Scheme of Study and the Syllabi for the VII semester B. Tech.- Biotechnology and the VIISemester M. Tech. - (5 -Year Integrated) Biotechnology Programmes for the students

admitted during the academic year 2011-12.

Semester VII

Course Code Course Name L-T-P-C

BBTCBT701R01/MBTCBT701 Equipment Design and Drawing 3-1-0-4

BBTCBT702R01/MBTCBT702 Downstream Processing - II 3-1-0-4

BBTCBT703R01/MBTCBT703 Bioethics & Biosafety 3-1-0-4

BBTCBT704R01/MBTCBT704 Bioreactor Engineering Lab 0-0-3-2

BBTCBT705R01/MBTCBT705 Downstream Processing Lab 0-0-3-2

BBTDBT701/ MBTDBT701BBTDBT707/ MBTDBT707BBTDBT703/ MBTDBT703BBTDBT704/ MBTDBT704BBTDBT705/ MBTDBT705BBTDBT706/ MBTDBT706

(Any 2)Protein Engineering Systems Biology Transport PhenomenaFree Radicals and Antioxidant BiologyGenomics and ProteomicsDevelopmental Biology of Plants and Animals

3-1-0-43-1-0-43-1-0-43-1-0-43-1-0-43-1-0-4

Total 15-5-6-24

3-1-0-4

BBTCBT701R01/MBTCBT701: EQUIPMENT DESIGN AND DRAWING

Course Objectives: To equip students with the basic concepts of design of processequipments and drawing of the same.

UNIT I 25 periods

Design of Shell & Tube Heat Exchangers and CondensersDesign of Calendria type evaporators Design of fermentor (chemostat) Design of Crystallizers

UNIT II 35 periods

Design of equipments for Distillation and Absorption (packed and plate column), Design of Extraction column (plate).Design of – Spray dryer, freeze dryer, rotary dryerDesign of membrane contactors for liquid separations

TEXTBOOKS

1. “Chemical Engineering”, 3/e, R.K. Sinnott, J.M. Coulson & J.F. Richardson (Eds.), Vol. 6, Butterworth Heinemann, 2002.

2. “Process Design of Equipments,” 3/e, Vols. 1 & 2, Shrikant D. Dawande, Central Techno Publications, 2003.

3. “Principals of mass transfer and separation process” Binay K.Dutta, Prentice-Hall of India, 2007.

REFERENCES

1. “Perry’s Chemical Engineer’s Handbook,” 7/e, R.H. Perry, D.W. Green, J.O. Maloney, McGraw-Hill, 19972. “Separation process principles”, Seader, Hanley, John Wiley & Sons, 1998.3. http://www.nptel.ac.in/courses/103103027/

LEARNING OUTCOMES

Unit I The learner will be able to apply the principles of transport process and makeprocess design and drawing of Shell & Tube Heat Exchangers, CondensersEvaporators, fermentor (chemostat) and crystallizers

Unit II The learner will be able to make a detailed process design and drawing of distillation, absorption, extraction, dryers and design of membrane contactors.

3-1-0-4

BBCBT702R01/MBTCBT702: DOWNSTREAM PROCESSING – II

Course Objectives: To equip students with skills to design and develop a separation protocolfor biologically important compounds and its scale up aspects.

UNIT I 15 periods

ADSORPTION: Theories of adsorption – Adsorption isotherms, industrial adsorbents,adsorption equipment for batch and continuous operations (co-current and counter-current),adsorption in fixed beds. Specific cases.

UNIT II 15 periods

CHROMATOGRAPHY: Chromatography – principles of chromatographic separation – gelfiltration, reverse- phase, hydrophobic interaction, ion-exchange, expanded-bed adsorption,bio-affinity and IMAC, supercritical fluid chromatography. Selection of process -selection ofparameters-pH, Buffer, ligand and methods. Design and selection of chromatographicmatrices; modes of operation; design of large-scale chromatographic separation processes-Gel filtration, Ion exchange

UNIT III 15 periods

CRYSTALLIZATION: Crystallization: Factors governing nucleation and crystal growth. Theoryof crystallization. Design of industrial crystallizers: batch and continuous crystallizers.

