocess. Data Acquisition Techniques: Computer Interfaces and peripheral devices; Fermentation software. Data smoothing and interpolation; State and parameter estimation; Direct regulatory control; cascade control of metabolism. Current practices of instrumentation and data acquisition in bioprocess industry. Bioreactor Design: The technical aspects involved in designing of a bioreactor. Design and operation strategies for Batch and Continuous bioprocess plants.

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10Res.BT123 Advanced Downstream Processing

Introduction : Role and importance of downstream processing in Biotechnology. Economics of downstream processing, cost cutting strategies, characteristics of biological mixtures, process design criteria for various bioproducts. Primary Separation and Recovery Process: Cell disruption method for intracellular products: chemical, mechanical and enzymatic methods. Principles, operation, design and scale up of sedimentation, flocculation, centrifugal settling and filtration. Enrichment Operations I: Precipitation and Extraction: Precipitation methods by isoelectric precipitation, salt fractionation, polymer and organic solvent. Extraction: Concepts, modeling and design aspects. Principles and applications of aqueous two-phase, super critical extraction and crystallization. Enrichment Operations II: Membrane Based Separations: Theory and applications of Ultrafiltration and microfiltration, design and configuration of membrane based separations, Structure and characteristics of membranes. Concepts, modeling and design aspects of reverse osmosis, dialysis, liquid membranes and Membrane reactors. Purification Techniques: Principle and practice of the Chromatography techniques: Gel permeation, Ion exchange, Reverse phase, Hydrophobic and Affinity chromatography. Recent advances in purification techniques of bioproducts. In-situ product removal and process integration. Case studies: Ethanol, Antibodies and mammalian proteins.

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10Res.BT124 Reaction Engineering

Introduction: Classification of reactions, molecularity and order of reaction, rate equation and rate of reaction, elementary and non - elementary reactions. Analysis of experimental reactor data: Evaluation of rate equation by integral method of analysis, integral and differential analysis for constant and variable volume system (zero, 1st and 2nd order irreversible reactions). Design of ideal reactors: Concept of ideality; development of design expressions for batch, tubular, and stirred tank reactors for both constant and variable volume reactions. Evaluation of rate equations, comparison of ideal reactors, multiple reactors systems. Non Ideal Flow: Interpretation of Residence Time Distribution: C, E and F curves, relation between C, E and mean residence time, step and impulse input response for the non ideal reactors. Kinetics of microbial growth and product formation: Phases of cell growth in batch cultures; simple unstructured kinetic models for microbial growth; Monod model; growth of filamentous organisms. Growth associated and non growth associated product formation kinetics; Leudeking – Piret models; substrate and product inhibition on cell growth and product formation Metabolic stoichiometry and energetics: Stoichiometry of cell growth and product formation – elemental balances, degrees of reduction of substrate and biomass; available electron balances; yield coefficients of biomass and product formation; maintenance coefficients. Energetic analysis of microbial growth and product formation, oxygen consumption and heat evolution in aerobic cultures; thermodynamic efficiency of growth. Heterogeneous reaction systems: Introduction to catalysis, properties of catalysts. Rate equations for surface kinetics, pore diffusion resistance combined with surface kinetics, porous catalyst particles, performance equation for reactors containing porous catalyst. Transport phenomena in biochemical reactors: Mass transfer in heterogeneous biochemical reaction systems. Oxygen transfer in submerged fermentation processes; oxygen uptake rates and determination of oxygen transfer coefficients (kla); role of aeration & agitation in oxygen transfer.

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10Res.BT125 Heat and Mass transfer

Heat transfer operations: Modes of heat transfer. Steady state conductions through single-layer, composite-layer, slabs, cylinders, spheres with constant thermal conductivity. Natural and forced convection. Correlation equations for natural and forced convection. Film co-efficient, overall Heat transfer co-efficient. Log mean temperature difference (LMTD), simple problems. Heat exchange equipment: Introduction, classification, construction and applications of different type of heat exchangers – double pipe heat exchanger, shell and tube heat exchanger. Determination of heat transfer area Diffusion: Types of diffusion, Measurement and calculation of diffusivities, theoretical estimation of diffusitivities, mass transfer coefficients and their correlations. Theories of mass transfer. Evaporation: Definition, applications, economy, capacity, evaporator operation. Single effect and multiple effect evaporators, material and energy balance equation, vapour recompression. Evaporator types: falling film, forced circulation, rotary vacuum evaporator. Drying: Definition, moisture content, drying curve, drying equipments-Tray drier, rotary drier and freeze drier. Distillation: Types of distillation – simple, flash, steam distillation. Azeotropic and extractive distillation. Distillation with and without reflux, multistage rectification of binary mixtures. McCabe Thiele Method- to find number of plates. Extraction: Principles of solid-liquid extraction and liquid-liquid extraction operation. Material balance for simple extraction process. Selection criteria for solvent. Working of Bollman, Mixer- Settler and York-Scheibel extractors.

