M.

TECH INDUSTRIAL BIOTECHNOLOGY

Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal University, Manipal

M. TECH. INDUSTRIAL BIOTECHNOLOGY

FIRST SEMESTER
Sub Code Subject Name L T P C Sub Code

SECOND SEMESTER
Subject Name L T P C

MAT 503 BIO 501 BIO 503 FIRST YEAR BIO 505

Mathematical methods in Chemical & Biochemical Engineering Bioprocess Engineering Molecular biology & rDNA technology Transport Phenomena in Bioprocessing

3 3 4 3 3

1 1 0 1 1

0 0 0 0 0

4 4 4 4 4

BIO 502 BIO 504 xxx.xxx.x BIO 514 BIO 512

Bioreactor Design and Analysis Bioprocess Modeling Analysis and Simulation Open Elective
Seminar

3 3 3 0 0

1 1 0 0 0

0 0 0 3 6

4 4 3 1 2

Advanced Bioseparation BIO 507 Processes Research Methodologies & Technical HUM 501 Communication
BIO 511

Bioprocess Engineering Lab - II

1 0

0 0

3 6

2 2

BIO *** BIO *** BIO ***

Program Elective Program Elective Program Elective

TOTAL

4 4 4

0 0 0

0 0 0

4 4 4

Bioprocess Engineering Lab - I

SECOND YEAR

BIO 699

TOTAL Project Work TOTAL

17

24

21
0

2
0

9
0

26
40

40

LIST OF PROGRAM ELECTIVES BIO 520 BIO 522 BIO 524 BIO 526 BIO 528 BIO 530 BIO 532 BIO 534 BIO 536 Advanced Bioinformatics Biofuels Engineering Biopharmaceuticals & Pharmaceutical Biotechnology Enzyme Biotechnology Solid Waste Management Statistical Design and analysis of experiments in biotechnology Design & development of Biological treatment processes Immunotechnology Biopolymer Technology

LIST OF OPEN ELECTIVES BIO 540 BIO 542 Animal and Plant Biotechnology Bionanotechnology

M.Tech INDUSTRIAL BIOTECHNOLOGY FIRST SEMESTER

MAT 503 MATHEMATICAL AND NUMERICAL TECHNIQUES IN CHEMICAL & BIOCHEMICAL ENGINEERING

[3 1 0 4]

Total No of periods: 48 Introduction, linear algebraic equations Eigenvalues and Eigenvectors of Matrices, sparse Matrices -Tensors and their applications. [12]

Non linear algebraic equations function evaluation-least square curve fit-Newton inter-polation formula-orthogonal polynomials and functions-ordinary differential equations initial value problems and Boundary value problems - finite difference techniques. [12]

Orthogonal collocations on finite difference - Galerkin finite elements-shooting techniques partial differential equations-finite difference technique (Method of lines) orthogonal collocation on finite elements. [12] The Galerkin finite Element technique-variational forms of PDEs. Sturm-Louiville theoryseparation of variables and Fourier Transforms-Greens function-uniqueness conditions for linear and Nonlinear systems, steady state characteristics of Nonlinear Dynamical systemsLinear stability and Limit cycles-secondary Bifurcations and chaos. [12]

Text Books:
1. Mathematical Methods in Chemical Engineering S.Pushpavanam, PHI, 1998. 2. Numerical methods for Engineer By Santhosh K.Gupta. Wiley Eastern Ltd. New Delhi. 3. Owen T. Hanna and Orville C. Sandall Computations methods in Chemical Engineering PHI, 1998. 4. Davis, H.T. and Thomson K., Linear Algebra and Linear operators in Engineering with applications of mathematica, Academic Press, 2000

BIO 501 Total No of periods: 48

BIOPROCESS ENGINEERING

[3 1 0 4]

Introduction to Biomolecules, Identification of Microorganisms: [08] Structure, properties and classification - carbohydrates, lipids, proteins and nucleic acids; Prokaryotes & Eukaryotes; Bacterial Taxonomy, Microscopy, general structural organization of bacteria and other microorganisms Upstream Processing: [09] Isolation, Preservation and Improvement of Industrial Micro-Organisms; Medium requirements for fermentation process; Criteria for good medium; Sterilization - batch and continuous heat sterilization of liquid media, filter sterilization of liquid media and Air. Design of sterilization equipment Principles of enzyme catalysis: [09] Proteins as enzymes; Classification of Enzymes; Mechanism of Enzyme Action; Determination of elementary step rate kinetics, patterns of substrate concentration dependence, modulation and regulation of enzyme activity . Kinetics of substrate utilization, product formation and biomass production: [09] Phases of cell growth in batch cultures - transient growth kinetics, Simple unstructured kinetic models for microbial growth, Growth of filamentous organisms; Environmental conditions affecting growth kinetics, substrate and product inhibition on cell growth and product formation; structured kinetic models, segregated kinetic models of growth. Energy and Material Balances: [09] Introduction to Engineering Calculations, Material-Balance calculations, Stoichiometry of microbial growth and Product formation, Energy Balance Calculations with and Without Reactions Production of Primary and secondary Metabolites: [04] A brief outline of processes for the production of some commercially important Organic acids, amino acids and alcohols, study of production processes for various classes of low molecular weight secondary metabolites: Antibiotics, quinones, aromatics, Vitamins and Steroid. Text books: 1. Cruger.W and A.Cruger, A Textbook of Industrial Microbiology (2e), Sinauer Associates, Sunderland,US, 2004. 2. Stryer.L, Biochemistry (4e), Freeman, 2002. 3. Michael Shuler and Fikret Kargi, Bioprocess Engineering: Basic Concepts (2e), Prentice Hall, Englewood Cliffs, NJ, 2002. 4. Bailey .J.E and D. F. Ollis, Biochemical Engineering Fundamentals (2e), Mc-Graw Hill, Inc., 1986. 5. Pauline M Doran, Bioprocess engineering principles (1e), Academic Press, 1995.

