M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTDepartment of BioTechnologyM.Sc Molecular Biology Syllabus2019
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTSemester I
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTSemester – ICodeCourse hemistry3-0-03MSUMB-102Laboratory Techniques3-0-03MSUMB-103Cell and Molecular Regulation of gene expression3-0-03BPracticalMSUMB-191Biochemistry & Analytical TechniquesLab0-0-63MSUMB-192Molecular Biology Lab0-0-63MSUMB-193Lab for Data analysis using statisticalsoftware0-0-62CMSUMB-181Seminar/ journal Presentation1Semester Total24MSUMB101: Biochemistrycredits 3Unit 1: Basic chemistry for biologistsFormation of chemical bonds, molecular orbital (MO) theory and linear
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTcombination of atomic orbitals (LCAO), basics of mass spectrometry, molecules, Avogadro number,molarity, chemical reactions, reaction stoichiometry, rates of reaction, rate constants, order of reactions,kinetic versus thermodynamic controls of a reaction, reaction equilibrium (equilibrium constant); light andmatter interactions (optical spectroscopy, fluorescence, bioluminescence, paramagnetism anddiamagnetism, photoelectron spectroscopy; chemical bonds (ionic, covalent, Van der Walls forces);electronegativity, polarity; VSEPR theory and molecular geometry, dipole moment, orbital hybridizations;acids, bases and pH - Arrhenious theory, pH, ionic product of water, weak acids and bases, conjugate acidbase pairs, buffers and buffering action etc; chemical thermodynamics - internal energy, heat andtemperature, enthalpy (bond enthalpy and reaction enthalpy), entropy, Gibbs free energy of ATP drivenreactions, spontaneity versus driven reactions in biology; bond rotations and molecular conformations Newman projections, conformational analysis of alkanes, alkenes and alkynes; functional groups, opticallyasymmetric carbon centers, amino acids, proteins, rotational freedoms in polypeptide backbone(Ramachandran plot).Unit 2 :Protein StructureWater – properties of water, essential role of water for life on earth pH, buffer, maintenance of blood pHand pH of gastric juice, pH optima of different enzymes (pepsin, trypsin and alkaline phosphatase),ionization and hydrophobicity, emergent properties of biomolecules in water, biomolecular hierarchy,macromolecules, molecular assemblies; Structure-function relationships: amino acids – structure andfunctional group properties, peptides and covalent structure of proteins, elucidation of primary and higherorder structures, Ramachandran plot, evolution of protein structure, protein degradation and introductionto molecular pathways controlling protein degradation, structure-function relationships in model proteinslike ribonuclease A, myoglobin, hemoglobin, chymotrypsin etc.; basic principles of protein purification;tools to characterize expressed proteins; Protein folding: Anfinsen’s Dogma, Levinthal paradox,cooperativity in protein folding, free energy landscape of protein folding and pathways of protein folding.Unit 3: EnzymeEnzyme catalysis – general principles of catalysis; quantitation of enzyme activity and efficiency; enzymecharacterization and Michaelis-Menten kinetics; relevance of enzymes in metabolic regulation, activation,inhibition and covalent modification; single substrate enzymes; restriction enzymes and nucleosidemonophosphate kinase; regulatory strategies with specific example of haemoglobin; isozymes; role ofcovalent modification in enzymatic activity; zymogens.Unit 4 :GlycobiologySugars-mono, di, and polysaccharides with specific reference to glycogen, amylose. lipids- structure andproperties of important members of storage and membrane.Unit 5 :Nucleic acidnucleosides, nucleotides, nucleic acids - structure, a historical perspective leading up to the proposition ofDNA double helical structure.Unit 6: BioenergeticsBioenergetics-basic principles; equilibria and concept of free energy; coupled interconnecting reactions inmetabolism; oxidation of carbon fuels; Ca signaling pathways; glycolysis and gluconeogenesis; Citric acidcycle, entry to citric acid cycle, citric acid cycle as a source of biosynthetic precursors; Oxidativephosphorylation, Photosynthesis – chloroplasts and two photosystems; proton gradient across thylakoidmembrane.Unit 7: Role of vitamins & cofactors in metabolismCalvin cycle and pentose phosphate pathway; glycogen metabolism, reciprocal control of glycogen synthesisand breakdown, elucidation of metabolic pathways; logic and integration of central metabolism; entry/ exit
