REGULATIONS 2015 B.TECH GENETIC ENGINEERING … · B.TECH GENETIC ENGINEERING . CURRICULUM - SYLLABUS . SEMESTER – I . S.NO Code Course L T P C THEORY. 1 MGE101 Molecular Genetics

REGULATIONS 2015 B.TECH GENETIC ENGINEERING CURRICULUM - SYLLABUS

SEMESTER – I

S.NO Code Course L T P C THEORY

1 MGE101 Molecular Genetics 3 1 0 4 2 MGE102 Molecular Immunology 3 0 0 3 3 MGE103 Research methodology, IPR & Instrumentation 3 1 0 4 4 MGE104 Statistical Genetics 3 1 0 4 5 MGE1E1 Elective I 3 0 0 3

PRACTICAL 6 MGE1L1 rDNA Technology Lab 0 0 4 2 Total 15 3 4 20

SEMESTER – II S.NO Code Course L T P C THEORY

1 MGE201 Computational methods in Molecular Genetics 3 1 0 4 2 MGE202 Plant Genomics and Proteomics 3 1 0 4 3 MGE203 Genomics and Transcriptomics 3 0 0 3 4 MGE2E1 Elective II 3 0 0 3 5 MGE2E2 Elective III 3 0 0 3

PRACTICAL 6 MGE2L1 Bioinformatics and Molecular modelling lab 0 0 4 2

Total 15 2 4 19

SEMESTER – III S.NO Code Course L T P C THEORY

1 MGE3E1 Elective-IV 3 0 0 3 2 MGE3E2 Elective-V 3 0 0 3 3 MGE3E3 Elective-VI 3 0 0 3

PRACTICAL 4 MGE3P1 Project-Phase 1

(Summer training prerequisite) 0 0 18 6

Total 9 0 18 15

SEMESTER – IV

S.NO Code Course L T P C PRACTICAL

1 MGE4P1 Project-Phase 2 0 0 24 12 Total 0 0 24 12

Total Credit Hour Summary Table

Semester

I

II

III

IV

Total

Total

20

19

15

12

66

LIST OF ELECTIVES

S.No

ELECTIVE

CODES

ELECTIVE SUBJECTS

L

T

P

C

1 MGE 001 Drug Discovery and clinical trials 3 0 0 3 2 MGE 002 Human Genetics 3 0 0 3 3 MGE 003 Pharmacogenomics 3 0 0 3 4 MGE 004 Nanomedicine & Nanobiotechnology 3 0 0 3 5 MGE 005 Stem cell Engineering 3 0 0 3 6 MGE 006 Transgenic Plants 3 0 0 3 7 MGE 007 Animal Biotechnology 3 0 0 3 8 MGE 008 Bioreactor and Bioprocess Technology 3 0 0 3 9 MGE 009 Molecular Mechanisms of Infectious

Disease 3 0 0 3

10 MGE 010 Genetic biodiversity and taxonomy 3 0 0 3 11 MGE 011 Applied mathematics for Genetic

Engineering 3 0 0 3

12 MGE 012 Bioseperation Technology 3 0 0 3 13 MGE 013 Bio confinement of Genetically

Modified Organisms 3 0 0 3

14 MGE 014 Industrial Microbiology 3 0 0 3 15 MGE 015 Tissue engineering & Regenerative

Medicine 3 0 0 3

16 MGE016 Advanced Bioinformatics 3 0 0 3 17 MGE017 Molecular Medicine and Mechanisms 3 0 0 3

18 MGE018 Protein Engineering and industrial

applications 3 0 0 3

19 MGE019 Metabolic process and Engineering 3 0 0 3

MGE101 Molecular Genetics 3 1 0 4

OBJECTIVES This course emphasizes on the current theories of mechanisms of inheritance and their implications for both basic knowledge on human diseases and its application in genetic mapping and genetic testing. OUTCOMES CO01:To understand the molecular basis for transcription, translation, replication, and

gene regulation. CO02: Other topics in molecular genetics for both prokaryotes and eukaryotes. CO03:To understand the underlying theoretical principles of the scientific methods and

approaches of molecular genetics. CO04: To be able to critically interpret experimental designs related to molecular genetics CO05:To acquire an appreciation for the impact of molecular genetics (particularly of human) in

physiology, evolution, and disease.

CO/PO Mapping S – Strong, M – Medium, W – Weak

COs Programme Outcomes (POs) PO1 PO2 PO3 PO4 PO5 PO6 PO7 PO8 PO9 PO10 PO11 PO12

CO1 S W S S CO2 M M S W CO3 M S W S CO4 S M W S COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT- 1- FUNDAMENTALS OF GENETICS 12 Mendelian inheritance: Mendel’s laws - Gene interactions: intra and inter allelic, pleiotropy, multiple alleles and multiple genes - Chromosomes and heredity: linkage and linkage groups - Gene: gene concept, unit of function, replication, recombination and mutation – Fine structure of gene: bar locus, complex loci, rII locus and complementation analysis - Gene function: inborn errors of metabolism, one gene/one enzyme hypothesis, pathways of gene action.

UNIT-II- GENOME ORGANIZATION 12 Genome organisation in prokaryotes and eukaryotes - DNA content and C-value paradox - methods to measure DNA content variation - Various types of DNA sequences – simple sequences, repetitive sequences, nonsense sequences, tandem gene clusters, satellites. Variety of DNA structures: double helix, Z-DNA, B-DNA, Mechanism of DNA replication: prokaryotes and eukaryotes. UNIT-III-MECHANISM OF TRANSCRIPTION 12 Mechanism of transcription: prokaryotes and eukaryotes - Operon and operon concept - Eukaryotic gene structure and expression - Mechanism of translation: prokaryotes and eukaryotes, Control of gene expression - RNA processing and editing, transcriptional and post transcriptional, translational and post transnational controls, Gene mutation: point mutation and transposable elements - DNA repair and recombination. UNIT-IV-MOLECULAR GENETICS OF PHAGE AND YEAST 12 Phage molecular genetics: genetic organization - lytic and lysogenic cycle, regulation of genes - foundations of phage genetics – T-odd coliphages – Single Strand DNA phages – RNA phage. Yeast molecular genetics: genome - mutants and genetic screens – genetic redundancy – cell type determination – cell cycle regulation of mitotic events – genetic interaction: two hybrid systems – gal pathway, gene regulation. UNIT-V-MOLECULAR GENETICS OF DROSOPHILA 12 Drosophila molecular genetics: genome - development genetics – mutants and genetic screens – P element biology – directed expression in drosophila – construction and use of genetic mosaics. Mouse molecular genetics: genome - directed gene expression – X inactivation and imprinting – gene dosage compensation – gene replacement and knockout.

Total Periods: 60 TEXT BOOKS: 1.Molecular Genetics of Bacteria, Third Edition (2007) L. Snyder, Blackwell Publishing

Company, Oxford, UK. 2.Molecular Genetics of Yeast - A Practical Approach, First Edition (1994) J.R. Johnston,

Oxford University Press, UK. 3.Principles of Genome Analysis and Genomics, Third Edition (2003) S.B. Primrose and R.M.

Twyman, Blackwell Publishing Company, Oxford, UK. 4.Mouse genetics: Concepts and Applications, First Edition (1995) L M. Silver, Oxford

University Press. REFERENCES: 1. Molecular Cell Biology, Third edition (1995) W.H.H. Lodish, A.Berk, and C.A. Kaiser,

Freeman & Co Ltd.

2. Molecular Biology of the Gene, Fifth Edition (2004) J.D. Watson, T.A. Baker, S. P. Bell, A. Gann, M. Levine, R. Losick, Pearson Education Inc.

MGE102 Molecular Immunology 3 0 0 3 OBJECTIVE Molecular Immunology is an introductory course in modern molecular immunology. It is geared towards students with strong backgrounds in basic biology, biochemistry, molecular biology and cell biology. OUTCOME CO01: We will focus on basic concepts in immunology with emphasis on the experimental

approaches that have led to our current understanding of the development and function of the immune system.

CO02: In addition, we will consider controversial topics and areas of current investigation. CO03: We expect students to become familiar with immunologic techniques that are used in

many scientific disciplines as well as clinical medicine



CO1 S M W S W S W S CO2 W S M W CO3 M S S CO4 S M W M M W COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT-I-CONCEPTS OF IMMUNOLOGY 9 General principles of immune system, molecules, cells and tissues of immune system, primary and secondary lymphoid organs (thymus, bursa of fabricius, lymph nodes, and spleen), B and T lymphocyte and their functions, lymphocyte cell mediated cytotoxicity.

UNIT-II-ANTIGENS AND ANTIBODIES 9 Concepts of antigen, antigenic determinant, antigenicity, immunogen and immunogenicity, factors affecting antigenicity, hapten, carrier effect, cross reactivity, adjuvant, Freund’s adjuvants and its significance, immunoglobulin, structure of immunoglobulin, types and properties of immunoglobulin, theories of antibody formation, clonal selection, Ig genes, immunoglobulin synthesis and metabolism, and antibody diversity. UNIT-III-HUMORAL AND CELL MEDIATED IMMUNITY 9 MHC, MHC antigen- Class I, Class II, Class III, antigen presentation, MHC restriction, immune response gene, immune response, humoral and cell mediated immune response, BCR, TCR & generation of biodiversity, lymphocytes, T cells regulation, graft rejection. UNIT-IV-ANTIGEN- ANTIBODY REACTION 9 Physico-chemical basis of Ag-Ab interaction, avidity, strength of binding between Ag and Ab and its measurement, detection of Ag-Ab interaction, precipitation, agglutination and complement fixation, complement system, and cytokines. UNIT-V-IMMUNOTECHNIQUES 9 One and two dimensional: single radial immuno diffusion, Ouchterlony immno diffusion, rocket immunoelectrophoresis, CIE, Graber and William technique, direct and indirect agglutination, ELISA, Direct, indirect and Sandwich immunofluorescence, hybridoma technology and monoclonal antibodies, Abzyme technique: Antiserum production, immuno histocompatibility, location of cells in tissues, immunoblotting, flow cytometry.

Total Periods: 45 TEXT BOOKS: 1.Essential Immunology, Eleventh Edition (2006) P. Delves, S. Martin, D. Burton and I. Roitt,

Wiley-Blackwell Publishers, UK. 2.Immunology, Third Edition (1997) J. Kuby, W H Freeman & Co Publishers. 3.Practical immunology, Fourth Edition (2002) F.C. Hay and O.M.R. Westwood, Wiley-

Blackwell Publishers. REFERENCES: 1.Immunology - A Short Course, Third Edition (1996) E. Benjamin, G. Sunshine, and S.