BIO 503 MOLECULAR BIOLOGY & r-DNA TECHNOLOGY Total No of periods: 48

[4 0 0 4]

Structure and Organization of Nucleic Acids: [05] Different forms of DNA and RNA, Organization of DNA in Prokaryotic and Eukaryotic Chromosomes. DNA Replication: [05] DNA Replication in Prokaryotes and Eukaryotes, Telomeric Replication in Eukaryotes, Replication of Viral DNA brief overview. Transcription and Translation: [05] Transcription in Prokaryotes and Eukaryotes, Post-transcriptional Modifications, Genetic Code, Wobble Hypothesis, Translation in Prokaryotes and Eukaryotes, Post-translational Modifications. Regulation of Gene Expression: [05] The Operon Concept Promoter, Operator, Terminator, Attenuator, Inducer, Repressor, Effect of cAMP Complex; lac operon. DNA Repair, Mutagenesis and Mutations: Biochemical mechanisms of DNA Repair, Types of Mutations, Modes of Mutagenesis. [06]

Basics of Recombinant DNA Technology: [04] Introduction to cloning, Method of creating recombinant DNA molecules, Cloning Vectors, Expression Vectors. Enzymes in Genetic Engineering: [04] Restriction Endonucleases and Exonucleases, Methylases, Ligases, Terminal Transferase, Polynucleotide Kinase, Phosphorylases, Phosphatases, RNase, DNase. Nucleic Acid Hybridization and DNA Libraries: [04] The hybridization reaction, Production and Labelling of Gene Probes, Southern Blotting, Northern Blotting, in situ hybridization, Construction of Genomic and cDNA libraries.

Molecular Analysis and Amplification Methods: Restriction Mapping, Adaptors & Linkers, PCR, RFLP, RAPD, Nucleic Acid Sequencing.

[05]

Applications of Recombinant DNA Technology: [05] Diagnostic Tools: SNPs, VNTRs. Drugs and Therapies: Therapeutic proteins from Transgenic plants and animals, Gene Therapy Combating Disease: Recombinant vaccines DNA Vaccines; Plant Breeding: Herbicide-resistance, Virus-resistance, Insect and pest-resistance, Stress tolerance. Others: DNA fingerprinting, Directed mutagenesis, Antisense Technology. Text books: 1. David Friefelder, Molecular Biology (2e), Jones and Bartlett Publishers Inc, 1987. 2. Primrose S.B and R. W. Old, Principles of gene manipulation - An introduction to genetic engineering (Vol. 2), Blackwell Scientific Publications, 1980. 3. Benjamin Lewin, Genes VIII , Prentice Hall , 2004. 4. Walker J.M and R.Rapley, Molecular Biology and Biotechnology, Indian Reprint by Panima Publishing Corporation, 2000. 5. Sambrook J et al, Molecular Cloning (Vol I, II and III), Cold Spring Harbor Laboratory (CSHL) Press, 1989. 6. Berger S.L. and A.R Kimmel, Methods in Enzymology (Vol.152), Academic Press, 1987.

BIO 505 TRANSPORT PHENOMENA IN BIOPROCESSING Total No of periods: 48

[3 1 0 4]

Introduction [03] Introduction to Transport Phenomena momentum, heat and mass transfer in bioprocessing Momentum transfer [13] Review of basic concepts Conservation of Mass, Conservation of Energy, Momentum Balance Momentum Balance in a Circular Pipe, Flow Velocity Profile Fermentation Broth Rheology Viscosity, Rheological Properties of Fermentation Broths, Factors affecting broth viscosity Mixing in a Bioreactor Flow regimes with and without baffles, various types of impellers and mixing equipment. Power Requirements for Mixing, Ungassed Newtonian Fluids, Gassed Fluids, Improving Mixing in Fermenters, Effect of Rheological Properties on Mixing, Role of Shear in Stirred Fermenters Heat Transfer [13] Review of basic concepts Various modes of heat transfer, viz., conduction convection and radiation. Design Equations for Heat Transfer Systems Energy Balance, Calculation of HeatTransfer Coefficients. Application of heat transfer in bioprocessing, Heat Management in Bioreactors, Relationship between heat transfer, cell concentration and stirring conditions Mass transfer [13] Review of basic concepts Diffusivity, theory of diffusion, analogy between mass, heat and momentum transfer, role of diffusion in bioprocessing. Definition of binary mass transfer coefficients, transfer coefficients at high mass transfer rates- boundary layer theory, penetration theory. Convective mass transfer Liquid-solid mass transfer, liquid-liquid mass transfer, gas liquid mass transfer. Oxygen transport to microbial cultures Gas liquid mass transfer fundamentals, oxygen requirement of microbial cultures. Oxygen requirements of microbial cultures oxygen mass transfer fundamentals. oxygen transfer and oxygen demand.

Oxygen transfer by aeration and agitation. Determination of oxygen mass transfer coefficient by various methods including dynamic gassing out and oxygen balance methods. Design considerations & Scale-up of fermentors Design criteria for fermentor, scale up criteria and examples. Text books: 1. Arthur T. Johnson, Biological Process Engineering: An Analogical Approach to Fluid Flow, Heat Transfer, and Mass Transfer Applied to Biological Systems, John Wiley and Sons, 1998.
2. Pauline M. Doran, Bioprocess Engineering Principles, Academic Press, 1995. 3. Blanch H.W and Douglas S. C, Biochemical Engineering, CRC Press, 1997. 4. Michael L Shuler and Fikret Kargi, Bioprocess Engineering: Basic Concepts, Prentice-Hall of India Pvt Ltd, 2008.