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTof various biomolecules from central pathways; principles of metabolic regulation; steps for regulation.Texts/References:1. M.T.Madiganand J.M. Martinko, BrockBiology of Microorganisms, 11th Edition,Pearson Prentice-Hall, 2006.2. L. Stryer, Biochemistry, 4th Edition, Freeman, 2002.3. G. Gottschalk, Bacterial Metabolism, 2nd Edition, Springer-Verlag, New-York, Berlin. 1986.MSUMB102:Lab Techniquescredits 3Unit1 :Chromatography Techniques- Paper Chromatography, Thin-layer chromatography,Displacementchromatography, Gas chromatography,High performance / pressure liquidchromatography, Ion exchange chromatography, Size-exclusion chromatography, Affinity chromatography.Unit 2: Electrophoretic techniques and blotting techniques - Theory and application ofPolyacrylamide and Agarose gel electrophoresis; Capillary electrophoresis; 2D Electrophoresis;Immunoelectrophoresis, Isoelectric focussing, Disc gel electrophoresis; Gradient electrophoresis; Pulsedfield gel electrophoresis, Western blot, Eastern blot, Southern blot, Northern blot.Unit 3 :Radioactivity - Radioactive & stable isotopes; Pattern and rate of radioactive decay; Units ofradioactivity; Measurement of radioactivity; Geiger-Muller counter; Solid & Liquid scintillation counters(Basic principle, instrumentation & technique); Applications of isotopes in biochemistry; Autoradiography.Unit 4 :Centrifugation - Basic principles; Mathematics & theory (RCF, Sedimentation coefficient etc);Types of centrifuge, Microcentrifuge, High speed & Ultracentrifuges; Preparative centrifugation; Differential& density gradient centrifugation; Applications (Isolation of cell components); Analytical centrifugation;Determination of molecular weight by sedimentation velocity & sedimentation equilibrium methods.Unit 5: MicroscopyOptical microscopy, Electron microscopy, Confocal microscopyUnit 6: Advanced techniquesDNA and Amino acid Sequencing, DNA CHIP, Microarray, Substractive Hybridization, RNase protectionassay, ELISA, Mass spectroscopy, Infra red spectroscopy, NMR, Circular DichroismMSUMB103:Cell and Molecular Biology credits 3Unit 1: organization of cell:Universal features of cells; cell chemistry and biosynthesis: chemicalorganization of cells; internal organization of the cell - cell membranes: structure of cell membranes andconcepts related to compartmentalization in eukaryotic cells; intracellular organelles: endoplasmicreticulum and Golgi apparatus, lysosomes and peroxisomes, ribosomes, cellular cytoskeleton, mitochondria,chloroplasts and cell energetics; nuclear compartment: nucleus, nucleolus and chromosomes.
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTUnit 2: Chromatin structure :Chromatin organization - histone and DNA interactome: structure andassembly of eukaryotic and prokaryotic DNA polymerases, DNA-replication, repair and recombination;chromatin control: gene transcription and silencing by chromatin-Writers,-Readers and –Erasers;Transcriptional control: Structure and assembly of eukaryotic and prokaryotic RNA Polymerases, promotersand enhancers, transcription factors as activators and repressors, transcriptional initiation, elongation andtermination; post-transcriptional control: splicing and addition of cap and tail, mRNA flow through nuclearenvelope into cytoplasm, breakdown of selective and specific mRNAs through interference by small noncoding RNAs (miRNAs and siRNAs), protein translation machinery, ribosomes-composition and assembly;universal genetic codes, degeneracy of codons, Wobble hypothesis; Iso-accepting tRNA; mechanism ofinitiation, elongation and termination; co- and post-translational modifications, mitochondrial genetic code.Unit 