Leskowitz, Wiley-Liss Publishers, New York. 2.Basic and Clinical Immunology, Fourth Edition (1982) D.P. Stites, J.D. Stobo and J.V.

Wells, Appleton & Lange Publishers.

MGE 103 Research methodology, IPR & Instrumentation 3 1 0 4 OBJECTIVES The course imparts knowledge and understanding about various research methodologies .This course helps in preparing students to perform research effectively. OUTCOMES CO01. To know about different types of research. CO02. To understand about research formulation. CO03. To know about research designs and methodology. CO04. To learn about presentations, thesis writing and publication of articles. CO05. It also helps the students to gain knowledge on literature review and thesis writing.



CO1 W M S S S S M CO2 W S M M CO3 S M W S CO4 M S W M S W COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT-1-Research formulation 12 Defining and formulating the research problem, selecting the problem, necessity of defining the problem, importance of literature review in defining a problem, Literature review - primary and secondary sources, reviews, monographs, patents, research databases, web as a source, searching the web, critical literature review, identifying gap areas from literature review and research databases, development of working hypothesis. UNIT-II-Research design and methods 12 Research design – basic principles, need of research design, features of good design, important concepts relating to research design, observation and facts, laws and theories, Prediction and explanation, research databases, development of models, developing a research plan – exploration, description, diagnosis, and experimentation.

UNIT-III-Execution of the research, data collection and analysis 12 Aspects of method validation, observation and collection of data, methods of data collection, sampling methods, data processing and analysis strategies and tools, data analysis with statistical packages (Sigma STAT, SPSS for Student t-test, ANOVA, etc), hypothesis testing, generalization and interpretation. UNIT-IV- Reporting and thesis writing 12 Structure and components of scientific reports, types of report, technical reports and thesis. Thesis writing – different steps and software tools (Word processing, etc) in the design and preparation of thesis, layout, structure (chapter plan) and language of typical reports, Illustrations and tables, bibliography, referencing and footnotes. Oral presentation – planning, software tools, creating and making effective presentation, use of visual aids, importance of effective communication. UNIT-V- Research ethics, IPR and scholarly publishing 12 Ethics – ethical issues, ethical committees (human & animal); IPR - intellectual property rights and patent law, commercialization, copy right, royalty, trade related aspects of intellectual property rights (TRIPS); Scholarly publishing – IMRAD concept and design of research paper, citation and acknowledgement, plagiarism, reproducibility and accountability.

Total Periods: 60 Text Books: (1) Research in education – John W. Best Jems V. Kahn (2) Research methodology – C. R. Kothari (3) Methodology and techniques of social research – Willkinson and Bhandarkar References: (1) Presentation skills – Michel Halton – Indian society for institute education (2) Practical introduction to copyrights – Gavin Mofariane (3) Thesis projects in sciences and engineering – Richard M. Devis (4) Scientist in legal system – Ann Labor Science (5) Thesis and assessment writing – Janolthon Anderson MGE104 Statistical Genetics 3 1 0 4 OBJECTIVES The objective of this class is to introduce students to advanced topics in genetic epidemiology, specifically related to human diseases and traits, with an emphasis on statistics and the mathematics behind the statistics. OUTCOMES CO01. The student should understand the assumptions, strengths, and weaknesses of the various

statistical tests, as well as be well prepared to undertake all aspects of a statistical genetics analysis.

CO02. Including study design, data cleaning and preparation, phenotype definition and modeling, estimation of heritability, linkage analysis, and association analysis.

CO03. Students complete a final project that involves analysis of a provided sample of simulated data, and present their results in both written and presentation formats.

CO/PO Mapping

S – Strong, M – Medium, W – Weak


CO1 M S W W CO2 S W M M W CO3 M S M CO4 M S W S S COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT-I-PATTERN OF INHERITANCE 12 Meaning of phenotype, genotype (homozygous, pure line, heterozygous, hybrid), dominant and recessive alleles. Mendel’s law of inheritance (Law of segregation and law of independent assortment) UNIT-II-ALLELIC RELATIONSHIPS 12 Single gene crosses (monohybrid cross, test cross, back cross), multi-gene crosses involving two or more genes, variations in allelic relationships, condiment alleles in complete dominance, lethal alleles. UNIT-III- STATISTICAL GENETICS OF SIMPLE CROSSES 12 Probability concepts, statistical distributions, normal distribution, binomial distribution, multinomial distribution, testing genetic ratios, chi-square test. UNIT-IV- QUANTITATIVE GENETICS 12 Qualitative versus quantitative traits, normal distribution, average measurements of variability, standard deviation, coefficient of variation, variance and variance method of estimations the number of genes, types of gene action.

UNIT V - STATISTICAL GENETICS OF POPULATIONS 12 Heritability, meaning of variance components, genetic similarity of relatives (depression analysis, correlation analysis), mendelian population, Hardy-Weinberg equilibrium, calculating gene frequencies: Autosomal loci with two alleles, autosomal loci with multiple alleles, testing a locus for equilibrium.

Total Periods: 60 TEXT BOOKS: 1.Genetics, Fourth Edition (2009) L.E. Susan, W.D. Stansfield and G. Bhowmik, Tata McGraw

Hill Publishing Company Limited, New Delhi. REFERENCES: 1.An Introduction to Genetic Statistics, Revised Edition (1969) O. Kempthorne, Jhon Wiley &

Sons, New York. 2.Introduction to Quantitative Genetics, Fourth Edition (1996) D.S. Falconer and T.F.C.

Mackay, Benjamin Cummings Publishers. MGE1L1 RECOMBINANT DNA TECHNOLOGY LAB 0 0 4 2 OBJECTIVE The lab deals with the principles of basic techniques that are essential for genetic engineering and recombinant DNA technology. OUTCOMES CO01. To strengthen the knowledge on various strategies of gene cloning CO02. To impart the knowledge on gene expression CO03. Able to do PCR and DNA sequencing.



CO1 W M S W M S M CO2 M S W M M CO3 M W W M CO4 S W M S S M COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni

5 Quiz 6 End Semester Examinations LABORATORY EXPERIMENTS 1.Cloning using restriction enzymes 2.Cloning of PCR products 3.Cloning in expression vector 4.Induction of expression of recombinant protein 5.Purification of recombinant proteins using His Tag 6.Automated DNA sequencing. MGE201 Computational Methods in Molecular Genetics 3 1 0 4 OBJECTIVES: 1. Understand the relationship between classical genetics and its genotype 2.Understand the central dogma of life 3. Understand the molecular genetics of model organisms and its application COURSE OUTCOMES : CO1 Understand the basics of microarrays in genomics, CO2 Apply the knowledge to next generation sequencing technology. CO3 Learn and apply the Estimation, Protein microarray CO4 Study and apply the gel electrophoresis CO5 Discuss the applications of Mass spectrometry

Co/Po Mapping S – Strong, M – Medium, W – Weak


CO1 M W S S CO2 S W M M W CO3 M W S S M CO4 S M W S COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations

UNIT I MICROARRAYS IN GENOMICS 12 Designing and producing microarrays; types of microarrays; cDNA microarray technology; Oligo-nucleotide arrays; Sample preparation, labeling, hybridization, generation of microarray data. Gene Expression analysis by cDNA and oligonucleotide arrays; ChIP-on-Chip; Bioinformatic analysis of large-scale microarray data for comparative transcriptomics UNIT II NEXT GENERATION SEQUENCING TECHNOLOGIES 12 Introduction to Next Generation Sequencing (NGS) technologies; Principles of NGS by Roche/454, Illumina, Life Technologies, Pacific Biosciences, Ion Torrent technologies; Applications of NGS to disease diagnosis and personalized medicine. UNIT III PROTEIN MICROARRAYS 12 Types of protein arrays; Protein microarray fabrication; Experimental analysis of proteins arrays. Data acquisition and processing; Applications of protein microarray types. UNIT IV TWO-DIMENSIONAL GEL ELECTROPHORESIS OF PROTEINS 12 Sample preparation, First-dimension IEF with IPG; Second dimensional separation of proteins; Image analysis of 2-DE gels; Protein expression profiling and comparative proteomics of complex proteomes using 2-DE. UNIT V MASS-SPECTROMETRY 12 Basics of Mass-spectrometry (MS) and bimolecular analysis; Common ionization methods for peptide/protein analysis (MALDI and ESI); Principles of Time of Flight (TOF), Ion Trap (IT), Quadrupole (Q), Fourier Transform-Ion cyclotron Resonance (FT-ICR), and Orbitrap mass analyzers; Collision-Induced Dissociation (CID) of peptides; Analysis of complex protein mixtures using Nano-liquid chromatography (Nano-LC) coupled to mass spectrometry analysis; Analysis of metabolites using Gas-chromatography coupled to Mass spectrometry; Mass-spectrometry analysis of Post-Translational Modifications of proteins (Phosphorylation and glycosylation). Accurate quantitation of peptides and small molecules using SRM/MRM approach.

Total Periods: 60 TEXTS/REFERENCES 1. Blanch, H.W., Clark, D.S. Introduction to Genomics, Marcel Dekker, 1997 2. Lee, James M. Mass Spectrometry, PHI, USA, 1982. 3. Bailey J.E. & Ollis, D.F. Microarray Fundamentals, 2nd Ed., McGraw Hill, 1986 4. Faber, Kurt “Advanced Blotting Techniques: A Textbook” 5th Edition. Springer 2008. 5. Recent Microarray technology (Vol I-III); Eds by K.Drauz and H. Waldmann. Willey-VCH

(ISBN: 3-527-29949-1)

MGE202 PLANT GENOMICS AND PROTEOMICS 3 1 0 4 OBJECTIVES: 1. To know the computational approaches to analyze the genomes and proteome 2. To understand genome maps and types 3. To learn the basics of protein-protein interactions COURSE OUTCOMES : CO1 Understand the basics of marker assisted selection, CO2 Apply the knowledge to double cross over. CO3 Learn and apply the Polyploidy and anuploidy. CO4 Study and apply the gel electrophoresis CO5 Discuss the applications of quantitative proteomics.