[06]

BIO 507 ADVANCED BIOSEPARATION PROCESSES Total No of periods: 48

[3 1 0 4]

Role of Downstream Processing in Biotechnology: [04] Role and importance of downstream processing in biotechnological processes. Problems and requirements of bioproduct purification. Economics and downstream processing in Biotechnology. Cost cutting strategies, characterstics of biological mixtures, process design criteria for various classes of bioproducts (high volume-low value products and low volumehigh value products), physicochemical basis of bio-separation processes. Primary Separation and Recovery Processes: [04] Cell disruption methods for intracellular products, removal of insolubles, biomass (and particulate debris) separation techniques; flocculation and sedimentation, centrifugation and filtration methods Precipitation methods: Precipitation with salts, organic solvents & polymers [04]

Extraction: [06] Batch extractions, staged extractions-cross current, co current, counter current extractions. Differential extractions, fractional extractions with a stationary phase, fractional extractions with two moving phases. Aqueous two-phase extraction: [06] reverse micelle extraction, supercritical fluid extraction, in-situ product removal/integrated bioprocessing Membrane-based separations (micro- & ultra-filtration): [06] Theory; design & configuration of membrane separation equipment; applications; reverse osmosis, dialysis, electro dialysis, Isoelectric focusing Adsorption: [06] Adsorption isotherms, industrial adsorbents, adsorption equipments for batch and continuous operations (co current and counter current), adsorption in fixed beds.

Chromatography: [06] Principles of chromatographic separation gel filtration, reversed phase, hydrophobic interaction, ion-exchange, expanded bed adsorption, bio affinity and IMAC, supercritical fluid chromatography. Case studies: [06] Preparation of commercial enzymes: Continuous isolation of enzyme prolyl-t RNA synthetase from mung bean, Intracellular foreign proteins from recombinant E.coli and extracellular enzyme (protease) recovery; Purification of biosurfactants from fermentation broths. Text books: 1. Belter P.A, Cussler E and Wei Shan Hu, Bioseparation Downstream Processing for Biotechnology, Wiley Interscience, 1988. 2. Asenjo and Juan A. Asenjo, Separation Processes in Biotechnology, CRC Press, 1990. 3. Wankat P.C, Rate Controlled Separation, Kluwer Publishers, 1990. 4. Wang D.I.C, Cooney C.L, Demain A.L, Dunnil.P, Humphery A.E. and Lilly M.D. Fermentation and Enzyme Technology, John Wiley and Sons, 1979.

HUM 501

RESEARCH METHODOLOGIES AND TECHNICAL COMMUNICATION

[1 0 3 2]

Total No of periods: 24 1. Mechanics of Research Methodology Basic concepts: Types of research, Significance of research, Research framework, Case study method, Experimental method, Sources of data, Data collection using questionnaire, Interviewing, and experimentation. Research formulation: Components, selection and formulation of a research problem, Objectives of formulation, and Criteria of a good research problem. Research hypothesis: Criterion for hypothesis construction, Nature of hypothesis, Need for having a working hypothesis, Characteristics and Types of hypothesis, Procedure for hypothesis testing. Sampling Methods: Introduction to various sampling methods and their applications. Data Analysis: Sources of data, Collection of data, Measurement and scaling technique, and Different techniques of Data analysis. 2. Thesis Writing and Journal Publication Writing thesis, Writing journal and conference papers, IEEE and Harvard styles of referencing, Effective Presentation, Copyrights, and avoiding plagiarism. References 1. Dr Ranjit Kumar, Research Methodology: A Step-by-Step Guide for Beginners, SAGE, 2005. 2. Geoffrey R. Marczyk, David DeMatteo & David Festinger, Essentials of Research Design and Methodology, John Wiley & Sons, 2004. 3. John W. Creswel , Research Design: Qualitative, Quantitative, and Mixed Methods Approaches, SAGE, 2004 4. Suresh C. Sinha and Anil K. Dhiman, Research Methodology (2 Vols-Set), Vedam Books, 2006. 5. C. R. Kothari, Research Methodology: Methods and Techniques, New Age International Publisher, 2008. 6. Donald R Cooper & Pamela S Schindler , Business Research Methods, McGraw Hill International, 2007. 7. R. Pannershelvam, Research Methodology, Prentice Hall, India, 2006 8. Manfred Max Bergman, Mixed Methods Research, SAGE Books, 2006. 9. Paul S. Gray, John B. Williamson, David A. Karp, John R. Dalphin, The Research Imagination, Cambridge University press, 2007. 10. Cochrain & Cox, Experimental Designs, II Edn. Wiley Publishers, 2006.

BIO 511

BIOPROCESS ENGINEERING LAB - I

[0 0 6 2]

Experiments are based on Bioprocess Engineering, Microbiology, Molecular biology & rDNA technology course works.

M.Tech INDUSTRIAL BIOTECHNOLOGY SECOND SEMESTER

BIO 502 BIOREACTOR DESIGN AND ANALYSIS Total No of periods: 48 Introduction and Review of Bio-reaction engineering concepts, Mass transfer effects in heterogeneous reaction Stirred tank batch bioreactor: stirred batch bio reactor for enzymes, cell cultures

[3 1 0 4]

[04] [03]

Continuous Stirred Tank Bioreactor : Continuous operation of mixed reactor, enzyme reactions in a mixed reactor, performance equation for M-M kinetics, substrate inhibition kinetics and product inhibition kinetics, chemostat with cell cultures steady state cell and substrate concentrations and productivity as a function of dilution rate, CSTR with immobilized enzymes, operation of CSTR in a constant feed rate policy-simulation for conversions with and without diffusion limitations, chemostat in series, Graphical design [06] Plug Flow and Packed Bed Bioreactor: Performance equation with Michelin-Menten kinetics, substrate inhibition and product inhibition, plug flow reactor for immobilized enzymes, operation of plug flow reactor in constant feed rate policy, simulation for conversion with and without diffusion limitations [06] Fedbatch reactor: Applications of fed reactor, Fed batch operation of mixed reactor, material balance on cell and substrate [03] Recycle system: Chemostat with recycle, Biological waste water treatment, Feed forward control of the activated sludge process [04] The Transient Behavior of Bioreactors: Stability analysis, Stability of the chemostat, Stability of chemostat with substrate inhibition, Operating diagram, Transient responses of the chemostat, control of the chemostat, Turbidostat operation, Nutristat operation [06] Design of a fermenter: Basic function of a fermenter for microbial or animal cell culture, basic bioreactor design criteria, overview of bioreactor types-stirred tank bioreactor, bubble column bioreactor, air-lift reactor, propeller loop reactor, jet loop reactor, schematic overview of a fermenter with control system, operating issues that affect reactor design, aeration and oxygen mass transfer in bioreactor system [04]

