m.tech industrial biotechnology

7/30/2019 M.tech Industrial Biotechnology

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M.TECH

INDUSTRIAL BIOTECHNOLOGY

Department of Biotechnology,

Manipal Institute of Technology (MIT),

Manipal University,

Manipal


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M. TECH.INDUSTRIAL BIOTECHNOLOGY

FIRST SEMESTER SECOND SEMESTER

FIRST

YEAR

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

MAT 503

Mathematical methods in

Chemical & Biochemical

Engineering 3 1 0 4 BIO 502

Bioreactor Design and

Analysis 3 1 0 4

BIO 501 Bioprocess Engineering 3 1 0 4 BIO 504

Bioprocess Modeling

Analysis and Simulation 3 1 0 4

BIO 503

Molecular biology & r-

DNA technology 4 0 0 4 xxx.xxx.x Open Elective 3 0 0 3

BIO 505

Transport Phenomena in

Bioprocessing 3 1 0 4 BIO 514 Seminar 0 0 3 1

BIO 507

Advanced Bioseparation

Processes 3 1 0 4 BIO 512

Bioprocess Engineering

Lab - II 0 0 6 2

HUM 501

Research Methodologies

&

Technical

Communication 1 0 3 2 BIO *** Program Elective 4 0 0 4

BIO 511

Bioprocess Engineering

Lab - I 0 0 6 2 BIO *** Program Elective 4 0 0 4

BIO *** Program Elective 4 0 0 4

TOTAL 17 4 9 24 TOTAL 21 2 9 26

SECOND

YEAR

BIO 699 Project Work 0 0 0 40

TOTAL 0 0 0 40


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LIST OF PROGRAM ELECTIVES

BIO 520 Advanced Bioinformatics

BIO 522 Biofuels Engineering

BIO 524 Biopharmaceuticals & Pharmaceutical Biotechnology

BIO 526 Enzyme Biotechnology

BIO 528 Solid Waste Management

BIO 530 Statistical Design and analysis of experiments in biotechnologyBIO 532 Design & development of Biological treatment processes

BIO 534 Immunotechnology

BIO 536 Biopolymer Technology

LIST OF OPEN ELECTIVES

BIO 540 Animal and Plant Biotechnology

BIO 542 Bionanotechnology


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M.TechINDUSTRIAL BIOTECHNOLOGY

FIRST SEMESTER


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MAT 503 [3 1 0 4]

MATHEMATICAL AND NUMERICAL TECHNIQUES IN CHEMICAL &

BIOCHEMICAL ENGINEERING

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 collocationon finite elements. [12]

The Galerkin finite Element technique-variational forms of PDEs. Sturm-Louiville theory-

separation of variables and Fourier Transforms-Greens function-uniqueness conditions for

linear and Nonlinear systems, steady state characteristics of Nonlinear Dynamical systems-

Linear 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 EngineeringPHI, 1998.

4. Davis, H.T. and Thomson K., Linear Algebra and Linear operators in Engineering withapplications of mathematica, Academic Press, 2000


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BIO 501 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 ofbacteria 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 sterilizationequipment

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 andregulation 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 molecularweight 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.


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BIO 503 MOLECULAR BIOLOGY & r-DNA TECHNOLOGY [4 0 0 4]


Structure and Organization of Nucleic Acids: [05]

Different forms of DNA and RNA, Organization of DNA in Prokaryotic and EukaryoticChromosomes.

DNA Replication: [05]

DNA Replication in Prokaryotes and Eukaryotes, Telomeric Replication in Eukaryotes,

Replication of Viral DNAbrief 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: [06]

Biochemical mechanisms of DNA Repair, Types of Mutations, Modes of Mutagenesis.

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.


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Molecular Analysis and Amplification Methods: [05]

Restriction Mapping, Adaptors & Linkers, PCR, RFLP, RAPD, Nucleic Acid Sequencing.

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 vaccinesDNA 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.


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BIO 505 TRANSPORT PHENOMENA IN BIOPROCESSING [3 1 0 4]


Introduction [03]

Introduction to Transport Phenomenamomentum, heat and mass transfer in bioprocessing

Momentum transfer [13]

Review of basic conceptsConservation 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 BioreactorFlow regimes with and without baffles, various types of impellers andmixing 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 Heat-

Transfer 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, gasliquid 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.
http://www.dcu.ie/~oshead/be322/Lectures/LectureH1.dochttp://www.dcu.ie/~oshead/be322/Lectures/LectureH1.doc


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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 [06]

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 ofIndia Pvt Ltd, 2008.


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BIO 507 ADVANCED BIOSEPARATION PROCESSES [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 volume-

high 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: [04]

Precipitation with salts, organic solvents & polymers

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.


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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 forBiotechnology, 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.


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HUM 501 RESEARCH METHODOLOGIES AND [1 0 3 2]

TECHNICAL COMMUNICATION


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 ResearchImagination, Cambridge University press, 2007.

10. Cochrain & Cox, Experimental Designs, II Edn. Wiley Publishers, 2006.


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BIO 511 BIOPROCESS ENGINEERING LAB - I [0 0 6 2]

Experiments are based on Bioprocess Engineering, Microbiology, Molecular biology & rDNA

technology course works.


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M.Tech


SECOND SEMESTER


16/37

BIO 502 BIOREACTOR DESIGN AND ANALYSIS [3 1 0 4]


Introduction and Review of Bio-reaction engineering concepts, Mass transfer effects inheterogeneous reaction [04]

Stirred tank batch bioreactor: stirred batch bio reactor for enzymes, cell cultures [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]


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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, micro & Macro fluid, conversioncalculation for Macrofluid [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.