CO1 S W M S S CO2 M S M S M CO3 W S W M CO4 S W M W

COURSE ASSESSMENT METHODS: DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations

UNIT-I -Introduction and Marker assisted selection 12 Meiosis and new genetic variability, Proof that crossing-over occurs at the four-strand stage, Double fertilization in higher plants, Independent assortment of two genes, testcrosses, Epistasis, Conditional probability and two linked loci, Genotypic proportions with two linked loci, Marker assisted selection and conditional probability.

UNIT-II- Double cross over and gene order 12 Estimation of linkage intensity in a testcross, Types of double crossovers, Detection of double crossovers, Types of double-crossovers, Estimation of linkage intensity that includes double crossover gametes, Interference in double crossovers. UNIT-III - Polyploidy and Aneuploidy 12 Random Chromosome segregation types in autotetraploids. The double reduction process in autotetraploids, Concepts in double reduction of autotetraploids, Maximal equational and random chromatid segregation ratios, Random chromosome versus maximum equational segregation, Determination of zygote ratios. UNIT-IV- Proteins and protein biochemical properties 12 Protein fractionation, separation and purification, Isoelectric focusing, Mass spectrometry fundamentals, Protein identification by MS technologies, Gel spot picking and image analysis demonstration, Protein de novo sequencing and top down proteomics. UNIT-V- Quantitative Proteomics 12 Protein array technology, Protein interaction and complex formation, protein digestion and peptide interaction, Protein quantification and Isoelectric focusing, HPLC fractionation of plant samples, Accurate molecular weight and/or complex analysis.

Total Periods: 60 Reference Books: 1. “Principles of Genome analysis and Genomics”- S.B. Primrose and R.M. Twyman –

Blackwell publishing, 2010. 2. “Genomics and Proteomics” functional and computational aspects”, Sandor suhai, Kluwer

Academic Press,December 2012.

Text Books: 1. “ICRF Handbook of Genome Analysis,” N.LS. Spurn S. Bryant, B.D. Young, Blackwell

Pulishing,2006. 2. “From Genes to Genomics: Concepts and Applications of Gene Technology” J. Dale,

VonM. Schantz, Wiley and Sons,2008. 3. “Discovering Genomics, proteomics S. Bioinformatics, “A. Malcolm Cambell S. Laurie J.

Heyer, Cold Spring HarborLaboratory Press s Benjamin Cummings,2008. MGE203 GENOMICS & TRANSCRIPTOMICS 3 0 0 3 OBJECTIVES: 1. To know the computational approaches to analyze the genomes and proteome. 2. To understand genome maps and types. 3. To learn the basics of protein-protein interactions.

COURSE OUTCOMES : CO1 Understand the basics of organisation and structure of genome. CO2 Apply the knowledge to genome mapping and sequencing. CO3 Learn and apply the functional genome analysis. CO4 Study and apply the highthroughput transcriptomic analysis. CO5 Discuss the applications of microarray technology and analysis.

Co/Po Mapping



CO1 S W W S W CO2 M S M M CO3 M S S S CO4 S M W W


UNIT I ORGANIZATION AND STRUCTURE OF GENOMES 9 General organization and structure of genomes of viruses, prokaryotes, eukaryotes, and organelles (chloroplast, mitochondrion) UNIT II GENOME MAPPING AND SEQUENCING 9 Isolation and cloning of genomic DNA, Genome mapping (genetic and physical), STS assembly, ESTs, RAPDs, RFLPs, AFLPs, SSLPs, SNPs, linkage analysis, Restriction mapping, FISH, Chromosome painting, microsatellites, Gene finding, annotation, ORF and functional prediction, Chain termination and chemical degradation sequencing methods, Whole genome shot-gun sequencing. UNIT III LARGE SCALE GENOMICS/ FUNCTIONAL GENOMICS ANALYSES 9 Genome-wide association (GWA) analysis; Comparative Genomic Hybridization (CGH); Serial Analysis of Gene Expression (SAGE); Massively parallel Signature Sequencing

(MPSS); Analysis of alteration in gene expression by Differential Display and Suppression Subtractive Hybridization. Introduction to Next Generation Sequencing (NGS) technologies for genome sequencing. UNIT IV MICROARRAY TECHNOLOGY AND ANALYSIS 9 Designing and producing microarrays; cDNA microarray technology; oligonucleatide arrays and designs; Sample preparation, labeling, hybridization, generation and analysis of microarray data. UNIT V HIGH-THROUGHPUT TRANSCRIPTOMICS ANALYSES 9 Gene Expression analysis by cDNA and oligonucleotide arrays; Methylome analysis using microarray; ChIP-on-Chip; Bioinformatic analysis of large-scale microarray data for comparative transcriptomics: Data normalization; Cluster analysis; Significance Analysis of Microarrays (SAM); Gene Ontology and Pathway analysis.

Total Periods: 45 TEXTS/REFERENCES 1. S.P. Hunt and F. J. Livesey, (2000) Functional Genomics 2. S. B. Primose (1998) Principles of Genome Analysis 3. C. R. Cantor and C. L. Smith (1999) Genomics_ The Science and Technology behind the

Human Genome Project 4. N. K. Spur, B. D. Young, and S. P. Bryant (1998) ICRF Handbook of Genome Analysis

Volume 1 & 2. 5. G. Gibson and S. V. Muse (2002) A primer of Genome Science 6. R. J. Reece (2004) Analysis of Genes and Genomes 7. S. Suhai (2002) Genomics and Proteomics_Functional and computational aspects. Kluwer

Academic press 8. Hans Joac and Thomas Roeder (2005) Microarrays 9. Steve Russell, Lisa A. Meadows and Roslin R. Russell (2009) Microarray Technology in Practice 10. Allison D. B., Page G. P., Beasley T. M., and Edwards J. W. (2006) DNA microarrays and

related genomics techniques – Design, Analysis, and Interpretation of Experiments. Chapman & Hall/CRC

11. Pevsner J. (2009) Bioinformatics and Functional Geneomics. Wiley-Balckwell 12. Rinaldis E. D. and Lahm A (2007)DNA Microarrays. Horizon bioscience. 13. Stekel D. (2003) Microarray Bioinformatics. Cambridge University Press

MGE2L1 BIOINFORMATICS AND MOLECULAR MODELING LAB 0 0 4 2 OBJECTIVES: 1. To know the computational approaches to analyze the genomes and proteome. 2. To understand genome maps and types. 3. To learn the basics of protein-protein interactions. COURSE OUTCOMES : CO1 Understand the basics of organisation and structure of genome. CO2 Apply the knowledge to genome mapping and sequencing. CO3 Learn and apply the functional genome analysis. CO4 Study and apply the highthroughput transcriptomic analysis. CO5 Discuss the applications of microarray technology and analysis.



CO1 S W M S W CO2 W S M W M CO3 M S S CO4 W M S M


1. BIOINFORMATICS - STRUCTURE ANALYSIS

Superposing structure and its analysis Analysis of SNP in structures Small Molecule Generation Peptide Building Carbohydrate Building Refinement of Molecules.

2. MOLECULAR GEOMETRY

Molecules considered as 2D structures Three dimensional shape of a molecule 2D and 3D representations Conformational complexity & Torsion angles

3. MOLECULAR PROPERTIES

Analysis of Physical &Chemical properties

4. MOLECULAR ENERGIES

Internal energy Thermodynamics Kinetics

5. MODELING & DRUG DESIGN Calculation of energies Modifying conformers populations

ELECTIVES MGE001 DRUG DISCOVERY AND CLINICAL TRIALS 3 0 0 3 OBJECTIVES:

1. To study about impact of polymorphism in human genome and applications. 2. To know about functional analysis of gene variation and genotyping techniques 3. To study about the pharmacogenomics application in diseases 4. To learn how to manage the pharmacogenomic information. 5.

COURSE OUTCOMES : CO1 Understand the basics of expression of genetic information. CO2 Apply the knowledge to coupling strategies. CO3 Learn and apply the clinical trials and regulation. CO4 Study and apply the clinical trial ethics. CO5 Discuss the applications of Pharmacovigilance.

Co/Po Mapping



CO1 S W CO2 W S M S M CO3 M S M CO4 S M W S M


UNIT I -INTRODUCTION 9 The Original Combinatorial Chemist – Biopolymers constitute natural libraries – Selection and evolution – The expression of genetic information – Combinatorial assembly of antibody genes

– Molecular solutions to Combinatorial problems. synthetic peptide libraries -Solid-Phase peptide synthesis – Peptide on pins – Other iterative disconvolution strategies, Examples of Split/Couple/Mix Peptide Libraries – Positional Scanning UNIT II- SUPPORTS, LINKERS, AND REAGENTS FOR PEPTIDE AND SMALL MOLECULE SYNTHESIS 9 Polystyrenes – PEG – Grafted supports – Coupling strategies – New resins and linkers – Ring – forming cleavage – loading. Supported Solution – Phase Synthesis - Polyethylene glycols – Dendrimers, Fluorous synthesis – Solution – Phase parallel synthesis scavenging resins – Ion Exchange resins – Supported reagents – Flourous reagents – Solid phase extraction – Gas Phase separation. UNIT III- ANALYTICAL METHODS FOR SOLID-PHASE SYNTHESIS 9 Product identification – Gel Phase NMR – High resolution magic angle spinning NMR on bead infrared Spectroscopy – Mass Spectroscopy – Non Spectroscopic Methods UNIT IV -INTRODUCTION TO CLINICAL TRIALS AND REGULATION 9 Fundamentals of clinical trials; Basic statistics for clinical trials; Clinical trials in practice; Reporting and reviewing clinical trials; Legislation and good clinical practice - Principles of the International Committee on Hormonisation (ICH)-GCP. Drug development and trial planning - pre-study requirements for clinical trials; Regulatory approvals for clinical trials; Consort statement; Trial responsibilities and protocols - Requirements of clinical trials protocols. UNIT V - MANAGEMENT AND ETHICS OF CLINICAL TRIALS & QUALITY CONTROL AND GUIDELINES 9 Project management in clinical trials. Application in clinical trial management; Risk assessment; Research ethics and Bioethics. Introduction to ethical codes and conduct; Introduction to animal ethics; Introduction to laws and regulation regarding use of animals in research. Quality assurance and governance - Pharmacovigilance; Research governance; Trial closure and pitfalls-trial closure; Reporting and legal requirements; Common pitfalls in clinical trial management.