Instrumentation and control: Methods of measuring process variables, measurement and control of dissolved oxygen, pH and foam measurements [04] Non-ideal flow: Non-ideal flow, RTD, E,C,F-curves, calculation for Macrofluid micro & Macro fluid, conversion [08]

Text books: 1. Blanch H.W and Douglas S. Clark, Biochemical Engineering, CRC Press, 1997. 2. Michael L Shuler and Fikret Kargi, Bioprocess Engineering: Basic Concepts, Prentice-Hall of India Pvt Ltd, 2008. 3. Stanbury P.F., Whitaker A. and Hall S.J, Principles of Fermentation Technology. Elsevier India Pvt Ltd, 2007. 4. Arthur T. Johnson, Biological Process Engineering: An Analogical Approach to Fluid Flow, Heat Transfer, and Mass Transfer Applied to Biological Systems, John Wiley and Sons, 1998. 5. Pauline M. Doran, Bioprocess Engineering Principles. Academic Press, 1995.
6. Rao D.G., Introduction to Biochemical Engineering. Tata McGraw-Hill, 2005.

BIO 504 BIOPROCESS MODELING, ANALYSIS & SIMULATION Total No of periods: 48

[3 1 0 4]

Perspective on modeling of physical, chemical and biological phenomena, uses and limitations of mathematical models in Bioprocess models- Basic classifications, fundamental features of models. Several examples involving algebraic equations, ordinary differential equations, difference equations partial differential equations, integral equations and integro-differential equations. [12] Elements of probability theory, stochastic models parameter estimation model forms for parameter estimation. Parameter estimation using moments, design of experiments for parameter estimation. Accuracy of parameter estimates. Design of experiments for model discrimination Regression and interpolation. [12] Review of numerical techniques for the solution of bioprocess models. Non linear systems analysis Phase Plane analysis in classical bioreactor models, phase plane plot for bioreactor with monad kinetics. [08] Introduction to nonlinear dynamics A simple population growth model. More complex growth models, chaotic behavior, cob web diagrams, stability of fixed point solutions. Introduction to bifurcations behavior in single and two variable systems. Introduction to chaos. The Lorenz equations. [08] Introduction to population balance modeling in bioprocess engineering The solution of population balance equations. Budding of yeast population Modeling of cells with dynamic morphology Modeling for biological populations with correlation between life spans of siblings. Modeling of Industrial sterilization processes [08] Text books: 1. Wayne Bequette.B, Process dynamics modeling and analysis and simulation,. Prentice Hall Inc, 2004. 2. John H. Seinfeld and Leon Lapidus., Mathematical Methods in Chemical Engg., (Vol. 3), Process Modeling, Estimations and Identification. Prentice Hall, 1974. 3. Ramakrishna. D, Population Balances. Academic Press, 2000. 4. Shyam S. Sablani., Handbook of Food and Bioprocess Modeling Techniques. C R C Press, 2006. 5. Volesky.B and J. Votruba., Modeling and Optimization of Fermentation Process (Process Simulation and Modelling). Elsevier Science and Technology, 1992.

List of OPEN ELECTIVES: Open Elective ELECTIVE-I BIO 540 BIO 542 Subjects 1. Animal and Plan Biotechnology 2. Bionanotechnology Teaching Department BIO BIO

BIO 540 Total No. of Hours: 36

ANIMAL AND PLANT BIOTECHNOLOGY

[3 0 0 3]

Plant Genome Organization Organization and features of mitochondrial, nuclear and choloroplast genome Structural features of gene families in plants, Totipotency, Regeneration of plants [04] Plant cell cultivation Biochemistry of major metabolic pathways, Autotrophic and heterotrophic growth, Plant growth regulators and elicitors, Cell suspension culture development: methodology, kinetics of growth and product formation, nutrient optimization, Plant products of industrial importance, Production of secondary metabolites by plant suspension cultures, Hairy root cultures and their cultivation. [06] Techniques in raising transgencies and IPR Direct and indirect methods: Mechanical, Femptosyringe, electroporation, biolistic, Chemical: Protoplast, Biological: Agrobacterium mediated plant transformation, chloroplast transformation, in-planta transformation. Patent, Plant breeders rights, Implementation of IPR protection, Emerging mechanisms for technology transfer, Enforcement laws and regulations [08] Animal Cell Organization and nutrient requirement Special features and organization of animal cells, Animal cell metabolism, Animal cell growth characteristics, Principles of sterile techniques, Regulation and nutritional requirements for mass cultivation of animal cell cultures. [06]

Animal cell cultivation Substrate and product transport through mammalian cell, Animal cell growth kinetics and shear force. Micro and Macro carrier attached growth, Cell culture in continuous, perfusion and hollow-fiber reactor. [06]

Techniques in animal biotechnology and IPR Hybridioma technology, Live stock improvement, Gene transfer methods in animals, Transgenic animals, Applications of Cloning and xenotransplantation, Animal cell preservation, IPR in Animal Biotechnology [06]

Text books: 1. Dixon R.A and Gonzales, Plant Cell Culture: A Practical Approach, IRL Press, 1995. 2. Lindsey. K and M.G.K. Jones, Plant Biotechnology in Agriculture, Prentice Hall, New 3. 4. 5. 6. Jersey, 1990. Biotol series, In vitro Cultivation of Plant cell, Butterworth Heinemann Ltd., 1994 Biotol series, In vitro Cultivation of Animal cell, Butterworth Heinemann Ltd. 1994. Ranga .M.M, Animal Biotechnology (3e), Agrobios, 2007. Bhojwani & Rajdhan, Animal and Plant Biotechnology, Elsevier, 1996.