Process integration: Synthesis of Downstream process, Automation in protein purification.Downstream Processing plant and equipment and downstream processing economics

UNIT IV 15 periods

DRYING: Importance of drying in processes - drying characteristics of materials - theory andmechanism of drying ––different types of drying – classification of dryers - continuousdrying – design features, performance of dryers - concepts of freeze drying, spray drying –auxiliary equipment required along with drying plants. Estimation of drying rate and dryingtime in Dryers.

TEXTBOOKS

1. “Product Recovery in Bioprocess Technology,” BIOTOL Series, VCH Publishers, 1992.

2. “Mass Transfer Operations,” 3/e, R. E. Treybal, McGraw-Hill, 1980

3. “Unit Operations of Chemical Engineering,” 7/e, W. L. McCabe & J. C. Smith, McGraw-Hill,New York, 2004.

REFERENCES

1.”Separation Process Principles”, 3/e, J.D. Seader, E.J. Henley, D. K. Roper, Wiley, 2011

“Bioseparations,” P. A. Belter & E. Cussler, Wiley, 1985.

2. “Separation Processes in Biotechnology,” J. Asenjo, M. Dekker, 1990.

3. Bioprocess Engineering principles, Pauline Doran, Publisher: Elsevier Science & Technology,1995.

LEARNING OUTCOMES

Unit I The learner will have an understanding of the concepts and equipment involved inadsorption

Unit II The learner will get complete knowledge of liquid chromatography techniques and itsscale up techniques

Unit III The learner will have an understanding of the principles and methods of crystallizationprocess

Unit IV The learner will have an understanding of the principles and methods of drying forprotein applications

3-1-0-4

BBTCBT703R01/MBTCBT703: BIOETHICS & BIOSAFETY

Course Objectives: To introduce bio-safety, bio-safety regulations and ethical concepts inbiotechnology

UNIT I 14 periodsBIOSAFETY AND HAZARD ASSESSMENT

Introduction to Bio-safety; Biosafety in laboratory- Laboratory associated infections and otherhazards; assessment of biological hazard & level of Biosafety; Prudent biosafety practices inlaboratory; Hazardous Materials Used in Biotechnology—Handling and Disposal includingradioactive materials; Good Manufacturing Practices (GMP); Good Laboratory Practices (GLP);Use of genetically modified organisms & their release in environment; special procedures forrDNA based product production.

UNIT II 12 periodsBIOSAFETY-REGULATORY FRAMEWORK IN INDIA

Recombinant DNA Advisory Committee (RDAC), Institutional Biosafety Committee (IBC),Review Committee on Genetic Manipulation, Genetic Engineering Approval Committee (GEAC),State Biosafety Coordination Committee (SBCC), District Level Committee (DLC). RecombinantDNA Guidelines (1990), Revised Guidelines for Research in Transgenic Plants (1998), SeedPolicy (2002), Prevention Food Adulteration Act (1955), The Food Safety and Standards Bill(2005), Plant Quarantine Order (2003), Regulation for Import of GM Products Under ForeignTrade Policy (2006-2007), National Environment Policy (2006). Rules for the manufacture,use/import/export and storage of hazardous microorganisms/genetically engineered organismsor cells (Ministry of Environment and Forests Notification, 1989).

UNIT III 12 periodsINTERNATIONAL BIOSAFETY-REGULATORY FRAMEWORK

International: Convention of Biological Diversity (1992); Cartagena Protocol on Biosafety;Objectives and salient features of Cartagena Protocol; Advanced Information Agreement (AIA)procedure; procedures for GMOs intended for direct use-risk assessment-risk management;handling, transport, packaging and identification of GMOs; Biosafety Clearing House;unintentional trans-boundary movement of GMOs; Benefits of becoming a party to theCartagena Protocol ; Bioterrorism & conventions on biological weapons.

