DETAILED CURRICULUM

of

Master of Science in Biotechnology(M.Sc. Biotechnology)

School of Science

Semester One

BiochemistryCredits

3

Course ObjectivesTheobjectivesof this courseare tobuilduponundergraduate levelknowledgeofbiochemicalprincipleswithspecificemphasis on different metabolicpathways.Thecourseshallmakethestudentsawareofvariousdiseasepathologieswithin thecontext of each topic.

Student Learning OutcomesOn completion of this course,students should be able to:• Gain fundamentalknowledgein biochemistry;

• Understand the molecularbasis of various pathologicalconditions from the perspectiveof biochemical reactions.

Unit IChemical basisof life7 lectures

Unit IIProtein structure4 lectures

Unit IIIEnzyme kinetics5 lectures

Unit IVGlycobiology2 lectures

Unit VStructure andfunctions ofDNA&RNAand lipids3 lectures

Unit VIBioenergetics8 lectures

Chemical basis of life:Miller-Urey experiment, abiotic formation of amino acidoligomers,compositionoflivingmatter;Water–propertiesofwater,essentialroleofwater for life onearthpH,buffer,maintenance ofbloodpHandpHofgastric juice,pH optima of different enzymes (pepsin, trypsin and alkaline phosphatase), ionizationand hydrophobicity, emergent properties of biomolecules in water, biomolecularhierarchy, macromolecules, molecularassemblies.

Structure-function relationships: amino acids – structure and functional groupproperties, peptides and covalent structure of proteins, elucidation of primary andhigherorder structures,Ramachandranplot, evolutionofprotein structure,proteindegradation and introduction to molecular pathways controlling protein degradation,structure-function relationships in model proteins like ribonuclease A, myoglobin,hemoglobin,chymotrypsinetc.;basicprinciplesofproteinpurification;toolstocharacterize expressed proteins; Protein folding: Anfinsen’s Dogma, Levinthalparadox,cooperativity in protein folding, free energy landscape of protein folding and pathwaysofprotein folding,moltenglobule state, chaperons,diseasesassociatedwithproteinfolding, introduction tomolecular dynamic simulation.

Enzymecatalysis–generalprinciplesofcatalysis;quantitationofenzymeactivityandefficiency; enzyme characterization and Michaelis-Menten kinetics; relevance ofenzymes in metabolic regulation, activation, inhibition and covalent modification;single substrate enzymes; concept of catalytic antibodies; catalytic strategies withspecific examples of proteases, carbonic anhydrases, restriction enzymes and nucleosidemonophosphate kinase; regulatory strategies with specific example of hemoglobin;isozymes; roleof covalentmodification inenzymaticactivity; zymogens.

Sugars - mono, di, and polysaccharides with specific reference to glycogen, amyloseand cellulose, glycosylation of other biomolecules - glycoproteins and glycolipids;lipids - structureandpropertiesof importantmembersof storageandmembranelipids; lipoproteins.

Self-assemblyof lipids,micelle,biomembraneorganization-sidednessandfunction;membraneboundproteins-structure,propertiesandfunction;transportphenomena;nucleosides, nucleotides, nucleic acids - structure, a historical perspective leading up tothepropositionofDNAdoublehelicalstructure;differenceinRNAandDNAstructureand their importance in evolution ofDNAas the geneticmaterial.

Bioenergetics-basic principles; equilibria and concept of free energy; coupledinterconnectingreactions inmetabolism;oxidationofcarbonfuels; recurringmotifs inmetabolism;IntroductiontoGPCR, Inositol/DAG//PKCandCa++signalingpathways;

glycolysis and gluconeogenesis; reciprocal regulations and non-carbohydrate sourcesof glucose; Citric acid cycle, entry to citric acid cycle, citric acid cycle as a source ofbiosynthetic precursors; Oxidative phosphorylation; importance of electron transferinoxidativephosphorylation; F1-F0ATPSynthase; shuttles acrossmitochondria;regulation of oxidative phosphorylation; Photosynthesis – chloroplasts and twophotosystems; proton gradient across thylakoid membrane; Calvin cycle andpentosephosphate pathway; glycogen metabolism, reciprocal control of glycogen synthesis andbreakdown, roles of epinephrine and glucagon and insulin in glycogen metabolism; Fattyacidmetabolism;proteinturnoverandaminoacidcatabolism;nucleotidebiosynthesis;biosynthesis of membrane lipids and sterols with specific emphasis on cholesterolmetabolism and mevalonate pathway; elucidation of metabolic pathways; logic andintegrationofcentralmetabolism;entry/exitofvariousbiomoleculesfromcentralpathways; principles ofmetabolic regulation; steps for regulation.

Unit VIIRole of vitamins& cofactorsin metabolism12 lectures

Calvin cycle and pentose phosphate pathway; glycogen metabolism, reciprocal controlofglycogensynthesisandbreakdown,rolesofepinephrineandglucagonandinsulinin glycogen metabolism; Fatty acid metabolism; protein turnover and amino acidcatabolism; nucleotide biosynthesis; biosynthesis of membrane lipids and sterols withspecific emphasis on cholesterol metabolism and mevalonate pathway; elucidation ofmetabolic pathways; logic and integration of central metabolism; entry/ exit of variousbiomolecules from central pathways; principles of metabolic regulation; steps forregulation; target of rapamycin (TOR)&Autophagy regulation in relation toC&Nmetabolism, starvation responses and insulin signaling.

Recommended Textbooks and References:1. Stryer, L. (2015). Biochemistry. (8th ed.) New York: Freeman.2. Lehninger,A.L. (2012).Principles ofBiochemistry (6th ed.).NewYork,NY:Worth.3. Voet,D.,&Voet, J.G. (2016).Biochemistry (5th ed.).Hoboken,NJ: J.Wiley&Sons.4. Dobson, C. M. (2003). Protein Folding and Misfolding. Nature, 426(6968), 884-890.

doi:10.1038/nature02261.5. Richards, F.M. (1991). The Protein Folding Problem. ScientificAmerican,

264(1), 54-63.doi:10.1038/scientificamerican0191-54.

Cell andMolecularBiologyCredits

Course ObjectivesTheobjectivesof thiscourseare tosensitize the students to the fact thataswegodownthescaleofmagnitudefromcells toorganelles tomolecules,theunderstandingofvariousbiologicalprocesses becomes deeper andinclusive.

Student Learning OutcomesStudent should be equipped to understandthree fundamental aspects in biologicalphenomenon:a)whattoseek;b)howtoseek; c) why toseek?

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Unit IDynamicorganizationof cell6 lectures

Universal featuresof cells; cell chemistry andbiosynthesis: chemicalorganizationofcells; internal organization of the cell - cellmembranes: structure of cellmembranesand concepts related to compartmentalization in eukaryotic cells; intracellularorganelles:endoplasmicreticulumandGolgiapparatus,lysosomesandperoxisomes,ribosomes, cellular cytoskeleton, mitochondria, chloroplasts and cell energetics; nuclearcompartment: nucleus, nucleolus and chromosomes.

Unit IIChromatin structureand dynamics12 lectures

Unit IIICellular signalling,transport andtrafficking3 lectures

Unit IVCellular processes8 lectures

Unit VManipulating andstudying cells3 lectures

Unit VIGenomeinstability and celltransformation8 lectures

Chromatinorganization-histoneandDNAinteractome:structureandassemblyofeukaryoticandprokaryoticDNApolymerases,DNA-replication, repair andrecombination; chromatin control: gene transcription and silencing by chromatin-Writers,-Readers and –Erasers; Transcriptional control: Structure and assembly ofeukaryotic and prokaryotic RNA Polymerases, promoters and enhancers, transcriptionfactors as activators and repressors, trancriptional initiation, elongation and termination;post-transcriptionalcontrol: splicingandadditionofcapandtail,mRNAflowthroughnuclearenvelopeintocytoplasm,breakdownofselectiveandspecificmRNAsthroughinterference by small non-coding RNAs (miRNAs and siRNAs), protein translationmachinery, ribosomes-composition and assembly; universal genetic codes, degeneracyofcodons,Wobblehypothesis; Iso-acceptingtRNA;mechanismofinitiation,elongationandtermination;co-andpost-translationalmodifications,mitochondrialgenetic codetranslationproduct cleavage,modification and activation.

Molecular mechanisms of membrane transport, nuclear transport, transport acrossmitochondria and chloroplasts; intracellular vesicular trafficking from endoplasmicreticulum through Golgi apparatus to lysosomes/cell exterior.

Cell cycle and its regulation; cell division: mitosis, meiosis and cytokinesis; celldifferentiation:stemcells, theirdifferentiationintodifferentcelltypesandorganizationinto specialized tissues; cell-ECM and cell-cell interactions; cell receptors and trans-membrane signalling; cell motility and migration; cell death: different modes of cell deathand their regulation.

Isolationofcellsandbasicsofcellculture;observingcellsunderamicroscope,differenttypesofmicroscopy;analyzingandmanipulatingDNA,RNAandproteins.

Mutations, proto-oncogenes, oncogenes and tumour suppressor genes, physical, chemicaland biological mutagens; types of mutations; intra-genic and inter-genic suppression;transpositions- transposable genetic elements in prokaryotes and eukaryotes, role oftransposons in genome; viral and cellular oncogenes; tumor suppressor genes; structure,function and mechanism of action; activation and suppression of tumor suppressorgenes; oncogenes as transcriptional activators.

Recommended Textbooks and References:1. Alberts, B., Johnson, A., Lewis, J., Raff,M., Roberts, K., &Walter,P.(2008).

Molecular Biology of the Cell (5thEd.). New York: Garland Science.2. Lodish,H. F.(2016).Molecular Cell Biology (8thEd.).NewYork:W.H.Freeman.3. Krebs,J.E.,Lewin,B.,Kilpatrick,S.T.,&Goldstein,E.S.(2014).Lewin'sGenesXI.

Burlington, MA: Jones & Bartlett Learning.4. Cooper,G.M.,&Hausman,R.E.(2013).TheCell:aMolecularApproach(6thEd.).

Washington: ASM ;Sunderland.5. Hardin, J., Bertoni, G., Kleinsmith, L. J.,& Becker,W.M. (2012). Becker's World of

the Cell. Boston (8thEd.). BenjaminCummings.6. Watson, J. D. (2008).Molecular Biology of the Gene (5th ed.). Menlo Park, CA:

Benjamin/Cummings.

Plant andAnimalBiotechnologyCredits

Course ObjectivesThe objectives of this course are tointroducestudentstotheprinciples,practices and application of animalbiotechnology, plant tissue culture,plant and animal genomics, genetictransformation and molecular breedingof plants andanimals.

Student Learning OutcomesStudents should be able to gainfundamental knowledge in animal andplant biotechnology and their applications.

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Unit IPlant tissue cultureandanimalcellculture10 lectures

Unit IIPlant geneticmanipulation10 lectures

Unit IIIAnimal reproductivebiotechnology andvaccinology8 lectures

Unit IVPlant and animalgenomics4 lectures

Plant tissue culture: historical perspective; totipotency; organogenesis; Somaticembryogenesis; establishment of cultures – callus culture, cell suspension culture, mediapreparation – nutrients and plant hormones; sterilization techniques; applications oftissue culture - micropropagation; somaclonal variation; androgenesis and its applicationsin genetics and plant breeding; germplasm conservation and cryopreservation; syntheticseed production; protoplast culture and somatic hybridization - protoplast isolation;cultureandusage;somatichybridization-methodsandapplications;cybridsandsomaticcellgenetics;plant cell cultures forsecondarymetaboliteproduction.Animalcellculture:briefhistoryofanimalcellculture;cellculturemediaandreagents;cultureofmammalian cells, tissuesandorgans;primary culture, secondaryculture,continuouscell lines, suspensioncultures;applicationofanimalcell culture forvirusisolationand in vitro testingofdrugs, testingof toxicityofenvironmentalpollutants incell culture,applicationofcell culture technology inproductionofhumanandanimalviral vaccines and pharmaceutical proteins.

Genetic engineering: Agrobacterium-plant interaction; virulence; Ti and Ri plasmids;opines and their significance; T-DNA transfer; disarmed Ti plasmid; Genetictransformation - Agrobacterium-mediated gene delivery; cointegrate and binaryvectorsandtheirutility;directgenetransfer-PEG-mediated,electroporation,particle bombardment and alternative methods; screenable and selectablemarkers;characterization of transgenics; chloroplast transformation; marker-free methodologies;advanced methodologies - cisgenesis, intragenesis and genome editing; molecularpharming - concept of plants as biofactories, production of industrial enzymes andpharmaceutically important compounds.

Animal reproductive biotechnology: structure of sperms and ovum; cryopreservation ofspermsandovaoflivestock;artificial insemination;superovulation,embryorecoveryand in vitro fertilization; culture of embryos; cryopreservation of embryos; embryotransfer technology; transgenic manipulation of animal embryos; applications oftransgenicanimal technology;animalcloning-basic concept, cloningforconservationfor conservation endangered species; Vaccinology: history of development of vaccines,introductiontotheconceptofvaccines,conventionalmethodsofanimalvaccineproduction,recombinantapproachestovaccineproduction,modernvaccines.

Overviewofgenomics–definition,complexityandclassification;needforgenomicslevelanalysis;methodsofanalyzinggenomeatvarious levels–DNA,RNA,protein,metabolites and phenotype; genome projects and bioinformatics resources for genomeresearch–databases;overviewofforwardandreversegeneticsforassigningfunctionfor genes.

Unit VMolecular mappingand marker assistedselection8 lectures

Molecularmarkers -hybridizationandPCRbasedmarkersRFLP,RAPD,STS, SSR,AFLP, SNP markers; DNA fingerprinting-principles and applications; introduction tomapping of genes/QTLs; marker-assisted selection - strategies for Introducing genesofbiotic andabiotic stress resistance inplants: geneticbasis fordisease resistance inanimals;moleculardiagnosticsofpathogensinplantsandanimals;detectionofmeatadulteration using DNA basedmethods.

Recommended Textbooks and References:1. Chawla,H. S. (2000). Introduction to PlantBiotechnology. Enfield,NH: Science.2. Razdan,M.K. (2003). Introduction to PlantTissueCulture. Enfield,NH: Science.3. Slater,A., Scott, N.W.,& Fowler,M. R. (2008). Plant Biotechnology: an Introduction

to Genetic Engineering. Oxford: OxfordUniversity Press.4. Buchanan, B. B., Gruissem,W.,& Jones, R. L. (2015). Biochemistry & Molecular

Biology of Plants. Chichester,WestSussex: JohnWiley&Sons.5. Umesha, S. (2013). Plant Biotechnology.The EnergyAnd Resources.6. Glick, B. R., & Pasternak, J. J. (2010).Molecular Biotechnology: Principles and

Applicationsof RecombinantDNA.Washington,D.C.: ASMPress.7. Brown,T.A.(2006).GeneCloningandDNAAnalysis:anIntroduction.Oxford:

Blackwell Pub.8. Primrose,S.B.,&Twyman,R.M.(2006).PrinciplesofGeneManipulationand

Genomics. Malden, MA: BlackwellPub.9. Slater,A., Scott, N.W.,& Fowler,M. R. (2003). Plant Biotechnology: The Genetic

Manipulation of Plants. Oxford: OxfordUniversity Press.10. Gordon, I. (2005). Reproductive Techniques in Farm Animals. Oxford:

CAB International.11. Levine,M.M. (2004).New Generation Vaccines.NewYork:M.Dekker.12. Pörtner, R. (2007). Animal Cell Biotechnology: Methods and Protocols. Totowa,

NJ: HumanaPress.