BIO 542 Total No of periods: 36

BIONANOTECHNOLOGY

[3 0 0 3]

Introduction and the scope of Bionanotechnology, Comparison of Biotechnology to Bionanotechnology [02] Bionanomachines and their Basics: Negligible gravity and inertia, atomic granularity, thermal motion, water environment and their importance in bionanomachines, The role of proteins, amino acids, nucleic acids, lipids and polysaccharides in modern biomaterials. Overview of natural Bionanomachines: Thymidylate Sythetase , ATP synthetase, Actin and myosin, Opsin, Antibodies and Collagen [03] Synthesis of Biomolecules: Recombinant Technology, Site-directed mutagenesis, Fusion Proteins. Quantum Dot structures and their integration with biological structures. Tools of Analysis: X-Ray crystallography, NMR spectroscopy, Electron microscopy and Atomic force microscopy. Molecular modeling tools: Graphic visualization, structure and functional prediction, Protein folding prediction and the homology modeling, Docking simulation and Computer assisted molecular design. [06] Structural principles of Bionanotechnology raw matertials: Factors governing biomolecular structure and stability, Protein folding; Self assembly, Self-organization, Molecular recognition and Flexibility of biomaterials. [05] Functional principles of Bionanotechnology: Information driven nanoassembly, Energetics, Role of enzymes in chemical transformation, allosteric motion and covalent modification in protein activity regulation, Structure and functional properties of Biomaterials, Bimolecular motors: ATP Synthetase and flagellar motors, Traffic across membranes: Potassium channels, ABC Transporters and Bactreriorhodapsin, Bimolecular sensing, Self replication, Machine-Phase Bionanotechnology. [10] Fields of Application: Designer proteins, Peptide nucleic acids, Nanomedicine, Drug delivery, DNA computing, Molecular design using biological selection, Harnessing molecular motors, Artificial life, Hybrid materials, Biosensors, Future of Bionanotechnology. [10] Text books: 1. David S Goodsell , Bionanotechnology, John Wiley & Sons, 2004. 2. Greco Ralph S , Nanoscale Technology in Biological Systems, CRC Press, 2005.

BIO 514

SEMINAR

[0 0 3 1]

This course is designed for the students to develop skills in searching technical literature, coordinating it and making a good presentation. Presentation of a good written report is also part of exercise. The students will give the seminar on a topic assigned to them, on soft skills or technical topics.

BIO 512

BIOPROCESS ENGINEERING LAB - II

[0 0 6 2]

Experiments are based on Fermentation Technology, Advanced Bioseparation Processes, Advanced Bioinformatics, Bioprocess Modelling and Simulation course works.

BIO ***

PROGRAM ELECTIVES

[4 0 0 4]

List of Program Electives: PROGRAM ELECTIVE CODE BIO 520 BIO 522 BIO 524 BIO 526 BIO 528 BIO 530 BIO 532 BIO 534 BIO 536 TEACHING DEPARTMENT SUBJECTS Advanced Bioinformatics Biofuels Engineering Biopharmaceuticals & Pharmaceutical Biotechnology Enzyme Biotechnology Solid Waste Management Statistical Design and analysis of experiments in biotechnology Design & development of Biological treatment processes Immunotechnology Biopolymer technology BIO BIO BIO BIO BIO BIO BIO BIO BIO

BIO 520 Total No of periods: 48

ADVANCED BIOINFORMATICS

[4 0 0 4]

Introduction: [08] Life, Proteins, Nucleic acids DNA, RNA, The flow of genetic information, Genetic code, Transcription, Translation and Protein Synthesis, Junk DNA and Reading Frames, Chromosomes, Genome & Computer Program, The Human Genome Project and the Digital code of Life, Applications of Bioinformatics. Biological Databanks: [08] Sequence Databases: Introduction, Primary and secondary databases, Nucleotide and protein sequence databases. Information retrieval from Biological databases, Retrieving Database Entries: Integrated Information Retrieval, The SRS & Entrez System, Structure databases: Introduction to Structures, Protein Data Bank (PDB), Molecular Modeling Database (MMDB) at NCBI, Structure file formats, visualizing structural information, structure viewers. Analytical Bioinformatics: [08] Introduction, The evolutionary basis of sequence alignment, the Modular Nature of proteins, Optional Alignment Methods, Database Similarity Searches: BLAST, FASTA, Low- Complexity Regions, Repetitive Elements. Pairwise sequence alignment - NEEDLEMAN and Wunsch, SmithWaterman algorithm; Multiple sequence alignments CLUSTAL, Motifs and Patterns, Primer design. Structural Bioinformatics: [08] Anatomy of Proteins - Secondary structures, Motifs, Domains, Tertiary and quaternary structuresRamachandran plot; RNA structure; Structure of Ribosome; RNA Secondary Structure Prediction, Structure of small molecules. Introduction to Set theory, Graph theory, Strings & Algorithms, Chemical graphs. Biodiversity Informatics: [10] Biological information; Biological diversity of life, Hierarchical Levels in Biodiversity, Genetic diversity; Different types of biodiversity, Biodiversity issues Hotspots & Warm spots, Essentials of Biodiversity Databases, Methods for species identification & classification, Biodiversity Databases Organizing biological species information; Tree of life project, Elements of phylogenetic Models, Phylogenetic Data Analysis, Substitution Model Building, Tree Building, and Tree Evaluation, Building the Data Model (Alignment), Determining the Substitution Model, Tree -Building