Total Periods: 45 TEXT BOOKS 1. Fenniri, Hicham, ‘Combinatorial Chemistry’, Oxford University Press, 2000 2. Block J.H. and Beale, J.M., ‘Wilson & Gisvolds Text book of Organic Medicinal and

Pharmaceutical Chemistry’, 11th Edition, Lippincott Williams & Wilkins, 2004 3. Fassina, G. “Combinatorial Chemistry and Technologies: Methods and Applications”, 2nd

Edition, CRC Press, 2005. REFERENCES 1. Lee, Chi-Jen; etal., “Clinical Trials or Drugs and Biopharmaceuticals.” CRC / Taylor &

Francis, 2011. 2. Matoren, Gary M. “The Clinical Research Process in the Pharmaceutical Industry.” Marcel

Dekker, 1984 MGE002 HUMAN GENETICS 3 0 0 3 OBJECTIVES: 1.To learn the inheritance pattern in human 2. To learn about the genome and its instability 3. To learn the strategies of genome mapping 4. To have an understanding of human pathology COURSE OUTCOMES : CO1 Understand the basics of pedigree and human genome organization. CO2 Apply the knowledge to gene expression in humans. CO3 Learn and apply the mutation and DNA repair. CO4 Study and apply the genome mapping. CO5 Discuss the applications of molecular pathology.



CO1 S M W S M CO2 W S M M S CO3 M S W M CO4 M S W W M


UNIT-I-PEDIGREES AND ORGANIZATION OF THE HUMAN GENOME 9 Mendelian pedigree patterns - Complications to the basic pedigree patterns - Factors affecting

gene frequencies - Non-mendelian characters - General organization of the human genome - Organization and distribution of human genes - Human multigene families and repetitive coding DNA - Extragenic repeated DNA sequences and transposable elements. UNIT-II-GENE EXPRESSION IN HUMANS 9 An overview of gene expression in human cells - Control of gene expression by binding of trans-acting protein factors to cis-acting regulatory sequences in DNA and RNA - Alternative transcription and processing of individual genes - differential gene expression and DNA methylation - Long-range control of gene expression and imprinting - unique organization and expression of Ig and TCR genes UNIT-III- MUTATION AND DNA REPAIR 9 An overview of mutation, polymorphism, and DNA repair - Simple mutations - Genetic mechanisms which result in sequence exchanges between repeats- Pathogenic mutations - The pathogenic potential of repeated sequences - DNA repair. UNIT-IV- GENOME MAPPING 9 Physical and transcript mapping - Genetic mapping of mendelian characters - Genetic mapping of complex characters – Human Genome projects - Identifying human disease genes UNIT-V- MOLECULAR PATHOLOGY 9 Mutations - Molecular pathology: from gene to disease - Molecular pathology: from disease to gene - Molecular pathology of chromosomal disorders - Gene tracking - Population screening - Cancer genetics - Complex diseases: theory and results.

Total Periods: 45 TEXT BOOKS:

1. Human Molecular Genetics, Third Edition (2003) T. Strachan and A.P. Read, Garland Science Publication. www.ncbi.nlm.nih.gov/books

REFERENCES: 1. Molecular Cell Biology, Sixth Edition (2007) H. Lodish, A. Berk, and C.A. Kaiser, W. H.

Freeman & Co Ltd. 2. Molecular Biology of the Gene, Sixth Edition (2007) J.D. Watson, T.A. Baker, S.P. Bell,

A. Gann, M. Levine, R. Losick, Benjamin Cummings Publication.

http://www.ncbi.nlm.nih.gov/books

MGE003 PHARMACOGENOMICS 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES : CO1 Understand the basics of Association Studies in Pharmacogenomics, CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry CO4 Study and apply the Aspects Influencing Genotyping CO5 Discuss the applications of Management Of Pharmacogenomic Information Co/Po Mapping S – Strong, M – Medium, W – Weak


CO1 M W S M M CO2 S M W M S CO3 S M S S CO4 M W S W COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT-I- INTRODUCTION TO PHARMACOGENOMICS 9 Pharmacogenomics: Historical perspectives and current status, Human Genome and Genomic Applications, Genetic Polymorphism of Metabolic Reactions, SNPs, Association Studies in Pharmacogenomics, Study on industries developing pharmacogenomic research. UNIT-II- FUNCTIONAL ANALYSIS OF GENE VARIATION 9

Transfection Assays With Allele-Specific Constructs: Functional Analysis of UDP-Glucuronosyltransferase Variants, CYP 2D6, CYP2C19 in drug metabolism, Snapshot of the Allele-Specific Variation in Human Gene Expression, Genome-Wide Analysis of Allele-Specific Gene Expression Using Oligo Microarrays, Roche Ampli Chip, HaploChIP: An In Vivo Assay. UNIT-III- GENOTYPING TECHNIQUES 9 Aspects Influencing Genotyping Method Selection, Denaturing HPLC for Mutation Detection and Genotyping, Pyrosequencing of Clinically Relevant Polymorphisms, Kinetic Fluorescence-Quenching Detection Assay for Allele Frequency Estimation, MALDI–TOF Mass Spectrometry, Fluorescence-Based Fragment Size Analysis, SNP Genotyping in DNA Pools, Genotyping of InDel Polymorphisms UNIT-IV- PHARMACOGENOMICS IN PERSONALIZED MEDICINE 9 Pharmacogenomics of Cardiovascular Diseases, Pharmacogenomics of Cancer treatment, Pharmacogenomics of Neurodegenerative Diseases, Pharmacogenomics in Depression, Pharmacogenomics and Respiratory diseases, Pharmacogenoomics in AIDS, Pharmacogenomics in Antibiotics. UNIT-V- MANAGEMENT OF PHARMACOGENOMIC INFORMATION 9 The Pharmacogenetics and Pharmacogenomics knowledge Base, Systems for the Management of Pharmacogenomic Information

Total Periods: 45 TEXT BOOKS: 1. Pharmacogenomics: Methods and Protocols (Methods in Molecular Biology) First Edition

(2005) Federico Innocenti, Humana Press Inc, New Jersey, USA. 2. Pharmacogenomics and Personalized Medicine (Methods in Pharmacology and

Toxicology) First Edition (2005) Nadine Cohen, Humana Press Inc, New Jersey, USA REFERENCES: 1. An A-Z Guide to Pharmacogenomics, First Edition (2006) M.C. Catania, Published by

American Association for Clinical Chemistry 2. Pharmacogenomics: Social, Ethical, and Clinical Dimensions, First Edition (2003)

Mark A. Rothstein, Wiley-Liss Publications

MGE004 NANOMEDICINE AND NANOBIOTECHNOLOGY 3 0 0 3 OBJECTIVES: 1. To learn various Fabrication And Characterization Of Nanomaterials COURSE OUTCOMES : CO1 : Understand the steps in Lithography techniques CO2 : Explain the features of Surface modification and conjugation to nanomaterials CO3 : Health and environmental impacts of nanotechnology. CO4 : Natural bio-nano machinery CO5 : Case study- nanotube synthase- ethical issues.



CO1 M W S M S M CO2 W S M W CO3 W S S CO4 S M W M M COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I- FABRICATION AND CHARACTERIZATION OF NANOMATERIALS 9 Introduction to Nanoscience and Nanotechnology; Milestones in Nanotechnology. Types of Nanomaterials (Quantum dots, Nanoparticles, Nanocrystals, Dendrimers, Buckyballs, Nanotubes); Gas, liquid, and solid –phase synthesis of nanomaterials; Lithography techniques (Photolithography, Dip-pen and Electron beam lithography); Thin film deposition; Electrospinning. Bio-synthesis of nanomaterials. UNIT II - PROPERTIES AND MEASUREMENT OF NANOMATERIALS NANOBIOLOGY AND BIOCONJUGATION OF NANOMATERIALS 9 Optical Properties: Absorption, Fluorescence, and Resonance; Methods for the measurement of nanomaterials; Microscopy measurements: SEM, TEM, AFM and STM. Confocal and TIRF imaging. Properties of DNA and motor proteins; Lessons from nature on making nanodevices; Reactive groups on biomolecules (DNA & Proteins); Surface modification and conjugation to

nanomaterials. Fabrication and application of DNA nanowires; Nanofluidics to solve biological problems. UNIT III- NANO DRUG DELIVERY AND NANOMEDICINE 9 Properties of nanocarriers; drug delivery systems used in nanomedicine; Enhanced Permeability and Retention effect; Blood-brain barrier; Active and passive targeting of diseased cells; Health and environmental impacts of nanotechnology. UNIT IV -STRUCTURAL PRINCIPLES AND FUNCTIONAL PRINCIPLES 9 Natural bio-nano machinery- construction- raw materials- protein folding- self-assembly- self- organization molecular recognition- flexibility. Nano assembly- energetics- chemical transformation- regulation. UNIT V- BIOMOLECULAR MOTORS AND PRESENT AND FUTURE 9 Biomaterials- Biomolecular motors- traffic across membranes- Biomolecular sensing- self-replication. Nanomedicine- DNA computers- Biosensors- Case study- nanotube synthase- ethical issues.

Total Periods: 45 TEXT BOOK 1. David S. Goodsell, Bionanotechnology- Lessons from Nature, Wiley-Liss, 2004. 2. Christof M. Niemeyer, Nanobiotechnology- Concepts, Applications and Perspectives, John

Wiley & Sons, 2004. 3. NanoBiotechnology Protocols (Methods in Molecular Biology) by Sandra J Rosenthal and

David W. Wright , Humana Press; 1 edition, 2005. 4. Bio-Nanotechnology_ Concepts and applications. Madhuri Sharon, Maheshwar Sharon, Sunil

Pandey and Goldie Oza, Ane Books Pvt Ltd, 1 edition 2012 5. Microscopy Techniques for Material Science. A. R. Clarke and C. N. Eberhardt (Editors) CRC

Press. 1st Edition, 2002 REFERENCE BOOKS 1. Mark A. Ratner, Daniel Ratner, Nanotechnology: A Gentle Introduction to the Next Big Idea, Prentice Hall PTR, 2003.