MicrobiologyCredits

3

Course ObjectivesThe objectives of this course are tointroduce field of microbiology withspecial emphasis on microbial diversity,morphology, physiology and nutrition;methods for control ofmicrobesandhost-microbe interactions.

Student Learning OutcomesStudents should be able to:• Identify major categories of

microorganisms and analyze theirclassification, diversity, andubiquity;

• Identify and demonstrate structural,physiological, genetic similaritiesanddifferencesofmajorcategoriesofmicroorganisms;

• Identify and demonstrate how tocontrol microbialgrowth;

• Demonstrate and evaluate interactionsbetween microbes, hosts andenvironment.

Unit IMicrobialcharacteristics5 lectures

Unit IIMicrobial diversity15 lectures

Introduction to microbiology and microbes, history & scope of microbiology,morphology, structure, growth and nutrition of bacteria, bacterial growth curve, bacterialculturemethods;bacterialgenetics:mutationandrecombination inbacteria,plasmids,transformation, transductionand conjugation; antimicrobial resistance.

Microbial taxonomy and evolution of diversity, classification of microorganisms,criteria for classification; classification of bacteria; Cyanobacteria, acetic acid bacteria,Pseudomonads, lactic and propionic acid bacteria, endospore forming bacteria,

Mycobacteria and Mycoplasma. Archaea: Halophiles, Methanogens, Hyperthermophilicarchae, Thermoplasm; eukarya: algae, fungi, slime molds and protozoa; extremophilesand unculturable microbes.

Unit IIIControl ofmicroorganisms5 lectures

Unit IVVirology10 lectures

Unit VHost-microbesinteraction5 lectures

Sterilization, disinfection and antisepsis: physical and chemical methods for controlof microorganisms, antibiotics, antiviral and antifungal drugs, biological control ofmicroorganisms.

Virus and bacteriophages, general properties of viruses, viral structure, taxonomy ofvirus, viral replication, cultivation and identification of viruses; sub-viral particles –viroids and prions.

Host-pathogen interaction, ecological impact of microbes; symbiosis (Nitrogen fixationand ruminant symbiosis); microbes and nutrient cycles; microbial communicationsystem;bacterialquorumsensing;microbialfuelcells;prebioticsandprobiotics.

Recommended Textbooks and References:1. Pelczar,M.J.,Reid,R.D.,&Chan,E.C.(2001).Microbiology(5thed.).

New York:McGraw-Hill.2. Willey, J.M., Sherwood,L.,Woolverton,C. J.,Prescott, L.M.,&Willey, J.M. (2011).

Prescott’s Microbiology. New York: McGraw-Hill.3. Matthai,W.,Berg,C.Y.,&Black,J.G.(2005).Microbiology,Principlesand

Explorations. Boston,MA: JohnWiley & Sons.

GeneticsCredits

3

Course ObjectivesThe objectives of this course are to takestudentsthroughbasicsofgeneticsandclassical genetics covering prokaryotic/phage genetics to yeast and highereukaryoticdomains.Oncoveringallclassical concepts of Mendelian geneticsacrosstheselife-forms,studentswillbeexposedtoconceptsofpopulationgenetics, quantitative geneticsencompassing complex traits, clinicalgenetics and genetics of evolution.

Student Learning OutcomesOnsuccessfulcompletionofthiscourse,student will be able :• Describe fundamental molecular

principles ofgenetics;• Understandrelationshipbetween

phenotype and genotype inhumangenetic traits;

• Describe the basicsofgeneticmapping;• Understand how gene expression

is regulated.

Unit IGenetics of bacteriaand bacteriophages15 lectures

Unit IIYeast genetics6 lectures

Concept of a gene in pre-DNA era; mapping of genes in bacterial and phagechromosomesbyclassicalgeneticcrosses; finestructureanalysis ofagene;geneticcomplementation and other genetic crosses using phenotypic markers; phenotype togenotype connectivityprior toDNA-basedunderstandingof gene.

Meiotic crosses, tetrad analyses, non-Mendelian and Mendelian ratios, gene conversion,models of genetic recombination, yeast mating type switch; dominant and recessivegenes/mutations, suppressor or modifier screens, complementation groups, transposonmutagenesis, synthetic lethality, genetic epistasis.

Unit IIIDrosophila geneticsas amodel ofhighereukaryotes5 lectures

Unit IVPopulation geneticsand genetics ofevolution5 lectures

Unit VQuantitative genetics ofcomplex traits (QTLs)2 lectures

Unit VIPlant genetics3 lectures

Monohybrid&dihybridcrosses,back-crosses,test-crosses,analysesofautosomalandsex linkages, screening of mutations based on phenotypes and mapping the same,hypomorphy, genetic mosaics, genetic epistasis in context of developmental mechanism.

Introduction to the elements of population genetics: genetic variation, genetic drift,neutral evolution; mutation selection, balancing selection, Fishers theorem, Hardy-Weinberg equilibrium, linkage disequilibrium; in-breeding depression & mating systems;population bottlenecks, migrations, Bayesian statistics; adaptive landscape, spatialvariation & genetic fitness.

Complex traits, mapping QTLs, yeast genomics to understand biology of QTLs.

Laws of segregation in plant crosses, inbreeding, selfing, heterosis, maintenance ofgenetic purity, gene pyramiding.

Recommended Textbooks and References:1. Hartl, D. L., & Jones, E.W.(1998). Genetics: Principles and Analysis. Sudbury,

MA: Jones andBartlett.2. Pierce, B.A. (2005).Genetics: a Conceptual Approach.NewYork:W.H.Freeman.3. Tamarin,R. H., & Leavitt, R.W.(1991). Principles of Genetics. Dubuque,

IA: Wm.C. Brown.4. Smith, J.M. (1998).Evolutionary Genetics. Oxford:OxfordUniversity Press.

Basics ofMathematicsand StatisticsCredits

Course ObjectivesThe objective of this course is to giveconceptual exposure of essential contentsof mathematics and statistics to students.

Student Learning OutcomesOn completion of this course,students should be able to :• Gain broad understandingin

mathematics and statistics;• Recognize importance and value of

mathematical and statistical thinking,training,andapproachtoproblemsolving, on a diverse variety ofdisciplines.

Unit IAlgebra6 lectures

Unit IICalculus4 lectures

Linearequations, functions:slopes-intercepts, formsof two-variable linearequations;constructing linear models in biological systems; quadratic equations (solving, graphing,featuresof, interpretingquadraticmodelsetc.), introductiontopolynomials,graphsofbinomials and polynomials; Symmetry of polynomial functions, basics of trigonometricfunctions, Pythagorean theory, graphing and constructing sinusoidal functions,imaginary numbers, complex numbers, adding-subtracting-multiplying complexnumbers, basics of vectors, introduction tomatrices.

Differential calculus (limits, derivatives), integral calculus (integrals, sequencesand series etc.).

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Unit IIIMathematicalmodels in biology4 lectures

Unit IVStatistics5 lectures

Population dynamics; oscillations, circadian rhythms, developmental patterns, symmetryin biological systems, fractal geometries, size-limits & scaling in biology, modelingchemical reaction networks and metabolic networks.

Probability: counting, conditional probability, discrete and continuous random variables;Errorpropagation;Populationsandsamples,expectation,parametric testsofstatisticalsignificance,nonparametrichypothesistests, linearregression,correlation&causality,analysis of variance, factorial experiment design.

Recommended Textbooks and References:1. Stroud, K. A., & Booth, D. J. (2009). Foundation Mathematics. New York,

NY: PalgraveMacmillan.2. Aitken,M., Broadhursts, B.,&Haldky,S. (2009)Mathematics for Biological

Scientists. Garland Science.3. Billingsley, P. (1986). Probability andMeasure.NewYork:Wiley.4. Rosner, B. (2000). Fundamentals of Biostatistics. Boston,MA:Duxbury Press.5. Daniel, W.W.(1987). Biostatistics, a Foundation for Analysis in the Health Sciences.

New York:Wiley.

Basics ofChemistryand PhysicsCredits

Course ObjectivesTheobjectivesof this courseare tocoverall essentials required to appreciatephysico-chemical principles underlyingbiological processes.

Student Learning OutcomesStudents should be able to have afirm foundation in fundamentals andapplication of current chemical andphysical scientific theories.

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Unit IBasic physicsfor biologists12 lectures:10 hours teaching +2 hours tutorials

Unit IIBasic chemistryfor biologists

Physicalquantitiesandtheirdynamics:definitionsanddimensions;vectors&scalars, displacement, velocity, acceleration, kinematic formulas, angular momentum,torqueetc. force,power,work,energy(kinetic&potential/electricchargeseparation,electromagneticspectrum,photonsetc.);springs&Hookeslaws;elasticandinelasticcollisions;Newton’slawofmotions (centripetal andcentrifugal forces etc.); simpleharmonic motions, mechanical waves, Doppler effect, wave interference, amplitude,period, frequency & wavelength; diffusion, dissipation, random walks, and directedmotions in biological systems; low Reynolds number - world of Biology, buoyantforces,Bernoulli’sequation,viscosity, turbulence, surface tension, adhesion; lawsof thermodynamics: Maxwell Boltzmann distribution, conduction, convection andradiation, internal energy, entropy, temperature and free energy, Maxwell’s demon(entropicforcesatworkinbiology,chemicalassemblies,self-assembledsystems,roleof ATP); Coulomb’s law, conductors and insulators, electric potential energy of charges,nerveimpulses,voltagegatedchannels, ionicconductance;Ohmslaw(basicelectricalquantities: current, voltage & power), electrolyte conductivity, capacitors and capacitance,dielectrics; various machines in biology i.e. enzymes, allostery and molecular motors(molecules to cells and organisms).

Basic constituents of matter - elements, atoms, isotopes, atomic weights, atomicnumbers,basicsofmassspectrometry,molecules,Avogadronumber,molarity,gasconstant, molecular weights, structural and molecular formulae, ions andpolyatomic

12 lectures:10 hours teaching +2 hours tutorials

ions; chemical reactions, reaction stoichiometry, rates of reaction, rate constants,order of reactions, Arrhenious equation, Maxwell Boltzmann distributions, rate-determining steps, catalysis, free-energy, entropy and enthalpy changes duringreactions; kinetic versus thermodynamic controls of a reaction, reaction equilibrium(equilibrium constant); light and matter interactions (optical spectroscopy, fluorescence,bioluminescence, paramagnetism and diamagnetism, photoelectron spectroscopy;chemical bonds (ionic, covalent, Van der Walls forces); electronegativity, polarity;VSEPRtheoryandmoleculargeometry,dipolemoment,orbitalhybridizations;statesof matter - vapor pressure, phase diagrams, surface tension, boiling and melting points,solubility,capillary action, suspensions, colloidsandsolutions; acids,bases andpH-Arrhenious theory, pH, ionic product of water, weak acids and bases, conjugateacid-basepairs,buffersandbufferingactionetc;chemical thermodynamics- internalenergy,heatand temperature,enthalpy (bondenthalpyandreactionenthalpy),entropy,GibbsfreeenergyofATPdriven reactions, spontaneityversusdriven reactions inbiology; redoxreactionsandelectrochemistry-oxidation-reductionreactions,standardcellpotentials,Nernstequation,restingmembranepotentials,electrontransportchains(ETC)inbiology,couplingofoxidativephosphorylationstoETC;theoriesofATPproductionanddissipationacrossbiologicalmembranes;bondrotationsandmolecularconformations-Newman projections, conformational analysis of alkanes, alkenes and alkynes; functionalgroups, optically asymmetric carbon centers, amino acids, proteins, rotational freedomsin polypeptide backbone (Ramachandran plot).

Recommended Textbooks and References:1. Baaquie,B.E. (2000).Laws of Physics: aPrimer. Singapore:NationalUniversity

of Singapore.2. Matthews, C. P.,& Shearer, J. S. (1897). Problems and Questions in Physics.

New York:MacmillanCompany.3. Halliday,D., Resnick, R., &Walker, J. (1993). Fundamentals of Physics.

New York: Wiley.4. Ebbing, D.D., &Wrighton,M. S. (1990). General Chemistry. Boston: Houghton

Mifflin.5. Averill, B., & Eldredge, P.(2007). Chemistry: Principles, Patterns, and Applications.

San Francisco: BenjaminCummings.6. Mahan, B.H. (1965).UniversityChemistry. Reading,MA:Addison-WesleyPub.7. Cantor,C. R., & Schimmel, P.R. (2004).Biophysical Chemistry. San Francisco:

W.H. Freeman.

LaboratoryI:Biochemistry& AnalyticalTechniquesCredits

Course ObjectivesTheobjectiveof thislaboratorycourse isto introducestudents toexperiments inbiochemistry. The course is designedto teach students the utility of set ofexperimental methods in biochemistryin a problem oriented manner.

Student Learning OutcomesOncompletionofthiscourse,studentsshould be able to:• Toelaborateconceptsofbiochemistry

with easy to run experiments;• Tofamiliarizewithbasic laboratory

instruments and understand theprinciple of measurements usingthose instruments with experimentsin biochemistry.

Syllabus 1. Preparing various stock solutions and working solutions that will be neededfor the course.

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2. Toprepare an Acetic-Na Acetate Buffer and validate the Henderson-Hasselbachequation.

3. TodetermineanunknownproteinconcentrationbyplottingastandardgraphofBSAusingUV-VisSpectrophotometerandvalidating theBeer-Lambert’sLaw.

4. Experimental verification that absorptionatOD260 ismore fordenaturedDNAas compared to native double stranded DNA. reversal of the same following DNArenaturation. Kinetics of DNA renaturation as a function of DNA size.

5. Identification of an unknown sample as DNA, RNA or protein usingavailablelaboratory tools. (OptionalExperiments)

6. Biophysicalmethods (CircularDichroismSpectroscopy, Fluorescence Spectroscopy).7. Determination of mass of small molecules and fragmentation patterns by Mass

Spectrometry.

LaboratoryII:MicrobiologyCredits

Course ObjectivesTheobjectiveofthislaboratorycourseistoprovidepracticalskillsonbasicmicrobiological techniques.

Student Learning OutcomesStudents should be able to:• Isolate, characterize and identify

common bacterialorganisms;• Determinebacterialloadofdifferent

samples;• Performantimicrobial sensitivity tests;• Preserve bacterial cultures.

Syllabus 1. Sterilization, disinfection and safety in microbiological laboratory.2. Preparation of media for cultivation of bacteria.3. Isolation of bacteria in pure culture by streak platemethod.4. Study of colony and growth characteristics of some common bacteria:

Bacillus, E. coli, Staphylococcus, Streptococcus, etc.5. Preparation of bacterial smear and Gram’s staining.6. Enumeration of bacteria: standard plate count.7. Antimicrobial sensitivity test anddemonstration of drug resistance.8. Maintenance of stock cultures: slants, stabs and glycerol stock cultures9. Determination of phenol co-efficient of antimicrobial agents.10. Determination ofMinimum Inhibitory Concentration (MIC)

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11. Isolation and identification of bacteria from soil/water samples.

Recommended Textbooks and References:1. Cappuccino, J. G., &Welsh,C. (2016).Microbiology: a Laboratory Manual.

Benjamin-Cummings PublishingCompany.2. Collins,C.H.,Lyne,P.M.,Grange,J.M.,&FalkinhamIII,J.(2004).Collinsand

Lyne’sMicrobiological Methods (8thed.).Arnolds.3. Tille, P.M., & Forbes, B. A. Bailey & Scott’s Diagnostic Microbiology.