3: Cellular signalling, transport and trafficking: Molecular mechanisms of membranetransport, nuclear transport, transport across mitochondria and chloroplasts; intracellular vesiculartrafficking from endoplasmic reticulum through Golgi apparatus to lysosomes/cell exterior.Unit 4: Cell cycle and its regulation;cell division: mitosis, meiosis and cytokinesis; celldifferentiation: stem cells, their differentiation into different cell types and organization into specializedtissues; cell-ECM and cell-cell interactions; cell receptors and trans-membrane signalling; cell motility andmigration; cell death: different modes of cell death and their regulation.Unit 5: Manipulating and studying cells: Isolation of cells and basics of cell culture; observingcells under a microscope, different types of microscopy; analyzing and manipulating DNA, RNA andproteins.Unit 6: Genome instability and cell transformation: Mutations, proto-oncogenes, oncogenesand tumour suppressor genes, physical, chemical and biological mutagens; types of mutations; intra-genicand inter-genic suppression; transpositions- transposable genetic elements in prokaryotes and eukaryotes,role of transposons in genome; viral and cellular oncogenes; tumor suppressor genes; structure, functionand mechanism of action; activation and suppression of tumor suppressor genes; oncogenes astranscriptional activators.Unit 7:Mammalian genetics:Mendel’s experiments, monohybrid and dihybrid cross, sexualreproduction applications of chi square test, deviation from Mendelian segregation, linkage, genetic map,Mendelism in human genetics: pedigree analysis, dosage compensation and sex determination, inheritancecharacteristics of sex-linked and autosomal traits,chromosome discovery, chromosomes as physicalbasis of inheritance, Polytene and lampbrush chromosomes, chromosomal aberrations and genetic load,sex-linked deleterious genes, extrachromosomal/non-Mendelian inheritance(episomes, mitochondria andchloroplasts), parental imprinting, Population Genetics-Variation and its modulation, effect of sexualreproduction on variation (Hardy-Weinberg Equilibrium), sources of variation, selection balancedpolymorphism, random events.Text/ Reference1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2008).Molecular Biology of theCell (5th Ed.). New York: Garland Science.2. Lodish, H. F. (2016). Molecular Cell Biology (8th Ed.). New York: W.H. Freeman.3. Cooper, G. M., & Hausman, R. E. (2013). The Cell: a Molecular Approach (6th Ed.).Washington: ASM;Sunderland.MSUMB104:Biostatisticscredits 3
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTUnit 1: Introduction to BiostatisticsBasic definitions and applications. Sampling: Representative sample, sample size, sampling biasand sampling techniques. Data collection and presentation: Types of data, methods of collectionof primary and secondary data, methods of data presentation, graphical representation byhistogram, polygon, ogive curves and pie diagram.Unit 2 : Measures of central tendency: Mean, Median, Mode.Measures of variability: Standard deviation, standard error, range, mean deviation and coefficientof variation. Correlation and regression: Positive and negative correlation and calculation of KarlPearsons co-efficient of correlation. Linear regression and regression equation and multiple linearregression, ANOVA, one and two way classification. Calculation of an unknown variable usingregression equation.Unit 3 :Tests of significanceTests of significance: Small sample test (Chi-square t test, F test), large sample test (Z test) andstandard error. Introduction to probability theory and distributions, (concept without deviation)binomial, poison and normal (only definitions and problems) Computer oriented statisticaltechniques. Frequency table of single discrete variable, bubble spot, computation of mean,variance and standard Deviations, t test, correlation coefficient. Randomized block design,complete block design, Usage of Statistical software.MSUMB105:Regulation of Gene Expressioncredits 3Unit 1 Regulation of gene expression in prokaryotes and their viruses:Constitutive, Inducible, and Repressible