MGE005 STEM CELL ENGINEERING 3 0 0 3 OBJECTIVES: To learn about the general concepts Stem cells and their Developmental Potential . COURSE OUTCOMES : CO1 : Outline the general concepts of Properties and application of Embryonic stem cells CO2 : Basic structures of in vitro and in vivo differentiation of human embryonic stem, CO3 : Hurdles to improving the efficiency of Therapeutic cloning, Stem cells and translational

medicine ethics. CO4 : Explain the concept of Haematopoietic Stem Cells CO5 : Illustrate the Basics of Tumour stem cells,



CO1 W M W W S CO2 W S M S M CO3 M S W M CO4 S M W M S S COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I 9 Stem Cells: Definition, classification and sources, Blastocyst culture, Xeno-free derivation and Cryopreservation, Properties and application of Embryonic stem cells. Characterization of Human Embryonic stem cells. UNIT II 9 Stem cells and their Developmental Potential, subcloning and controlled differentiation of human embryonic stem cells. in vitro and in vivo differentiation of human embryonic stem cells. Feeder free culture of human embryonic stem cells.

UNIT III 9 Therapeutic cloning: Derivation and propagation of human embryonic stem cells by somatic cell nuclear transfer, Hurdles to improving the efficiency of Therapeutic cloning, Stem cells and translational medicine ethics. UNIT IV 9 Haematopoietic Stem Cells: Basic science to Clinical applications, Growth factors and the regulation of haematopoietic stem cells, Haematopoietic stem cells for gene therapy, Haematopoietic cells for leukaemia. UNIT V 9 Skeletal muscle stem cells, Liver stem cells, Tumour stem cells, Stem cell therapies in animal models: Their outcome and possible benefits in humans. TEXT BOOKS: 1. Stem Cells: From Bench to Bedside-Ariff Bongso, Eng Hin Lee . 2. Stem Cells-C S Potten. REFERENCES: 1. Nagy A, Gertenstein M,Vintersten K,Behringer R(2003).Manipulating the Mouse Embryo

,New York:Cold Spring Harbor Press. 2. Gilbert SF.(2000) Developmental biology,6th edition Sunderland,MA:Sinauer

Associates,Inc.

MGE006 TRANSGENIC PLANTS 3 0 0 3 OBJECTIVES: To be able to employ Genetic Engineering in plants. COURSE OUTCOMES : CO1 : Understand the development of new genetic traits CO2 : Methods in Plant Biotechnology CO3 : Identify the role of Immobilized cell systems CO4 : Understand the Alternative methods of plant transformation-in planta floral dip method. CO5 : Explain importance and generating genetically modified plants



CO1 M S W S CO2 W S M M S

CO3 M S W W S CO4 W M W M S

COURSE ASSESSMENT METHODS

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT-I 9 Genetic Engineering in plants: Structure and organization of plant genome, regulation of plant genome expression, transcriptional, translational and post transcriptional regulation of plant genome. Transposons, Transfer of DNA to plant cells- Direct transformation by electroporation and particle gun bombardment. Agrobacterium, Ti plasmid vector Theory and techniques for the development of new genetic traits, conferring resistance to herbicide, pesticide, plant pathogens. UNIT-II 9 Methods in Plant Biotechnology: Amplification of DNAs by Polymerase Chain Reaction (PCR).Gene transfer technology Vectors, Gene transfer using Particles Bombardment, Microinjection method, Sterilization of plant tissues. Methods of micro-propagation, Application of micropropagation, Marker assisted selection (RAPD, RFLP, AFLP, SNP`s etc.). Methods for crop improvement. UNIT-III 9 Application of Plant Biotechnology: Application of plant Biotechnology: Herbicide resistance, disease resistance, novel proteins, vaccines, antibodies and antigens. Immobilized cell systems and Biotransformation. Plant Genome Project: Rice genome project. Hairy root culture and its importance. UNIT-IV 9 Vector, constitutive and tissue specific promoters, reporter genes, selections markers and terminators for plant transformation. Biology of Agrobacterium mediated gene transfer. Biolistic method of transformation. Alternative methods of plant transformation-in planta floral dip method, silicon carbide, pollen tube pathway etc. UNIT V 9 Concerns with genetically modified plants (antibiotic marker, frankenstein food, super weeds, etc) and probable solutions. Indian regulatory systems for laboratory testing, field trail and commercial release of transgenic plants. Bioconfinement strategies for cultivated crops.

Biosafety and ethics in generating genetically modified plants. Potential benefits of genetically modified plants

Total Periods: 45 Text Books 1. Reinert J and Bajaj YPS (1990) Applied and Fundamental aspects of Plant Cell, Tissue and

organ Culture. Springer Verlag, Berlin. 2. Narayanaswamy S (1994) Plant Cell and Tissue Culture. Tata McGraw Hill, New Delhi. 3. Roberts JA and R Hooley (1988) Plant Growth Regulators. Chapman and Hall. New York. References: 1. Bengochea T and Doods JH (1986) Plant Protoplasts, A Biotechnological Tool for Plant

Improvement. Chapman and Hall. London. 2. Gamborg OL and GC Phillips (1995) Plant Cell, Tissue and organ culture. Narosa Publishing

House, New Delhi. 3. Dodds JH and Roberts LW (1995) Experiments in plant Tissue Culture. Cambridge University

Press, Cambridge. 4. Razdan MK (1993) An Introduction to Plant Tissue Culture, Oxfsord & IBH Pub. Co, Pvt.,

Ltd., New Delhi 5. Kumar U (1999) Methods in Plant Tissue Culture, Agro Botanica, New Delhi. MGE007 ANIMAL BIOTECHNOLOGY 3 0 0 3 OBJECTIVES: To be able to animal cell culture technology. COURSE OUTCOMES: CO1 : To Structure and organization of an animal cell CO2 : Introduction to the balanced salt solutions and growth medium, CO3 : Introduction – Cell transformation CO4 : Understand the Somatic cell genetics CO5: Understand the Protein Expression



CO1 M S W W CO2 W S M S CO3 S W S M W CO4 W M S M

COURSE ASSESSMENT METHODS

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT-I BASICS OF ANIMAL CELL AND ITS CULTURING: 9 Structure and organization of an animal cell, Types of animal cell culture – cell culture, organ/tissue culture, organotypic culture and histotypic culture, Equipments and materials needed for animal cell culture technology. UNIT-II ANIMAL CELL CULTURE MEDIUM AND ITS COMPONENTS AND THEIR SIGNIFICANCE: 9 Introduction to the balanced salt solutions and growth medium, Brief discussion on the chemical, physical and metabolic functions of different constituents of culture medium, Role of carbon-di-oxide and role of serum and its supplements in maintaining cells in culture medium, Serum and protein free defined media and their application UNIT-III BASIC TECHNIQUES OF MAMMALIAN CELL CULTURE IN VITRO 9 Primary and established cell lines, Biology and characterization of the cultured cells, measuring parameters of growth. Maintenance of cell culture, Cell separation, Cell transformation, Cell synchronization, Measurement of viability and cytotoxicity, Apoptosis – characteristic features and molecular mechanisms, Measurement of cell death. UNIT-IV ENGINEERING ANIMAL CELLS: 9 Somatic cell genetics, Cell culture based vaccines, Genetic engineering of mammalian cells in culture, Scaling up of animal cell culture, Stem cell cultures – embryonic and adult stem cells and their applications. UNIT-V APPLICATIONS OF ANIMAL CELL CULTURE: 9 Three dimensional culture and tissue engineering, Applications of animal cell culture technology (heterologous, Primary culture/CEF culturing, Protein Expression). TEXT BOOKS: 1. Culture of Animal Cells, Fl. Ian Froshney. Wiley-Liss. 2. Animal Cell Culture - Practical Approach, Ed. John R.W. Masters, OXFORD,

REFERENCE BOOKS: 1. Cell Growth and Division: A Practical Approach. Ed. R. Basega, IRL Press. 2. Cell Culture Lab Fax. Eds. M Butler & M. Dawson, Bios Scientific Publications Ltd..Oxford. 3. Animal Cell Culture Techniques. Ed. Martin Clynes, Springer. 4. Methods in Cell Biology, Vol. 57, Animal Cell Culture Methods. Ed. Jenni P Mather and

David Barnes. Academic Press. MGE008 BIOREACTOR AND BIOPROCESS TECHNOLOGY 3 0 0 3 OJECTIVES: 1. Understand explicitly the concepts 2. Biomass Growth and product formation COURSE OUTCOMES : CO1 : Understand and systematic analysis of black box stoichiometries CO2 : Principles of model building for biotechnological processes CO3 : Design and operation of continuous cultures CO4 : Case studies on Production of green chemicals CO/PO Mapping S – Strong, M – Medium, W – Weak


CO1 W S M M S CO2 W S M W S CO3 M W S S CO4 S M W M S M COURSE ASSESSMENT METHODS

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I BLACK BOX MODEL 9 Yield coefficients, black box stoichiometries, elemental balances, heat balance, degrees of reduction balances, systematic analysis of black box stoichiometries, identification of gross measurement errors.

UNIT II MODELING OF VARIOUS FERMENTATION PROCESSES 9 Principles of model building for biotechnological processes, unstructured models on the population level, structured models on the cellular level, morphologically structured model, genetically structured models, cybernetic model, modelling of recombinant systems. UNIT III DESIGN OF FERMENTATION PROCESSES 9 Kinetics of substrate utilization, biomass growth and product formation, inhibition on cell growth and product formation. Design and operation of continuous cultures, chemostat in series, batch and fed batch cultures, total cell retention cultivation. UNIT IV BIOREACTOR DESIGN & CONSTRUCTION 9 Basic design and construction of CSTR, bioreactor design of agitator/agitator motor, power consumption in aerated bioreactor, design of sparger, mixing time estimation, oxygen mass transfer capability in bioreactor, Removal of Heat in bioreactor, Main parameters to be monitored and controlled in fermentation processes. UNIT V CASE STUDIES IN FERMENTATION DERIVED PRODUCTS 9 Case studies on Production of green chemicals, algal biofuels, recombinant Insulin. Case studies should deal with medium design, reactor design & process optimization etc.

Total Periods: 45 TEXT BOOKS 1. Shuler, M.L. and Kargi, F. Bioprocess Engineering : Basic concepts, 2nd ed., Prentice- Hall,

2002. 2. Doran Pauline M, Bioprocess Engineering Principles, Academic Press, 1995 3. Nielsen, J. and Villadsen, J. “Bioreaction Engineering Principles”. Springer, 2007. 4. Blanch, H.W and Clark D.S., “Biochemical Engineering”, Marcel Dekker,1997 REFERENCES 1. Bailey,J.E. and Ollis, D.F. Biochemical Engineering Fundamentals", 2nd ed.,McGraw Hill

1986. 2. Stanbury, P.F., Stephen J. Hall & A. Whitaker, Principles of Fermentation Technology, Science

& Technology Books.