LaboratoryIII: Plantand AnimalBiotechnologyCredits

Course ObjectivesTheobjectivesof this course are toprovidehands-on training in basic experiments ofplant and animal biotechnology.

Student Learning OutcomesOn completion of course, students shouldbe able to gain basic skills in plant andanimal biotechnology.

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SyllabusPlant Biotechnology

SyllabusAnimal Biotechnology

1. Prepare culturemediawithvarious supplements forplant tissue culture.2. Prepare explants for inoculationunder aseptic conditions.3. Attempt in vitro andro and gynogenesis in plants.4. PreparekaryotypesandstudythemorphologyofsomaticchromosomesofAllium

cepa,A. sativum,A. tuberosumandcomparethemonthebasisofkaryotypes.5. UndertakeplantgenomicDNAisolationbyCTABmethodanditsquantitationby

visual as well as spectrophotometeric methods.6. PerformPCRamplificationof‘n’numberofgenotypesofaspeciesforstudyingthe

geneticvariationamongtheindividualsofaspeciesusingrandomprimers.7. Studygenetic fingerprinting profiles of plants and calculatepolymorphic

information content.8. Axillary shoot multiplication.9. Callus Culture10. de novo regeneration

1. Count cells of an animal tissue and check their viability.2. Prepareculturemediawithvarioussupplementsforplantandanimaltissueculture.3. Prepare single cell suspension from spleen and thymus.4. Monitor andmeasure doubling time of animal cells.5. Chromosome preparations from cultured animal cells.6. Isolate DNA from animal tissue by SDSmethod.

Semester Two

GeneticEngineeringCredits

3

Course ObjectivesThe objectives of this course are to teachstudents with various approaches toconducting genetic engineering and theirapplications in biological research aswellas in biotechnology industries. Geneticengineeringisatechnologythathasbeendevelopedbasedonourfundamentalunderstanding of the principles ofmolecularbiologyandthis isreflected inthe contents of this course.

Student Learning OutcomesGiven the impact of genetic engineeringin modern society, the students shouldbe endowed with strong theoreticalknowledge of this technology. Inconjunction with the practicals inmolecular biology & genetic engineering,the students should be able to take upbiological research as well as placement inthe relevant biotech industry.

Unit IIntroduction andtools for geneticengineering6 lectures

Unit IIDifferent typesof vectors7 lectures

Unit IIIDifferent typesof PCR techniques7 lectures

Unit IVGene manipulationand protein-DNAinteraction7 lectures

Unit VGene silencingand genome editingtechnologies13 lectures

Impactofgeneticengineeringinmodernsociety;generalrequirementsforperformingagenetic engineering experiment; restriction endonucleases and methylases; DNA ligase,Klenow enzyme, T4 DNA polymerase, polynucleotide kinase, alkaline phosphatase;cohesive andblunt end ligation; linkers; adaptors; homopolymeric tailing; labellingof DNA: nick translation, random priming, radioactive and non-radioactive probes,hybridization techniques: northern, southern, south-western and far-western and colonyhybridization, fluorescence in situ hybridization.

Plasmids;Bacteriophages;M13mpvectors;PUC19andBluescriptvectors,hagemids;Lambda vectors; Insertion and Replacement vectors; Cosmids; Artificial chromosomevectors(YACs;BACs);Principlesformaximizinggeneexpressionexpressionvectors;pMal;GST;pET-basedvectors; Proteinpurification;His-tag;GST-tag;MBP-tag etc.;Intein-based vectors; Inclusion bodies; methodologies to reduce formation of inclusionbodies; mammalian expression and replicating vectors; Baculovirus and Pichia vectorssystem,plantbasedvectors,TiandRiasvectors,yeastvectors,shuttlevectors.

PrinciplesofPCR:primerdesign;fidelityofthermostableenzymes;DNApolymerases;typesofPCR–multiplex,nested;reverse-transcriptionPCR,real timePCR,touchdownPCR,hot startPCR, colonyPCR, asymmetricPCR, cloningofPCRproducts;T-vectors; proof reading enzymes; PCR based site specific mutagenesis; PCR inmolecular diagnostics; viral and bacterial detection; sequencing methods; enzymaticDNAsequencing;chemicalsequencingofDNA;automatedDNAsequencing;RNAsequencing; chemical synthesis of oligonucleotides; mutation detection: SSCP,DGGE, RFLP.

Insertionof foreignDNAintohost cells; transformation, electroporation, transfection;constructionof libraries; isolationofmRNAand totalRNA; reverse transcriptase andcDNAsynthesis; cDNAandgenomic libraries; constructionofmicroarrays–genomicarrays, cDNA arrays and oligo arrays; study of protein-DNA interactions:electrophoreticmobility shift assay; DNase footprinting; methyl interference assay, chromatinimmunoprecipitation; protein-protein interactionsusing yeast two-hybrid system;phage display.

Gene silencing techniques; introduction to siRNA; siRNA technology; Micro RNA;construction of siRNA vectors; principle and application of gene silencing; geneknockoutsandgenetherapy;creationoftransgenicplants;debateoverGMcrops;introductiontomethodsofgeneticmanipulationindifferentmodelsystemse.g. fruit flies

(Drosophila), worms (C. elegans), frogs (Xenopus), fish (zebra fish) and chick; Transgenics-genereplacement;genetargeting;creationoftransgenicandknock-outmice;diseasemodel; introduction togenomeediting byCRISPR-CASwith specific emphasis onChinese and American clinicaltrials.

Recommended Textbooks and References:1. Old,R.W.,Primrose,S.B.,&Twyman,R.M.(2001).PrinciplesofGene

Manipulation: an Introduction to Genetic Engineering. Oxford: BlackwellScientific Publications.

2. Green, M. R., & Sambrook, J. (2012).Molecular Cloning: a Laboratory Manual.ColdSpringHarbor,NY:ColdSpringHarborLaboratory Press.

3. Brown, T.A. (2006).Genomes (3rd ed.). NewYork:Garland Science Pub.4. Selectedpapers from scientific journals, particularlyNature& Science.5. TechnicalLiteraturefromStratagene,Promega,Novagen,NewEnglandBiolabetc.

ImmunologyCredits

3

Course ObjectivesTheobjectivesofthiscoursearetolearnaboutstructuralfeaturesofcomponentsofimmune systemaswell as their function.Themajor emphasis of this coursewill beon development of immune system andmechanisms by which our body elicitsimmuneresponse.Thiswillbeimperativefor students as itwill help them topredictabout nature of immune response thatdevelops against bacterial, viral or parasiticinfection, and prove it by designing newexperiments.

Student Learning OutcomesOn completion of this course,students should be able to:• Evaluate usefulness of immunology

in different pharmaceutical companies;• Identify proper research lab working

in area of their own interests;• Apply their knowledge and designimmunological experiments todemonstrate innate, humoral orcytotoxic T lymphocyte responses andfigure out kind of immune responses inthesettingofinfection(viralorbacterial).

Unit IImmunology:fundamental conceptsandoverviewoftheimmunesystem5 lectures

Unit IIImmune responsesgeneratedbyBandTlymphocytes8 lectures

Unit IIIAntigen-antibodyinteractions6 lectures

Components of innate and acquired immunity; phagocytosis; complement andinflammatory responses; pathogen recognition receptors (PRR) and pathogen associatedmolecular pattern (PAMP); innate immune response; mucosal immunity; antigens:immunogens, haptens; Major Histocompatibility Complex: MHC genes, MHC andimmune responsiveness and disease susceptibility, Organs of immune system, primaryand secondary lymphoid organs.

Immunoglobulins - basic structure, classes & subclasses of immunoglobulins, antigenicdeterminants; multigene organization of immunoglobulin genes; B-cell receptor;Immunoglobulin superfamily; principles of cell signaling; basis of self & non-selfdiscrimination;kineticsof immune response,memory;B cellmaturation, activationand differentiation; generation of antibody diversity; T-cell maturation, activation anddifferentiationandT-cell receptors; functionalTCell subsets; cell-mediated immuneresponses, ADCC; cytokines: properties, receptors and therapeutic uses; antigenprocessing and presentation- endogenous antigens, exogenous antigens, non-peptidebacterialantigensandsuper-antigens; cell-cell co-operation,Hapten-carrier system.

Precipitation,agglutinationandcomplementmediatedimmunereactions;advancedimmunological techniques: RIA, ELISA, Western blotting, ELISPOT assay,immunofluorescence microscopy, flow cytometry and immunoelectron microscopy;surfaceplasmonresonance,biosensorassaysforassessingligand–receptorinteraction;CMI techniques: lymphoproliferation assay, mixed lymphocyte reaction, cell cytotoxicityassays, apoptosis,microarrays, transgenicmice, gene knock outs.

Unit IVVaccinology8 lectures

Unit VClinical immunology8 lectures

Unit VIImmunogenetics5 lectures

Active and passive immunization; live, killed, attenuated, subunit vaccines; vaccinetechnology: role and properties of adjuvants, recombinant DNA and protein basedvaccines, plant-based vaccines, reverse vaccinology; peptide vaccines, conjugate vaccines;antibody genes and antibody engineering:chimeric, generation of monoclonal antibodies,hybridmonoclonalantibodies;catalyticantibodiesandgenerationofimmunoglobulingenelibraries,idiotypicvaccinesandmarkervaccines,viral-likeparticles(VLPs),dendriticcellbasedvaccines,vaccineagainst cancer,Tcellbasedvaccine,ediblevaccineand therapeutic vaccine.

Immunity to infection : bacteria, viral, fungal andparasitic infections (with examplesfrom each group); hypersensitivity: Type I-IV; autoimmunity; types of autoimmunediseases;mechanismandroleofCD4+Tcells;MHCandTCRinautoimmunity;treatment of autoimmune diseases; transplantation: immunological basis of graftrejection; clinical transplantation and immunosuppressive therapy; tumor immunology:tumorantigens; immuneresponsetotumorsandtumorevasionoftheimmunesystem, cancer immunotherapy; immunodeficiency: primary immunodeficiencies,acquired or secondary immunodeficiencies, autoimmune disorder, anaphylactic shock,immunosenescence, immune exhaustion in chronic viral infection, immune tolerance,NK cells in chronic viral infection and malignancy.

Majorhistocompatibility complexgenesand their role inautoimmuneand infectiousdiseases,HLAtyping,humanmajorhistocompatibilitycomplex(MHC),Complementgenes of the human major histocompatibility complex: implication for linkagedisequilibrium and disease associations, genetic studies of rheumatoid arthritis,systemiclupus erythematosus and multiple sclerosis, genetics of human immunoglobulin,immunogenetics of spontaneous control ofHIV,KIR complex.

Recommended Textbooks and References:1. Kindt, T. J., Goldsby, R. A., Osborne, B. A., & Kuby, J. (2006). Kuby Immunology.

New York:W.H.Freeman.2. Brostoff, J., Seaddin, J.K.,Male, D.,&Roitt, I.M. (2002).Clinical Immunology.

London: Gower Medical Pub.3. Murphy,K., Travers,P.,Walport,M., & Janeway,C. (2012). Janeway’s

Immunobiology.New York:GarlandScience.4. Paul,W.E. (2012). Fundamental Immunology. NewYork:Raven Press.5. Goding, J. W.(1996). Monoclonal Antibodies: Principles and Practice: Production

and Application of Monoclonal Antibodies in Cell Biology, Biochemistry, andImmunology. London: Academic Press.

6. Parham, P.(2005). The Immune System. New York:Garland Science.

BioinformaticsCredits

3

Course ObjectivesTheobjectivesof thiscourseare toprovidetheoryandpracticalexperienceof theuseofcommoncomputational toolsanddatabases which facilitate investigation ofmolecular biology and evolution-relatedconcepts.

Student Learning OutcomesStudent should be able to :• Developanunderstandingofbasic

theory of these computational tools;• Gainworkingknowledgeofthese

computational tools and methods;• Appreciate their relevance for

investigating specific contemporarybiological questions;

• Critically analyse and interpretresultsof their study.

Unit IBioinformatics basics5 lectures

Unit IIDNAsequenceanalysis10 lectures

Unit IIIMultiple sequenceanalysis5 lectures

Unit IVProtein modelling5 lectures

Unit VProtein structureprediction andvirtual library10 lectures

Bioinformatics basics: Computers in biology and medicine; Introduction to Unixand Linux systems and basic commands; Database concepts; Protein and nucleic aciddatabases;Structuraldatabases;BiologicalXMLDTD’s;patternmatchingalgorithmbasics; databases and search tools: biological background for sequence analysis;Identification of protein sequence from DNA sequence; searching of databases similarsequence; NCBI; publicly available tools; resources at EBI; resources on web; databasemining tools.

DNAsequenceanalysis:genebanksequencedatabase;submittingDNAsequencestodatabases and database searching; sequence alignment; pairwise alignment techniques;motifdiscoveryandgeneprediction; localstructuralvariantsofDNA,theirrelevanceinmolecular levelprocesses, and their identification; assemblyofdata fromgenomesequencing.

Multiplesequenceanalysis;multiplesequencealignment; flexiblesequencesimilaritysearchingwith theFASTA3programpackage; use ofCLUSTALWandCLUSTALXformultiple sequence alignment; submitting DNA protein sequence to databases: where andhow to submit, SEQUIN, genome centres; submitting aligned sets of sequences, updatingsubmitted sequences, methods of phylogenetic analysis.

Protein modelling: introduction; force field methods; energy, buried and exposedresidues; side chains and neighbours; fixed regions; hydrogen bonds; mapping propertiesontosurfaces;fittingmonomers;RMSfitofconformers;assigningsecondarystructures;sequence alignment- methods, evaluation, scoring; protein completion: backboneconstruction and side chain addition; small peptide methodology; software accessibility;buildingpeptides;proteindisplays; substructuremanipulations,annealing.

Proteinstructureprediction:proteinfoldingandmodelgeneration;secondarystructureprediction; analyzing secondary structures; protein loop searching; loop generatingmethods; homology modelling: potential applications, description, methodology,homologous sequence identification; align structures, align model sequence; constructionof variable and conserved regions; threading techniques; topology fingerprint approachfor prediction; evaluation of alternate models; structure prediction on a mysterysequence; structure aided sequence techniques of structure prediction; structural profiles,alignmentalgorithms,mutationtables,prediction,validation,sequencebasedmethodsof structure prediction, prediction using inverse folding, fold prediction; significanceanalysis, scoring techniques, sequence-sequence scoring; protein function prediction;elements of in silico drug design;Virtual library: Searching PubMed, current content,science citation index and current awareness services, electronic journals, grants andfunding information.

Recommended Textbooks and References:1. Lesk,A.M. (2002). IntroductiontoBioinformatics.Oxford:OxfordUniversityPress.2. Mount, D.W.(2001). Bioinformatics: Sequence and Genome Analysis. Cold Spring

Harbor,NY:Cold SpringHarbor Laboratory Press.3. Baxevanis, A. D.,&Ouellette, B. F.(2001). Bioinformatics: a Practical Guide to the

Analysis of Genes and Proteins. NewYork:Wiley-Interscience.4. Pevsner, J. (2015). Bioinformatics and Functional Genomics. Hoboken,

NJ.:Wiley-Blackwell.5. Bourne, P.E.,&Gu, J. (2009).Structural Bioinformatics.Hoboken,NJ:Wiley-Liss.6. Lesk, A. M. (2004). Introduction to Protein Science: Architecture, Function, and

Genomics.Oxford: Oxford UniversityPress.

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Genomics andProteomicsCredits

Course ObjectivesTheobjectivesof thiscourse is toprovideintroductory knowledge concerninggenomics, proteomics and theirapplications.