Gene Expression; Positive and Negative Control of geneexpression b) Operons: Lac, Trp, Ara in Bacteria c) Switch between lysogeny and lysis inBacteriophage Lambda d) Translational control of gene expression and post translationalregulatory mechanism , Horizontal gene transferUnit 2 Regulation of Gene expression in Eukaryotes:a) Spatial and temporal gene regulation of gene expressionb) Transcriptional control: RNA polymerases, cis-elements, transcription factorsc) Post transcriptional control: Alternate splicing, capping and poly-adenylation, RNA –editing,cytoplasmic control of mRNA stabilityd) Environmental impact on transcription: Heat shock genes and Rubiscoe) Chromosome organization and long range control: Transcription in lampbrush and polytenechromosomes and chromatin loops, puffs and domains, matrix attachment regions, remodeling ofchromatin structure, enhancers, long range and epigenetic control mechanisms, ENCODE projectf) Translational control of gene expression and post translational regulatory mechanismg) RNA interference: mechanisms and enzymology; RISC complex formation; regulation of geneexpression by miRNP pathway; plant-virus interactions and silencing of RNA. Epigenetics,methylation, acetylation & Histone modification, Transcriptomics, MetabolomicsTexts/References
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUT1. Watson, J. D. (2008). Molecular Biology of the Gene (5th ed.). Menlo Park,CA:Benjamin/Cummings.2. Benjamin Lewin, Gene IX, 9th Edition, Jones and Barlett Publishers, 2007.MSUMB191: Lab on Biochemistry and AnalyticalTechniquescredits 31. To prepare an Acetic-NaAcetate Buffer system and validate the Henderson-Hasselbach equation.2. To determine an unknown protein concentration by plotting a standard graph of BSA using UV-VisSpectrophotometer and validating the Beer- Lambert’s Law.3. Titration of Amino Acids and separation of aliphatic, aromatic and polar amino acids by TLC.4. An enzyme purification theme (such as E.coli Alkaline phosphatase or any enzyme of the institutionschoice).a) Preparation of cell-free lysatesb) Ammonium Sulfate precipitationc) Ion-exchange Chromatagraphyd) Gel Filtratione) Affinity Chromatographyf) Generating a Purification Tableg) Assessing purity by SDS-PAGE Gel Electrophoresish) Assessing purity by 2-D gel Electrophoresisi) Enzyme Kinetic Parameters: Km, Vmax and Kcat.5. Biophysical methods (Circular dichroism spectroscopy, fluorescence spectroscopy).6. Determination of mass of small molecules and fragmentation patterns by Mass SpectrometryMSUMB192: Molecular Biology lab1. Concept of lac-operon:a. lactose induction of β-galactosidase.b. Glucose Repression.c. Diauxic growth curve of E. coli.2. UV mutagenesis to isolate amino acid auxotroph.3. Phage titre with λ phage/M13.4. Genetic Transfer-Conjugation, gene mapping.5. Plasmid DNA isolation and DNA quantitation.credits 3
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUT6. Restriction Enzyme digestion of plasmid DNA.7. Agarose gel electrophoresis.8. Polymerase Chain reaction.9. DNA Ligation.10. Preparation of competent cells.11. Transformation of E.coli with standard plasmids, Calculation of transformation efficiency.12. Confirmation of the insert, Miniprep of recombinant plasmid DNA, Restriction mapping.13. Expression of recombinant protein, concept of soluble proteins and inclusion body formation in E.coli,SDS-PAGE analysis14. Purification of His-Tagged protein on Ni-NTA columnsa. Random Primer labelingb. Southern hybridization.MSUMB193: Data analysis using statisticalsoftwarecredits 184.108.40.206.5.Introduction to different statistical software.Determination of mean, median, mode of given data set.Determination of standard deviation and standard error of a given data set.Preparation of different types of graph from a given data set.Determination of statistical significance of the experimental data: Paired and unpaired t test and pvalue determination6. Nonparametric Mann-Whitney test, including confidence interval of difference of medians.7. Wilcoxon test with confidence interval of median.8. Usage of two and three way anova.9. Kaplan-Meier survival analysis.