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10Res.BT126 Biorector Design and Economics

Fermentation Process – General requirements of fermentation Process; An overview of aerobic and anaerobic fermentation processes and their application in industry. Basic design and construction of fermenters and its ancillaries; Material of construction, Vessel geometry, Bearing assemblies, Motor drives, Aseptic seals; Flow measuring devices, Valves, Agitator and Spurges Design, Sensor. Medium requirements for fermentation processes – examples of simple and complex media; Design and usage of commercial media for industrial fermentations; Thermal death kinetics of microorganisms; Batch and continuous heat – sterilization of Liquid media; Filter sterilization of liquids. Stoichiometry of Cell growth and Product formation – Elemental balances, available- electron balances, degrees of reduction; yield coefficients of biomass and product formation; maintenance of coefficients; oxygen consumption and heat evolution in aerobic cultures. Phases of cell growth in batch culture; Simple unsaturated kinetic models for microbial growth; growth associated and non-growth associated product formation kinetics; Mono and Leudekng – piret models; Introduction to structured models for growth and product formation. Mass transfer in heterogeneous biochemical reaction systems; Oxygen transfer in submerged fermentation processes; Oxygen uptake rates and determination of oxygen transfer coefficients (kLa); role of aeration and agitation in oxygen transfer. Heat transfer processes in biological systems. Operational models of reactors, - Batch, continuous, Fed Batch, repetitive batch, recycle and continuous cultivation; Novel bioreactors; Stirred tank, Air lift & Loop reactors, Packed bed and Hollow fiber membrane bioreactors, Bioreactors for waste treatment processes; Scale-up of bioreactors, SSF bioreactors. Marketability of the product, availability of technology, raw materials, equipment, human resources, land and utilities, site characteristics, waste disposal, govt. regulations and other legal restrictions, community factors and other factors affecting investment and production costs. Fixed capital investments including land, building, equipment and utilities, installation costs, (including equipment, instrumentation, piping, electrical installation and other utilities), working capital investments Direct Production costs (including raw materials, human resources, maintenance and repair, operating supplies, power and other utilities, royalities, etc.), fixed charges (including depreciation, taxes, insurance, rental costs etc.). Administration, safety and other auxiliary services, payroll overheads, warehouse and storage facilities etc. Return on original investment, interest rate of return, accounting for uncertainty and variations and future developments.

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10Res.BT127

Biosensors: Design and Applications

Overview of biosensors, History, concepts and applications. Bioinstrumentation and bio-electronic devices, Fundamental elements of biosensor devices and designs. Molecular recognition: Enzymes, Antibodies and DNA. Modification of bio-recognition molecules for selectivity and sensitivity. Kinetics and thermodynamics of bio-recognition reactions. Applications of Biosensor-based instruments to the bioprocess industry. Target analysis, various recognition, signals, and device types. Considerations, calibration, dynamic Range, signal to noise, sensitivity, selectivity, interference. Fundamentals of surfaces and interfaces, Electrochemistry for biosensors, Principles of potentiometry and potentiometric biosensors; amperometry and amperometric biosensors; Voltammetry: principles and techniques; Bio-electrochemistry and direct biosensors, Electrical and Electrochemical Impedance: Principles and Applications. Conductimetric and Impedimetric Biosensors. Enzyme sensors, affinity sensors: antibodies, oligo-nucleotides, measuring binding in affinity sensors, SPR, quartz crystal microbalance, FRET, Membrane protein sensors: ion channels, receptors, whole cell sensors – bacteria, yeast, mammalian cells, non-biological and bio-mimicry: molecularly imprinted polymers, non-biological organic molecules, electro-chemiluminescence, pH sensors, artificial receptors Immobilization: adsorption, encapsulation - (hydro-gel, sol-gel glass, etc.), covalent attachment, diffusion issues Optical Biosensor, Microlithography for biosensors, FETS and Bio-FETS, MEMS and Bio-MEMS. Lab-on-a-chip: TAS and m-TAS devices, Sensors based on Fiber Optic, Surface Plasmon Resonance (SPR) biosensors, Surface Characterization of Hybrid Bilayer Membrane Sensors, Quartz Crystal Nanogravimetry (QCN) biosensors, quantum dots, magnetic beads, PEBBLE sensors, Coupled mass transport and kinetics of enzyme-catalyzed and molecular binding reactions, Biosensor Arrays and Chemometrics, Multi-element array biosensors: electronic nose and electronic tongue, Signal Processing and Data Fusion for Biosensors Measuring complex samples, multi-analyte detection, continuous measurements, reagent less biosensors, implantable sensors, biocompatibility issues. Applications of biosensors in Agriculture, food safety, food processing: state of the field, market potential, unique design criteria and needs. Biomedical sensors: Microfabricated Sensors and the Commercial Development Of the i-Stat Point-Of-Care system, Noninvasive Biosensors in Clinical Analysis. Applications of Biosensor-based instruments; Blood chemistry sensors, sensors for Genetic testing, Physical sensors, Electrical sensors: Electrocardiographs Electroencephalograph etc., Electrosurgical equipments. Applications of biosensors in Bio-security, environmental : state of the field, market potential, unique design criteria and needs, current sensors in use.