Student Learning OutcomesStudents should be able to acquireknowledge and understanding offundamentals of genomics and proteomics,transcriptomics and metabolomics andtheir applications in various applied areasof biology.

Unit IBasics of genomicsandproteomics5lectures

Brief overview of prokaryotic and eukaryotic genome organization; extra-chromosomalDNA: bacterial plasmids, mitochondria and chloroplast.

Unit IIGenome mapping5lectures

Unit IIIGenome sequencingprojects10 lectures

Unit IVComparativegenomics5 lectures

Unit VProteomics5 lectures

Unit VIFunctional genomicsand proteomics10 lectures

Genetic and physical maps; markers for genetic mapping; methods and techniques usedforgenemapping,physicalmapping, linkageanalysis, cytogenetic techniques,FISHtechnique ingenemapping, somatic cellhybridization, radiationhybridmaps, in situhybridization, comparative genemapping.

HumanGenomeProject,genomesequencingprojectsformicrobes,plantsandanimals,accessing and retrieving genome project information from theweb.

Identificationandclassificationoforganismsusingmolecularmarkers-16SrRNAtyping/sequencing,SNPs;useofgenomestounderstandevolutionofeukaryotes, trackemerging diseases and design new drugs; determining gene location in genome sequence.

Aims, strategies and challenges in proteomics; proteomics technologies: 2D-PAGE,isoelectric focusing, mass spectrometry, MALDI-TOF, yeast 2-hybrid system, proteomedatabases.

Transcriptome analysis for identification and functional annotation of gene, Contigassembly, chromosome walking and characterization of chromosomes, mining functionalgenes in genome, gene function- forward and reverse genetics, gene ethics; protein-proteinandprotein-DNAinteractions;proteinchipsandfunctionalproteomics;clinicalandbiomedical applicationsofproteomics; introduction tometabolomics, lipidomics,metagenomics and systemsbiology.

Recommended Textbooks and References:1. Primrose, S. B., Twyman,R.M., Primrose, S. B., & Primrose, S. B. (2006).

Principles of Gene Manipulation and Genomics. Malden, MA: Blackwell Pub.2. Liebler, D.C. (2002). Introduction to Proteomics: Tools for the New Biology.

Totowa, NJ: Humana Press.3. Campbell, A.M., &Heyer, L. J. (2003). Discovering Genomics, Proteomics, and

Bioinformatics. San Francisco: Benjamin Cummings.

3

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MolecularDiagnosticsCredits

3

Course ObjectivesTheobjectivesof thiscourseare tosen-sitize students about recent advances inmolecular biology and various facets ofmolecular medicine which has potential toprofoundlyaltermanyaspectsofmodernmedicine including pre- or post-natalanalysis of genetic diseases and identifica-tionofindividualspredisposedtodiseaserangingfromcommoncoldto cancer.

Student Learning OutcomesStudents should be able to understandvarious facetsofmolecularproceduresandbasicsofgenomics,proteomicsandmetabolomics that could be employed inearlydiagnosisandprognosisofhumandiseases.

Unit IGenome biology inhealth and disease5 lectures

Unit IIGenome: resolution,detection & analysis10 lectures

Unit IIIDiagnosticmetabolomics5 lectures

Unit IVDetection and identityof microbial diseases5 lectures

Unit VDetection ofinherited diseases5 lectures

Unit VIMolecular oncology5 lectures

Unit VIIQuality assuranceand control5 lecture

DNA, RNA, Protein: An overview; chromosomal structure & mutations; DNA polymor-phism: human identity; clinical variability and genetically determined adverse reactionsto drugs.

PCR: Real-time; ARMS; Multiplex; ISH; FISH; ISA; RFLP; DHPLC; DGGE; CSCE; SSCP;Nucleic acid sequencing: new generations of automated sequencers; Microarray chips;EST;SAGE;microarraydatanormalization&analysis;molecularmarkers: 16S rRNAtyping;Diagnostic proteomics: SELDI-TOF-MS; Bioinformatics data acquisition& analysis.

Metabolite profile for biomarker detection the body fluids/tissues in various metabolicdisorders by making using LCMS & NMR technological platforms.

Direct detection and identification of pathogenic-organisms that are slow growing orcurrentlylackingasystemof invitrocultivationaswellasgenotypicmarkersofmicrobialresistance to specific antibiotics.

Exemplifiedby twoinheriteddiseases forwhichmoleculardiagnosishasprovidedadramatic improvement of quality of medical care: Fragile X Syndrome: Paradigm of newmutationalmechanismofunstable triplet repeats,von-HippelLindaudisease: recentacquisition in growing number of familial cancer syndromes.

Detectionof recognizedgenetic aberrations in clinical samples from cancer patients;typesofcancer-causingalterationsrevealedbynext-generationsequencingofclinicalisolates; predictive biomarkers for personalized onco-therapy of human diseases such aschronic myeloid leukemia, colon, breast, lung cancer and melanoma as well as matchingtargeted therapies with patients and preventing toxicity of standard systemic therapies.

Quality oversight; regulations and approved testing.

Recommended Textbooks and References:1. Campbell, A.M., &Heyer, L. J. (2006). Discovering Genomics, Proteomics,

and Bioinformatics. San Francisco: BenjaminCummings.2. Brooker,R. J. (2009).Genetics: Analysis &Principles.NewYork,NY:McGraw-Hill.

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3. Glick,B.R.,Pasternak, J.J.,&Patten,C.L. (2010).MolecularBiotechnology:Principles and Applications of Recombinant DNA. Washington, DC: ASM Press.

4. Coleman,W.B., & Tsongalis, G. J. (2010).Molecular Diagnostics: for the ClinicalLaboratorian. Totowa,NJ: HumanaPress.

ResearchMethodologyand ScientificCommunica-tionSkillsCredits

Course ObjectivesThe objectives of this course are togive background on history of science,emphasizing methodologies used todo research, use framework of thesemethodologies for understanding effectivelab practices and scientific communicationand appreciate scientific ethics.

Student Learning OutcomesStudents should be able to:• Understand history and methodologies

of scientific research, applying these torecent publishedpapers;

• Understand and practice scientificreading, writing andpresentations;

• Appreciate scientific ethics throughcase studies.

3

Unit IHistoryofscienceandscience methodologies8 lectures

Unit IIPreparationforresearch2 lectures

Unit IIIProcess ofcommunication20 lectures

Unit IVScientificcommunication10 lectures

Empirical science; scientific method; manipulative experiments and controls; deductiveand inductive reasoning; descriptive science; reductionist vs holistic biology.

Choosing a mentor, lab and research question; maintaining a lab notebook.

Concept of effective communication- setting clear goals for communication; determiningoutcomes and results; initiating communication; avoiding breakdowns whilecommunicating; creating value in conversation; barriers to effective communication;non-verbal communication-interpreting non-verbal cues; importance of body language,power of effective listening; recognizing cultural differences; Presentation skills - formalpresentation skills; preparing and presenting using over-head projector, PowerPoint;defending interrogation; scientific poster preparation & presentation; participatingin group discussions; Computing skills for scientific research - web browsing forinformation search; search enginesand theirmechanismof searching;hiddenWebandits importanceinscientific research; internetasamediumof interactionbetweenscientists; effective email strategyusing the right toneandconciseness.

Technical writing skills - types of reports; layout of a formal report; scientific writingskills- importanceofcommunicatingscience;problemswhilewritingascientificdocument; plagiarism, software for plagiarism; scientific publication writing: elementsof a scientific paper including abstract, introduction, materials & methods, results,discussion, references; drafting titles and framing abstracts; publishing scientific papers -peer reviewprocess andproblems, recentdevelopments suchasopenaccessandnon-blind review; plagiarism; characteristics of effective technical communication; scientificpresentations; ethical issues; scientificmisconduct.

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Recommended Textbooks and References:1. Valiela,I.(2001).DoingScience:Design,Analysis,andCommunicationofScientific

Research.Oxford: Oxford UniversityPress.2. OnBeingaScientist:aGuidetoResponsibleConductinResearch.(2009).

Washington,D.C.: National Academies Press.3. Gopen,G.D.,& Smith, J.A. The Science of Scientific Writing. American Scientist,

78 (Nov-Dec 1990), 550-558.4. Mohan,K.,&Singh,N. P.(2010). Speaking English Effectively. Delhi:Macmillan

India.5. Movie: Naturally Obsessed, TheMaking of a Scientist.

LaboratoryIV:MolecularBiology andGeneticEngineeringCredits

Course ObjectivesTheobjectivesof this courseare toprovidestudentswithexperimentalknowledgeofmolecular biology and genetic engineering.

Student Learning OutcomesStudentsshouldbeable togainhands-onexperience ingenecloning,proteinexpression and purification. Thisexperience would enable them to beginacareer inindustry thatengages ingenetic engineering as well as in researchlaboratories conducting fundamentalresearch.

2

Syllabus 1. Plasmid DNA isolation and DNA quantitation2. Restriction Enzyme digestion of plasmid DNA3. Agarose gel electrophoresis4. PolymeraseChainReaction and analysis by agarose gel electrophoresis5. Vector and Insert Ligation6. Preparation of competent cells7. TransformationofE.coliwithstandardplasmids,Calculationof

transformation efficiency8. Confirmation of the insert by Colony PCR andRestrictionmappin

Recommended Textbooks and References:1. Green, M. R., & Sambrook, J. (2012). Molecular Cloning: a Laboratory Manual.

Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

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Laboratory V:ImmunologyCredits

2

Course ObjectivesTheobjectivesof this laboratory courseare todevelopanunderstandingaboutpractical aspects of components ofimmunesystemaswellas their function.Basic aswell as advancedmethodswillbe taught todetectdifferentantigenandantibody interactions, isolation of differentlymphocyte cellsetc. andhowtheycanbeused in respective researchwork.

Student Learning OutcomesStudents should be able to:• Evaluate usefulness of immunologyin

different pharmaceutical companies;• Identify proper research labworking

in area of their own interests;• Apply their knowledge and design

immunological experiments todemonstrate innate, humoral orcytotoxic T lymphocyte responses andfigureoutkindof immuneresponsesin setting of infection (viral orbacterial) by looking at cytokineprofile.

Syllabus 1. Selection of animals, preparation of antigens, immunization and methodsof blood collection, serum separation and storage.

2. Antibody titre by ELISAmethod.3. Doublediffusion, Immuno-electrophoresis andRadial Immunodiffusion.4. Complement fixation test.5. Isolation and purification of IgG from serumor IgY fromchicken egg.6. SDS-PAGE, Immunoblotting, Dot blotassays.7. Blood smear identification of leucocytes by Giemsa stain.8. Separation of leucocytes by dextran method.9. DemonstrationofPhagocytosis of latex beads and their cryopreservation.10. SeparationofmononuclearcellsbyFicoll-Hypaqueandtheircryopreservation.11. Demonstration of ELISPOT.12. Demonstration of FACS.

Semester Three

BioprocessEngineering &TechnologyCredits

3

Course ObjectivesTheobjectivesof thiscourseare toeducatestudentsaboutthefundamentalconceptsof bioprocess technology and its relatedapplications,thuspreparingthemtomeetthechallengesofthenewandemergingareas of biotechnology industry.

Student Learning OutcomesStudents should be able to:• Appreciate relevance of microorganismsfrom industrialcontext;

• Carry out stoichiometric calculationsand specifymodelsof their growth;

• Giveanaccountofdesignandoperations of various fermenters;

• Present unit operations together withthefundamentalprinciples forbasicmethods in production technique forbio-based products;

• Calculate yield and production rates ina biological production process, andalso interpret data;

• Calculatetheneedforoxygenandoxygen transfer;

• Critically analyze any bioprocess frommarket point ofview;

• Give an account of importantmicrobial/enzymatic industrialprocesses in food and fuel industry.

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Unit IBasic principlesof biochemicalengineering4 lectures

Unit IIStoichiometry andmodels of microbialgrowth4 lectures

Unit IIIBioreactor designand analysis8 lectures

Unit IVDownstreamprocessing andproduct recovery8 lectures

Unit VFermentationeconomics4 lectures

Unit VIApplications ofenzyme technologyin food processing4 lectures

Unit VIIApplications of micro-bial technology in foodprocess operations andproduction, biofuelsandbiorefinery4 lectures

Isolation, screeningandmaintenanceof industrially importantmicrobes;microbialgrowthanddeathkinetics(anexamplefromeachgroup,particularlywithreferencetoindustrially useful microorganisms); strain improvement for increased yield and otherdesirable characteristics.

Elementalbalanceequations;metaboliccoupling–ATPandNAD+;yieldcoefficients;unstructuredmodelsofmicrobial growth; structuredmodels ofmicrobial growth.

Batch and continuous fermenters; modifying batch and continuous reactors: chemostatwith recycle, multistage chemostat systems, fed-batch operations; conventionalfermentationv/sbiotransformation; immobilizedcellsystems; largescaleanimalandplant cell cultivation; fermentation economics; upstream processing: media formulationand optimization; sterilization; aeration, agitation and heat transfer in bioprocess; scaleupand scaledown;measurement andcontrol ofbioprocessparameters.

Separation of insoluble products - filtration, centrifugation, sedimentation, flocculation;Celldisruption; separationofsolubleproducts: liquid-liquidextraction,precipitation,chromatographic techniques, reverse osmosis, ultra and micro filtration, electrophoresis;final purification: drying; crystallization; storage andpackaging.

Isolation of micro-organisms of potential industrial interest; strain improvement; marketanalysis;equipmentandplantcosts;media; sterilization,heatingandcooling;aerationandagitation;bath-process cycle timesandcontinuouscultures; recoverycosts;waterusage and recycling; effluent treatment and disposal.

Mechanismofenzymefunctionandreactionsinprocesstechniques;enzymaticbioconversionse.g.starchandsugarconversionprocesses;high-fructosecornsyrup;interesterified fat; hydrolyzed protein etc. and their downstream processing; baking byamylases, deoxygenation and desugaring by glucoses oxidase, beer mashing and chillproofing;cheesemakingbyproteasesandvariousotherenzymecatalytic actions infood processing.

Fermented foods and beverages; food ingredients and additives prepared by fermentationand their purification; fermentation as a method of preparing and preserving foods;microbesandtheiruseinpickling,producingcoloursandflavours,alcoholicbeveragesand other products; process wastes-whey, molasses, starch substrates and other foodwastesforbioconversiontousefulproducts;bacteriocinsfromlacticacidbacteria–productionandapplications in foodpreservation; biofuelsandbiorefinery

Recommended Textbooks and References:1. Shuler,M. L., &Kargi, F. (2002). Bioprocess Engineering: Basic Concepts.

Upper Saddle River, NJ: Prentice Hall.2. Stanbury,P.F.,&Whitaker,A. (2010). Principles of Fermentation Technology. Oxford:

Pergamon Press.3. Blanch,H.W.,&Clark,D.S. (1997).Biochemical Engineering.NewYork:M.Dekker.4. Bailey, J.E., &Ollis, D. F.(1986). Biochemical Engineering Fundamentals.NewYork:

McGraw-Hill.

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5. El-Mansi,M.,&Bryce,C. F.(2007).FermentationMicrobiology andBiotechnology.Boca Raton: CRC/Taylor & Francis.

EmergingTechnologiesCredits

3

Course ObjectivesThis course is broad-based in natureencompassing several new technologiesthat current experimental researchersare employing to probe complex systembiology questions in life-sciences. Theobjectivesof this course are to teachbasicsofthenewprinciplestostudentssoastoappreciate current-day research tool-kitbetter.