UNIT IV 12 periodsBioethics

Introduction to bio-ethics; Ethical issues in genetic engineering, patenting human genes,cloning, genetic testing & screening; Biotechnology & social responsibility; The legal & socio-economic impact of Biotechnology; Public acceptance issue in Biotechnology-issue of access,ownership, monopoly, traditional knowledge, public versus private funding.

UNIT V 10 periods

Regulatory requirements for Drug development and Clinical research

Basics of regulation of drug development; application and various phases of clinical trial,specialized areas of drug development & commercialization.

TEXTBOOKS

1. Thomas J.A., Fush R.L., (2002), Biotechnology & safety Assessment, 3/e, Academic press.

2. Fleming D.A., Hunt D.L., (2002), Biological safety Principles & practices, 3/e, ASM Press,Washington.

3. Biotechnology- A Comprehensive treatise (Vol 12), Legal economic & ethical DimensionsVCH.

REFERENCES

1. Nilima Kshirsagar, Tejasree N Kulkarni, Anish Desai, Jatin Shah; Regulatory requirements fordrug development and clinical research (2013), ICMR, New Delhi.

2. Sasson A, Biotechnologies & Development, UNESCO Publications.

3. Regulatory Framework for GMOs in India (2006) Ministry of Environment and Forest,Government of India,New Delhi

4. Cartagena Protocol on Biosafety (2006) Ministry of Environment and Forest, Government ofIndia, New Delhi

LEARNING OUTCOMES

Unit IIntroduces the learners to bio-safety in laboratory, GLP and GMP; use ofradioisotopes in laboratory and hazard management; understand the hazards inhandling genetically modified organisms.

Unit II Introduces the learner to various national committees that set guidelines for use ofrDNA, GMO.

Unit III Introduces the learner to various international convention protocols and regulatorypolicies that control handling transport of GMOs.

Unit IV Introduces the learner to ethical issues in biotechnology.

Unit V Introduces the learner to ethical and regulatory issues in drug development andclinical research.

0-0-3-2

BBTCBT704R01/MBTCBT704: BIOREACTOR ENGINEERING LABORATORY

Course objectives: The laboratory course is aimed to provide hands-on experience to learnerson different fundamental aspects of bioprocess engineering.

List of Experiments

1. Assessment of the effect of pH on enzyme activity

2. Assessment of the effect of substrate concentration on enzyme activity

3. Assessment of the effect of temperature and heat on enzyme activity

4. Assessment of the effect of inhibitor concentration on enzyme activity

5. Production and optimization of amylase from corn in solid state fermentation.

6. Enzyme immobilization by entrapment in calcium alginate gel

7. Microbial growth kinetics and substrate utilization kinetics in batch culture.

8. Medium optimization by PLACKETT BURMAN METHOD

9. Lactic acid production from milk under aerobic and anaerobic condition.

10. kLa estimation by sodium sulphite oxidation method

11. kLa estimation by dynamic gassing out method.

12. Monitoring process variables during batch cultivation of bacterial strain.

LEARNING OUTCOMES

Upon completion of experiments, the learners will be able to:

Expt No. Outcome

1 Calculate the optimum pH of enzymatic reaction

2 Estimate the enzyme kinetic parameters such as Vm and Km

3 Estimate the optimum temperature and stability of enzymatic reaction4 Identify the type of enzyme inhibition5 Estimate the activity of amylase and find out moisture content6 Measure the immobilized enzyme kinetic parameters and compare with

free enzyme kinetic parameters7 Estimate the substrate utilization rate and yield coefficient8 Use Placket Burman method to identify the important variable in

fermentation9 Compare the productivity of lactic acid under different conditions 10 Estimate volumetric mass transfer coefficient 11 Estimate the power requirement by volumetric mass transfer coefficient12 Observe pH, dissolved oxygen concentration, temperature, substrate and

cell concentration during the fermentation

0-0-3-2

BBCBT705R01/MBTCBT705: DOWNSTREAM PROCESSING LABORATORY

Course objectives:

Provides an opportunity to experimentally verify the theoretical concepts already learnt in the courses: Downstream processing-I & II.

To expertise in the separation and purification systems involved in bio-product recovery. To learn, develop a successful separation protocol of the target bio-molecule.