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTSemester II
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTSemester IICodeCourse obiology & DevelopmentalBiology3-0-03MSUMB-202Genomics & Genetic Engineering3-0-03MSUMB-205Applied Bioinformatics3-0-03MSUMB-206Choice based courses(from MOOCS basket)BPracticalMSUMB-291Genetic engineering Lab0-0-63MSUMB-292Immunology Lab0-0-632CMSUMB-281Seminar/ Journal Club PresentationSemester Total124
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTMSUMB 201: Neurobiology & DevelopmentalBiologycredits 3Unit 1 Introduction to the Nervous system, cellular and molecular building blocks, the structure ofnervous systemsUnit 2 The Electrical Potential of a resting neuron, the nerve impulse, synaptic transmission,neurotransmitters and their release, integration of synaptic actionUnit 3 Properties of sensory systems, coding and control of sensory information, motor systems:muscle and its control, reflexes and pattern generation, sensory influence on motor output, thebrain and motor output.Unit 4 Development, developmental plasticity, behavioural plasticity: learning, hormones and thenervous systemUnit 5 The neural basis of behavior, gene regulation in the nervous systemUnit 6 Gametogenesis, Types and structure of eggs, Fertilization, Mechanism of fertilization,fertilization in sea urchin, sperm activation, ovum activation, egg-sperm adhesion, acrosomereaction, prevention of polyspermy, cleavage and blastulation, types of cleavage and patterns ofcleavage, Fate map, Gastrulation, different types of morphogenetic movements, placenta, In vitroFertilization.Texts/References1. Foundations of Neurobiology, Fred Delcomyn2. From Neuron to Brain, Nicholls, Martin and Wallace: Sinauer Associates3. Developmental Biology, GilbertMSUMB 202: Genomics & Proteomicscredits 3MetagenomicsMetagenome Sequencing and Analysis , Presequencing Considerations, MPLING and DataGeneration, Sequence Processing , Tools and Databases for Metagenomic Analysis, Application ForMetagenomic Data AnalysisHuman GenomicsHuman Genome and its Evolution, Overview of the Human Genome ,Protein Coding Genes in theHuman Genome ,RNA Coding Genes and Gene Expression Control Regions , GenomicHeterogeneity of the Human Genome , Genetic Changes That Made Us Human , Ancient HumanGenomes, UCSC Human Genomr Browser
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTTranscriptomicsWhat is the Transcriptome and how it is evaluated? Type of RNA molecules within Transcriptome,Transcriptome Evaluation Method: Microarray Analysis , DNA Microarrays, The Diversity of theTranscriptome, Transcriptome Analysis Throughout RNA-seq, Identification of Biomarkers andExpression Signatures, Methods for Gene Co-expression Network Visualizationand Analysis,Construction and Analysis of GCNsEpigenomicsDNA Methylation, Epigenetic Mechanisms of Gene Regulation, Strategies for Epigenome Analysis,ChIP, ChIP-on-Chip, ChIP-Seq, Profiling of DNA Methylation, MeDIP-seq, Sequencing theEpigenome, Integrating Epigenomic Results, Visualizing the Epigenome, Epigenetics of AgingProteomicsProtein Structure , Amino Acids, Peptide Bonds , Primary Structure , Secondary , Tertiary Structure ,Quaternary ,Experimental Determination of Amino Acid Sequences andProtein Structures Protein2D Gels ,Protein Western Blots . ,Mass Spectrometry, Chemical Identification of Amino Acids inPeptides , Analysis of Protein 3D Structure by X Ray Diffractionand ,Other Assays for Protein Compositions and Interactions , Computational Methods forModeling Molecular Structures , Molecular-Force-Field ,Molecular Dynamics ,Hydrogen Bonds . . ,Computation and Minimization of , Solutions to the Problem of Minimization of RMSDoverRotations, Solutions to the Problem of Minimization of RMSD over Rotations and SolventAccessible Surface of a Protein, Computational Prediction of Protein Structure and Function ,Inferring Structures of Proteins, Protein , De Novo Methods , Comparative Protein Modeling ,Visualization of protein modeling by Swiss PDB package, Application of Biopolymer package inprotein modeling, Necessary application of modeling in proteomics, Protein–Ligand BindingAnalysis , Classification Based on Proteomic AssaysTexts/ReferencesBranden and Tooze “Introduction to Protein Structure”R. R. Sinden, “DNA Structure & Function”A. R. Leach “Molecular Modelling- Principles & Function”Mount “Bioinformatics” Cold Spring HarbourArthur Lesk “Introduction to BioinformaticsMSUMB 203: Immunologycredits 3Unit 1 : Fundamental concepts and anatomy of the immune systemComponents of innate and acquired immunity; Phagocytosis; Complement and Inflammatoryresponses; pathogen recognition receptors (PRR) and pathogen associated molecular pattern(PAMP); Haematopoesis; Organs and cells of the immune system- primary and secondarylymphoid organs; Lymphatic system; Lymphocyte circulation; Lymphocyte homing; Mucosal andCutaneous associated Lymphoid tissue.(MALT&CALT); Mucosal Immunity; Antigens immunogens, haptens; Major Histocompatibility Complex - MHC genes, MHC and immuneresponsiveness and disease susceptibility, HLA typing.