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GROUP - C

10Res.BT131

Applied Bioinformatics

Basic Concepts of Molecular Biology: Proteins, Nucleic Acids: DNA, RNA. Molecular Genetics: Genes and Genetic code, Transcription, Translation and Protein synthesis, Chromosomes Genome: Maps and Sequences, Sequencing Techniques, Human Genome project, Sequence Databases. Biological Databases: Types of databases – Primary and Secondary biological databases. Primary databases, secondary databases, genotype databases, molecular structure databases and genome databases. Hidden Markov Models: Forward and Backward algorithm, Viterbi algorithm, Applications: Modelling Protein sequence families, multiple alignments. Protein Modeling and Insilico Drug Design: Protein structure, signal peptides, transmembrane proteins, analysis of protein structures. Protein modeling, modeling protein structures using High Throughput methods. Insilico drug design, Virtual Library design, vHTS and Scaffold Hopping, Predictive Science (Biological Activity, ADMET). Structure based Drug Design (SBDD), Lead Optimization, Structural Mining: Protein Ligand work analysis. Study of drug-interactions, Docking. Perl and Bioinformatics: Basics of PERL, Intermediate and Advanced, Biological databases, Sequence analysis and alignment, Evolutionary analysis. Metabolomics, Working with Discovery Studio (Molecular Modeling): 2D and 3D visualization, 2D and 3D molecular descriptors, Quantum mechanics / molecular, mechanics. SAR analysis, 2D and 3D QSAR. Bayesian statistics, neural networks, recursive partitioning, GFA, etc. Library analysis and Library design. Predictive ADME and toxicology (TOPKAT®), Conformation generation and Analysis. Structure-based and structure-guided design, docking, scoring. Virtual screening and compound ranking/scoring. Receptor-ligand interactions analysis, Fragment-based design, de novo design (LUDI), Pharmacophore generation (Catalyst), Scaffold hopping, 3D database screening, Simulations, molecular mechanics/dynamics (CHARMm). Explicit/implicit solvation models, Transmembrane protein modeling, Homology modeling, Antibody modeling, Electrostatics calculations, protein ionization and pK prediction, Protein modeling (MODELER®) and analysis, protein engineering. Protein-protein docking and refi nement, Sequence analysis, sequence alignment, phylogenetic analysis, • X-Ray (CNX), structure refi nement and analysis.


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10Res.BT132 Computer Programming and Biostatistics

Introduction to C++: Introduction Object Oriented Programming concepts, data types, Operators, statements, variables, arrays, structures, objects and classes, Encapsulation, Polymorphism and Inheritance. Bioperl: Overview, Bioperl Objects, Brief descriptions (Seq, PrimarySeq, LocatableSeq, RelSegment, LiveSeq, LargeSeq, RichSeq, SeqWithQuality, SeqI), Location objects, Interface objects and implementation objects, Representing large sequences (LargeSeq), Representing changing sequences (LiveSeq), Using Bioperl: Accessing sequence data from local and remote databases, Accessing remote databases (Bio::DB::GenBank, etc), Indexing and accessing local databases Bio::Index::*, bp_index.pl, bp_fetch.pl, Bio::DB::*), Transforming sequence files (SeqIO), Transforming alignment files (AlignIO), Performing Sequence analysis – Global alignment, Local alignment, Multiple sequence alignment, Parsing BLAST alignment report, Parsing multiple sequence alignment. Biojava: Alphabets and Symbols, Basic Sequence Manipulation, Translation, Proteomics, Sequence IO, Annotations, Locations and Features, BLAST and FASTA, Counts and Distributions, Weight Matrices and Dynamic Programming, User interfaces, BioSQL and Sequence Databases, Genetic Algorithms, Protein Structure, Ontologies. Introduction to BioJava applications: DengueInfo, Dazzle, Biosense, Bioclipse, PROMPT, Cytoscape, BioWeka, Geneious, MassSieve, Strap, Jstacs. Basics of Statistics: Data and Variabls, Measurement scale. Descriptive statistics, frequency distributions and data presentation, relative frequency, histogram. Measures of central tendency. Probability distribution functions: The Binomial distribution, The Poisson distribution, the uniform distribution, the normal distribution, Characteristics of a random variable, Expectation, Moments of a distribution, Moment generating functions. Distribution functions of more than one random variable. Joint distributions, Conditional distributions, Marginal distributions, Independent random variables. Estimation Theory: Maximum likelihood estimation Example: linear regression, Bayesian framework. Markovian Dynamics: Dynamical processes, Markov processes, Tests of significance, Confidence intervals, Central Limit Theorem, Analysis of variance, linear models and multiple regressions. Validation in Genomics: CpG island methylation revisited; E-values for protein database searches based on tandem mass spectrometry scoring.

