SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

PROGRAMME : M. TECHSYSTEMS BIOLOGY

CURRICULUMSEMESTER - 1

Sl. No. COURSE CODE COURSE TITLE L T P C PAGE No.

1. SMT5103 Applied Mathematics 3 1 0 4 1

2. SBI5108 Introduction to Systems biology 3 1 0 4 11

3. SBI5109 Metabolic pathways 3 1 0 4 12

4. SBI5110 Proteomics 3 1 0 4 13

5. SBI5111 Transcriptomics 3 1 0 4 14

6. SBI5112 Metagenomics 3 1 0 4 15

PRACTICAL

7. SBI6533 System Biology lab 0 0 6 3 65

TOTAL CREDITS: 27

SEMESTER - 2

Sl. No. COURSE CODE COURSE TITLE L T P C PAGE No.

1. SBI5113 Introduction to Mathematical Biology 3 1 0 4 16

2. SBI5114 Translatomics 3 1 0 4 17

3. Elective I 3 1 0 4

4. Elective II 3 1 0 4

5. Elective III 3 1 0 4

6. S61PT Professional Training 0 0 10 5

PRACTICAL

7. SBI6534 Mat Lab 0 0 6 3 65

TOTAL CREDITS: 28

SEMESTER - 3

Sl. No. COURSE CODE COURSE TITLE L T P C PAGE No.

1. SBI5202 Next Generation Sequencing 3 1 0 4 19

2. Elective IV 3 1 0 4

3. Elective V 3 1 0 4

4. Elective VI 3 1 0 4

5. Project Work - Phase I

L - LECTURE HOURS, T – TUTORIAL HOURS, P – PRACTICAL HOURS, C – CREDITS

M.E. / M.Tech REGULAR xiii REGULATIONS 2015

SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

PRACTICAL

6. SBI6536 Statistics Using R Package Lab 0 0 6 3 67

TOTAL CREDITS: 19

SEMESTER - 4

Sl. No. COURSE CODE COURSE TITLE L T P C PAGE No.

7. S61PROJ Project Work – Phase I and II 0 0 40 20

TOTAL CREDITS: 20

TOTAL CREDITS FOR THE COURSE: 94

LIST OF ELECTIVES

Sl. No. COURSE CODE COURSE TITLE L T P C PAGE No.

1. SBT5107 Cell Biology and Molecular Genetics 3 1 0 4 33

2. SBI5601 Structural and functional Genomics 3 1 0 4 78

3. SBI5602 Microarrays- Techniques and Applications 3 1 0 4 79

4. SBI5603 Data Mining in Bioinformatics 3 1 0 4 80

5. SBI5605 Machine Learning for Bioinformatics 3 1 0 4 82

6. SBI5610 Computational Chemistry 3 1 0 4 87

7. SBI5611 Immunoinformatics and Computational Vaccinology 3 1 0 4 88

8. SBI5613 Phenomics 3 1 0 4 90

9. SBI5614 Gene variation and Diseases 3 1 0 4 91

10. SBI5615 Metabolomics 3 1 0 4 92

11. SBT 5606 Stem cell research 3 1 0 4 112

12. SBT5610 Bioethics, Biosafety and IPR 3 1 0 4 116

M.E. / M.Tech REGULAR xiv REGULATIONS 2015

SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 1 REGULATIONS 2015

SMT5103 APPLIED MATHEMATICS

(Common to M.Tech Bio-Technology & Bio-Informatics)

L T P Credits Total Marks

3 1 0 4 100

UNIT 1 MATRIX THEORY 11 Hrs. QR decomposition – Eigen values using shifted QR algorithm - Singular Value Decomposition - Pseudo inverse- Least square approximations.