List of Experiments

1. Cell Disruption: High-pressure homogenization2. Cross Flow Filtration3. Aqueous Two Phase Extraction4. Reverse Miscellar Extraction5. Ionic liquid based two phase extraction6. Ammonium Sulphate Precipitation7. Isoelectric Precipitation 8. Removal of small molecules using dialysis9. Ion Exchange Chromatography (IEX)10. Hydrophobic Interaction Chromatography(HIC)

LEARNING OUTCOMES

Expt. No. Outcome1 The student will be able to employ small scale cell disruption methods2 The student will be able to harvest cells by cross flow filtration3 The student will be able to use aqueous two phase extraction for protein

separation. 4 The student will be able to separate invertase using reverse miscellar extraction

systems5 The student will be able to separate proteins using ionic liquid-based two phase

extraction6 The learner will be able to separate protein by ammonium sulphate precipitation7 The student will be able to employ isoelectric precipitation of proteins. 8 The student will be able to dialyze the protein9 The student will be able to purify a protein using ion exchange chromatography10 The student will be able to purify a protein using HIC

3-1-0-4

BBTDBT701/MBTDBT701: PROTEIN ENGINEERING

Course Objectives: To provide a fundamental knowledge of the methods used to engineerprotein molecules with novel properties and study the impact of the alterations on differentprotein functions.

Unit I 15 periods

Protein Structure and Folding

Motifs in protein structure: amino acids; polypeptide structure; secondary structures - alphahelix, beta sheets and loops; Ramachandran plot; topology diagrams; motifs – helix-turn-helix,helix-loop-helix, hairpin beta, greek key motif and beta-alpha-beta-multi domain proteins. Protein folding: protein renaturation - determinants of protein folding; protein disulphideisomerase; molecular chaperones- conformational diseases.

Unit II 15 periods

Protein Production & Engineering Methods

Protein expression; choice of expression systems; use of E. coli and S. cerevisiae for proteinproduction; post-translational manipulations; optimization of protein production; initialpurification. In vitro mutagenesis: principle and variations - in vitro chemical mutagenesis – oligonucleotide -based mutagenesis - cassette mutagenesis – PCR based mutagenesis - saturationmutagenesis favoring the mutants; applications. Protein engineering using non-canonical aminoacids - methodologies; applications-side chain packing - backbone mutations- dissectingcollagen mutations

Unit III 15 periods

Strategies for Protein Design

Protein design; strategies for the design of structure - self-assembly - ligand-induced assembly -assembly via covalent cross-linking - assembly of peptides on a synthetic template Strategies for the design of function - novel functions by retrofitting natural proteins -incorporation of binding sites into de novo proteins - design of catalytically active proteins -membrane proteins and ion channels - design of new materials.

Unit IV 15 periods

Modulating protein structures and interaction by computational design

The core repacking problem; predicting native protein core sequences; early core designs; fullrepacks and surface design; hydrogen bonding and polar residues in the core; altering proteinfolds; experimental evaluation. Geometry based design; stereochemistry based design; Applications of computationallydesigned proteins - biosensors - therapeutic proteins and antibodies.

TEXTBOOKS

1. Introduction to Protein Structure, 2/e, C. Branden and J. Tooze, Garland Science, USA, 1999.2. Protein Engineering and Design, 1/e, Paul R. Carey, Academic Press Inc, USA, 1996. 3. Protein Engineering and Design, 1/e, Sheldon J. Park, Jennifer R. Cochran, Taylor and Francis Inc., CRC Press, USA, 2010.

REFERENCE

1. Protein Engineering: A Practical Approach, 1/e, A. R. Rees, M. J. E. Sternberg, R. Wetzel, Oxford University Press, USA, 1993.

LEARNING OUTCOMES

Unit IThe learner will be able to understand physical aspects of protein structure, itscomponents and folding.

Unit IIThe learner will get the exposure on recombinant protein production and mutagenesismethods to engineer new protein constructs.

Unit IIIThe learner can obtain knowledge in various strategies to design protein structureand function.