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10Res.BT133 Genomics, Proteomics and Microarray

Introduction: Genomics and Proteomics. Structure, organization and features of Prokaryotic & Eukaryotic Genomes. Vectors, Genome mapping. Polymorphisms: Molecular markers – RFLP, AFLP, RAPD, SCAR, SNP, ISSR, and Protein markers - Allozymes and Isozymes, Telomerase, FISH - DNA amplification markers and Cancer biomarkers. Genome sequences databases and Genome annotation, Gene discovery. Gene Ontology. Haplotyping and Diplotyping. Genome Sequencing: Early sequencing efforts. DNA sequencing methods - Maxam-Gilbert Method, Sanger Dideoxy method, Fluorescence method, shot-gun approach and ultra-high-throughput DNA Sequencing using Microarray technology. Genome sequencing projects on E.coli. Arabidopsis and rice; Human-genome project and the genetic map. Recent developments and next generation sequencing. Raw genome sequence data, expressed sequenced tags (ESTs), Gene variation and associated diseases, diagnostic genes and drug targets. Genotyping - DNA Chips, diagnostic assays, diagnostic services. Comparative genomics and Functional Genomics. Studies with model systems such as Yeast, Drosophila, C. elegans, Arabidopsis. SAGE. Functional Genomics: C-Values of eukaryotic genomes. Organization of microbial, plant and animal genomes, repetitive and coding sequences. Identification and tagging of markers for important traits, T-DNA & trasposon tagging. Cloning of genes by map-based cloning, Construction & Screening of cDNAs libraries, differential display via RT-PCR. Micro-array in functional genomics. Genome annotation : Extrinsic, Intrinsic (Signals and Content), Conservative information used in gene prediction. Frameworks for Information integration – Exon chaining, Generative models: Hidden Morkov Models, Discriminative learning and Combiners. Evaluation of Gene prediction methods – Basic tools, Systematic evaluation and Community experiments (GASP, EGASP and NGASP). Proteomics: Scope, Experimental methods for studying proteomics, methods of protein isolation, purification and quantification. Methods for large scale synthesis of proteins. Applications of peptides in biology. Analysis of proteins - high throughput screening, engineering novel proteins, Mass-Spectroscopy based protein expression and post-translational modification analysis. Bioinformatics analysis - clustering methods, proteome functional information. Functional annotation of Proteins: Introduction, Protein sequence databases, UniProt, UniProtKB – Sequence curation, Sequence annotation, Functional annotation, annotation of protein structure, post-translational modification, protein-protein interactions and pathways, annotation of human sequences and diseases in UniProt and UniProtKB. Protein family classification for functional annotation – Protein signature methods and Databases, InterPro, InterProScan for sequence classification and functional annotation. Annotation from Genes and Protein to Genome and Proteome. Microarray: Basics of Biochips and Microarray Technology, Historical Development, Biochip technologies. Applications Of Biochip Technology: Molecular diagnostics, Pharmacogenomics, application of microarray technology in drug discovery and development, Gene expression studies, Use of DNA chip technology for drug safety, Use of microchips for drug delivery, Use of biochips in healthcare, Use of microarrays in population genetics and epidemiology, Use of microarrays in forensics, DNA chip technology for water quality management, Application of micro arrays in the agro-industry; use of microarrays in Genetic disease monitoring; Point of Care (P.O.C) applications, Limitations of biochip technology. Commercial Aspects of Biochip Technology: Markets for biochip technologies, Commercial support for the development of biochips, Government support for biochip development, Business strategies, and Patent issues. DNA Computing: Introduction, Junctions, other shapes, Biochips and large-scale structures, Discussion of Robinson and Kallenbach's methods for designing DNA shapes, DNA cube, computing with DNA, Electrical analogies for biological circuits, Challenges, Future Trends.

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10Res.BT134 Data warehousing and Data mining

Introduction to Data Warehousing: Heterogeneous information; the integration problem; the Warehouse Architecture; Data Warehousing; Warehouse DBMS. Aggregations: SQL and aggregations; aggregation functions; grouping. Data Warehouse Models and OLAP Operations: Decision support; Data Marts; OLAP vs OLTP; the Multi-Dimensional data model; Dimensional Modelling; ROLAP vs MOLAP; Star and snowflake schemas; the MOLAP cube; roll-up, slicing, and pivoting. Some Issues in Data Warehouse Design: Monitoring; wrappers; integration; data cleaning; data loading; materialised views; warehouse maintenance; OLAP servers; metadata. Building Data Warehouses: Conceptual Data Modeling, Entity-Relationship (ER) modeling, Dimension modeling. Data warehouse design using ER approach. Aspects of building data warehouses. Introduction to Data Mining: Data Mining; A View of the KDD Process; Problems and Techniques; Data Mining Applications; Prospects for the Technology. The Crisp-Dm Methodology: Approach; Objectives; Documents; Structure; Binding to Contexts; Phases, Task, Outputs. Data Mining Inputs and Outputs: Concepts, Instances, Attributes; Kinds of Learning; Providing Examples; Kinds of Attributes; Preparing Inputs. Knowledge Representations; Decision Tables and Decision Trees; Classification Rules; Association Rules; Regression Trees and Model Trees; Instance-Level Representations. Data Mining Algorithms: One-R; Naïve Bayes Classifier; Decision Trees; Decision Rules; Association Rules; Regression; K-Nearest Neighbour Classifiers. Evaluating Data Mining Results: Issues in Evaluation; Training and Testing Principles; Error Measures, Holdout, Cross Validation; Comparing Algorithms; Taking Costs into Account; Trade-Offs in the Confusion Matrix.