UNIT 2 CALCULUS OF VARIATIONS 13 Hrs. Concept of Functionals - Euler’s equation – functional dependent on first and higher order derivatives – Functionals on several dependent variables – Iso perimetric problems - Variational problems with moving boundaries

UNIT 3 MULTIVARIATE ANALYSIS 13 Hrs. Multiple Regression Analysis - Principal Component Analysis – Canonical Correlation Analysis – Factor Analysis – Discriminant Analysis – Cluster Analysis (No Derivations)

UNIT 4 NUMERICAL METHODS – I 11 Hrs. Numerical solution of Ordinary Differential equation – Euler’s method – Modified Euler’s method - Runge - Kutta Method of fourth order- Runge - Kutta method of simultaneous first order differential equation- Runge - Kutta method of second order differential equation-Milne’s Predictor Corrector method- Adam-Bashforth predictor - corrrector method

UNIT 5 NUMERICAL METHODS – II 12 Hrs. Numerical solution of Partial Differential Equations- Classification- Elliptic equations-Solution of Laplace equation by Liebmann’s Iteration process- Poisson equation- Parabolic equation - Bender Schmidt Method- crank Nicholson Difference Method- Solution for Hyperbolic equation

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Narayanan S., Manicavachagom Pillay T.K., Ramanaiah G., Advanced Mathematics for Engineering students, Volume I, 2nd

Edition, S.Viswanathan Printers and Publishers, 1992. 2. Venkataraman M.K., Engineering Mathematics – First Year, 2nd Edition, National Publishing Company, Chennai, 2000. 3. Kreyszig.E, Advanced Engineering Mathematics, 8th Edition, John Wiley & Sons, Singapore, 2001. 4. Jain M.K., Iyengar SRK and Jain R.L., Numerical Methods for Scientific and Engineering Computation, Wiley Eastern Ltd.,

1987 5. Balagurusamy E., Numerical Methods – Tata McGraw Hill, 2000 6. Veerarajan T., Engineering Mathematics for First Year, 2nd Edition, Tata McGrawHill Publishers, 2008. 7. Dr. Kandasamy P. Numerical Methods, S.Chand & Company, New Delhi, 2003.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 11 REGULATIONS 2015

SBI5108 INTRODUCTION TO SYSTEMS BIOLOGY L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to reconstruct the integrated cellular networks of biological systems using computational

techniques for understanding the nature of a disorder in malfunction. Students are enabled to visualise a biological entity as an integrated aspect of a specific system.

UNIT 1 GENERAL INTRODUCTION 12 Hrs. Introductory Concepts – Various definitions of system biology, top-down and bottom-up approaches Modeling in biology – Properties of models – Cell cycle modeling,Transcription networks : Basic Concepts – The Cognitive problem of the cell – Elements of transcription networks – Dynamics and response time in simple gene regulation – The human interactome – On mathematical modeling of biological phenomena

UNIT 2 REGULATION 12 Hrs. Patterns, Randomized networks and Network motifs – Autoregulation – Negative and positive autoregulation - Feed forward loop network motif – Structure and dynamics – Convergent evolution of FFLs - Temporal Expression programs - Global structure of transcription networks

UNIT 3 SYSTEMS BIOLOGY OF DEVELOPMENT, SIGNAL TRANSDUCTION & NEURONS 12 Hrs. Developmental transcription networks – Positive feedback, Regulaged feedback, Long transcription cascades and developmental timing – Robust patterning in development - Network motifs in Signal transduction networks – Information processing using multi layered perceptron – Composite Network motifs – Neuronal network of C. elegans.

UNIT 4 PROTEIN AND GENE CIRCUITS 12 Hrs. Robustness principle in protein circuits –Bacterial chemotaxis – Chemotaxis protein circuit of E. Coli - Models explaining exact adaptation – Fine tuned and Barkai – Leibler model – Robust adaptation and integral feedback – Individuality and robustness in bacterial chemotaxis – Optimal expression level of a protein under constant conditions – Optimal regulation in variable environments – Synthetic gene regulatory systems and gene circuits.