MGE009 MOLECULAR MECHANISMS OF INFECTIOUS DISEASE 3 0 0 3 OBJECTIVES 1. Provides an opportunity to experimentally verify the theoretical concepts already studied

modern molecular pathogenesis studies 2. Understand pathogen types and modes of entry. 3. Develop their skills in the preparation, qualitative and quantitative analysis.

COURSE OUTCOMES: CO1. Determination of Host defense mechanisms. CO2. Historical perspective. CO3. virulence-associated factors and virulence lifestyle factors.. CO4. Classical approaches based on serotyping CO/PO Mapping S – Strong, M – Medium, W – Weak


CO1 S M W S S M CO2 W S M S CO3 M S W S M CO4 M S W M S COURSE ASSESSMENT METHODS

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT-I 9 Host-Parasite interactions, Host defense mechanisms and molecular mechanisms involved in Pathogenesis of diseases caused by E.Coli and Vibrio Cholerae. UNIT-II 9 Historical perspective - discovery of microscope, Louis Pasteur's contributions, Robert Koch's postulates, early discoveries of microbial toxins, toxic assays, vaccines, antibiotics and birth of molecular genetics and modern molecular pathogenesis studies, Various pathogen types and modes of entry.

UNIT-III 9 Attributes & components of microbial pathogenesis, Host defense: skin, mucosa, cilia, secretions, physical movements, limitation of free iron, antimicrobial compounds, mechanism of killing by humoral and cellular defense mechanisms, complements, inflammation process, general disease symptoms, Pathogenic adaptations to overcome the above defenses. UNIT-IV 9 Virulence, virulence factors, virulence-associated factors and virulence lifestyle factors. Molecular genetics and gene regulation in virulence of pathogens like Vibrio Cholerae, E.coli, Shigella, Plasmodium, Influenza virus. Virulence assays: adherence, invasion, cytopathic, cytotoxic effects. Criteria & tests in identifying virulence factors, attenuated mutants, molecular characterization of virulence factors, signal transduction & host responses. UNIT-V 9 Classical approaches based on serotyping. Modern diagnosis based on highly conserved virulence factors, immuno & DNA-based techniques. New therapeutic strategies based on recent findings on molecular pathogenesis of a variety of pathogens, Vaccines - DNA, subunit and cocktail vaccines.

Total Periods: 45 TEXT BOOKS 1. Iglewski B.H and Clark V.L "Molecular basis of Bacterial Pathogenesis", Academic Press,

1990. 2. Peter Williams, Julian Ketley& George Salmond, "Methods in Microbiology: Bacterial

Pathogenesis, Vol. 27", Academic Press, 1998. REFERENCES 1. Recent reviews in Infect. Immun., Mol. Microbiol, Biochem. J., EMBO etc. 2. Nester, Anderson, Roberts, Pearsall, Nester, "Microbiology: A Human Perspective",

McGraw-Hill, 3rd Edition, 2001. 3. Eduardo A. Groisman, Principles of Bacterial Pathogenesis, Academic Press, 2001

MGE010 GENETIC BIODIVERSITY AND TAXONOMY 3 0 0 3 OBJECTIVES 1. Provides an opportunity to experimentally verify the theoretical concepts already studied.

hierarchy of categories. 2. Understand explicitly the Evolution of gene families 3. Origin and Evolution & Economically important microbes and animals. . COURSE OUTCOMES : CO1.Determination of basic concepts of biosystematics taxonomy CO2. Detailed account of destabilizing forces.

CO3. Pattern of changes in nucleotide and amino acid sequence. CO4. Ecological significance of molecular variations CO/PO Mapping S – Strong, M – Medium, W – Weak


CO1 M W S W CO2 W S M S M CO3 M S S M CO4 W W M COURSE ASSESSMENT METHODS

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I 9 Definition and basic concepts of biosystematics taxonomy and - classification.- History of Classification - Trends in biosystematics : Chemotaxonomy, cytotaxonomy and molecular - Species concepts : species category, different species concepts, subspecies - and other infra-specific categories. - Theories of biological classification: hierarchy of categories. UNIT II 9 Concepts of evolution and theories of organic evolution-Neo Darwinism and population genetics: - Hardy-Weinberg law of genetic equilibrium -detailed account of destabilizing forces: - Natural selection - Mutation - Genetic Drift - Migration - Meiotic Drive. UNIT III 9 Trends in Evolution -Molecular Evolution- Gene evolution -Evolution of gene families - Assessment of molecular variation. UNIT IV 9 Origin of higher categories - Phylogenetic .gradualism and punctuated equilibrium. - Major trends in the origin of higher categories - Micro and macro evolution. - Molecular population genetics - Pattern of changes in nucleotide and amino acid sequence. UNIT V 9 Ecological significance of molecular variations (genetic - polymorphism) -Genetic & Speciation - Phylogenetic and biological concept of species. – Patterns and mechanism of reproductive

isolation.- Modes of speciation (allopatry & sympatry) - Origin and Evolution & Economically important microbes and animals.

Total Periods: 45 TEXTBOOKS: 1. Biodiversity Hardcover – S. Chakraborty

REFERENCE BOOKS: 1. Human Genetic DiversityFunctional Consequences for Health and Disease Julian C. Knight 2. Genetic Diversity in Plants Edited by MahmutÇalişkan, MGE011 APPLIED MATHEMATICS FOR GENETIC ENGINEERING 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES : CO1 Understand the basics of Association Studies in Pharmacogenomics, CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry CO4 Study and apply the Aspects Influencing Genotyping CO5 Discuss the applications of Management Of Pharmacogenomic Information



CO1 S W M S W CO2 W S M M W CO3 M S S S CO4 W M W M COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I - MATRICES 9

http://www.amazon.in/s/ref=dp_byline_sr_book_1?ie=UTF8&field-author=S.+Chakraborty&search-alias=stripbooks

http://www.intechopen.com/books/editor/genetic-diversity-in-plants

Review types of matrices, properties. Inverse matrix Cramer’s rule for solving a system of linear equations. – Rank of Matrix – Consistency and Inconsistency of a system of m linear equations in ‘n’ unknowns –Cayley ,Hamilton theorem – Eigen values and eigen vectors of a real matrix UNIT II – TRIGONOMETRY 9 Review of complex numbers. De Moiver’s theorem and its applications. Expansion of sin cosn in terms of sin cos θ and Expansion of tan nθ in terms of tan θ . Expansion of sin cosθ and in terms of sines and cosines of multiples of θ . Hyperbolic functions and inverse hyperbolic functions. UNIT III - DIFFERENTIAL CALCULUS 9 Differentiation and Derivatives of simple functions – Successive Differentiation – Various forms of Algebraic and Trigonometric functions – Problems. UNIT IV - INTEGRAL CALCULUS 9 Various types of integration –by – Reduction formula for, sincos, sin cos ax n nnn m ex x xx(without proof)-Problems . UNIT V - APPLICATIONS OF DIFFERENTIAL CALCULUS & INTEGRAL CALCULUS 9 Applications of differential calculus & integral calculus. Tangent & Normal-Radius of curvature – Velocity and acceleration . Integral calculus - Length & Area.

Total Periods: 45 TEXT BOOK: 1. Grewal B.S, Higher EnggMaths, Khanna Publications, 38th Edition. 2. Veerajan, T., Engineering Mathematics, Tata McGraw Hill Publishing Co., New Delhi,2000. REFERENCE BOOKS: 1. Kreyszig.E, Advanced Engineering Mathematics, 8th edition, John Wiley & Sons. Singapore,

2001. 2. Kandasamy P etal. Engineering Mathematics, Vol.I (4th revised edition), S.Chand&Co., New

Delhi,2000. MGE012 BIOSEPERATION TECHNOLOGY 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES: CO1 Understand the basics of Association Studies in Pharmacogenomics, CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry

CO4 Study and apply the Aspects Influencing Genotyping CO5 Discuss the applications of Management Of Pharmacogenomic Information



CO1 M S W M S CO2 W M W S CO3 S W M M CO4 W M S M COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I - INTRODUCTION TO BIOSEPARATION 9 Characterization of biomolecules and fermentation broth. Guidelines to recombinant protein purification. UNIT II - SOLID-LIQUID SEPARATION AND CELL DISRUPTION 9 Solid liquid separation- microfiltration and centrifugation – theory and design for scaleup operation. Cell disruption – Homogeniser ,dynomill – principle, factors affecting disruption, batch and continuous operation. Cell disruption by chemical methods. UNIT III - CONCENTRATION AND PURIFICATION 9 Liquid- liquid extraction – theory and practice with emphasis on Aqueous two phase extraction. Solid liquid extraction. Precipitation techniques using salt and solvent. Separation by ultrafiltration, Dialysis, Electrophoresis. UNIT IV – CHROMATOGRAPHY 9 Theory, practice and selection of media for – Gel filtration chromatography, Ion exchange chromatography, Hydrophobic interaction chromatography, reverse phase chromatography, Affinity chromatography – Metal affinity chromatography, dye affinity chromatography, immunosorbent affinity chromatography & Expanded bed chromatography. Scale up criteria for chromatography, calculation of no of theoretical plates and design.

UNIT V FINAL POLISHING AND CASE STUDIES 9 Freeze drying, spray drying and crystallization. Purification of cephalosporin, aspartic acid, Recombinant Streptokinase, Monoclonal antibodies, Tissue plasminogen activator, Taq polymerase, Insulin.