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTUnit 2: Immune responses generated by B and T lymphocytesImmunoglobulins-basic structure, classes and subclasses of immunoglobulins, antigenicdeterminants; Multigene organization of immunoglobulin genes; VDJ Recombination, B-cellreceptor; Immunoglobulin superfamily; Principles of cell signaling; Immunological basis of self non-self discrimination; Kinetics of immune response, memory; B cell maturation, activation anddifferentiation; Generation of antibody diversity; T-cell maturation, activation and differentiationand T-cell receptors; Functional T Cell Subsets; Cell-mediated immune responses, ADCC;Cytokines-properties, receptors and therapeutic uses; Antigen processing and presentationendogenous antigens, exogenous antigens, non-peptide bacterial antigens and super-antigens;Cell-cell co-operation, Hapten- carrier systemUnit 3: Antigen-antibody interactionsPrecipitation, agglutination and complementmediated immune reactions; Advancedimmunological techniques - RIA, ELISA, Westernblotting,ELISPOTassay,immunofluorescence, flow cytometry and immunoelectron microscopy; Surface plasma resonance,Biosenor assays for assessing ligand-receptor interaction, CMI techniques- lymphoproliferationassay, Mixed lymphocyte reaction, Cell Cytotoxicity assays, Apoptotosis, Microarrays, Transgenicmice, Gene knock outs, CD nomenclature, Identification of immune Cells; Principle ofImmunofluorescence Microscopy, Flurochromes; Staining techniques for live cell imaging and fixedcells; Flow cytometry, Instrumentation, Applications.Unit 4: VaccinologyActive and passive immunization; Live, killed, attenuated, sub unit vaccines; Vaccine technologyRole and properties of adjuvants, recombinant DNA and protein based vaccines, plantbased vaccines, reverse vaccinology; Peptide vaccines, conjugate vaccines; Antibody genesand antibody engineering- chimeric and hybrid monoclonal antibodies; Catalytic antibodies andgeneration of immunoglobulin gene libraries.Unit V Clinical ImmunologyImmunity to Infection: Bacteria, viral, fungal and parasitic infections (with examples from each group);Hypersensitivity - Type I-IV; Autoimmunity; Types of autoimmune diseases; Mechanism and role of CD4 Tcells; MHC and TCR in autoimmunity; Treatment of autoimmune diseases; Transplantation-Immunologicalbasis of graft rejection; Clinical transplantation and immunosuppressive therapy; Tumor immunology Tumor antigens; Immune response to tumors and tumor evasion of the immune system, Cancerimmunotherapy; Immunodeficiency- Primary immunodeficiencies, Acquired or secondaryimmunodeficiencies. Immunoglobulin therapy, Specific and nonspecific immunotherapy for Asthma andallergic diseases.Text/ Reference1. Kuby, RA Goldsby, Thomas J. Kindt, Barbara, A. Osborne Immunology, 6th Edition, Freeman, 2002.2. Brostoff J, Seaddin JK, Male D, Roitt IM., Clinical Immunology, 6 th Edition, Gower Medical Publishing,2002.