UNIT 5 KINETICS AND GENE REGULATION 12 Hrs. Kinetic proof reading of the genetic code – Recognition of self and non – self by the immune system – Proof reading of diverse recognition processes in the cell – Demand rules for gene regulation. Structure of microbial genetic unit– Savageau demand rule – Rules based on minimal error load– Demand rules for multi regulator systems - Simplicity in biology.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. An introduction to systems biology. Design Principles of biological circuits. Chapman and Hall CRC. Uri Alon. 2007 2. Eberhard Voit, A First Course in Systems Biology , 2012. 3. Marian Walhout , Marc Vidal, Job Dekker Handbook of Systems Biology: Concepts and Insights, 2012.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 12 REGULATIONS 2015

SBI5109 METABOLIC PATHWAYS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE The study of this paper will help the student in having a good understanding of the pathways of different reactions

in a metabolic pathway.

UNIT 1 BIOENERGETICS AND BIOLOGICAL OXIDATION 12 Hrs. The living cell: a unique chemical system, introduction to metabolism, methods of studying metabolism, transport mechanism, bioenergetics, Free energy and entropy. Phosphoryl group transfers and ATP. Enzymes involved in redox reactions. The electron transport chain - organization and role in electron capture.Oxidative phosphorylation - Electron transfer reactions in mitochondria. F1F0 ATPase - Structure and mechanism of action. The chemiosmotic theory , Inhibitors of respiratory chain and oxidative phosphorylation - Uncouplers and ionophores. Regulation of oxidative phosphorylation

UNIT 2 CARBOHYDRATEMETABOLISM 12 Hrs. Glycolysis and gluconeogenesis - Pathway, key enzymes and coordinate regulation. The citric acid cycle and regulation.The pentose phosphate pathway.Metabolism of glycogen and regulation.Metabolism of galactose and fructose.The glyoxylate cycle.Cori cycle. Futile cycles, anaplerotic reactions.Hormonalregulation of carbohydrate metabolism, Energetics of metabolic cycle

UNIT 3 LIPID METABOLISM 12 Hrs. Introduction, hydrolysis of triacylglycerols and oxidation of fatty acids, Oxidation of odd numbered fatty acids, fate of propionate, role of carnitine, degradation of complex lipids. Fatty acid biosynthesis (acetyl CoA carboxylase, fatty acid synthase), Lipidbiosynthetic pathway for triacylglycerols, phosphoglycerides and sphingomyelin, Prostaglandins. Metabolism of cholesterol and its regulation, Formation of ketone bodies, Hormone regulating lipid metabolism.

UNIT 4 AMINO ACID METABOLISM 12 Hrs. Amino Acids – Metabolism of amino acid (Transamination, decarboxylation, oxidative andnon:oxidative deamination of amino acids). Special metabolism of methionine, histidine, phenylalanine, tryptophan, lysine, valine, leucine and isoleucine, Urea cycle and its regulation.

UNIT 5 PURINE AND PYRIMIDINE METABOLISM 12 Hrs. Nucleotides – Biosynthesis and degradation of purine and pyrimidine nucleotides and its regulation. Denovo pathway,Purine salvage pathway, inter conversion of nucleotides.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. J. G. Salway, Metabolism at a Glance, Paperback 2004. 2. Principles of Biochemistry, A.L. Lehninger, Vth, W.H. Freeman & Company,2008 3 Stryer, Biochemistry , Vth, W. H. Freeman,2002. 4. D. Voet, J and G Voet, Biochemistry, Wiley,2001 5. Harper, Biochemistry , 28th, McGraw-Hill Medical,2009. 6. David Rawn, Biochemistry, IV, Wiley, 2014 7. Zubay and Zubay, Biochemistry III, William C Brown Pub,1995.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 13 REGULATIONS 2015

SBI5110 PROTEOMICS L T P Credits Total Marks 3 1 0 4 100

COURSE OBJECTIVE Students gain knowledge to explore and perform global analysis of proteome data from various species.