Unit IVThe learner will able to understand the different aspects involved in protein structuredesign and interactions using computational and geometry based approaches.

3-1-0-4

BBTDBT707: SYSTEMS BIOLOGY

Course objective: (i) To introduce basic network biology principles and to demonstrate whysystems level understanding in biology is essential; (ii) to illustrate biological network basedinformation processing, regulation and control mechanisms through systems modeling.

UNIT I 15 periods

SYSTEMS BIOLOGY- FUNDAMENTALS

Scope, Historic perspective and Network biology: Traditionally biology - descriptive science;Status of quantification - comparison with traditional engineering systems; Central dogma-functional organization of biological networks, Hierarchical links and emergence of phenotypiccharacteristics; Biochemical reaction networks: Principles - Enzyme kinetics, Michaelis-Mentenkinetics, Mass actions kinetics, Input Output response, Steepness, Threshold phenomenon,Ultrasensitivity, Hill equation, Steady state and Dynamics response; Emergent properties ofbiological networks: Complexity, Adaptability, Bistability, Robustness and Evolvability.

UNIT II 15 periods

TRANSCRIPTION NETWORK

Introduction to network motifs and detection from random networks, Elements of transcriptionnetworks, Emergent properties of biological networks, Dynamics and response time of simplegene regulation, Autoregulation-A network motif, Response time and Robustness.

UNIT III 15 periods

FEED FORWARD LOOPS & TEMPORAL AND GLOBAL STRUCTURE OF TRANSCRIPTIONNETWORKS

Types of Feed Forward Loops (FFLs) in networks motifs and their specific properties-Dynamics,Sign sensitive delay, Response acceleration, Convergent evolution of FFLs; Temporalexpression programs-Single input module (SIM), Topological generalization, Multi-Output FFL,Bi-Fans, Dense overlapping regulons, Network motifs and global structure

UNIT IV 15 periods

NETWORK MOTIF USAGE & CASE STUDIES

Network motif usage in (i) Developmental transcription networks, (ii) Signal transductionnetworks, (iii) Neuronal networks; Case studies: (i) Robustness of protein circuits – the exampleof chemotaxis, E. coli chemotaxis network, exact adaptation (ii) Robustness patterning indevelopment - Morphogen profiles, Fruit fly patterning (iii) Threshold and Negative feedbackloop in rhythmic processes (oscillations) of complex biological system, Circadian Rhythm.

REFERENCE

1. “Introduction to Systems Biology. URI ALON. Chapman and Hall/CRC Mathematical andComputational Biology, 2007.

2. “Systems Modeling in Cellular Biology: From Concepts to Nuts and Bolts,” Edited ByZOLTAN SZALLASI, JÖRG STELLING, VIPUL PERIWAL. Princeton Hall of India. ISBN:978-81-203-3172-3, 2007.

3. “Computational Modeling of Genetic and Biochemical Networks," Edited by JAMES M.BOWER and HAMID BOLOURI, MIT press, 2004.

4. Relevant research articles.

LEARNING OUTCOMES

Unit I The learner will get an introductory understanding and overview of systems levelnetwork modelling in biology. The learner will be able to appreciate whyquantifications in biology is essential. The learner will be able to represent biologicalsystems in terms of mathematical expressions.

Unit II The learner will get familiarised with the transcription networks in general and thelearner will be able to identify, quantify and analyse simple motifs in transcriptionnetworks.

Unit III The learner will be able to identify, quantify and analyse feed forward loops intranscription networks. In addition they will also be able to appreciate the role ofnetwork motifs in orchestrating the temporal and global behaviour in biologicalsystems.

Unit IV The learner will be able to understand the usage of assorted range of network motifsby diverse biological systems to elicit specific phenotypic characteristics. In additionthe learner will get familiarised with three case specific examples.

3-1-0-4

BBTDBT703/MBTDBT703: TRANSPORT PHENOMENA

Course Objective: To help the learners understand the concept of mathematical modelling,equations of change and develop models for new systems

UNIT I 11 periods

Mechanism of momentum, heat & mass transport; Newton’s law of viscosity; Fourier’s laws ofheat conduction; Fick’s laws of diffusion; pressure & temperature dependence of viscosity;conductivity & diffusivity; theory of viscosity; conductivity & mass diffusivity; Non-Newtonianfluids.