Methods, Searching for Trees, Rooting Trees, Evaluating Trees and Data, Phylogenetic software on the web. Commercial Bioinformatics Bioinformatics companies, IPR and Bioinformatics, Novel ideas, Bioinformatics patents, copyright & Patenting. Text books: 1. David W Mount, Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor, 2. 3. 4. 5. 6. 7. 2001. Arthur M. Lesk, Introduction to Bioinformatics, Oxford University Press, 2002. Smith D.W., Biocomputing Informatics and the Genome Projects, Academic Press, 1993. Stuart M Brown., Bioinformatics: A biologists guide to biocomputing and the internet, Eaton Publishing Company, 2000. Doolittle.R.F., Computational methods for macromolecular sequence analysis, Academic Press, 1996. Salzberg.S.L., D.B.Searls, S.Kasif (Eds.)., Computational methods in Molecular Biology. Elsevier, 1998. John N. Abelson, Melvin I. Simon and Russell F. Doolittle (Eds.), Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences (Methods in Enzymology, Volume 183). Academic Press, 1990. [06]

BIO 522 Total no. of periods: 48

BIOFUELS ENGINEERING

[4 0 0 4]

Introduction: [08] Description of Biofuels; Energy Use & Efficiency; Biofuel Production; Alternative Energies; Biochemical Pathways Review for Organoheterotrophic, Lithotrophic & Phototrophic Metabolism; Importance of COD; Biofuel Feedstocks: Starch, Sugar, Lignocellulosic, Agro & Industrial by-products. Production of Bioethanol: [08] Process Technology for Bioethanol production using Sugar; Starch and Lignocellulosic Feedstocks: Selection of micro-organisms and feedstock; Associated Unit Operations; Determination of Bioethanol yield; Recovery of Bioethanol; Recent Advances; Process Integration Production of Biodiesel: [08] Chemical, Thermodynamic & Reaction Kinetic Aspects of Biodiesel Production: Transesterification and Supercritical Esterification, Saponification and Hydrolysis, Acid & Base Catalysis; Sources of Oils; Methods of Biodiesel Production General procedure and Large scale production; Quality Control Aspects. Production of Biohydrogen: [08] Enzymes involved in H2 Production; Photobiological H2 Production: Biophotolysis and Photofermentation; H2 Production by Fermentation: Biochemical Pathway, Batch Fermentation, Factors affecting H2 production, Carbon sources, Process and Culture Parameters; Detection and Quantification of H2 Microbial Fuel Cells: [08] Biochemical Basis; Fuel Cell Design: Anode & Cathode Compartment, Microbial Cultures, Redox Mediators, Exchange Membrane, Power Density; MFC Performance Methods: Substrate & Biomass Measurements, Basic Power Calculations, MFC Performance: Power Density, Single-Chamber vs Two-Chamber Designs, Wastewater Treatment Effectiveness; Future Directions

Microbial Modeling of Biofuel Production: [08] Microbial Growth Models: Unstructured, Single Limiting Nutrient Models, Inhibition Models, Models for Multiple Limiting Substrates, Yield Parameters; Kinetic Rate Expressions; Bioreactor Operation and Design for Biofuel Production: Batch, CSTR, CSTR with Cell Recycle, Fed-Batch Systems, Plug Flow Systems; Modeling of Glucose Utilization and Hydrogen Production; Batch and CSTR Fermentations and Simulations Text books: 1. Caye M. Drapcho, N.P. Nhuan and T. H. Walker, Biofuels Engineering Process Technology , Mc Graw Hill Publishers, New York, 2008. 2. Jonathan R.M, Biofuels Methods and Protocols (Methods in Molecular Biology Series), Humana Press, New York, 2009. 3. Lisbeth Olsson (Ed.), Biofuels (Advances in Biochemical Engineering/Biotechnology Series, Springer-Verlag Publishers, Berlin, 2007.

BIO 524

BIOPHARMACEUTICALS AND PHARMACEUTICAL BIOTECHNOLOGY [4 0 0 4] Total No of Periods: 48 Pharmaceuticals, biologics and biopharmaceuticals [08] Introduction to pharmaceutical products, Biopharmaceuticals and pharmaceutical biotechnology, Biopharmaceuticals: current status and future, Pharmaco-Kinetics- absorption of drugs, distribution of drugs, protein binding of drugs, Basic Issues in the Manufacture of Macromoleucles, Traditional pharmaceuticals of biological origin-animal origin, plant origin, microbial origin. Pharmacokinetics [08] Biotransformation of drugs, Preclinical Pharmacokinetics , Compartment modeling- one compartment open model , two compartment open model, multi compartment model, non linear kinetics, bioavailability and bioequivalence, excretion of drugs, pharmacokinetics effects of food and fasting. The drug development and manufacturing process [08] Drug discovery, Patenting- Patent types, The patent application, Patenting in biotechnology, Preclinical trials, Clinical trials, The role and remit of regulatory authorities-The Food and Drug Administration, The investigational new drug application, The new drug application, European regulations, Guides to good manufacturing practice, Formulation and Delivery Issues of Therapeutic Proteins, Biotechnology-Derived Drug Products: Formulation Development, Stability Testing, Filling, and Packaging. Pharmaceutical dosage forms: [16] Dosage Forms and Basic Preparations, Excipients for Pharmaceutical Dosage Forms, Compressed tablets, wet granulation, dry granulation or slugging, direct compression, tablet formulation, coating, capsules, sustained action dosage form, parental, oral liquids, ointments, recombinant blood products and therapeutic enzymes, hormones of therapeutic interest Pharmaceutical products, Analysis and Control: laxatives analgesics non steroidal contraceptives external antiseptics antacids and other, antibiotics biological hormones vitamins - preservation, analytical methods and test for various drugs and pharmaceuticals, packaging techniques quality control

Drug safety evaluation: [08] Strategy and Phasing for Drug Safety Evaluation in the Discovery and Development of Pharmaceuticals, Regulation of Human Pharmaceutical Safety, Acute Toxicity Testing in Drug Safety Evaluation, Special Concerns for the Preclinical Evaluation of Biotechnology Products, Immunotoxicology in Pharmaceutical Development, The Application of In Vitro Techniques in Drug Safety Assessment, Pharmaceutical Quality Assurance

Text books: 1. Heinrich Klefenz , Industrial pharmaceutical biotechnology, John Wiley sons, 2002. 2. Susanna Wu-Pong, Yongyut Rojanasakul, and Joseph Robinson, Biopharmaceutical drug and design and development, Humana Press, 2007. 3. Gary Walsh, Biopharmaceuticals: Biochemistry and Biotechnology (2e), John Wiley & Sons, 2003. 4. Herbert A Kirst, Wu-Kuang Yeh; Milton J, Enzyme Technologies for pharmaceutical and biotechnological applications, WILEY-VCH Verlag, 2003.