Student Learning OutcomesStudents should be to learn history,theoretical basis and basic understandingof latest technologies in area ofbiotechnology.Theyshouldalsobe ableto learn about various applications ofthese technologies. The students may alsolearnoneapplicationindepththroughanassignment and/orseminar.

Unit IOptical microscopymethods10 lectures

Unit IIMass spectroscopy5 lectures

Unit IIISystems biology5 lectures

Unit IVStructural biology5 lectures

Unit VCRISPR-CAS6 lectures

Basic Microscopy: Light Microscopy: lenses and microscopes, resolution: Rayleigh’sApproach,Darkfield;PhaseContrast;Differential InterferenceContrast; fluorescenceand fluorescence microscopy: what is fluorescence, what makes a molecule fluorescent,fluorescencemicroscope;opticalarrangement, lightsource; filtersets: excitationfilter,dichroicmirror,andbarrier,opticallayoutforimagecapture;CCDcameras;backillumination, binning; recording color; three CCD elements with dichroic beamsplitters,boosting the signal.Advanced Microscopy: Confocal microscope: scanning optical microscope, confocalprinciple, resolution andpoint spread function, light source: gas lasers& solid-state,primary beamsplitter; beam scanning, pinhole and signal channel configurations,detectors;pixelsandvoxels;contrast, spatial sampling: temporalsampling:signal-to-noise ratio, multichannel images. nonlinear microscopy: multiphoton microscopy;principlesof two-photonfluorescence,advantagesof two-photonexcitation, tandemscanning (spinning disk) microscopes, deconvolving confocal images; image processing,three-dimensional reconstruction; advanced fluorescence techniques: FLIM, FRET,and FCS, Fluorescence Lifetime, Fluorescence Resonant Energy Transfer (FRET),Fluorescence Correlation Spectroscopy (FCS), Evanescent WaveMicroscopy; Near-Fieldand Evanescent Waves, Total Internal Reflection Microscopy; Near-Field Microscopy;BeyondtheDiffractionLimit:StimulatedEmissionDepletion(STED),Super-ResolutionSummary, Super-Resolution Imaging with Stochastic Optical Reconstruction Microscopy(STORM) and Photoactivated LocalizationMicroscopy (PALM).

Ionization techniques; mass analyzers/overview MS; FT-ICR and Orbitrap, fragmentationof peptides; proteomics, nano LC-MS; Phospho proteomics; interaction proteomics, massspectroscopy in structural biology; imaging mass spectrometry.

High throughput screens in cellular systems, target identification, validation ofexperimental methods to generate the omics data, bioinformatics analyses, mathematicalmodeling and designing testable predictions.

X-raydiffractionmethods, solution&solid-stateNMR,cryo-electronmicroscopy,small-angle X-ray scattering, Atomic forcemicroscopy.

Historyof itsdiscovery, elucidationof themechanism including introduction to allthe molecular players, development of applications for in vivo genome engineering forgeneticstudies, promiseof the technologyasanextgeneration therapeuticmethod.

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Unit VINanobodies4 lectures

Introduction to nanobodies, combining nanobody with phage-display method fordevelopmentofantibodyagainstnativeproteins,nanobodyasatool forproteinstructure-functionstudies, useofnanobodies formolecular imaging, catabolicantibodies using nanobodies.

Recommended Textbooks and References:1. Campbell, I.D. (2012).Biophysical Techniques.Oxford:OxfordUniversityPress.2. Serdyuk, I. N., Zaccai, N. R., & Zaccai, G. (2007).Methods in Molecular Biophysics:

Structure,Dynamics, Function.Cambridge:CambridgeUniversityPress.3. Phillips, R., Kondev, J.,& Theriot, J. (2009). Physical Biology of the Cell. NewYork:

Garland Science.4. Nelson,P.C.,Radosavljević,M.,&Bromberg, S. (2004).Biological Physics: Energy,

Information, Life. New York:W.H.Freeman.5. Huang, B., Bates, M., & Zhuang, X. (2009). Super-Resolution Fluorescence

Microscopy.AnnualReviewofBiochemistry,78(1),993-1016.doi:10.1146/annurev.biochem.77.061906.092014.

6. Mohanraju, P.,Makarova, K. S., Zetsche, B., Zhang, F.,Koonin, E. V.,& Oost, J.V.(2016).Diverse EvolutionaryRoots andMechanisticVariationsof theCRISPR-CasSystems. Science, 353(6299).doi:10.1126/science.aad5147.

7. Lander,E. (2016).TheHeroesofCRISPR.Cell, 164(1-2), 18-28.doi:10.1016/j.cell.2015.12.041.

8. Ledford,H.(2016).TheUnsungHeroesofCRISPR.Nature,535(7612),342-344.doi:10.1038/535342a.

9. Jinek,M., Chylinski,K., Fonfara, I.,Hauer,M.,Doudna, J.A.,&Charpentier, E.(2012). A Programmable Dual-RNA-Guided DNA Endonuclease in AdaptiveBacterial Immunity. Science, 337(6096), 816-821. doi:10.1126/science.1225829.

10. Hamers-Casterman,C.,Atarhouch,T.,Muyldermans,S.,Robinson,G.,Hammers,C., Songa, E. B., Hammers, R. (1993). Naturally Occurring Antibodies Devoid of LightChains. Nature, 363(6428), 446-448.doi:10.1038/363446a0.

11. Sidhu, S. S., &Koide, S. (2007). Phage Display for Engineering andAnalyzingProtein Interaction Interfaces.CurrentOpinion in Structural Biology, 17(4), 481-487.doi:10.1016/j.sbi.2007.08.007.

12. Steyaert, J., & Kobilka, B. K. (2011). Nanobody Stabilization of G Protein-CoupledReceptorConformational States.CurrentOpinion inStructuralBiology,21(4), 567-572. doi:10.1016/j.sbi.2011.06.011.

13. Vincke, C., & Muyldermans, S. (2012). Introduction to Heavy Chain Antibodies andDerived Nanobodies. Single Domain Antibodies, 15-26. doi:10.1007/978-1-61779-968-6_2.

14. Verheesen, P.,&Laeremans, T.(2012). Selection by Phage Display of SingleDomain Antibodies Specific to Antigens in their Native Conformation. SingleDomainAntibodies, 81-104. doi:10.1007/978-1-61779-968-6_6.

15. Li, J.,Xia,L.,Su,Y.,Liu,H.,Xia,X.,Lu,Q.Reheman,K. (2012).Molecular Imprintof Enzyme Active Site by Camel Nanobodies. Journal of Biological Chemistry J. Biol.Chem., 287(17), 13713-13721.doi:10.1074/jbc.m111.336370.

16. Sohier, J.,Laurent,C.,Chevigné,A.,Pardon,E.,Srinivasan,V.,Wernery,U.Galleni,M. (2013). Allosteric Inhibition of VIM Metallo-β-Lactamases by a Camelid Nanobody.Biochemical Journal, 450(3), 477-486. doi:10.1042/bj20121305.

17. Chakravarty, R., Goel, S., &Cai,W.(2014).Nanobody: The “Magic Bullet” forMolecularImaging?Theranostics,4(4),386-398.doi:10.7150/thno.8006.

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Critical Analy-sis of ClassicalPapersCredits

Course ObjectivesThe objectives of this course are tofamiliarize students with classic literatureto make them appreciate how ground-breaking discoveries were made without,necessarily, use of high-end technologies.

Student Learning OutcomesStudents shouldbeable to train in theexercise of hypothesisbuildingandmethods of addressing the hypothesis withreadily available technology.

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How does the Course Module work? Students may be divided in groups and each group may be responsible for oneclassical paper.Each week theremay be a 1.5 hour presentation cumdiscussion for each of the papers. At the end of thesemester each student will be asked to write a mini-review (2-3 pages long) on any one classical paper, other than theone he/she presented/discussed.

A list of sixteen classic papers and some suggested reference materials:

SyllabusMolecular Biology

SyllabusCell Biology

1. Studies on thechemical natureof the substance inducing transformation ofPneumococcal types: Induction of transformation by a desoxyribonucleic acidfraction isolated from Pneumococcus type III.Avery OT,Macleod CM, McCarty M.; J Exp Med. 1944 Feb 1;79(2):137-58.Note:ThispaperdemonstratesthatDNAisthetransformingPrincipleoriginallydescribed by FredrickGriffith.

2. Independent functions of viral protein and nucleic acid in growth of bacteriophageHersheyADandChaseM.; J Gen Physiol. 1952May;36(1):39-56.Note:Note:Thispaperdemonstrates thatDNA,andnotprotein,componentofphages enter bacterial cells.

3. Molecularstructureofnucleicacids;astructurefordeoxyribosenucleicacidWatsonJD andCrick FH;Nature. 1953Apr25;171(4356):737-8Note: In this onepagepaperWatsonandCrick first described thestructureofDNA double helixStudy help - Watson_Crick_Nature_1953_annotated

4. Transposablemating type genes in Saccharomyces cerevisiaeJames Hicks, Jeffrey N. Strathern & Amar J.S. Klar; Nature 282, 478-483,1979Note: This paper provided evidence for ‘cassette hypothesis’ of yeast mating typeswitches i.e. interconversion of mating types in yeast (S. cerevisiae) occurs byDNA rearrangement.

5. Messelson & Stahl experiment demonstrating semi-conservative replication of DNA.MeselsonMandStahlFW.;ProcNatlAcadSciUSA.1958 Jul 15;44(7):671-82Note: The experiment demonstrating semi-conservative mode of DNA replication isreferred to as "themost beautiful experiment in biology"

6. Invivo alterationof telomere sequences and senescence causedbymutatedTetrahymena telomerase RNAsGuo-LiangYu,JohnD.Bradley,LauraD.Attardi&ElizabethH.Blackburn;Nature 344, 126-132, 1990Note:Thispaperdemonstratesthatthetelomerasecontainsthetemplatefortelomere synthesis

1. A protein-conducting channel in the endoplasmic reticulumSimonSMANDBlobelG.;Cell.1991May3;65(3):371-80Note:Thispaperdemonstrates theexistenceofaproteinconductingchannelStudy help - A brief history of Signal Hypothesis

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SyllabusDevelopmentalBiology/ Genetics

2. Identification of 23 complementation groups required for post-translational eventsin the yeast secretorypathwayNovick P, Field C, Schekman R.; Cell. 1980 Aug;21(1):205-15Note: In thisgroundbreakingpaperRandySchekman'sgroupusedamutagenesisscreen for fast sedimenting yeast mutants to identify genes involved in cell secretion

3. Ayeastmutantdefectiveatanearlystageinimportofsecretoryproteinprecursorsinto the endoplasmicreticulumDeshaies RJ and Schekman R.; J Cell Biol. 1987 Aug;105(2):633-45Note:UsinganotheryeastmutationscreenSchekmanlab identifiesSec61,acomponent of ER protein Conducting Channel (PCC)Suggested reference paper - A biochemical assay for identification of PCC.

4. Reconstitution of the Transport of Protein between Successive Compartmentsof the GolgiBalchWE, DunphyWG, BraellWA,Rothman JE.; Cell. 1984 Dec;39(2 Pt 1):405-16Note: This paper describes setting up of an in vitro reconstituted system fortransport between golgi stacks which eventually paved the way for identification ofmost of themolecular players involved in these steps includingNSF,SNAPetc.

5. Acomplete immunoglobulin gene is created by somatic recombinationBrackC,HiramaM,Lenhard-SchullerR, TonegawaS.; Cell. 1978 Sep;15(1):1-14Note: This study demonstrates DNA level molecular details of somaticrearrangementofimmunoglobulingenesequencesleadingtothegenerationoffunctionally competentantibodygeneratinggene followingrecombination.

6. A novel multigene family may encode odorant receptors: a molecular basis forodor recognitionBuck L and Axel R; Cell. 1991 Apr 5;65(1):175-87Note: This paper suggests that different chemical odorants associate with differentcell-specific expression of a transmembrane receptor in Drosophila olfactoryepithelium where a large family of odorat receptors is expressed.

7. Kinesin walks hand-over-handYildiz A, TomishigeM, Vale RD, Selvin PR.; Science. 2004 Jan 30;303(5658):676-8Note:This paper shows that kinesinmotorworks as a two-headeddimericmotorwalking hand-over-hand rather than like an inchworm on microtubule tract usingthe energy of ATPhydrolysis.

1. Mutations affecting segment number and polarity inDrosophilaChristiane Nusslein-Volhard and Eric Weischaus; Nature 287, 795-801, 1980Note: This single mutagenesis screen identified majority of the developmentallyimportant genes not only in flies but in other metazoans as well.

2. Informationfor thedorsal--ventralpatternof theDrosophilaembryo isstoredas maternalmRNAAndersonKVandNüsslein-VolhardC;Nature. 1984 Sep 20-26;311(5983):223-7Note: This landmark paper demonstrated that early dorsal-ventral patterninformationisstoredasmaternalmRNAinfliesanddevisedthemethodofidentifying genes encoding suchgenes

3. Hedgehog signalling in the mouse requires intraflagellar transport proteinsHuangfuD,LiuA,RakemanAS,MurciaNS,NiswanderL,AndersonKV.;Nature. 2003 Nov6;426(6962):83-7Note:Oneof thearchitects oforiginal flymutagenesis screens conductedamousemutagenesscreenwhichidentifiedageneKif3aasamajorcomponentofhedgehogsignaling pathway. Eventually this discovery revolutionizes our understanding ofmechanismsof action of signalingpathways by demonstrating central role ofcillia in it.SuggestedReferencepaper-Designandexecutionofaembryoniclethalmutationscreen inmouse.

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Bioentrepre-neurshipCredits

2

Course ObjectivesResearch and business belong togetherand both are needed. In a rapidlydeveloping life science industry, thereis an urgent need for people whocombine business knowledge with theunderstanding of science & technology.Bio-entrepreneurship, an interdisciplinarycourse, revolves around the central themeofhowtomanageanddevelop lifesciencecompanies and projects. The objectivesof this course are to teach studentsabout concepts of entrepreneurshipincluding identifying a winning businessopportunity, gathering funding andlaunching a business, growing andnurturing the organization and harvestingthe rewards.

Student Learning OutcomesStudents should be able to gainentrepreneurial skills, understandthe various operations involved inventure creation, identify scope forentrepreneurship in biosciences andutilize the schemes promoted throughknowledge centres and various agencies.The knowledge pertaining to managementshould also help students to be able tobuild up a strong network within theindustry.

Unit IInnovation andentrepreneurshipin bio-business8 lectures

Unit IIBio markets -business strategyand marketing8 lectures

Unit IIIFinance andaccounting8 lectures

Unit IVTechnologymanagement8 lectures

Introduction and scope in Bio-entrepreneurship, Types of bio-industries and competitivedynamics between the sub-industries of the bio-sector (e.g. pharmaceuticals vs. Industrialbiotech), Strategy and operations of bio-sector firms: Factors shaping opportunitiesfor innovationandentrepreneurship inbio-sectors, andthebusiness implicationsofthose opportunities, Alternatives faced by emerging bio-firms and the relevant toolsfor strategic decision, Entrepreneurship development programs of public and privateagencies (MSME,DBT,BIRAC,Make In India), strategic dimensions of patenting&commercialization strategies.

Negotiatingtheroadfromlab tothemarket (strategiesandprocessesofnegotiationwith financiers, government and regulatory authorities), Pricing strategy, Challengesin marketing in bio business (market conditions & segments; developing distributionchannels, thenature, analysis andmanagementof customerneeds),Basic contractprinciples,different typesof agreementandcontract terms typically found in jointventure anddevelopment agreements,Dispute resolution skills.