UNIT II 10 periods

Introduction to shell balances; boundary conditions. Velocity distributions in laminar flow; flow of fallingfilm; flow through circular tube; flow through an annulus; adjacent flow of two immiscible fluids; creepingflow around a solid sphere.

UNIT III 15 periods

Equations of change for isothermal systems: Equation of continuity; equation of motion;equation of mechanical energy; Euler’s equation of motion; Navier-Stokes equation; steady-state flow problems; dimensional analysis of equation of change.

UNIT IV 12 periods

Temperature distributions in solids: Heat conduction with an electrical heat source; heatconduction with nuclear heat source; viscous heat source; chemical heat source; compositewalls; cooling fin.

UNIT V 12 periods

Concentration distributions in laminar flow:

Diffusion through a stagnant gas; diffusion with heterogeneous chemical reaction,homogeneous chemical reaction; diffusion into a falling liquid film; forced-convection masstransfer; diffusion & chemical reaction inside a porous catalyst; effectiveness factor.

TEXTBOOKS

1. “Transport Phenomena,” 2/e, Bird, Stewart & Lightfoot, John Wiley & Sons, 2001.

2. “Transport Process & Unit Operations,” 3/e, J. Christie & G. Koplis, Prentice-Hall of India, 2003.

3. “Transport Phenomena,” J. Thomson, Pearson Education Asia Ltd., 2001.

REFERENCES

1. “Fundamentals of Momentum, Heat & Mass Transfer,” J. R. Welty, R. E. Wilson & L. E. Wick, John Wiley (ISE), 2001.

2. “Momentum, Heat & Mass Transfer,” Bennett & Mayers, McGraw-Hill, 1982.

LEARNING OUTCOMES

Unit I At the end of this unit the learner will be able to explain the mechanisms oftransport and make analogy of transport processes; understand transportproperties and predict transport properties.

Unit II At the end of this unit the learner will be able to write shell momentumbalance and develop mathematical models for fluid flow systems

Unit III At the end of this unit the learner will be able to understand and applyequation of continuity and motion

Unit IV At the end of this unit the learner will be able to write shell energy balanceand develop models for heat conduction with various heat sources

Unit V At the end of this unit the learner will be able to write shell mass balanceand develop models mass of transport systems

3-1-0-4

BBTDBT704/MBTDBT704: FREE RADICALS AND ANTIOXIDANT BIOLOGY

Course Objectives: Provide an understanding on Free Radicals, its formation in cell systems,attenuation and detection techniques; mechanism of Anti-cancer drug in prevention ofcarcinogenesis.

UNIT - I 15 PeriodsFree Radicals and Cellular Damage

Oxidative Stress- Conditions favouring free radicals-Dysfunctional of Complex I-I/R stressfactors. Free radicals- Reactive Oxygen species [ROS]- Reactive Nitrogen Species- Chemistry& Synthesis. ROS Production -Xanthine/Xanthine Oxidase system-lipoxygenase system-NADPH Oxidase-Aconitase Enzyme.Role of Fe [II] in ROS generation- Fenton’s Reaction.RNSProduction-Nitric Oxide synthetase- their classification-iNOS- eNOS&nNOS; Arginine-Citrullinereaction. Organelle involved in free radical formation-Mitochondria- sites of Free radicalformation-electron transport chain-Complex I& Complex III.