Total Periods: 45 TEXT BOOKS 1. Roger G Harrison et al “Bioseparation Science and Engineering” Oxford University Press, 2003 2. Belter PA and Cussler E, “ Bioseparations ”, Wiley 1985 REFERENCE BOOKS 1. Wankat P.C, “ Rate controlled separations ”, Elsevier, 1990 2. Asenjo J.M., “ Separation processes in Biotechnology ” Marcel Dekker Inc. 1993. MGE013 BIOCONFINEMENT OF GENETICALLY MODIFIED ORGANISMS 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES: CO1 Understand the basics of Association Studies in Pharmacogenomics, CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry CO4 Study and apply the Aspects Influencing Genotyping CO5 Discuss the applications of Management Of Pharmacogenomic Information



CO1 S W S S CO2 W S M M S CO3 M S S CO4 S M W M M W

COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations Unit I - INTRODUCTION TO BIOCONFINEMENT 9 Genetically Engineered Organisms –Bioconfinement - Methods of Bioconfinement, International Aspects - History of Confinement - Social Acceptability of Bioconfinement Methods Unit II - NEED FOR BIOCONFINEMENT 9 Risk factors - Effects on Nontarget Species - Delaying the Evolution of Resistance - Food Safety and Other Issues - Need for Bioconfinement. Unit III - BIOCONFINEMENT OF PLANTS AND ANIMALS 9 Genetically Engineered Trees - Transgenic Grasses - Transgenic Algae-Effectiveness at Different Spatial and Temporal Scales - Monitoring and Managing Confinement Failure -bioconfinement of fish, and insects . Unit IV - BIOCONFINEMENT OF VIRUSES, BACTERIA, AND OTHER MICROBES 9 Introduction - Potential Effects or Concerns, and Need for Bioconfinement in Viruses, Fungi, and Bacteria Unit V - BIOLOGICAL AND OPERATIONAL CONSIDERATIONS FOR BIOCONFINEMENT 9 Execution of Confinement - International Aspects - Bioconfinement - Bioconfinement Research

Total Periods: 45 TEXT BOOK

1. Biological confinement of genetically engineered organisms by national research council :National Academic press.

MGE014 INDUSTRIAL MICROBIOLOGY 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES: CO1 Understand the basics of Association Studies in Pharmacogenomics, CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry CO4 Study and apply the Aspects Influencing Genotyping

CO5 Discuss the applications of Management Of Pharmacogenomic Information



CO1 W S M W S CO2 S M S CO3 M S M S CO4 S W S S M COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I - INTRODUCTION AND HISTORY 9 Definition, scope and roles of microbiology and its relation to other disciplines;-fundamentals and characteristics of the roles of microbes in bioprocess technology; nomenclature and classification of microbes- review of microbes commonly used in bioprocess industries: bacteria, actinomycetes, yeasts, fungi, viruses and algae-history of industrial microbiology- Role of microorganisms in petroleum degradation and bioleaching. UNIT II - MICROORGANISMS OF INDUSTRIAL IMPORTANCE 9 Selection of Microorganisms; Primary and Secondary Screening; Types of stock culture, Strain Improvement Strategies; Strain Identification & Strain Preservation of Industrial

Microorganisms for overproduction of Primary and Secondary metabolites; Medium requirements for fermentation process-carbon, nitrogen, minerals, vitamins and other nutrients-examples of simple and complex media. UNIT III - PRODUCTION OF PRIMARY AND SECONDARY METABOLITES 9 A brief outline of processes for the production of some commercially important Organic acids (citric acid, taconic acid , lactic acid , acetic acid , gluconic acid ) and amino acids (glutamic acid , lysine, aspartic acid, phenylalanine etc.) and Alcohols (ethanol, 2,3,-butanediol etc.) Study of production process for various classes of low molecular weight secondary metabolites: Antibiotics-beta-lactams (Penicillins, Cephalosporins etc.), Aminoglycosides (streptomycin, kanamycin etc.), macrolides (erythromycin), quinines, aromatics etc.; Vitamins and Steroids. UNIT IV - PRODUCTION OF COMMERCIALLY IMPORTANT ENZYMES AND PROTEINS 9 Proteases, Amylases, Lipases, Cellulases, Pectinases, Isomerases and other commercially important enzymes for the food and pharmaceutical industries; Production of recombinant proteins having therapeutic and diagnostic applications; production of vaccines. UNIT V- FERMENTATION 9 Definition of fermentation; fermentor/bioreactor; fermentation media; raw materials – molasses and types, corn steep liquor, sulphite waste liquor and whey. Buffers, precursors, inhibitors, and antifoam agents. inoculum preparation.- Types of Fermentation Processes: Surface, Submerged and Solid state fermentation, Batch and Continuous fermentation.-Down stream processing – Precipitation, filtration, centrifugation, distillation, cell disruption, solvent recovery, drying.

Total Periods: 45 TEXT BOOK 1. Crueger and A. Crueger; Biotechnology: A Textbook of Industrial Microbiology (Eng. Ed. T.

D. Brook). Sinaeur Associates, 1990. 2. L. E. Casida, Jr.; Industrial Microbiology.Wiley Eastern Ltd., 1989. REFERENCE BOOK 1. G. Reed (Ed.); Prescott and Dunn’s Industrial Microbiology (4th Ed.).CBS Publishers, 1987. 2. H. J. Rehm, G. Reed and H. Pape (Eds.) Biotechnology (A Comprehensive Treatise vols. 1-8).

MGE015 TISSUE ENGINEERING AND REGENERATIVE MEDICINE 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES: CO1 Understand the basics of Association Studies in Pharmacogenomics,

CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry CO4 Study and apply the Aspects Influencing Genotyping CO5 Discuss the applications of Management Of Pharmacogenomic Information Co/Po Mapping S – Strong, M – Medium, W – Weak


CO1 M W S M S CO2 W S M S M CO3 M S W W CO4 S M S M COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I - INTRODUCTION 9 Introduction to tissue engineering: Basic definition; current scope of development; use in therapeutics, cells as therapeutic agents, cell numbers and growth rates, measurement of cell characteristics morphology, numberviability, motility and functions. Measurement of tissue characteristics, appearance, cellular component, ECM component, mechanical measurements and physical properties. UNIT II - TISSUE ARCHITECTURE 9 Tissue types and Tissue components, Tissue repair, Basic wound healing events, Applications of growth factors: Role of VEGF. Angiogenesis, Basic properties, Cell-Matrix & Cell-Cell Interactions, Control of cell migration in tissue engineering. UNIT III - BIOMATERIALS 9 Biomaterials: Properties of Biomaterials ,Surface, bulk, mechanical and biological properties. Scaffolds & tissue engineering, Types of Biomaterials, biological and synthetic materials, Biopolymers, Applications of biomaterials, Modifications of Biomaterials, Role of Nanotechnology.

UNIT IV - BASIC BIOLOGY OF STEM CELLS 9 Stem Cells : Introduction, Types & sources of stem cell with characteristics: hematopoietic differentiation pathway, Potency and plasticity of stem cells, sources, embryonic stem cells, hematopoietic and mesenchymal stem cells, Stem Cell markers, FACS analysis, Differentiation, Stem cell systems- Liver, neuronal stem cells, cancer stem cells, induced pleuripotent stem cells. UNIT V CLINICAL APPLICATIONS 9 Stem cell therapy, Moleculartherapy, In vitro organogenesis, Neurodegenrative diseases, spinal cord injury, heart disease, diabetes, burns and skin ulcers, muscular dystrophy, orthopedic applications, Stem cells and Gene therapy, Physiological models tissue engineering therapies ,product characterization, component safety efficacy. Preservation –freezing and drying.

Total Periods: 45 TEXTS/REFERENCES 1. Bernhard O.Palsson,SangeetaN.Bhatia,”Tissue Engineering” Pearson Publishers 2009. 2. Meyer, U.; Meyer, Th.; Handschel, J.; Wiesmann, H.P. .Fundamentals of Tissue Engineering and Regenerative Medicine.2009. 3. Bernard N. Kennedy ((editor). New York : Nova Science Publishers, c2008.Stem cell transplantation, tissue engineering, and cancer applications 4.Raphael Gorodetsky, Richard SchäferCambridge stem cell based repair tissues. MGE016 ADVANCED BIOINFORMATICS 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES : CO1 Understand the basics of Association Studies in Pharmacogenomics, CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry CO4 Study and apply the Aspects Influencing Genotyping CO5 Discuss the applications of Management Of Pharmacogenomic Information Co/Po Mapping S – Strong, M – Medium, W – Weak


CO1 M S S S CO2 M S S W CO3 M S W M CO4 S W W W

COURSE ASSESSMENT METHODS: DIRECT INDIRECT

1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT-I - Motif and cis-Regulatory Module (CRM) Modeling 9 Learning motif models, Learning models of cis-regulatory modules, Gibbs sampling, Dirichlet priors, Parameter tying, Heuristic search, HMM structure search, Sequence Entropy and mutual information, Duration modeling, Semi-Markov models. UNIT-II- Gene Finding 9 The gene finding task, Maximal dependence decomposition, Interpolated Markov models, Back-off models, Pairwise HMMs, Genscan, Twinscan, SLAM. UNIT-III - RNA-Sequencing 9 RNA-Seq technology, transcript quantification with RNA-Seq, specialized RNA databases DBEST, EPD (eukaryotic promoter database)-HGMD(human gene muation database)-g-protein coupled receptor database. UNIT-IV- RNA Analysis 9 Predicting RNA secondary structure, Nussinov/energy-minimization algorithms, Stochastic context free grammars, Inside/Inside-Outside/CYK algorithms, Searching sequences for a given RNA secondary structure, RSEARCH, RNA gene recognition via comparative sequence analysis, microRNA gene/target prediction. UNIT-V - Large-Scale and Whole-Genome Sequence Alignment 9 Large-scale alignment, Whole-genome alignment, Parametric alignment, Suffix trees, Locality sensitive hashing, k-mer tries, Sparse dynamic programming, Longest increasing subsequence problem, Markov random fields, MUMmer, LAGAN/MLAGAN, Mauve, Mercator.

Total Periods: 45 REFERENCE BOOKS:

1. Sequence, Structure and DatabanksA Practical Approach By: Des Higgins (Ed), Willie Taylor (Ed) Edition: 1st edition, October 2000.

2. Developing bioinformatics computer skills By: Cynthia Gibas, Per Jambeck Edition: 1st edition, April 2001 Publisher: O'Reilly & Associates.

3. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition by Andreas D. Baxevanis and B. F. Francis Ouellette (Eds) May 2006; 2nd Edition; Willey&Sons.

http://www.bioinformatics.org/w/index.php?title=Des_Higgins&action=edit&redlink=1

http://www.bioinformatics.org/w/index.php?title=Willie_Taylor&action=edit&redlink=1

http://www.bioinformatics.org/w/index.php?title=Willie_Taylor&action=edit&redlink=1

http://www.bioinformatics.org/w/index.php?title=Cynthia_Gibas&action=edit&redlink=1

http://www.bioinformatics.org/w/index.php?title=Per_Jambeck&action=edit&redlink=1

TEXT BOOKS:

1. Introduction to Computational Genomics: A Case Studies Approach by Nello Cristianini and Matthew W. Hahn, ISBN: 0521671914, Publisher: Cambridge University Press (December 31, 2006).