UNIT 1 INTRODUCTION 12 Hrs. Definition of Proteomics - The Proteome and the Genome - The Life and Death of a Protein - Proteins as Modular Structures - Functional Protein Families - Deducing the Proteome from the Genome - Gene Expression, Codon Bias, and Protein Levels.

UNIT 2 ANALYTICAL PROTEOMICS 12 Hrs. Protein sample preparation, Separation of macromolecules and organelles in cells by ultra-centrifugation - Analysis techniques both in situ and in isolation such as spectroscopy, chromatography and electrophoresis, Separation techniques – 2-D gel and polyacrylamide gel electrophoresis (PAGE). Image analysis tools.

UNIT 3 PROTEIN IDENTIFICATION AND DIGESTION 12 Hrs. Protein identification – mass determination and Edman degradation,Determination of 3-D structures by x-ray crystallography and NMR,Data handling with Bioinformatics tools for storing, archiving and retrieving. Protein Digestion - Overview of Proteases - Nonspecific Proteases.

UNIT 4 MINING PROTEOMES 12 Hrs. Mining Proteomes- Selecting Proteomes for analysis - Mining Approach 2D-SDS-PAGE and MALDI-TOF MS- Mining Approach Multidimensional Peptide Chromatography and LC-Tandem MS Analysis. Electron spray ionization (ESI) Protein Expression Profiling - Comparative Proteomics with 2D Gels - Comparative Proteomics with LC-MS and Isotope Tags. Identifying Protein–Protein Interactions and Protein Complexes. Database available for identification of mass spectrometry data. Programs uised to identify mass spectra (PeptIdent, MultiIdent, Profound, Pepsea, Mascot, Ms-fit,Mowse, Sequest, Pepfrag, MS-tag, Serpa).

UNIT 5 TOOLS AND APPLICATIONS 12 Hrs. Tools of Proteomics - MS/MS Fragment Ion Calculator, Peppy, Expecter,Phenyx, Maxquant, OMSA,Protein Digestor ,DNA Translator ,Composition Calculator, Protein Arrays ,Applications of Proteomics.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. A. Malcolm Campbell & Laurie J. Heye, Genomics, Proteomics and Bioinformatics., .CSHL Press and Benjamin Cummings.

ISBN 0-8053-4722-4, 2003 2. Daniel C. Liebler, Introduction to Proteomics, Humana Press.ISBN 0-8960-3992-7, 2002 3. R.M. Twyman, Principles of Proteomics, Garland Scientific/BIOS Scientific Publishers.ISBN 1-8599-6273-4, 2004. 5. Timothy Palzkil, Kluwer, Proteomics. Academic. ISBN 0-7923-7565-3, 2001 6. P. Jolles and H, Jornvall, Proteomics in Functional Genomics – Protein Structure Analysis, Birkhauser. ISBN 3-7643-5885-8,

2000 7. Reiner Westermeier and Tom Naven, Proteomics in Practice – A Lab Manual of Proteome Analysis.. Wiley-VCH Verlag.

ISBN 3-527-30354-5, 2002

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 14 REGULATIONS 2015

SBI5111 TRANSCRIPTOMICS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students gain knowledge in the expression of mRNA molecule of a particular individual in a given time

UNIT 1 INTRODUCTION TO TRANSCRIPTOMICS 12 Hrs. Introduction to omes and omics, Definition of transcriptome, Transcriptomics resources: Bgee, smirnaDB, CLIPZ,, EIMMo. analysis of transcriptome – techniques used in Transcriptomics like DNA microarray. cDNA, mRNA, SiRNA, MiRNA – function, regulation and Application. Examples of basic research in transcriptomics.

UNIT 2 TECHNIQUES USED IN TRANSCRIPTOMICS 12 Hrs. Characterizing a transcriptome: de novo transcriptome sequencing, pyrosequencing, RNA-seq, Affymetrix, SAGE, Chip-Seq, sequencing vs. microarrays, clustering and other analysis, differential expression analysis, data flood, co-expression, expression dynamics, alternative splicing, transcription regulatory networks.