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10Res.BT135 Java for Bioinformatics & Biomedical Application

Introduction to Java: Basics, Introduction to Java Applications, The Java Programming Environment, Fundamental Programming Structures in Java, Objects and Classes in Java, Polymorphism and Abstract Classes, Inheritance, Interfaces and Inner Classes, Program Design & Considerations , Graphical Components & Visual Design ,Java Utilities , Exception Handling, Exception Handling, File I/O, Applets, Linked Data Structures, Multithreading. Bioinformatics and Java: Current state of biomedical research. Cancer biomedical informatics and Grid program. caBIG organization and architecture. Model-View-Controller framework. Web services and service oriented architecture, caGrid. Sequence Search: Peforming BLAST analysis, Developing SwingBlast application. Designing SwingBlast Java application - adding events to applications, Designing SwingBlast GUI, Coding SwingBlast GUI. Description of Blast Classes, Implementing JQBlast. Enhacing SwingBlast application – Retrieving sequence from GenBank using BioJava and without using BioJava. Facilitating PubMed Searches: JavaServer pages and Java Servelets – HTTP and CGI, HTTP Protocol, GET and POST methods. Servelets and JavaServer pages technologies - Java API for Servelets and JSPs, JavaServer pages Standard Tag Library (JSTL), Apache Tomcat server. The NCBI PubMed literature search and retrieval service. Accessing biomedical literature through Entrez. Development of web application with Servelets and JSPs. Creating a Gene Prediction and BLAST Analysis Pipel ine: Gene prediction programs. Performing Gene prediction with Genscan - Running genscan analysis, Analyzing Genscan output. Craeting SwingGenscan, Coding for SwingGenScan, SwingGenScan user Iunterface and Running SwingGenScan. Cancer Biomedical Informatics Grid (caBIG): Cancer Biomedical informatics Grid: Structure and Organisation of caBIG, Data Integration and ETL, Cancer Common Ontology Representation Environment (caCORE). Cancer Bioinforamtics and Infrastructure Object (caBIO). Downloading and configuring caBIO. Creating JcaBIO application - JcaBIO classes and Application, Coding the SwingCaBIO application and Running JcaBIO application.

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10Res.BT136 Molecular Modeling and Simulation

Introduction to Molecular Modeling: Modeling basics. Generation of 3D Coordinates Crystal data, Fragment libraries, and conversion of 2D Structural data into 3D Form, Force fields, and Geometry optimization, Energy minimizing Procedures, use of Charges, Solvent effects and Quantum Mechanical methods. Conformational analysis. Computational tools for Molecular modeling, conformational analysis using - Systematic Search Procedures, Monte carlo and molecular dynamics methods. Determining features of proteins(Interaction potential, Molecular Electrostatic Potential, molecular interaction fields, properties on molecular surface and Pharmacophore identification. 3D QSAR Methods. Modeling and Simulation Technique: Modeling and Simulation of Dopamine D3 Receptor Antagonists. Comparative Protein Modeling – Conformational Properties of Protein Structure, Types of Secondary Structural Elements, Homologous Proteins. Procedures for sequence Alignments, Determination and Generation of Structurally Conserved Regions, Construction of Structurally Variable Regions, Side-Chain modeling, Secondary Structure Prediction, Threading Methods. Optimization and Validation of Protein Models. Virtual Screening and Docking: Introduction to Docking – Preparation of Partners, Compound Library, representation of Proteins and Ligands. Docking Algorithms. Simulation approaches for Protein model. Simulation of a Fluid Phase Lipid Bilayer Membrane, de novo Simulations of the Folding of GCN4 and its Mutants. Building a model of HIV-I Reverse Transcriptase (possible mechanisms for AZT resistance).

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10Res.BT137

Metabolic Engineering

Introduction to Cellular Metabolism: Metabolic engineering and its multidisciplinary nature; Review of cellular metabolism; Models for cellular reactions; Material balances and data consistency-Block box model, elemental balances, heat balance and analysis. Regulation of Metabolic Pathways: Regulation of enzyme activity- Reversible and irreversible inhibition systems, regulation of enzyme concentration- Control of transcription and translation. Global control: Regulation at whole cell level- regulation of metabolic networks. Metabolic Pathway Manipulations: Enhancement of product yield and productivity- Ethanol, Amino acids and Solvents. Extension of substrate- Sucrose utilization and pentose metabolism for ethanol production. Product spectrum and novel products- Antibiotics, Polyketides, Vitamins, Biological pigments. Improvements of cellular properties-Nitrogen metabolism, Oxygen utilization, Overflow metabolism and genetic stability maintenance. Xenobiotics degradation of Polychlorinated Biphenyls (PCBs) and Benzene, Toluene, p-Xylene Mixtures (BTX). Metabolic Flux Analysis: Methods for determination of metabolic fluxes by isotope labeling- Fractional label enrichment, complete enumeration of TCA cycle metabolite isotopomers from labeled pyruvate and acetate. Applications of metabolic flux analysis: Amino acid production by Glutamic acid bacteria and mammalian cell cultures. Flux analysis of metabolic networks- Bottom-up Approach, Top-Down Approach. Metabolic Control Analysis (MCA): MCA theorems, determination of flux control coefficient. MCA of linear and branched pathways. Theory of large deviations