2. Post-genome Informatics by Minoru Kanehisa,January 2008, Cambridge University. 3. Bioinformatics: From Genomes to Drugs Bioinformatics: Thomas Lengauer, July 25, 2010,

2nd edition Vol 2.John Wiley & Son.

MGE017 MOLECULAR MEDICINE AND MECHANISM 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES : CO1 Understand the basics of Association Studies in Pharmacogenomics, CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry CO4 Study and apply the Aspects Influencing Genotyping CO5 Discuss the applications of Management Of Pharmacogenomic Information



CO1 M W S S W CO2 W S M S M CO3 M S S M CO4 W M S M COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations

UNIT I INTRODUCTION TO MOLECULAR MEDICINE 9 Organization of the Human Genome, Chromosomes and Genes – Recombinant DNA and Genetic Techniques – Transcriptional Control of Gene Expression – transmission of Human Genetic Disease – Human Genome Project – Cell Cycle Oncogenes and Tumor suppressor Genes – Molecular Diagnostic Testing – Genetic Counseling – Transgenic Mice as Models of Disease, Introduction to gene therapy. UNIT II CARDIOLOGY 9 Molecular Cardiology – Congenital Heart Disease – Inherited Cardiomyopathies – Coronary Atherosclerosis – Endothelium – Derived Nitric Oxide and Control of Vascular Tone – Hypertension – Cardiac Arrhythmias – Cardiovascular Gene Therapy. UNIT III PULMONOLOGY 9 Asthma – Cystic Fibrosis – Pulmonary Emphysema – Surfactant Deficiency – Lung Cancer: The Role of Tumor Suppressor Genes – Strategies for controlling the diseases. UNIT IV ENDOCRINOLOGY 9 Mechanisms of Hormone Action – Diabetes Mellitus – Pituitary Function and Neoplasia Growth Hormone Deficiency Disorders – Thyroid Disorders – Disorders of the parathyroid Gland – Congenital Adrenal Hyperplasia – Adrenal Disease – Multiple Endocrine Neoplasia Type 2 – Molecular Mechanisms of Hypoglycemia Associated with increased Insulin Production. UNIT V NEPHROLOGY 9 Renal Development – Mechanisms of Leukocyte Extravasation – Ischemic Acute Renal Failure – Potassium Secretory Channels in the Kidney – Alport Syndrome – Nephrogenic Diabetes Insipidus – Polycystic Kidney Disease – Renal Neoplasms: Wilms’ Tumor and Renal-Cell Carcinoma.

Total Periods: 45 TEXTS/REFERENCES 1. Jameson, J.L., Francis, S.C., “Principles of Molecular Medicine”, Humand Press, 1998. 2. Ross, D.W. “Introduction to Molecular Medicine”, 3rd Edition, Springer, 2002. 3. Ross, D.W. “Introduction to Oncogenes and Molecular Medicine”,Springer, 1998. 4. Pasternak, J.J. “An Introduction to Human Molecular Genetics”, 2nd Edition, Wiley Liss,

2005 5. Strachan, Tom and Andrew P. Read. “Human Molecular Genetics, Bios, 1996.

MGE018 PROTEIN ENGINEERING AND INDUSTRIAL APPLICATIONS 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES: CO1 Understand the basics of Association Studies in Pharmacogenomics, CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry CO4 Study and apply the Aspects Influencing Genotyping CO5 Discuss the applications of Management Of Pharmacogenomic Information



CO1 M S W S M CO2 W S M M M CO3 W M S W CO4 M S W S M COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I INTRODUCTION 9 Amino acids, primary structure of proteins, amino acid composition, industrial significance, primary structure determination by chemical methods including automated sequencing and by gene sequencing, significance of primary structure determination, peptide synthesis, secondary structure and super secondary structures UNIT II PROTEIN ARCHITECTURE 9 Tertiary structure of proteins, types of proteins, domains, quaternary structure, protein complexes, protein-protein interactions

UNIT III STRUCTURE-FUNCTION RELATIONSHIP 9 DNA-binding proteins: prokaryotic transcription factors, Helix-turn-Helix motif in DNA binding, Trp repressor, Eucaryotic transcription factors, Zn fingers, helix-turn helix motifs in homeodomain, Leucine zippers, Membrane proteins: General characteristics, Transmembrane segments, prediction, bacteriorhodopsin and Photosynthetic reaction center, Immunoglobulins: IgG Light chain and heavy chain architecture, abzymes and Enzymes: Serine proteases, understanding catalytic design by engineering trypsin, chymotrypsin and elastase, substrate assisted catalysis other commercial applications. UNIT IV PROTEIN ENGINEERING METHODS 9 Protein engineering methods, amino acid side chain reactions, chemical modification of proteins, site-directed mutagenesis, posttranslational modifications and engineering UNIT V INDUSTRIAL APPLICATIONS OF PROTEIN ENGINEERING 9 Examples of industrial protein engineering applications Engineering of serine proteases, engineering of antibodies, engineering of proteins for thermal stability, engineering of proteins for preventing aggregation, His-tagged proteins in purification, engineering proteins for secretion, de novo protein synthesis.

Total Periods: 45 TEXT BOOKS 1. Voet, D. and Voet, G., “Biochemistry”. 3rd Edition, John Wiley and Sons, 2001. 2. Branden C. and Tooze J., “Introduction to Protein Structure”, 2nd Edition, Garland Publishing,

1999. 3. Creighton, T.E. “Proteins : Structure and Molecular Properties”, 2nd Edition, W.H. Freeman,

1993. REFERENCES 1. Whitford, David “Proteins : Structure and Function”. John Wiley & Sons, 2005. 2. Holland, I Barry et al., “ABC Proteins : From Bacteria to Man”. Academic Press

Elsevier,2003. 3. Alberghina, L. “Protein Engineering in Industrial Biotechnology”. Harwood Academic

Publications, 2000. 4. Moody P.C.E. and Wilkinson A.J. “Protein Engineering”. IRL Press, Oxford, 1990. 5. Rees, A.R., Sternberg, M.J.E. and Wetzel, R. “Protein Engineering: A PracticalApproach”. IRL

Press, 1992 MGE019 METABOLIC PROCESS AND ENGINEERING 3 0 0 3 OBJECTIVES: 1. To understand the basics of Pharmacogenomics: Historical perspectives COURSE OUTCOMES :

CO1 Understand the basics of Association Studies in Pharmacogenomics, CO2 Apply the knowledge to Transfection Assays With Allele-Specific Constructs CO3 Learn and apply the Estimation, MALDI–TOF Mass Spectrometry CO4 Study and apply the Aspects Influencing Genotyping CO5 Discuss the applications of Management Of Pharmacogenomic Information.

Co/Po Mapping



CO1 M S W M M M CO2 W S M M CO3 W S W S CO4 S W S M COURSE ASSESSMENT METHODS:

DIRECT INDIRECT 1 Internal Tests 1 Course and Survey 2 Assignments 2 Faculty Survey 3 Seminar 3 Industry 4 Online test 4 Alumni 5 Quiz 6 End Semester Examinations UNIT I METABOLIC FLUX ANALYSIS 9 Introduction to metabolic engineering, comprehensive models of cellular reactions with stoichiometry and reaction rates; metabolic flux analysis of exactly/over/under determined systems. Shadow price, sensitivity analysis. UNIT II TOOLS FOR EXPERIMENTALLY DETERMINING FLUX THROUGH PATHWAYS 9 Monitoring and measuring the metabolome, Methods for the experimental determination of metabolic fluxes by isotope labeling metabolic fluxes using various separation-analytical techniques. GC-MS for metabolic flux analysis, genome wide technologies: DNA /phenotypic microarrays and proteomics. UNIT III CONSTRAINT BASED GENOMIC SCALE METABOLIC MODEL 9 Development of Genomic scale metabolic model, Insilico Cells: studying genotype-phenotype relationships using constraint-based models, case studies in E. coli, S.cerevisiae metabolic network reconstruction methods, optimization of metabolic network, Identification of targets for metabolic engineering; software and databases for genome scale modeling UNIT IV METABOLIC CONTROL ANALYSIS AND KINETIC MODELING 9 Fundamental of Metabolic Control Analysis, control coefficients and the summation theorems,

Determination of flux control coefficients. Multi-substrate enzyme kinetics, engineering multifunctional enzyme systems for optimal conversion, and a multi scale approach for the predictive modelling of metabolic regulation. UNIT V CASE STUDIES IN METABOLIC ENGINEERING 9 Metabolic engineering examples for bio-fuel, bio-plastic and green chemical synthesis. Study of genome scale model in various systems for the production of green chemicals using software tools. Validation of the model with experimental parameters.

Total Periods: 45 TEXT BOOKS 1. Stephanopoulos, G.N. “Metabolic Engineering: Principles and Methodologies”. Academic

Press / Elsevier, 1998. 2. Lee, S.Y. and Papoutsakis, E.T. “Metabolic Engineering”. Marcel Dekker, 1998. 3. Nielsen, J. and Villadsen, J. “Bioreaction Engineering Principles”. Springer, 2007. 4. Smolke, Christiana D., “The Metabolic Pathway Engineering Handbook Fundamentals”, CRC

Press Taylor & Francis, 2010. REFERENCES 1. Voit, E.O. “Computational Analysis of Biochemical Systems : A Practical Guide for

Biochemists and Molecular Biologists”. Cambridge University Press, 2000. 2. Scheper, T. “Metabolic Engineering” Vol 73 (Advances in Biochemical Engineering

Biotechnology) Springer, 2001. 3. Cortassa, S. et al, “ An Introduction to Metabolic and Cellular Engineering”, World Scientific

Publishing, 2002. 4. Kholodenko, Boris N and H. V. Westerhoff “Metabolic Engineering in the Post Genomic Era”,

Horizon Bioscience, 2004.

Documents

REGULATIONS 2015 B.TECH GENETIC ENGINEERING … · B.TECH GENETIC ENGINEERING . CURRICULUM - SYLLABUS . SEMESTER – I . S.NO Code Course L T P C THEORY. 1 MGE101 Molecular Genetics