UNIT 3 GENE EXPRESSION, MICROARRAYS 12 Hrs. Transcriptomics- importance of transcription, tools and techniques in transcriptomics, microarray technology, sequencing based approaches to study transcriptomes, applications of new generation transcriptome sequencing, gene expression profiling, non coding RNA discovery and detection.

UNIT 4 TOOLS AND SOFTWARES USED FOR TRANSCRIPTOMICS 12 Hrs. Genome sequencing projects- technology of sequencing and assembly- role of bioinformatics in genome annotation- current status of genome sequencing projects- Genomic browsers and databases- Orthology prediction- Search for transcription factor binding sites - Computational prediction of miRNA target genes- De novo prediction of regulatory motifs in genome- Single nucleotide polymorphisms (SNP) in medical genetics. Transcriptomics tools( Expression profiler, DNA arrays, GEPAS, VAMPIRE, MIDAW).

UNIT 5 APPLICATION OF TRANSCRIPTOMICS 12 Hrs. Experimental techniques: microarrays, EST, SAGE. Microarray data: normalization and analysis. Genevestigator and OncoMine - browsing microarray-derived gene expression profiles, tissue and stage-of-development-specific patterns of expression, coexpression of genes, pre-computed lists of differentially expressed genes. Application of transcriptomics in disease identification. Standalone analysis of publicly available microarray expression data: GEO database, ArrayExpress, TAIR, MIAME. TM4 analysis suite.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Richard A.Goldsby, Thomas. J.Kindt, Barbara. A.Osborne, JanisKuby, Immunology, 5thEdition, W.H.Freeman and Company,

2003. 2. Peter J. Delves, Seamus J. Martin, Dennis R. Burton, Ivan Roitt, Essential Immunology, Blackwell Scientific Publication,

2000. 3. William E.Paul, Fundamentals of Immunology, 5thEdition, Lipincott Williams & Wilkins, Philadelphia, 2003. 4. Roderick Nairn, Mathew Helbert, Immunology for Medical students, 1stEdition, American Society for Microbiology Press,

WashingtonD.C., 2002. 5. James.R.Minor, Brain D.Fontaine, Concepts in Immunology and immunotherapeutics, 3rdEdition, American Society of Health

system,Pharmacists, Noida, 2003. 6. Weir. D. M and Steward. J Immunology.7thEdition W.B.Saunders Company, 1998.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 15 REGULATIONS 2015

SBI5112 METAGENOMICS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to explore the application of high throughput techniques of genomics to understand the

substantial advances in microbial ecology, evolution, and diversity.

UNIT 1 INTRODUCTION 12 Hrs. Why Metagenomics - Definition –tools, comparison and various applications. What can microbes do - Invisible communities - Global impact - Understanding microbial communities - Why Genomics is not enough - Metagenomics and its applications in various fields - Revisiting the concepts of genome, species, diversity - Microbes - Work, reaction, evolution.

UNIT 2 GENOMICS TO METAGENOMICS 12 Hrs. Sequencing - Pioneering project - Acid Mine Drainage Project - The Sargasso Sea Metagenomic Survey and Community profiling - The Human Microbiome Project - Viral Metagenomics

UNIT 3 DESIGNING A METAGENOMICS PROJECT 12 Hrs. Parallels with microbial genome sequencing - Metagenomics - Step by step - Habitat Strategy, Sampling strategy, Macromolecule recovery - Getting the most out of metagenomics studies - 16S rRNA based surveys, 16S rRNA Phylogenetic and functional anchors - Generation of large scale DNA sequence, assembling whole genomes, Gene centric analyses

UNIT 4 DATA MANAGEMENT AND BIOINFORMATICS CHALLENGES 12 Hrs. Genomic data - Metagenomic data - The importance of metadata - Databases for metagenomic data - software - analysis of metagenomic sequence data - Major stakeholders, education and training. Metagenomics data analysis and applications