BIO 526 Total Number of Periods: 48

ENZYME BIOTECHNOLOGY

[4 0 0 4]

Introduction: Disease resistant crops-Engineering bacterial and fungi resistance in cropsHerbicide resistant crops (HRCs) - potential risks and increased costs associated with the use of HRcs- Bacillus thuringensis (BT) for insect control-recycling of toxic wastes- Novel food products- Transgenic animals- General risks of releasing genetically engineeried organisms into the environment. Use of biotechnology and genetic engineering Public perceptions of biotechnology- Use of biotechnology as a way to preserve biodiversity- Further depletion of biodiversity- Harm to nontarget organisms- Transnational companies (TNCs) may exploit farmers in developing countries. [14]

The Catalysts of Life: Historical, occurrence and distribution of catalysts- NomenclatureAntienzymes-Isoenzymes- Isolation and purification of enzymes- The active site-Enzyme specificity-Sunstrate concentration-Temperature- Temperature coefficient- types of InhibitionsMechanisms of Allosteric effects-chemical kinetics-catalysis. [08] Cutinase- A Lipolytic Enzyme: Three Dimensional structure of Native cutinase- The tertiary fold , secondary structure, Hydrogen Bonds and Salt Bridges- The catalytic Triad- Structural comparision between Cutinase and the other Hydrolase Fold members- The oxyaninon Hole mutants- Dynamics of Cutinase- Molecular Dynamics-packaging Forces-the Atomic Structure of Native cutinase-The analysis of the Anisotropy. [08] Industrial Enzymes by Protein Engineering: Bacillus subtilis Natural Protease- Stabilizing pseudomonas isoamylase- Stabilizing Carbamylase from Agrobacterium Radiobacter. [08] Poly (A) Polymerases: General characteristics of Poly (A) Polymerase- Changes in Poly (A) Polymerase activity in response to various stimuli- Phosphorylation of Poly (A) Polymerase and its potential regulatory role- Exonuclease associated with purified nuclear Poly (A) PolymeraseImmunology of Poly (A) Polymerase- Probable functions of Poly (A) Polymerase,Probable recognition sites for Poly (A) addition. [10]

Text books: 1. Prakash .M, Enzyme Biotechnology (1e), Discovery Publishing House, 2007. 2. Michael L. Shuler and Fikret Kargi. Bioprocess Engineering, Pearson Prentice Hall, 2002.

BIO 528 Total no of periods: 48

SOLID WASTE MANAGEMENT

[4 0 0 4]

Introduction to solid waste management: [05] Waste generation in technological society, integrated solid waste management, operation of solid state waste management systems. Legislative Trends and Impacts: major legislation, Government agencies. Sources, Types and Composition of solid wastes: [12] Determination of the composition of municipal solid wastes in the field, Physical, chemical and biological properties of MSW; transformations of solid waste; Properties and classification of Hazardous wastes; transformations of Hazardous waste constituents found in MSW; Management of hazardous wastes in MSW. Engineering Principles: [12] Solid waste generation and collection Rates, Collection of solid waste, Separation and Processing and Transformation of solid waste, Transfer and Transport, Disposal of solid wastes and residual matter: The landfill method, classification and types; Layout and preliminary design of landfills Biological and chemical conversion technologies: [12] Biological principles, aerobic composting, low and high solids Anaerobic digestion, development of anaerobic digestion processes and technologies for treatment of the organic fraction of MSW; other biological transformation processes. Energy production from biological conversion products, Fermentation and compost processes: Basic processes, feed stocks, products, design parameters, reactor types, Application and economics, case histories. Solid waste management and planning issues: [07] Meeting federal and state mandated diversion goals:- source reduction and recycling, Implementation of solid waste management options; planning, siting and permitting of waste management facilities.

Text books:
1. George Tchobanoglous, Integrated solid waste management: Engineering principles and management issues, Mcgraw Hill, 1993. 2. William D Robinson, The solid waste handbook: A practical guide, John Willy & sons, 1986.

BIO 530

STATISTICAL DESIGNS AND ANALYSIS OF EXPERIMENTS IN BIOTECHNOLOGY [4 0 0 4] Total No of periods: 48 Presentation & analysis of data: Errors in Data and calculations, presentation of experimental data, data analysis, general procedures for plotting data, process flow diagrams [06] Introduction to statistical design: Classical versus statistical approaches to experimentation, diagnosing the experimental environment, good design requirements. Introduction to factorial designs, definitions and principles, Basic Two-level factorial design experiments, 2k factorial design [10]

Screening designs: Fractionating factorial designs, fractional factorial designs, PlackettBurmann screening designs [10] Process Optimization experiments: Response surface methodology concepts & methods, design considerations, central composite designs and Box-Behnken response surface design [12] Case studies: Optimizations of Media components, fermentation process and purification process with specific case studies by using statistical software. [10] Text book: 1. Lawson J & Erjavec J, Modern Statistics for Engineering and Quality Improvement (1e), Duxbury Press, 2001. 2. Montgomery Douglas C , Design and analysis of experiments (6e), John Wiley, 2009. 3. Pauline Doran, Bioprocess Engineering Principles (1e), Academic Press, 1995.