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUT3. Janeway et al., Immunobiology,4th Edition, Current Biology publications., 1999.4. Paul, Fundamental of Immunology, 4th edition, Lippencott Raven,MSUMB 204: Genetic Engineeringcredits 3Unit 1: Tools for genetic engineering:Impact of genetic engineering in modern society; general requirements for performinga genetic engineering experiment; restriction endonucleases and methylases; DNA ligase, Klenowenzyme, T4 DNA polymerase, polynucleotide kinase, alkaline phosphatase; cohesive and blunt endligation; linkers; adaptors; homopolymeric tailing; labelling of DNA: nick translation, randompriming, radioactive and non-radioactive probes; hybridization techniques: northern, southern,south-western and far-western and colony hybridization, fluorescence in situ hybridization.Unit 2: VectorsPlasmids; Bacteriophages; M13 mp vectors; PUC19 and Bluescript vectors, phagemids; Lambdavectors; Insertion and Replacement vectors; Cosmids; Artificial chromosome vectors (YACs; BACs);Principles for maximizing gene expression: expression vectors, pMal, GST, pET-based vectors;Protein purification: His-tag; GST-tag; MBP-tag etc. Intein-based vectors; Inclusion bodies;methodologies to reduce formation of inclusion bodies; mammalian expression and replicatingvectors; Baculovirus and Pichia vectors system, plant based vectors, Ti and Ri plasmids as vectors,yeast vectors, shuttle vectors.Unit 3: PCR and cloning:primer design; fidelity of thermostable enzymes; DNA polymerases; types of PCR – multiplex,nested; reverse-transcription PCR, real time PCR, touchdown PCR, hot start PCR, colony PCR,asymmetric PCR, cloning of PCR products; TA cloning vectors; proof reading enzymes; PCR basedsite specific mutagenesis; PCR in molecular diagnostics; viral and bacterial detection; sequencingmethods; enzymatic DNA sequencing; chemical sequencing of DNA; automated DNA sequencing;RNA sequencing; chemical synthesis of oligonucleotides; mutation detection: SSCP, DGGE, RFLP,RAPD, AFLP, DNA microsatellite, DNA marker, Polymorphism, Positional cloning, functionalcloning, therapeutic cloning.Unit 4: cDNA analysisInsertion of foreign DNA into host cells; transformation, electroporation, transfection;construction of libraries; isolation of mRNA and total RNA; reverse transcriptase and cDNAsynthesis; cDNA and genomic libraries; construction of microarrays – genomic arrays, cDNA arraysand oligo arrays; study of protein-DNA interactions: electrophoretic mobility shift assay; DNaseIfootprinting; methyl interference assay, chromatin immunoprecipitation; protein-proteininteractions using yeast two-hybrid system; phage display.Unit 5: Gene silencing and genome editing technologiesGene silencing techniques; Transposon and jumping gene, introduction to siRNA; siRNAtechnology; Micro RNA; construction of siRNA vectors; principle and application of gene silencing;gene knockouts and gene therapy; creation of transgenic plants; debate over GM crops;
M.Sc Mol. Biology. Syllabus 2019: Department of Biotechnology MAKAUTintroduction to methods of genetic manipulation in different model systems e.g. fruit flies(Drosophila), worms (C. elegans), frogs (Xenopus), fish (zebra fish) and chick; Transgenics - genereplacement; gene targeting; creation of transgenic and knock-out mice; disease model;introduction to genome editing by CRISPR-CAS with specific emphasis on Chinese and Americanclinical trials.Texts/References1. Gene XII, Lewin’s2. Molecular cell Biology, David Baltimore and Harvey LodishMSUMB205 : Applied Bioinformaticscredits 3Unit 1: Sequence-alignment related problemsSequence databases; Similarity matrices; Pairwise alignment; BLAST; Statistical significance ofalignment; Sequence assembly, Multiple sequence alignment; Clustal; Phylogenetics: distancebased approaches, maximum parsimony.Unit 2: Pattern analysis in sequencesMotif representation: consensus, regular expressions; PSSMs; Markov models;Regulatorysequence identification using Meme; Gene finding: composition based finding, sequence motifbased finding.Units 3: Structure-related problemsRepresentation of molecular structures(DNA, mRNA, protein), secondary structures, domainsand motifs; Structure classification (SCOP, CATH); Visualization software (Pymol, Rasmol etc.);Experimental determination of structures(X-ray crystallography, NMR); Structure databases;Secondary structure prediction; RNA structure prediction; Mfold; Protein structure predictionby comparative modelling approaches(homology modelling, threading); Ab initio structureprediction: force fields, backbone conformer generation by Monte Carlo approaches, side-chainpacking; Energy minimization; Molecular dynamics; Rosetta; Structure comparison (DALI, VASTetc.); CASP;Protein-ligand docking; Computer-aided drug design(pharmacophoreidenti
Determination of molecular weight by sedimentation velocity & sedimentation equilibrium methods. Unit 5: Microscopy Optical microscopy, Electron microscopy, Confocal microscopy . Alternate splicing, capping and poly-adenylation, RNA -editing, cytoplasmic control of mRNA stability d) Environmental impact on transcription: Heat shock genes .
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The journal Molecular Biology covers a wide range of problems related to molecular, cell, and computational biology, including genomics, proteomics, bioinformatics, molecular virology and immunology, molecular development biology, and molecular evolution. Molecular Biology publishes reviews, mini-reviews, and experimental and theoretical works .
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