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GROUP - D

10 Res.BT141 Tissue Engineering

Cell and Tissue Engineering: Techniques of cell and tissue culture. Isolation,selection.and maintenance of primary and early passage cultures. Stem cells: Embryonic and adult stem cells. Pluripotent stem cells: Ectodermal cells - skin and nervous system. Mesodermal cells - muscles, bones, heart and blood vessels.cell adhesion theory. Effect of biomaterial on physiological behaviour. Introduction to cell characteristics, regulation, assays, mathematical models for cell migration and tissue growth Biomaterials-Tissue Interactions: The principles of materials science and cell biology. Natural and Synthetic polymers. Hydrogels based on N—isopropylacrylamide and biodegradable bioceramicsMethods for biomaterials surface characterization and analysis of protein adsorption. Analysis of Molecular and cellular interactions with biomaterials in terms of unit cell processes, such as matrix by synthesis, degradation, and contraction. Mechanisms underlying wound healing and tissue remodeling following implantation in various organs. Tissue and Organ regeneration.

Scaffold Design and Fabrication: Scaffold processing methods: Solvent casting, membrane lamination, freeze-drying, polymer-ceramic composite forms, phase separation, gas foam processing. Microencapsulation methods: Agarose-PSS a (polysterene sulphonic acid), alginate (Ca2+-Induced gelation). Design of Medical Devices / Implants: The principles underlying the design of medical implants, The systematic use of cell-matrix control volumes; the role of stress analysis in the design process; anatomic fit, shape and size of implants; selection of biomaterials; instrumentation for surgical implantation procedures; preclinical testing for safety and efficacy, including risk/benefit ratio assessment evaluation of clinical performance and design of clinical trials. Case studies : orthopedic devices, soft tissue implants, artificial organs, and dental implants.

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10 Res.BT142 Bioethics, biosafety and IPR

Biosafety and Risk Assessment: Introduction; Historical Background; Introduction to Biological Safety Cabinets; Primary Containment for Biohazards; Biosafety levels; specific microorganisms; Recommended biosafety levels for Infectious agents and Infected Animals; Biosafety guidelines - Government of India; Definition of GMOs & LMOs; Roles of Institutional Biosafety Committee, RCGM, GEAC etc. for GMO applications in food and agriculture; Environmental release of GMOs; Risk Analysis; Risk Assessment; Risk management and communication; Overview of National Regulations and relevant International Agreements including Cartagena Protocol, GMP and GLP. Bioethics and Legal Issues: Ethical issues; Public perception related to Biotechnology from developed and developing countries. Legal and socio-economic impacts of biotechnology, public awareness on genetically modified life forms (case study). Ethical implication of biotechnological products and technique. Social and ethical implication of biological weapons. Introduction to Intellectual Property: Types of IP: Patents, Trademarks, Copyright & Related Rights, Industrial Design, Traditional Knowledge, Geographical Indications, Protection of New GMOs; International framework for the protection of IP. IP as a factor in R&D; IPs of relevance to biotechnology with case studies; Introduction to GATT, WTO, WIPO and TRIPS. Biotechnology and Intellectual Property Rights: Biotechnology and the Law-Objective, Evolution, Basic Structure of Gene Techniques, Applications, Commercial Potential of Biotech Inventions, Rationale for Intellectual Property Protection. Patenting Biotechnology Inventions-Objective, Concept of Novelty, Concept of inventive step, Microorganisms, Moral Issues in Patenting Biotechnological inventions. Plant varieties Protection-Objectives, Justification, International Position, Plant Varieties Protection in India, Bio-Prospecting and Bio-Piracy, Alternative ways, Protectability, need for a Sui-Generis regime Concept of ‘Prior Art’ and Basics of Patents: Invention in context of “prior art”; Patent databases; Searching International Databases; Country-wise patent searches (USPTO, EPO, India etc.); Analysis and report formation. Types of patents; Indian Patent Act 1970; Recent Amendments; WIPO Treaties; Budapest Treaty; PCT and Implications; Role of a Country Patent Office; Procedure for filing a PCT application Patent Filing, Infringement and Enforcement of IPR: Patent application- forms and guidelines, fee structure, time frames; Filing of a patent application; Precautions before patenting-disclosure/non-disclosure; Types of patent applications: provisional and complete specifications; International patenting-requirement, procedures and costs; Financial assistance for patenting-introduction to existing schemes; Publication of patents-gazette of India, status in Europe and US Patenting by research students, lecturers and scientists-University/organizational rules in India and abroad, credit sharing by workers, financial incentives, Patent infringement- meaning, scope, litigation, case studies and examples. Enforcement of Intellectual Property Rights - Civil Remedies, Criminal Remedies, Border Security measures. Practical Aspects of Licensing - Benefits, determinative factors, important clauses, licensing clauses.