BIO 532

DESIGN AND DEVELOPMENT OF BIOLOGICAL TREATMENT PROCESSES [4 0 0 4] Total No of periods: 48 Bacterial metabolism in wastewater treatment systems: Introduction, decomposition of organic carbon compounds in natural and manmade systems, aerobic and anaerobic decomposition of glucose, protein, carbohydrates, proteins, lipids etc., Nitrogen removal during treatment, enhanced biological phosphate removal, biological removal, biotransformations, and biosorption of metal ions, aerobic and anaerobic degradation of xenobiotics [09] Activated sludge process: Single and two stage process, special developments, technological and microbiological aspects, plant configurations, design [08] Modeling of aerobic waste water treatment process: Introduction, purpose of modeling, activated sludge model, presentations, waste water characteristics various disinfection methods for waste water [08] High rate anaerobic waste water treatment: Introduction, basic principles, reactor design parameters, reactor operation [07] Biological Nutrient removal: Suspended growth and attached growth nutrient removal processes and design criteria Nitrogen (Nitrification and denitrification), & Phosphorus precipitation , biological), Biological removal of toxic and recalcitrant organic wastes [10] Water reuse: Wastewater reclamation, risk assessment, various reclamation technologies, storage agricultural reuse, industrial reuse, groundwater recharge [06]

Text book:
1. Jrdening H.J. and J.Winter , Environmental Biotechnology - Concepts and Applications,

Cambridge University Press, 2006.

2. George Tchobanoglous and Franlin L. Burton, Wastewater Engineering- Treatment, Disposal and Reuse, Tata McGraw Hill Publishing Co. Ltd, 1990.

BIO 534 Total No of periods: 48

IMMUNOTECHNOLOGY

[4 0 0 4]

The Immune System: Introduction - innate and adaptive immunity. Lymphocytes - their origin and differentiation; antigens - their structure and classification; complement and their biological functions; types of immune responses; anatomy of immune response. [07] Humoral Immunity: B-lymphocytes and their activation; structure and function of immunoglobulins; immunoglobulin classes and subclasses. Genetic control of antibody production. monoclonal antibodies and diagnosis. idiotypes and idiotypic antibodies. Major histocompatibility complex. Blood Typing: AB, O & Rh. [07] Cellular Immunology: Thymus derived lymphocytes (T cells) their classification. antigen presenting cells (APC) -macrophages. dendritic cells. langerhans cells - their origin, activation and functions; mechanisms of phagocytosis; identification of cell types of immune system; immunosuppression. Immune tolerance. [07] Antigen Antibody interactions: precipitation, agglutination, neutralization. Immunological and antibody based assays: RIA, ELISA, Chemiluminescence, ELIspot, FACS, western blotting, Immuno fluorescence, immuno precipitation, immuno diffusion, immunoelectrophoresis. Immuno Histochemistry and IHC methods. Immuno electron microscopy. [08] Stem cells: Brief mention about stem cells and applications to immunology, Immunosuppressive drugs. HLA and disease, mechanisms of immunity to tumor antigens. [06] Autoimmunity: Auto antibodies in humans, pathogenic mechanisms, experimental models of auto immune disease, treatment of auto immune disorders. [06] Molecular Immunology: Preparation of vaccines, application of rDNA technology to production of antibodies. Immunotherapy. [07] Text Books: 1. Roitt I , Essential Immunology , Blackwell Scientific Publications, Oxford press ,1991. 2. Kuby J and WH Freeman, Immunology (6e), New York, 2007. 3. Benjarnini E. and Leskowitz s., Immunology A short course, Wiley Liss, NY, 1991. 4. Sambrook J et al ., Molecular cloning (Vol I, II and III)., Cold Spring Harbor laboratory Press. New York, USA, (1989, 2000). 5. Gabriel Virella, Introduction to Medical Immunology (4e), Lippincott Williams & Wilkins (1999).

BIO 536 Total No of periods: 48

BIOPOLYMER TECHNOLOGY

[4 0 0 4]

Introduction: Biopolymers The current scenario, different biopolymers produced from various renewable resources, characteristics, merits and demerits over conventional polymers [06] Biopolymer Technology and Applications: Biopolymers and Artificial Biopolymers in Biomedical Applications, an Overview, Novel Synthesis of Biopolymers and Their Medical Applications, Composite Films Based on Poly (Vinylalcohol) and Lignocellulosic Fibres: Preparation and Characterizations, Composite Materials Based on Gelatin and Fillers from Renewable Resources: Thermal and Mechanical Properties, Properties of PHAs and Their Correlation to Fermentation Conditions [12] Biosynthesis and Modifications: Synthesis and modification of different Biopolymers like xanthum gum, PHA, PHB etc.,

[06]

Biosurfactants: Source, characteristics and properties of Biosurfactants; Production of Biosurfactants via the fermentation and biotransformation routes; Production of Biosurfactants with immobilized cells; Integrated bioprocess for continuous production of Biosurfactants including downstream processing; Applications of Biosurfactants Food Industry, Environmental Control. [08] Material Testing and Analytical Methods: An Overview of Available Testing Methods, Comparison of Test Systems for the Examination of the Fermentability of Biodegradable Materials, Structure-Biodegradability Relationship of biopolymers [08] Case studies: Optimization of production and purification of Xanthum gum and other biopolymers like PHA, PHB [08] Text Books: 1. Emo Chiellini , Emo Chiellini and Helena Gil, Biorelated Polymers: Sustainable Polymer Science and Technology, Springer 2001. 2. Johnson .R.M, L.Y. Mwaikambo and N. Tucker, Biopolymers, Rapra Technology, 2003. 3. Naim Kosaric (Ed). Biosurfactants. Marcell Dekker Inc, 1993.

M.Tech INDUSTRIAL BIOTECHNOLOGY SECOND YEAR

BIO 699

PROJECT WORK

[0 0 0 40]

The students (individually) at the beginning of second year will be assigned project work to be carried out in Industry/Institute under the supervision of a guide. The project should be completed and submitted for evaluation at the end of the year.