Business plan preparation including statutory and legal requirements, Business feasibilitystudy,financialmanagementissuesofprocurementofcapitalandmanagementofcosts,Collaborations & partnership, Information technology.

Technology – assessment, development & upgradation, Managing technology transfer,Quality control & transfer of foreign technologies, Knowledge centers and Technologytransfer agencies, Understanding of regulatory compliances and procedures (CDSCO,NBA, GCP,GLA,GMP).

Recommended Textbooks and References:1. Adams, D. J.,& Sparrow, J.C. (2008). Enterprise for Life Scientists: Developing

InnovationandEntrepreneurship in theBiosciences. Bloxham: Scion.2. Shimasaki, C.D. (2014). Biotechnology Entrepreneurship: Starting, Managing, and

LeadingBiotechCompanies.Amsterdam:Elsevier.AcademicPress isan imprintof Elsevier.

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3. Onetti, A., & Zucchella, A. Business Modeling for Life Science and BiotechCompanies: Creating Value and Competitive Advantage with the Milestone Bridge.Routledge.

4. Jordan, J. F. (2014). Innovation, Commercialization, and Start-Ups in Life Sciences.London: CRC Press.

5. Desai, V.(2009).The Dynamics of Entrepreneurial Development and Management.New Delhi: Himalaya Pub.House.

IntellectualPropertyRights,Biosafety andBioethicsCredits

3

Course ObjectivesThe objectives of this course are:• Toprovide basic knowledge on

intellectual property rights and theirimplications in biological research andproduct development;

• TobecomefamiliarwithIndia’sIPR Policy;

• Tolearn biosafety and risk assessmentof products derived from biotechnolo-gyandregulationofsuchproducts;

• Tobecomefamiliarwithethical issuesin biological research. This coursewill focus on consequences ofbiomedical research technologies suchas cloning of whole organisms, geneticmodifications, DNAtesting.

Student Learning OutcomesOn completion of this course,students should be able to:• Understand the rationale for and

against IPR and especially patents;• Understand why India has adopted

an IPR Policy and be familiar withbroad outline of patent regulations;

• Understand different types ofintellectual property rights in generaland protection of products derivedfrom biotechnology research andissues related to application andobtaining patents;

• Gain knowledge of biosafety andrisk assessment of productsderivedfrom recombinant DNA researchand environmental release ofgeneticallymodified organisms,national and international regulations;

• Understandethical aspects related tobiological, biomedical, health care andbiotechnology research.

Unit IIntroduction toIPR5 lectures

Unit IIPatenting5 lectures

Introductiontointellectualproperty;typesofIP:patents,trademarks,copyright&related rights, industrial design, traditional knowledge, geographical indications,protectionofnewGMOs; International framework for theprotection of IP; IP as a factorinR&D;IPsof relevance tobiotechnologyandfewcasestudies; introductiontohistoryofGATT,WTO,WIPOandTRIPS; plant varietyprotection and farmers rights act; conceptof ‘priorart’: invention in context of “priorart”;patentdatabases - country-wise patentsearches (USPTO, EPO, India); analysis and report formation.

Basics of patents: types of patents; IndianPatentAct 1970; recent amendments;WIPOTreaties;BudapestTreaty;PatentCooperationTreaty(PCT)andimplications;procedurefor filingaPCTapplication; roleofaCountryPatentOffice; filingofapatentapplication;precautionsbeforepatenting-disclosure/non-disclosure -patent application- formsand guidelines including those of National Bio-diversity Authority (NBA) and otherregulatorybodies, feestructure, time frames; typesofpatentapplications:provisionalandcompletespecifications;PCTandconventionalpatentapplications; internationalpatenting-requirement, procedures and costs; financial assistance for patenting-introduction to existing schemes; publication of patents-gazette of India, status in Europeand US; patent infringement- meaning, scope, litigation, case studies and examples;commercializationofpatentedinnovations; licensing–outrightsale, licensing,royalty;patenting by research students and scientists-university/organizational rules in India andabroad,collaborativeresearch-backwardandforwardIP;benefit/creditsharingamongparties/community, commercial (financial)andnon-commercial incentives.

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Unit IIIBiosafety10 lectures

Unit IVNational andinternationalregulations5 lectures

Unit VBioethics15 lectures

Biosafety and Biosecurity - introduction; historical background; introduction tobiological safety cabinets; primary containment for biohazards; biosafety levels; GRASorganisms, biosafety levels of specific microorganisms; recommended biosafety levelsfor infectiousagentsand infectedanimals;definitionofGMOs&LMOs;principlesofsafetyassessmentoftransgenicplants–sequentialsteps inriskassessment;conceptsoffamiliarityandsubstantialequivalence;risk–environmental riskassessmentandfoodandfeedsafetyassessment; problemformulation–protectiongoals,compilationofrelevant information, riskcharacterizationanddevelopmentofanalysisplan; riskassessment of transgenic crops vs cisgenic plants or products derived from RNAi, genomeediting tools.

International regulations–Cartagenaprotocol,OECDconsensusdocuments andCodexAlimentarius; Indianregulations–EPAactandrules,guidancedocuments,regulatoryframework–RCGM,GEAC,IBSCandotherregulatorybodies;Draftbillof Biotechnology Regulatory authority of India - containments – biosafety levels andcategory of rDNA experiments; field trails – biosafety research trials – standard operatingprocedures-guidelinesofstategovernments;GMlabeling–FoodSafetyandStandardsAuthority of India (FSSAI).

Introduction, ethical conflicts in biological sciences - interference with nature,bioethics in health care - patient confidentiality, informed consent, euthanasia,artificial reproductive technologies, prenatal diagnosis, genetic screening, gene therapy,transplantation. Bioethics in research – cloning and stem cell research, Human andanimal experimentation, animal rights/welfare, Agricultural biotechnology - Geneticallyengineeredfood,environmentalrisk, labelingandpublicopinion.Sharingbenefitsandprotectingfuturegenerations -Protectionofenvironmentandbiodiversity–biopiracy.

Recommended Textbooks and References:1. Ganguli,P.(2001). IntellectualPropertyRights: UnleashingtheKnowledgeEconomy.

New Delhi: Tata McGraw-Hill Pub.2. National IPR Policy, Department of Industrial Policy&Promotion,Ministry of

Commerce, GoI3. Complete Reference to Intellectual Property Rights Laws. (2007).

Snow White PublicationOct.4. Kuhse, H. (2010). Bioethics: an Anthology. Malden,MA: Blackwell.5. Officeof theControllerGeneralofPatents,Design&Trademarks;Departmentof

Industrial Policy&Promotion;Ministry ofCommerce& Industry;Governmentof India. http://www.ipindia.nic.in/

6. KarenF.Greif and JonF.Merz,Current Controversies in the Biological Sciences-Case Studies of Policy Challenges from New Technologies, MIT Press

7. World Trade Organisation.http://www.wto.org8. World Intellectual PropertyOrganisation. http://www.wipo.int9. InternationalUnionfortheProtectionofNewVarietiesofPlants.http://www.upov.int10. National Portal of India. http://www.archive.india.gov.in11. National BiodiversityAuthority. http://www.nbaindia.org12. Recombinant DNA Safety Guidelines, 1990 Department of Biotechnology, Ministry

of Science and Technology, Govt. of India. Retrieved from http://www.envfor.nic.in/divisions/csurv/geac/annex-5.pdf

13. Wolt,J.D.,Keese,P.,Raybould,A., Fitzpatrick, J.W.,Burachik,M.,Gray,A.,Wu,F.(2009).ProblemFormulationintheEnvironmentalRiskAssessmentforGeneticallyModified Plants. Transgenic Research, 19(3), 425-436. doi:10.1007/s11248-009-9321-9

14. Craig,W.,Tepfer,M., Degrassi, G., & Ripandelli, D. (2008). An Overview of GeneralFeaturesof Risk Assessments of GeneticallyModified Crops. Euphytica,164(3), 853-880. doi:10.1007/s10681-007-9643-8

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15. Guidelines for Safety Assessment of Foods Derived from GeneticallyEngineeredPlants. 2008.

16. Guidelines and Standard Operating Procedures for Confined Field Trials ofRegulated Genetically Engineered Plants. 2008. Retrieved fromhttp://www.igmoris.nic.in/guidelines1.asp

17. Alonso,G.M. (2013).SafetyAssessmentofFoodandFeedDerived fromGMCrops:UsingProblemFormulationtoEnsure“FitforPurpose”RiskAssessments.Retrieved from http://biosafety.icgeb.org/inhousepublicationscollectionbiosafetyreviews.

ProjectProposalPreparation&PresentationCredits

2

Course ObjectivesThepurposeofthiscourseistohelpstu-dentsorganize ideas,material andobjec-tives for theirdissertationand tobeginde-velopmentofcommunicationskillsandtoprepare thestudents topresent their topicof research and explain its importance totheir fellowclassmatesandteachers.

Student Learning OutcomesStudents should be able to demonstratethe following abilities:• Formulate a scientific question;• Present scientific approach to solve

the problem;• Interpret, discuss and communicate

scientificresultsinwrittenform;• Gainexperience inwritinga scientific

proposal;• Learnhowtopresentandexplain

their research findings to theaudience effectively.

SyllabusProject ProposalPreparation

SyllabusPosterPresentation

SyllabusOral Presentation

Selectionof research lab and research topic:Students should first select a labwhereintheywouldliketopursuetheirdissertation.Thesupervisororseniorresearchersshouldbeable tohelp the students to readpapers in theareasof interest of the labandhelp themselectatopicfortheirproject.Thetopicoftheresearchshouldbehypothesisdriven.Reviewofliterature:Studentsshouldengageinsystematicandcriticalreviewofappropriate and relevant information sources and appropriately apply qualitative and/orquantitativeevaluationprocessestooriginaldata;keepinginmindethicalstandardsofconduct in the collection and evaluation of data and other resources.WritingResearchProposal:Withthehelpoftheseniorresearchers,studentsshouldbeable to discuss the research questions, goals, approach, methodology, data collection, etc.Students shouldbeable toconstruct a logical outline for theproject includinganalysissteps andexpectedoutcomes andprepare a complete proposal in scientific proposalformat for dissertation.

Studentswillhave topresent the topic of theirproject proposal after fewmonthsof theirselectionof the topic. They shouldbeable toexplain thenovelty and importanceof theirresearch topic.

Attheendof theirproject,presentationwillhave tobegivenbythestudents toexplainworkdonebythemindetail.Alongwithsummarizingtheirfindings theyshouldalsobe able to discuss the future expected outcome of their work.

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LaboratoryVI:BioprocessEngineering&TechnologyCredits

Course ObjectivesThe objectives of this laboratory course aretoprovidehands-ontraining tostudents inupstream and downstream unitoperations.

Student Learning OutcomesStudents should be able to:• Investigate, design and conduct

experiments, analyze and interpretdata, and apply the laboratoryskillsto solve complex bioprocessengineering problems;

• Apply skills and knowledge gained willbeuseful insolvingproblemstypicalofbio industries and research.

4

Syllabus 1. Basic Microbiology techniquesa) Scale up from frozen vial to agar plate to shake flask culture.b) Instrumentation:Microplate reader, spectrophotometer,microscopy.c) Isolation of microorganisms from soil samples.

2. Experimental set-upa) Assembly of bioreactor andsterilization.b) Growth kinetics.c) Substrate and product inhibitions.d) Measurement of residualsubstrates.

3. Data Analysisa) Introduction toMetabolic Flux Analysis (MFA).

4. Fermentationa) Batch.b) Fed-batch.c) Continuous.

5. Unit operationsa) Microfiltrations: Separation of cells from broth.b) Bioseparations:Variouschromatographic techniques and extractions.

6. Bioanalyticsa) Analytical techniqueslikeHPLC,FPLC,GC,GC-MSetc. formeasurement

of amounts ofproducts/substrates.

Recommended Textbooks and References:1. Shuler,M.L.,&Kargi, F.(2002).Bioprocess Engineering: Basic Concepts.Upper

Saddle River, NJ: PrenticeHall.2. Stanbury, P.F.,&Whitaker,A. (2010). Principles of Fermentation Technology.

Oxford: PergamonPress.3. Blanch, H.W.,&Clark, D. S. (1997). Biochemical Engineering. NewYork:

M. Dekker.4. Bailey, J.E., &Ollis, D. F.(1986). Biochemical Engineering Fundamentals.NewYork:

McGraw-Hill.5. El-Mansi,M., & Bryce, C. F. (2007). FermentationMicrobiology and Biotechnology.

Boca Raton: CRC/Taylor &Francis.

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LaboratoryVII:Bioinfor-maticsCredits

2

Syllabus

Course ObjectivesThe aim of this course is to providepractical training in bioinformaticmethods including accessing major publicsequence databases, use of differentcomputational tools to find sequences,analysis of protein and nucleic acidsequences by various software packages.

1. UsingNCBIandUniprotwebresources.

Student Learning OutcomesOn completion of this course,students should be able to:• Describe contents andproperties of

most important bioinformaticsdatabases;

• Perform text- and sequence-basedsearches and analyze and discussresultsinlightofmolecularbiologicalknowledge;

• Explainmajor steps inpairwise andmultiple sequence alignment, explainprinciple and execute pairwisesequence alignment by dynamicprogramming;

• Predict secondary and tertiarystructures of protein sequences.

2. Introduction and use of various genome databases.3. Sequence information resource: Using NCBI, EMBL, Genbank, Entrez, Swissprot/

TrEMBL, UniProt.4. Similarity searches using tools like BLASTand interpretationof results.5. Multiple sequence alignment usingClustalW.6. Phylogenetic analysis of protein and nucleotide sequences.7. Useof gene predictionmethods (GRAIL, Genscan, Glimmer).8. Using RNA structure predictiontools.9. Useof various primer designing and restriction site prediction tools.10. Useofdifferent protein structure predictiondatabases (PDB, SCOP,CATH).11. Construction and study of protein structures usingDeepview/PyMol.12. Homology modelling ofproteins.13. Useof tools formutationandanalysisof theenergyminimizationof

protein structures.14. UseofmiRNAprediction, designing and target prediction tools.

Semester Four

DissertationCredits

(Semester IV: 20 Credits)

Course ObjectivesThe objectives of this course are toprepare the students to adapt to theresearchenvironment and understandhow projects are executed in a researchlaboratory.Itwillalsoenablestudentstolearn practical aspects of research andtrain students in the art of analysis andthesis writing.

Student Learning OutcomesStudentsshouldbeabletolearnhowtoselect anddefend a topic of their research,howtoeffectivelyplan,execute, evaluateand discuss their experiments. Studentsshould be able to demonstrate considerableimprovement inthe followingareas:• In-depth knowledge of the chosen

area of research.• Capability to critically and

systematically integrateknowledgeto identify issues that must beaddressed within framework ofspecific thesis.

• Competence in researchdesign

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and planning.• Capability to create, analyse and

critically evaluate different technicalsolutions.

• Ability to conduct researchindependently.

• Ability to perform analyticaltechniques/experimental methods.

• Project management skills.• Report writing skills.• Problem solving skills.• Communication and interpersonal

skills.

SyllabusPlanning &performingexperiments

SyllabusThesiswriting

Basedon theprojectproposal submitted inearlier semester, students shouldbeable toplan,andengagein,an independentandsustainedcritical investigationandevaluateachosenresearch topicrelevant tobiological sciencesandsociety. Theyshouldbeabletosystematically identify relevant theory and concepts, relate these to appropriate method-ologiesandevidence,applyappropriatetechniquesanddrawappropriateconclusions.Senior researchers should be able to train the students such that they canwork inde-pendently andare able tounderstand theaimofeachexperimentperformedby them.Theyshouldalsobeabletounderstandthepossibleoutcomesofeachexperiment.