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10 Res.BT143 Management, Entrepreneurship and Biobusiness

Management: Introduction: Meaning nature and characteristics of Management, scope and functional areas of management, Management and administration, roles of management, levels of management. Development of Management Thought: Early management approaches and modern management approaches. Functions of Management: Planning and Forecasting, Organizing, Directing and Controlling. Managing Engineering Design and Development: Product and Technology Life Cycles, Nature of Research and development, Research Strategy and organization, selecting R & D Projects, Protection of Ideas. Creativity, Nature of Engineering Design, Systems Engineering / New Product Development, Control System in Design, Product Liability and Safety, Designing for Reliability, other “abilities” in Design. Managing Production Operations: Assuring product quality, Productivity, Work measurement, Maintenance and Facilities (Plant) engineering and other manufacturing functions. Entrepreneur: Meaning of an Entrepreneur, Role of entrepreneurs in Economic Development, Entrepreneurship in India, Entrepreneurship Barriers. Role of Micro Small & Medium Enterprises (MSME) in Economic Development, Impact of Liberalization, Privatization and Globalization on MSME, Effect of WTO/GATT. Different Schemes; TECSOK, KIADB, KSSIDC, KSIMC, DIC-Single Window Agency, MSME, NSIC, SIDBI, KSFC. Preparation of Project: Meaning of Project, Project Identification, Project Selection, Project Report – Contents, Formulation and Project Appraisal. Identification of Business Opportunities: Market Feasibility studies, Technical Feasibility Studies; Financial Feasibility Studies and Social Feasibility studies. Technologies and Bio-Safety: Principles of business management and concept of Biobusiness, Fundamentals and constituents of Biotech for biobusiness, SWOT analysis of Indian Biobusiness. Recombinant DNA technology, Monoclonal antibody technology, Bioprocess technology, Fermentation, recovery and purification techniques. Guidelines for recombinant DNA research, release of genetically modified organisms (GMOs). Commercialization: Analysis of factor influencing international competitiveness in biotechnology, type of firms commercializing biotechnology, financing, tax incentives, issues and policies. Bioscience enterprises- raw biocommodities, hybridization, tissue culture, biofermentation, biofertilizers. Project Cost and Market Potential: Total product cost, capital investment and profitability, manufacturing cost estimation, capital investment estimation, Risk capital and working capital, manufacturing cost estimation for an intracellular protein, using cost analysis for R & D decision making.

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10 Res.BT144 Clinical Biotechnology

Introduction: Introduction to Clinical study and design of clinical studies. Epidemiological research and treatment studies: Double-blind and Single-blind Randomized controlled trial, Non-blind trial, Nonrandomized trial-quasi-experiment. Observational studies: Cohort study- Prospective cohort and Retrospective cohort. Time series study, Case-control study and Nested case-control study. Community survey and Ecological study. Seasonal studies: Conduction of studies in seasonal indications such as Allergies and Influenza. Statistical Analysis and Interpretation: Background and purpose, trial design consideration, Parallel group design, cross over design, factorial design. Introduction to Statistical Application Software (SAS), procedures and clinical data management. Drug Design and Synthesis: Synthesis of compounds in accordance with the molecular structure and biological activity concept: Analgesics, neuromuscular blocking agents, anti-fertility drugs and bactericidal & bacteriostatic agents (sulphonamides, mercury compounds and antiseptics). Study of Therapeutic Proteins and Related Case Stud ies: Blood and Blood products: Clotting factors, anticoagulants, Thrombolytic Agents, Tissue plasminogen activator and streptokinase. Safety guidelines in Blood Transfusion. Therapeutic Proteins: Antibodies, Enzymes, Hormones, Growth factors (Erythropoietin), Vaccines (HIV and Cancer), Interferon and Interleukins. Cancer Biology and Therapy: Introduction to cancer biology and modes of treatment: radiotherapy, chemotherapy, surgery, Biological therapy, immunotherapy and gene therapy. Clinical Toxicology: Basic concept in toxicology. Types and mechanism of toxin action- Epoxidation & drug toxicity, N-oxidation & drug toxicity and sulphur xenobiotics. Hepatotoxicity and Nephrotoxicity. Biotransformation of toxins, inactivation and removal from the body. Clinical Research Governance and Ethics: Overview on regulatory affairs for pharmaceuticals, neutraceuticals and medical devices. Good Clinical Practices (GCP) and International quality standard and related guidelines (ICH-E6). Risk assessment and trial monitoring. Legal and ethical issues on biotechnology, medical research and related clinical practice.

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10 Res.BT145 Renewable Energy Sources

An introduction to energy sources: Energy consumption as a measure of prosperity, world energy futures, brief discussion of conventional energy sources and their availability, non-conventional energy sources. Comparison between conventional and Non-conventional methods, Applications of Non–conventional energy. Solar energy: Solar constants, solar radiation earth’s surface, solar radiation geometry, solar radiation measurements. Relevant problems on design and analysis.