Cellular Damages by Free Radicals

Membrane Damages-Oxidation of Proteins-Fatty acids- Lipid Peroxidation-Oxidation ofSulfhydryl groups. ROS induced DNA Damages- Oxidation of Guanine Residues-8hydroxyguanine [8-OH-dG] adduct formation-detection assays-Comet Assay, TUNEL Assay-DNA Ladder Assay. Protein Oxidation-Lipid Peroxidation and its detection. Poly (ADP-ribose)Polymerase

UNIT - II 15 PeriodsEndogenous Antioxidants in Free Radical Reduction

Anti-oxidants – Definition. Diet Derived small Molecules as anti-oxidants : Vitamin C-Vitamin E-Bilirubin- Ubiquinone – N-Acetyl Cysteine- Chemistry of Free radical quenching. EndogenousAnti-oxidants :- Superoxide Dismutase [SOD]-Mn-SOD, Cu-Zn SOD & Fe-SOD; Catalase. Non-Enzymatic Antioxidants-Glutathione-Thioredoxin -detoxification in mitochondria- their assays-localization.

UNIT - III 15 PeriodsCellular Responses to Oxidative Damages

Physiological Role of Free Radicals- Signal transduction-MAPK Cascade. Carcinogenesis- CellProliferation- Role of NF-kB- Signaling Cascade- Cell survival Mechanisms-PI3-K/Akt pathway-Ras/Raf/MEKK/ERK1/2. Anti-Cancer Drug-Doxorubicin triggered Apoptosis- Cell DeathPathway- Extrinsic Pathway-ATM/ChK1/p53 Pathway- Intrinsic-Bax/Cytochrome-C/CaspasesTriggered Apoptotic Pathway-. Inflammation-Parkinson Disease-Ischemic-Reperfusion [I/R]

UNIT - IV 15 PeriodsFree Radicals Detection Techniques

ROS Detection-TBARS; Cyt C/NBT; Fluoresence Assays in cell cultures –CMH2DCFDA- HEAssay- Flow Cytometric method-Quantification of ROS. EPR Detection- Spin Trapping-MPO-DEPEMPO. RNS Detection : NOS Activity measurement-Nitration Assay- peroxy nitrite Probes.

TEXTBOOK

1. Free Radicals in Biology and Medicine [2007] Barry Halliwell and John Gutteridge(eds).,Fourth Edition., Oxford University Press., 781 pages

REFERENCES

1. Redox Signaling and Regulation in Biology and Medicine [2009] Claus Jacob and PaulG Winyard (eds)., Fourth Edition., Oxford University Press., 441 pages

2. Advanced Protocols in Oxidative Stress – Vol I (2008) Donald Armstrong (ed) Fourthedition., Humana Press., 477 Pages.

LEARNING OUTCOMES

Unit I At the end of this Unit, students get an understanding on free radicals of oxygen,nitrogen, their sites of formation, their deleterious effects on cell system andmetabolism.

Unit II Having learnt on deleterious effects caused by free radicals, students understand oncell’s protection system. They get to know the various possible ways of defensesystems, their attenuation pathways.

Unit III Going in depth, they now correlate on free radical generation towards prevention of cancer growth along with cell signaling pathways offering protection in normal cells.

Unit IV Having learnt bio-chemical pathways, they are exposed to various techniques available on free radicals detection, both as invitro & in-situ methods.

3-1-0-4

BBTDBT705/MBTDBT705: GENOMICS AND PROTEOMICS

Course Objective: To learn about the large scale of protein and genes, particularly theirstructures and functions, information flow within a cell, gene organization and network andgenome variation at the DNA level towards the fundamental understanding on the life processand disease.

UNIT I 15 periods

INTRODUCTION TO GENOMICS: What is genomics; The human genome; phenotype-genotype; contents of human genome; genes that encode proteome; varieties of genomeorientation; genome sequencing projects; variations within and between populations; humangenome sequencing; the human genome and medicine.

GENOME MAPPING AND SEQUENCE: Maps and guides; whole genome sequencing -preliminary sequencing-completed sequencing- genome annotation; partial sequences; proteinfunction prediction from DNA sequence; proteins from gene; altering gene expression;imprinting, methylation and cancer.

UNIT II 15 periods

GENOME VARIATION: Variation in human genome; mutation and allele; human SNPs-role ofSNPs in skin pigmentation and malaria resistance; mitochondrial SNPs; variations in medicationresponsiveness; changes in non disease QTL due to SNPs.