Attheendoftheirproject,thesishastobewrittengivingallthedetailssuchasaim,methodology, results, discussion and future work related to their project. Students mayaimtogettheir researchfindingspublished inapeer-reviewedjournal. If theresearchfindings have application-oriented outcomes, the students may file patent application.

RecommendedElectives

BiologicalImagingCredits

2

Course ObjectivesTheobjectivesof thiscourseare toprovidecompleteoverviewofstate-of-artlive-cellimaging techniques using microscopescurrentlyavailable inliterature.Live-cell imaging techniques allow real-timeexaminationof almost every aspect ofcellular function under normal andexperimentalconditions.Withlive-cellimagingexperiments,mainchallengesaretokeepcellsaliveandhealthyoveraperiodof time.Thegrowingnumberoflive-cell imaging techniques means onecan obtain greater amounts of informationwithout stressing out cells.

Student Learning OutcomesOn completion of this course, studentsshallbeabletogainacompleteoverviewofsuper-resolutionfieldfromfundamentalsto state-of-artmethods and applicationsin biomedical research. The students shalllearnthecomparativeadvantagesanddisadvantages of each technique, coversall key techniques in field of biomedicalscience.Thestudentsshallalso learnhowtouse new tools to increase resolution insub-nanometer-scale images of living cellsand tissue, which leads to new informationabout molecules, pathways and dynamicsand state-of-the-art examples ofapplications using microscopes.

Unit IWidefield fluorescentmicroscopy3 lectures

One of the most basic techniques for live-cell imaging is widefield fluorescentmicroscopy. Standard inverted research grade microscopes can yield valuable results ifyouareimagingadherentcells, largeregionsofinterest (suchasorganelles)orverythintissue sections (less than5micrometer). Inwidefield, aCCDcamera is usuallyused to

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capture images and the epi-fluorescence illumination source can be a mercury lamp,xenon lamp, LED’s, etc. Each of light sources require carefully matched interferencefilters for specific excitationandemissionwavelengthsofyour fluorophoreof interest.With widefield microscopy, your specimen is only exposed to excitation light forrelativelyshorttimeperiodsasthefullapertureofemissionlightiscollectedbytheobjectives.Widefield fluorescencemicroscopy canbeused in combinationwithothercommon contrast techniques such as phase contrast and differential interference contract(DIC) microscopy. This combination is useful when performing live-cell imaging toexamine general cell morphology or viability while also imaging regions of interestwithin cells.

Unit IIConfocal laserscanning microscopy(CLSM)3 lectures

Unit IIISpinning disc confocalmicroscopy(SDCM)2 lectures

Unit IVLight-sheetfluorescencemicroscopy(LSFM, or SPIM)2 lectures

Unit VSuper-resolvedfluorescencemicroscopy8 lectures

Unit VIRe-scan confocalmicroscopy4 lectures

CLSMhas ability to eliminate out-of-focus light and information. It is also possible toobtainopticalserial sectionsfromthickerspecimens.Aconjugatepinhole inopticalpathof confocal microscope prevents fluorescence from outside of focal plane from beingcollectedbyphotomultiplier detectoror imagedbycamera. InCLSM,a singlepinhole(andsingle focusedlaserspot) isscannedacrossspecimenbyscanningsystem.Thisspotformsareflectedepi-fluorescence imagebackon originalpinhole.Whenspecimen is infocus,fluorescentlightfromitpassesthroughpinholetodetector.Anyout-of-focuslightisdefocusedatpinholeandvery littleof this signalpasses through todetectormeaningthatbackground fluorescence isgreatly reduced.Thepinholeacts as aspatial filter foremission light from thespecimen.

Thismethodutilisesa ‘NipkowDisc’which isamechanicalopaquediscwhichhasaseriesofthousandsofdrilledoretchedpinholesarranged inaspiralpattern.Eachilluminatedpinholeondisc is imagedbymicroscopeobjective toadiffraction-limitedspot on region of interest on specimen. The emission from fluorophores passes backthoughNipkowdiscpinholesandcanbeobservedandcapturedbyaCCDcamera.Theeffectofspinningdiscisthatmanythousandsofpointsonspecimenaresimultaneouslyilluminated.UsingSDCMtoexamineaspecimenmeansthatreal-timeimaging(30-frames-per-secondorfaster)canbeachieved,whichisextremelyuseful ifyouarelookingatdynamic changeswithin livingcellsover awidespectrumof time-scales.

Thismethodenablesonetoperformlive-cell imagingonwholeembryos, tissuesandcell spheroids in vivo in a gentlemannerwithhigh temporal resolutionand in threedimensions.Oneisabletotrackcellmovementoverextendedperiodsoftimeandfollowdevelopmentoforgansand tissuesonacellular level.Thenextevolutionof light-sheetfluorescence microscopy, termed lattice light-sheet microscopy as developed by EricBetzig (Nobel Prize Laureate 2014 for PALM super-resolution microscopy) will evenallow live-cell imagingwith super-resolved in vivo cellular localization capabilities.

Super-Resolution in a Standard Microscope: From Fast Fluorescence Imaging toMolecular Diffusion Laws in Live Cells; Photoswitching Fluorophores in Super-ResolutionFluorescenceMicroscopy;ImageAnalysisforSingle-MoleculeLocalizationMicroscopy Deconvolution of Nanoscopic Images; Super-Resolution FluorescenceMicroscopy of the Nanoscale Organization in cells; Correlative Live-Cell and Super-Resolution Microscopy and Its Biological Applications; SAX Microscopy and ItsApplication to Imaging of 3D-Cultured Cells; Quantitative Super-Resolution Microscopyfor Cancer Biology andMedicine.

Structured Illumination Microscopy; Correlative Nanoscopy: AFM Super-Resolution(STED/STORM) ; Stochastic Optical Fluctuation Imaging.

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Recommended Textbooks and References:1. RajagopalVadivambal,DigvirS. Jayas. (2015).Bio-Imaging: Principles, Techniques,

and Applications. ISBN 9781466593671 - CAT#K20618.2. AlbertoDiaspro,MarcA.M. J.vanZandvoort. (2016). Super-Resolution Imaging in

Biomedicine. ISBN 9781482244342 - CAT#K23483.3. Taatjes, Douglas, Roth, Jürgen (Eds.). (2012). Cell Imaging TechniquesMethods and

Protocols. ISBN 978-1-62703-056-4.

ComputationalBiologyCredits

2

Course ObjectivesTheobjectiveofthiscourseistoprovidestudents with theory and practicalexperienceofessentials toaidforgenomic,proteomicandmetabolomicscoursesanddrug designprogram.

Student Learning OutcomesOncompletionof this course, thestudents are expected to:• Develop an understanding of the

basic theory of these computationaltools;

• Develop required database extraction,integration, coding for computationaltoolsandmethodsnecessary forall Omics;

• Create hypothesis for investigatingspecific contemporary biologicalquestions, provide help to experimentwithordevelopappropriatetools;

• Critically analyze and interpretresultsoftheirstudywithrespecttowholesystems.

Unit IIntroduction tocomputational biologybasics and biologicaldatabases4 lectures

Unit IIPairwise andmultiple sequencealignments5 lectures

Unit IIIGenome analysis6 lectures

Unit IVStructurevisualization3 lectures

Computers in biology and medicine; Overview of biological databases, nucleic acid &protein databases, primary, secondary, functional, composite, structural classificationdatabase, Sequence formats & storage, Access databases, Extract and create subdatabases, limitations of existing databases.

Localalignment,Globalalignment,Scoringmatrices-PAM,BLOSUM,Gapsandpenalties,Dotplots.Dynamicprogrammingapproach:NeedlemanandWunschAlgorithm, Smith and Waterman Algorithm, Hidden Markov Model: Viterbi Algorithm.Heuristic approach: BLAST, FASTA. Building Profiles, Profile based functionalidentification.

Polymorphisms in DNA sequence, Introduction to Next Generation Sequencingtechnologies, Whole Genome Assembly and challenges, Sequencing and analysis of largegenomes, Gene prediction, Functional annotation, Comparative genomics, Probabilisticfunctionalgenenetworks,Humangenomeproject,Genomicsandcrop improvement.Study available GWAS, ENCODE, HUGO projects, extract and build sub databases;Visualization tools including Artemis and Vista for genome comparison; Functionalgenomics case studies.

Retrieving and drawing structures, Macromolecule viewing platforms, Structurevalidation and correction, Structure optimization, Analysis of ligand-proteininteractions; Tools such as PyMol or VMD.

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Unit VMolecularmodelling6 lectures

Unit VIStructure-baseddrug development6 lectures

Unit VIILigand-based drugdevelopment6 lectures

Significance and need, force field methods, energy, buried and exposed residues; sidechains and neighbours; fixed regions; hydrogen bonds; mapping properties onto surfaces;RMS fit of conformers and protein chains, assigning secondary structures; sequencealignment: methods, evaluation, scoring; protein curation: backbone construction andside chain addition; different types of protein chain modelling: ab initio, homology,hybrid, loop; Template recognition and alignments; Modelling parameters andconsiderations; Model analysis and validation; Model optimization; Substructuremanipulations, annealing, protein folding and model generation; loop generatingmethods; loop analysis; Analysis of active sites using different methods in studyingprotein–protein interactions.

Molecular docking: Types and principles, Semi-flexible docking, Flexible docking; Ligandand protein preparation, Macromolecule and ligand optimization, Ligand conformations,Clustering,Analysisofdockingresultsandvalidationwithknowninformation.Extra-precision docking platforms, Use of Small-molecule libraries, Natural compound librariesfor virtual high throughputscreenings.

Quantitative structure activity relationships; Introduction to chemical descriptors like2D, 3D and Group-based; Radar plots and contribution plots and Activity predictions,Pharmacophoremodeling,Pharmacophore-basedscreeningsofcompoundlibrary,analysis and experimentalvalidation.

Recommended Textbooks and References:1. Mount,D.W.(2001). Bioinformatics: Sequence and Genome Analysis. Cold Spring

Harbor,NY:Cold SpringHarbor Laboratory Press.2. Bourne, P.E., &Gu, J. (2009). Structural Bioinformatics. Hoboken,

NJ: Wiley-Liss.3. Lesk, A. M. (2004). Introduction to Protein Science: Architecture, Function, and

Genomics. Oxford: Oxford University Press.4. Campbell,M&Heyer, L. J. (2006), Discovering Genomics, Proteomics and

Bioinformatics, PearsonEducation.5. Oprea, T. (2005). Chemoinformatics in Drug Discovery,Volume 23.

Wiley Online Library.6. Gasteiger, J.&Engel,T.(2003),Chemoinformatics: aTextbook,WileyOnlineLibrary.

DrugDiscovery andDevelopmentCredits

Course ObjectivesThis course will give a broad overview ofresearch and development carried out inindustrial setup towards drug discovery.

Student Learning OutcomesOncompletionofthiscourse,studentsshould be able to understand basics ofR&Dindrugdiscoveryandshouldbeabletoapplyknowledgegained in respectivefieldsofpharmaceutical industry.

2

Unit ITarget identificationand molecularmodelling7 lectures

Identification of target or drug leads associatedwith a particular disease by a numberof different techniques including combinations of molecular modeling, combinatoriallibraries and high-throughput screening (HTS); Conceptualizing the automation of theHTS process and the importance of bioinformatics and data processing in identificationof lead compounds; Rational drug design, based on understanding the three-dimensional

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structures and physicochemical properties of drugs and receptors; Modelling drug/receptor interactions with the emphasis on molecular mechanisms, molecular dynamicssimulations and homology modelling; Conformational sampling, macromolecularfolding, structural bioinformatics, receptor-based and ligand-based design and dockingmethods, in silico screening of libraries, semi-empirical andab-initiomethods,QSARmethods,moleculardiversity,designofcombinatorial librariesofdrug-likemolecules,macromolecular and chemicaldatabases.

Unit IILead optimization5 lectures

Unit IIIPreclinicaldevelopment5 lectures

Unit IVDrugmanufacturing4 lectures

Unit VClinical trialdesign4 lectures

Unit VIFundamentals ofregulatory affairsand bioethics4 lectures

Identificationof relevant groupsonamolecule that interactwith a receptor andareresponsible for biological activity; Understanding structure activity relationship;Structure modification to increase potency and therapeutic index; Concept ofquantitativedrugdesignusingQuantitativestructure–activityrelationshipmodels(QSARmodels) based on the fact that the biological properties of a compound are afunctionofitsphysicochemicalparameterssuchassolubility,lipophilicity,electroniceffects, ionization, stereochemistry, etc.; Bioanalytical assay development in support ofin vitro and in vivo studies (LC/MS/MS, GC/MS and ELISA).

Principles of drug absorption, drug metabolism and distribution - intestinal absorption,metabolicstability,drug-druginteractions,plasmaproteinbindingassays,metaboliteprofile studies, Principles of toxicology, Experimental design for preclinical and clinicalPK/PD/TKstudies,Selectionofanimalmodel;RegulatoryguidelinesforpreclinicalPK/PD/TK studies; Scope ofGLP,SOP for conduct of clinical&nonclinical testing, controlon animal house, report preparation and documentation Integration of non-clinical andpreclinical data to aid design of clinical studies.

RequirementsofGMPimplementation,DocumentationofGMPpractices,CoA,RegulatorycertificationofGMP,QualitycontrolandQualityassurance, conceptandphilosophy of TQM, ICH and ISO 9000; ICHguidelines forManufacturing,Understanding ImpurityQualificationData, Stability Studies.

Objectives of Phase I, II, III and IV clinical studies, Clinical studydesign, enrollment,sites and documentation, Clinical safety studies: Adverse events and adverse drugreactions, Clinical PK, pharmacology, drug-drug interaction studies, Statistical analysisand documentation.

Global Regulatory Affairs and different steps involved, Regulatory Objectives, RegulatoryAgencies;FDAguidelinesonINDandNDAsubmissions,Studiesrequired for INDandNDAsubmissions foroncology,HIV,cardiovascular indications,On-labelvs.off-labeldruguseGCPandRequirements ofGCPCompliance, Ethical issues andCompliancetocurrentethicalguidelines,EthicalCommitteesandtheirsetup,AnimalEthicalissuesand compliance.

Recommended Textbooks and References:1. Krogsgaard-Larsen et al. Textbook of Drug Design and Discovery. 4th Edition.

CRC Press.2. Kuhse, H. (2010).Bioethics: an Anthology. Malden,MA: Blackwell.3. Nally, J. D. (2006) GMP for Pharmaceuticals. 6th edition. CRCPress4. Brody, T. (2016) Clinical Trials: Study Design, Endpoints and Biomarkers, Drug

Safety, and FDAand ICHGuidelines. Academic Press.

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EnvironmentalBiotechnologyCredits

2

Course ObjectivesThis course aims to introducefundamentals of EnvironmentalBiotechnology. The course will introducemajorgroupsofmicroorganisms-toolsinbiotechnologyandtheirmostimportant environmental applications.The environmental applications ofbiotechnology will be presented indetailandwillbesupportedbyexamplesfromthe national and international literature.

Student Learning OutcomesOncompletionofcourse,studentswillbeable tounderstanduseofbasicmicrobiological, molecular and analyticalmethods, which are extensively used inenvironmental biotechnology.