Solar energy collectors: Physical principles of conversion of solar radiation into heat – flat plate Collectors, advantages of flat plate collectors, applications, concentration collectors, focusing type, advantages & disadvantages of concentrating type collectors over flat plate collectors. Solar energy storage: Requirement of solar energy storage system, solar pond, solar thermal power production. Application of solar energy: Solar water heating, space heating, brief discussion of Solar electric power generation, photo voltaic system for power generation, applications of solar photo voltaic systems, advantages & disadvantages, solar distillation, solar furnace, solar cooking, solar green house. Relevant problems on design and analysis. Wind energy: Basic principles of wind energy conversion, Nature of wind, power in the wind, maximum power wind energy conversion, site selection consideration, basic concepts of WECS, Classification of WECS, advantages & disadvantages of WECS. Application of wind energy. Environmental Aspects, Recent applications and development, relevant problems on design and analysis. Energy from Bio-mass: Bio-mass as a renewable source of energy, different types of bio-mass fuels, gas –liquid-solid, bio-mass conversion technologies ,Wet-process-dry process, Photosynthesis, Bio-gas generation, factors affecting Bio-digestion, classification of bio-gas plants, continuous & batch types, fixed drum types, & flogging drum types, advantages & disadvantages, Janatha model: KVIC type, gasification of biogas and different types of gasifier. Relevant problems on design and analysis.

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10 Res.BT146 Nanobiotechnology

Introduction: History of Nanotechnology and Nanobiotechnology, scope and Applications. Introduction and overview of Quantum concepts. Nanomaterials and Nanobiomaterials: Structures and properties of Carbon based, metal based and bionanomaterails: Fullerenes, Bucky Ball, Nanotubes, Quantum Dots, Magnetic, Nano Shells, Dendrimers, Nanocarriers, Nanocrystals, Nanowires, Nanomembranes, hybrid biological/inorganic, protein & DNA based nanostructures. Introduction & overview of 1st, 2nd and 3rd generation biomaterials. Characterization of Nanostructures: UV-Visible spectroscopy, Electron Microscopy-Scanning electron microscopy (SEM), Atomic Force microscopy (AFM), Transmission electron microscopy (TEM), Scanning Probe microscopy (SPM), Scanning tunnel microscopy (STM); Fourier Transform infrared spectroscopy (FTIR); X-ray spectroscopy. Nano Synthesis and Fabrication: Introduction & overview of Nanofabrication: Bottom up-self assembly and Top down approaches using processes like Ball milling, Sol-gel Process, Chemical Vapour deposition (CVD). Plasma or flame spraying synthesis, Ion-Bean sculpting electrodeposition and various lithography techniques. Nanolithography and Soft lithography. Biosensors: types, applications and developments. Biosensor in modern medicine. Application of Nanobiotechnology : Medical Nanobiotechnology: Diagnostics: Imaging: Benefits and Applications. Nanotherpeutics: cancer treatment – Nanotechnology based chemotherapy (Smart Bomb), Pebbles, wound care products, Implantable materials for vascular interventions, Implantables materials for orthopaedics and dentistry. Active implantable devices and biomics. Nanosurgery. Pharmaceutical Nanobiotechnology: Drug delivery – Nanoparticles used as drug delivery systems, types of drug loading, drug release (sustained and targeted release mechanism), Biodegradable polymers. Application in the field of Nano Surgery and Tissue Engineering. Biomems and Nems: Micro & Nano-Electromechanical systems – Fabrication process – choice of materials – advantages and limits of various approaches, Applications, Thermal Radiations, Magnetic, Chemical and Mechanical Transducers –Sensing and Actuators. Nano Safety Issues: Nanotoxicology: Toxicology health effects caused by Nanoparticles, Ethics, Challenges and Future.

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10 Res.BT147 Resreach Methodology

What is research? – Reflection, Science & Research. Basic & Applied Research, Steps in Research, Literature Collection: Review of literature, review process and bibliography, research/discriminative reading, consulting source material, Research Objectives and hypothesis, Research method and materials, Research action, Data collection and analysis plan, Research budget and resources. Introduction – identification of the research question, hypotheses, and justification for the topic Literature review – updated version of the initial literature review developed for the research proposal; should review in detail at least four analytical works. Research Design – detailed discussion of the conceptualization and operationalization of variables. Data Gathering – thorough description of methods of data gathering and sources. Analytical Techniques – detailed discussion of data gathering and analytical methods, including explanation of their suitability of these techniques compared with others and any possible problems arising from the methods selected. Data Analysis and Presentation – application and execution of analytical techniques, and interpretations of findings. Issues related to plagiarism, copyright laws, acknowledging the sources etc to be discussed with case studies. Format for manuscript writing, documentation, organization of reference material, bibliography, end note etc to be discussed with case studies.

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Grou p-A Group -B Group -C Group -D · Waste water treatment – primary waste water treatment:...

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