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BIO 504 BIOPROCESS MODELING, ANALYSIS & SIMULATION [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 ofmodels. 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 systemsanalysis PhasePlane analysis in classical bioreactor models, phase plane plot for bioreactor

with monad kinetics. [08]

Introduction to nonlinear dynamicsA 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,. PrenticeHall 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.


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List of OPEN ELECTIVES:

Open Elective Subjects Teaching

Department

ELECTIVE-I BIO 540 1. Animal and Plan Biotechnology BIO

BIO 542 2. Bionanotechnology BIO

BIO 540 ANIMAL AND PLANT BIOTECHNOLOGY [3 0 0 3]

Total No. of Hours: 36

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]


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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

Jersey, 1990.

3. Biotol series,In vitro Cultivation of Plant cell, Butterworth Heinemann Ltd., 1994

4. Biotol series,In vitro Cultivation of Animal cell, Butterworth Heinemann Ltd. 1994.

5. Ranga .M.M,Animal Biotechnology(3e), Agrobios, 2007.

6. Bhojwani & Rajdhan,Animal and Plant Biotechnology, Elsevier, 1996.


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BIO 542 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 forcemicroscopy. 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 Flexibilityof biomaterials. [05]

Functional principles of Bionanotechnology: Information driven nanoassembly, Energetics,

Role of enzymes in chemical transformation, allosteric motion and covalent modification inprotein 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.


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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 partof 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.


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BIO *** PROGRAM ELECTIVES [4 0 0 4]

List of Program Electives:

PROGRAM

ELECTIVE

CODE SUBJECTS

TEACHING

DEPARTMENT

BIO 520 Advanced Bioinformatics BIO

BIO 522 Biofuels Engineering BIO

BIO 524 Biopharmaceuticals & Pharmaceutical Biotechnology BIO

BIO 526 Enzyme Biotechnology BIO

BIO 528 Solid Waste Management BIO

BIO 530

Statistical Design and analysis of experiments in

biotechnology

BIO

BIO 532 Design & development of Biological treatment processes BIO

BIO 534 Immunotechnology BIO

BIO 536 Biopolymer technology BIO


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BIO 520 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, Smith-

Waterman algorithm; Multiple sequence alignments CLUSTAL, Motifs and Patterns, Primer

design.

Structural Bioinformatics: [08]

Anatomy of Proteins - Secondary structures, Motifs, Domains, Tertiary and quaternary structures-

Ramachandran 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 issuesHotspots & 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


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Methods, Searching for Trees, Rooting Trees, Evaluating Trees and Data, Phylogenetic software

on the web.

Commercial Bioinformatics [06]

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,

2001.

2. Arthur M. Lesk,Introduction to Bioinformatics, Oxford University Press, 2002.

3. Smith D.W.,Biocomputing Informatics and the Genome Projects, Academic Press, 1993.

4. Stuart M Brown., Bioinformatics: A biologists guide to biocomputing and the internet,

Eaton Publishing Company, 2000.

5. Doolittle.R.F., Computational methods for macromolecular sequence analysis, Academic

Press, 1996.

6. Salzberg.S.L., D.B.Searls, S.Kasif (Eds.)., Computational methods in Molecular Biology.

Elsevier, 1998.

7. 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.
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BIO 522 BIOFUELS ENGINEERING [4 0 0 4]

Total no. of periods: 48

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


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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 andHydrogen 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,BiofuelsMethods 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.


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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, Pre-

clinical 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 ofTherapeutic 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 antisepticsantacids and other, antibiotics biological hormones

vitamins - preservation, analytical methods and test for various drugs and pharmaceuticals,

packaging techniquesquality control


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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 inDrug 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 andbiotechnological applications, WILEY-VCH Verlag, 2003.


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BIO 526 ENZYME BIOTECHNOLOGY [4 0 0 4]

Total Number of Periods: 48

Introduction: Disease resistant crops-Engineering bacterial and fungi resistance in crops-

Herbicide resistant crops (HRCs) - potential risks and increased costs associated with the use ofHRcs- 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- Nomenclature-

Antienzymes-Isoenzymes- Isolation and purification of enzymes- The active site-Enzyme

specificity-Sunstrate concentration-Temperature- Temperature coefficient- types of Inhibitions-

Mechanisms 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) Polymerase-

Immunology 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.


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BIO 528 SOLID WASTE MANAGEMENT [4 0 0 4]

Total no of periods: 48

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 andmanagement issues, Mcgraw Hill, 1993.

2. William D Robinson, The solid waste handbook: A practical guide, John Willy & sons,

1986.


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BIO 530 STATISTICAL DESIGNS AND ANALYSIS OF EXPERIMENTS IN

BIOTECHNOLOGY [4 0 0 4]


Presentation & analysis of data: Errors in Data and calculations, presentation of experimentaldata, 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, Plackett-

Burmann 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.


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BIO 532 DESIGN AND DEVELOPMENT OF BIOLOGICAL TREATMENT

PROCESSES [4 0 0 4]


Bacterial metabolism in wastewater treatment systems: Introduction, decomposition oforganic 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, bio-

transformations, and biosorption of metal ions, aerobic and anaerobic degradation of xeno-

biotics [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 removalprocesses 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.


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BIO 534 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).


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BIO 536 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 ofthe 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.
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M.Tech


SECOND YEAR


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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.

m.tech industrial biotechnology

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