COMPARATIVE GENOMICS – Unity and diversity of life – differences in genomes - genomes ofhuman and chimpanzees- genomes of mice and rats

UNIT III 15 periods

GENOMES OF PROKARYOTES AND EUKARYOTES: Evolution and phylogenetic relationshipin prokaryotes and eukaryotes; genomes of archaea and pathogenic bacteria; yeast genome;evolution of plant; genomes of sea squirt, chicken and dog.

DNA MICROARRAYS: Cancer and genomic microarrays- better ways to diagnose and treatcancer; breast cancer categorization with microarrays; improving health care with DNAMicroarrays- efficacy of TB vaccine; predicting effective drugs in different types of cancers;genomic responses to leptin treatments and fat; accumulation.

UNIT IV 15 periods

PROTEOMICS: Gene ontology terms; introduction to protein structure and function- enzymecatalysis-motor proteins-allosteric regulation-serpins; protein aggregation diseases; measuringproteins-2D gels-mass spectrometry; ; protein microarray; the role of single-protein moleculesand single-cell proteomes.

GENOMIC CIRCUITS: Dissecting a gene’s circuitry-gene regulation-molecular dissection ofdevelopment- gene expression in Endo 16-regulation of transcription; natural gene circuits -gene toggle switches - lambda phage switch; engineering principles to determine genomereliability; engineered genetic toggle switches.

TEXTBOOKS

1. Arthur M. Lesk “Introduction to Genomics”, 2e, Oxford University press, 2012

2. A. Malcolm Campbell, Laurie J. Heyer, “Discovering Genomics, Proteomics &Bioinformatics”, 2e, Pearson Education, 2007.

REFERENCE

1. Werner Dubitzky, Martin Granzow, Daniel P. Berrar, Fundamentals of data mining ingenomics and proteomics, 1e, Springer, 2007

LEARNING OUTCOMES

Unit IThe learner will get fundamental knowledge on genomes and experimental stepstowards genome mapping and sequencing.

Unit IIThe learner can understand the genomic variations, its importance in lifeprocess/disease.

Unit IIIThe learner can study the significance genomic data to understand evolution andapplications of DNA microarray to study various diseases

Unit IVThe learner can gain fundamental knowledge in the proteomics tools to understand different biological functions and the role of proteins in the genome circuits.

3-1-0-4

BBTDBT706/MBTDBT706: DEVELOPMENTAL BIOLOGY OF PLANTS AND ANIMALS

Course Objectives: To help the learners recognise the steps involved in organismdevelopment from a single cell

Unit I 15 periodsEARLY EMBRYOLOGY

Introduction, Comparative and evolutionary embryology, Animal embryology, early embryonicdevelopment - invertebrates and vertebrates, mitosis and meiosis, primordial germ cells,gametes-cellular components, fertilization.

Unit II 15 periodsMOLECULAR MECHANISM

Molecular events in the universal mechanism of animal development, signalling mechanisms,Coenorhabditis elegans- developmental control; Drosophila- genesis of body plan, patterning ofantero-posterior axis.

Unit III 15 periodsLATE EMBRYOLOOGY

Cell movement and shaping of vertebrate body-Xenopus embryo; Mouse- embryo development,Late embryonic development-neuronal development, organogenesis and the patterning ofappendages, metamorphosis, regeneration and aging.

Unit IV 15 periodsPLANT EMBRYOLOGY

Plant development, germ line cells, fertilization, seed, and germination, plant hormones indevelopment, oriented cell division, vegetative growth, reproductive growth and senescence.

TEXT BOOKS1. “Molecular biology of the cell”, 5th ed. Bruce Alberts, Garland science, USA, 2008. 2. “Developmental Biology”, 6th ed. S. F. Gilbert, Sinauer Associates, USA, 2000.

LEARNING OUTCOMES

Unit I The student will be able to explain cellular details of gametes and recognise steps involved in embryo formation.

Unit II The learner will be able to describe the molecular mechanism of early and late embryology.

Unit III The learners will be able to distinguish the steps involved in organ development and they can infer how mature organisms develop.

Unit IV The learners will distinguish and recognise steps involved in plant development from a single cell to multi cellular plant