Unit IIntroduction toenvironment6 lectures

Unit IIBioremediation6 lectures

Unit IIIRole of microorgan-isms in bioremediation6 lectures

Unit IVBiotechnologyand agriculture11 lectures

Unit VBiofuels11 lectures

Introductiontoenvironment;pollutionanditscontrol;pollution indicators;wastemanagement: domestic, industrial, solid and hazardous wastes; strain improvement;Biodiversityand its conservation;Roleofmicroorganisms ingeochemical cycles;microbial energy metabolism, microbial growth kinetics and elementary chemostattheory, relevantmicrobiological processes,microbial ecology.

Bioremediation: Fundamentals, methods and strategies of application (biostimulation,bioaugmentation) – examples, bioremediation of metals (Cr, As, Se, Hg), radionuclides(U,Te),organic pollutants (PAHs,PCBs, Pesticides, TNT etc.), technological aspects ofbioremediation (in situ, ex situ).

Application of bacteria and fungi in bioremediation: White rot fungi vs specializeddegrading bacteria: examples, uses and advantages vs disadvantages; Phytoremediation:Fundamentalsanddescriptionofmajormethodsofapplication(phytoaccumulation,phytovolatilization, rhizofiltrationphytostabilization).

Bioinsecticides: Bacillus thuringiensis, Baculoviruses, uses, genetic modificationsandaspectsofsafety in theiruse;Biofungicides:Descriptionofmodeofactionsandmechanisms(e.g. Trichoderma,Pseudomonas fluorescens);Biofertilizers:Symbioticsystems between plants – microorganisms (nitrogen fixing symbiosis, mycorrhiza fungisymbiosis),Plantgrowthpromoting rhizobacteria (PGPR)–uses,practicalaspectsandproblems in application.

Environmental Biotechnology and biofuels: biogas; bioethanol; biodiesel; biohydrogen;Description of the industrial processes involved, microorganisms and biotechnologicalinterventionsforoptimizationofproduction;Microbiologicallyenhancedoilrecovery(MEOR); Bioleaching of metals; Production of bioplastics; Production of biosurfactants:bioemulsifiers; Paper production: use ofxylanases andwhite rot fungi.

Recommended Textbooks and References:1. G.M. Evans and J.C. Furlong (2003), Environmental Biotechnology: Theory

and Applications, Wiley Publishers.2. B. Ritmann and P.L. McCarty, (2000), Environmental Biotechnology: Principle &

Applications, 2ndEd., McGraw Hill Science.3. ScraggA., (2005)EnvironmentalBiotechnology. PearsonEducationLimited.4. J. S. Devinny,M. A. Deshusses and T.S.Webster, (1998), Biofiltration for Air

Pollution Control, CRC Press.5. H. J. Rehm and G. Reed, (2001), Biotechnology – A Multi-volume Comprehensive

Treatise, Vol. 11, 2ndEd., VCH Publishers Inc.

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6. H. S. Peavy,D.R. Rowe andG. Tchobanoglous, (2013), Environmental Engineering,McGraw-Hill Inc.

MicrobialTechnologyCredits

Course ObjectivesThe objectives of this course are tointroduce students to developments/advances made in field of microbialtechnology for use in human welfareandsolvingproblems of the society.

Student Learning OutcomesOncompletionofthiscourse,studentswould develop deeper understandingof the microbial technology and itsapplications.

2

Unit IIntroduction tomicrobial technology8 lectures

Unit IIEnvironmentalapplications ofmicrobial technology6 lectures

Unit IIIPharmaceuticalapplications ofmicrobial technology8 lectures

Unit IVFood applications ofmicrobial technology7 lectures

Unit VAdvances in microbialtechnology8 lectures

Microbial technology in human welfare; Isolation and screening of microbes importantfor industry – advances in methodology and its application; Advanced genome andepigenome editing tools (e.g., engineered zinc finger proteins, TALEs/TALENs, andtheCRISPR/Cas9systemasnucleasesforgenomeediting,transcriptionfactorsforepigenome editing, and other emerging tools) for manipulation of useful microbes/strains and their applications; Strain improvement to increase yield of selectedmolecules,e.g., antibiotics, enzymes,biofuels.

Environmentalapplicationofmicrobes;Oreleaching;Biodegradation-biomassrecycleandremoval;Bioremediation-toxicwasteremovalandsoilremediation;GlobalBiogeochemical cycles; Environment sensing (sensor organisms/ biological sensors);International and National guidelines regarding use of genetically modified organisms inenvironment, food andpharmaceuticals.

Recombinant protein and pharmaceuticals production in microbes – commonbottlenecks and issues (technical/operational, commercial and ethical); Attributesrequired in industrialmicrobes (Streptomyces sp., Yeast) tobeused asefficient cloningand expression hosts (biologicals production); Generating diversity and introduction ofdesirable properties in industrially important microbes (Streptomyces/Yeast); Microbialcell factories; Downstream processing approaches used in industrial productionprocess(Streptomyces sp., Yeast).

Applicationofmicrobesandmicrobialprocessesinfoodandhealthcareindustries -foodprocessing and food preservation, antibiotics and enzymes production, microbes intargeted delivery application – drugs and vaccines (bacterial and viral vectors); Non-recombinantwaysof introducingdesirableproperties inGenerally recognizedassafe(GRAS)microbes tobeused in food (e.g.,Yeast)- exploiting theexistingnaturaldiversityor the artificially introduced diversity through conventional acceptable techniques(mutagenesis,protoplast fusion,breeding,genomeshuffling,directedevolution etc.).

Microbialgenomicsfordiscoveryofnovelenzymes,drugs/antibiotics;Limitsofmicrobialgenomicswithrespecttouseinhumanwelfare;Metagenomicsandmetatranscriptomics– theirpotential,methodstostudyandapplications/use (animaland plant health, environmental clean-up, global nutrient cycles & global sustainability,understanding evolution), Global metagenomics initiative - surveys/projects andoutcome,metagenomiclibraryconstructionandfunctionalscreeninginsuitablehosts–toolsand techniques fordiscovery/identificationofnovel enzymes,drugs(e.g., protease, antibiotic) etc.

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Recommended Textbooks and References:1. Lee, Y.K. (2013). Microbial Biotechnology: Principlesand Applications.

Hackensack, NJ: WorldScientific.2. Moo-Young,M. (2011).Comprehensive Biotechnology. Amsterdam: Elsevier.3. Nelson,K.E. (2015).EncyclopediaofMetagenomics.Genes,Genomesand

Metagenomes: Basics, Methods, Databases and Tools. Boston,MA: SpringerUS.4. The New Science of Metagenomics Revealing the Secrets of Our Microbial Planet.

(2007).Washington,D.C.: National Academies Press.5. Journals:(a)Nature,(b)NatureBiotechnology,(c)Appliedmicrobiologyand

biotechnology, (d) Trends in Biotechnology, (e) Trends inMicrobiology,(f) Current opinion in Microbiology, (g) Biotechnology Advances,(h) Genome Research)

6. Websites: http://jgi.doe.gov/our-science/

ProteinEngineeringCredits

2

Course ObjectivesThe aim of this course is to introducemethods and strategies commonly used inprotein engineering.

Student Learning OutcomesOncompletionofthiscourse,studentsshould be able to:• Analyse structure and construction of

proteins by computer-basedmethods;• Describe structure and classificationof proteins;

• Analyse purity and stability of proteinsandexplainhowto store them inbest way;

• Explainhowproteinscanbeusedfordifferent industrial and academicpurposes such as structuredetermination, organic synthesis anddrug design.

Unit IIntroduction toprotein engineering5 lectures

Unit IIStability of proteinstructure5 lectures

Unit IIIApplications5 lectures

Proteinengineering–definition, applications;Featuresorcharacteristicsofproteinsthat can be engineered (definition and methods of study) – affinity and specificity;Spectroscopicproperties; Stability tochanges inparameters aspH, temperatureandamino acid sequence, aggregation propensities, etc. Protein engineering with unnaturalamino acids and itsapplications.

Methods of measuring stability of a protein; Spectroscopic methods to studyphysicochemical properties of proteins: far-UV and near-UV CD; Fluorescence; UVabsorbance; ORD; Hydrodynamic properties–viscosity, hydrogen-deuterium exchange;Brief introduction to NMR spectroscopy – emphasis on parameters that can bemeasured/obtained from NMR and their interpretation.

Forcesstabilizingproteins–Vanderwaals, electrostatic,hydrogenbondingandweaklypolar interactions, hydrophobic effects; Entropy – enthalpy compensation; Experimentalmethods of protein engineering: directed evolution like gene site saturation mutagenesis;Module shuffling; Guided protein recombination, etc., Optimization and high throughputscreening methodologies like GigaMetrix, High throughput microplate screens etc.,Application to devices with bacteriorhodopsin as an example; Engineering antibodyaffinity by yeast surface display; Applications to vaccines, Peptidomimetics and its use indrug discovery.

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Unit IVComputationalapproaches5 lectures

Unit VCase studies1 lecture

Computational approaches to protein engineering: sequence and 3D structureanalysis, Data mining, Ramachandran map, Mechanism of stabilization of proteinsfrom psychrophiles and thermophiles vis-à-vis those from mesophiles; Protein design,Directed evolution for protein engineering and its potential.

Case Studies.

Recommended Textbooks and References:1. Editedby TECreighton, (1997),Protein Structure: a Practical Approach,

2ndEdition, Oxford university press.2. Cleland andCraik, (2006),Protein Engineering, Principles and Practice, Vol7,

Springer Netherlands.3. MuellerandArndt,Protein Engineering Protocols, 1stEdition,HumanaPress.4. Ed. RobertsonDE,Noel JP, (2004), Protein Engineering Methods in Enzymology,

388, Elsevier AcademicPress.5. J Kyte; (2006), Structure in Protein Chemistry, 2ndEdition, Garlandpublishers.

Nano-biotechnologyCredits

2

Course ObjectivesThe course aims at providing a general andbroad introduction to multi-disciplinaryfieldofnanotechnology.Itwillfamiliarizestudentswith the combinationof thetop-downapproachofmicroelectronicsand micromechanics with the bottom-up approach of chemistry/biochemistry;adevelopment that is creatingnewandexciting cross-disciplinary research fieldsand technologies. The course will also givean insight into complete systems wherenanotechnology can be used to improveour everyday life.

Student Learning OutcomesOn successful completion of this course,students should be able to describe basicscience behind the properties of materialsat nanometre scale, and the principlesbehind advanced experimental andcomputational techniques for studyingnanomaterials.

Unit IIntroduction tonanobiotechnology5 lectures

Unit IINano – films5 lectures

Unit IIINano – particles5 lectures

Unit IVApplicationsofnano–particles5 lectures

Introduction to Nanobiotechnology; Concepts, historical perspective; Differentformats of nanomaterials and applications with example for specific cases; CellularNanostructures; Nanopores; Biomolecular motors; Bio-inspired Nanostructures,Synthesis and characterization of different nanomaterials.

Thin films; Colloidal nanostructures; Self Assembly, Nanovesicles; Nanospheres;Nanocapsules and their characterisation.

Nanoparticlesfordrugdelivery, concepts,optimizationofnanoparticleproperties forsuitability of administration through various routes of delivery, advantages, strategies forcellular internalization and long circulation, strategies for enhanced permeation throughvarious anatomical barriers.

Nanoparticles for diagnostics and imaging (theranostics); concepts of smart stimuliresponsive nanoparticles, implications in cancer therapy, nanodevices for biosensordevelopment.

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Unit VNano–materials5 lectures

Unit VINano–toxicity5 lectures

Nanomaterials for catalysis, development and characterization of nanobiocatalysts,application of nanoscaffolds in sythesis, applications of nanobiocatalysis in theproduction of drugs and drug intermediates.

IntroductiontoSafetyofnanomaterials,Basicsofnanotoxicity,ModelsandassaysforNanotoxicityassessment;Fateofnanomaterials indifferentstratasofenvironment;Ecotoxicitymodels and assays; LifeCycleAssessment, containment.

Recommended Textbooks and References:1. GeroDecher, Joseph B. Schlenoff, (2003);Multilayer Thin Films: Sequential Assembly

of NanocompositeMaterials,Wiley-VCHVerlagGmbH&Co.KGaA2. DavidS.Goodsell, (2004);Bionanotechnology: Lessons fromNature;Wiley-Liss3. NeelinaH.Malsch (2005), Biomedical Nanotechnology, CRC Press4. GregT.Hermanson, (2013);BioconjugateTechniques, (3rd Edition); Elsevier5. Recent review papers in the area of Nanomedicine.

VaccinesCredits

2

Course ObjectivesThiscoursewillprovidestudentswithan overview of current developmentsindifferent areas of vaccines.

Student Learning OutcomesBytheendof this course, studentsshould be ableto:• Understand fundamentalconcepts

ofhumanimmunesystemandbasicimmunology;

• Differentiate and understand immuneresponses inrelation to infectionand vaccination;

• Understand requirement and designingof different types of vaccines;

• Understand importance ofconventional and new emergingvaccine technologies.

Unit IFundamentals ofimmune system6 lectures

Unit IIImmune responseto infection9 lectures

Unit IIIImmune responseto vaccination8 lectures

Unit IVVaccine types &design3 lectures

Overview of Immune system; Human Immune system: Effectors of immune system;Innate & Adaptive Immunity; Activation of the Innate Immunity; AdaptiveImmunity;TandBcellsinadaptiveimmunity;Immuneresponseininfection;Correlates of protection.

Protective immune response inbacterial; viral andparasitic infections; Primary andSecondary immune responses during infection; Antigen presentation and Role ofAntigen presenting cells: Dendritic cells in immune response; Innate immune response;Humoral (antibodymediated) responses;Cellmediated responses: roleofCD4+andCD8+T cells;Memory responses:Memory and effector T andB cells,Generation andMaintenance of memory T and B cells.

Vaccination and immune response; Adjuvants in Vaccination; Modulation of immuneresponses: Induction of Th1 and Th2 responses by using appropriate adjuvants andantigen delivery systems - Microbial adjuvants, Liposomal and Microparticles as deliverysystems; Chemokines and cytokines; Role of soluble mediators in vaccination; Oralimmunization and Mucosal Immunity.

History of vaccines, Conventional vaccines; Bacterial vaccines; Viral Vaccines; Vaccinesbased on routes of administration: parenteral, oral, mucosal; Live attenuated andinactivated vaccine; Subunit Vaccines and Toxoids; Peptide Vaccine.

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Unit VVaccine technologies4 lectures

NewVaccineTechnologies;RationallydesignedVaccines;DNAVaccination;Mucosalvaccination; New approaches for vaccine delivery; Engineering virus vectors forvaccination; Vaccines for targeted delivery (Vaccine Delivery systems); Disease specificvaccine design: Tuberculosis Vaccine; Malaria Vaccine; HIV/AIDS vaccine; Newemerging diseases and vaccine needs (Ebola, Zika).

Recommended Textbooks and References:1. Janeway,C. A., Travers, P.,Walport,M., & Shlomchik,M. J. (2005). Immuno Biology:

the ImmuneSystem in HealthandDisease. USA:Garland Science Pub.2. Kindt, T. J., Osborne, B. A., Goldsby, R. A., & Kuby, J. (2013). Kuby Immunology.

New York:W.H.Freeman.3. Kaufmann, S.H. (2004).Novel VaccinationStrategies.Weinheim:Wiley-VCH.4. Journal Articles (relevant issues) from: Annual Review of Immunology, Annual

Review of Microbiology, Current Opinion in Immunology, Nature Immunology,Expert review ofvaccines.