UNIT 5 GLOBAL METAGENOMICS INITIATIVE 12 Hrs. The vision - Characteristics of large scale projects - Big Science component - Expected benefits - Theory and principles - Learning from previous Large scale projects - The Human genome project, The Arabidopsis Genome Project - Lessons for Metagenomics. Earth microbiome project, Global ocean surver metagenomics (Indian ocean and French Polynesia). Global ocean sampling expedition.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Streit, Wolfgang, Daniel, Rolf, Metagenomics, Methods and Protocols, springer protocols, 2010 2. Casas V, and Rohwer F ,Phage metagenomics. In Hughes,KT and Maloy, SR (eds.) Methods in Enzymology 421: Advanced

bacterial genetics: use of transposons and phage for genomic engineering ,Amsterdam: Elsevier, 2007. 3. Gillespie DE, Rondon MR, Williamson LL, and Handelsman J,Metagenomic libraries from uncultured microorganisms. In:

Osborn AM and Smith CJ (eds.) Molecular microbial ecology, Taylor and Francis. 2005 4. http://www.nap.edu/openbook.php?record_id=11902

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 65 REGULATIONS 2015

10. DNA / RNA Secondary Structure Evolution i) MFold ii) PlotFold

11. e-PCR, Gene Ontology 12. Sequence Submission in repository

MOLECULAR MODELING LAB 1. Construction of molecules 2. Secondary structure prediction 3. Molecular visualization – JMOL, VMD 4. Homology modelling – Insight II, Modeller 5. Docking- Autodock, Discovery Studio, Schrodinger 6. Molecular dynamics - AMBER 7. QSAR

SBI6533 SYSTEMS BIOLOGY LAB L T P C Total Marks 0 0 6 3 100

1. Modeling and Visualization 2. E cell 3. Gepasi 4. Copasi 5. Construction and Analysis of gene expression networks 6. Mat lab I 7. Mat Lab II 8. CellDesigner 9. Cytoscape

SBI6534 MAT LAB L T P C Total Marks 0 0 6 3 100

HIGH-THROUGHPUT SCREENING 1. Exploring Genome-wide Differences in DNA Methylation Profiles. 2. Identifying Differentially Expressed Genes from RNA-Seq Data. 3. Exploring Protein-DNA Binding Sites from Paired-End ChIP-Seq Data. 4. Visualize and integrate Short -read alignments.

SEQUENCE ANALYSIS 1. Calculating and Visualizing Sequence Statistics. 2. Aligning Pairs of Sequences. 3. Working with Whole Genome Data. 4. Comparing Whole Genomes. 5. Assessing the Significance of an Alignment. 6. Using Scoring Matrices to Measure Evolutionary Distance. 7. Nucleotide sequence analysis. 8. Protein and amino acid sequence analysis.

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 16 REGULATIONS 2015

SBI5113 INTRODUCTION TO MATHEMATICAL

BIOLOGY L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE The student will be exposed to build a mathematical concept for a biological phenomena occurring in a cell.

UNIT 1 I INTRODUCTION AND CALCULUS 12 Hrs. Mathematics as a language - Need of learning mathematics - Applications of mathematics in Biology - Graphs and functions - Linear function, Quadratic function, Exponential function - Periodic functions, Combination of simple functions, Examples from Biology - Differentiation and its application in Biology - Product rule in differentiation, Derivatives of Sine and Cosine functions, Plotting derivatives, Differential calculus to understand actin polymerization - Growth curve - Force and energy, DNA unzipping, Plotting mathematical functions

UNIT 2 DIFFERENTIAL EQUATIONS 12 Hrs. Simple differential equations, First order differential equations, Examples: Polymerizing and depolymerizing filaments, Cell growth - Concentration gradient, Second order differential equations. Motion of an object under external force : Newton’s equations

UNIT 3 APPLICATIONS OF CALCULUS AND VECTOR ALGEBRA IN BIOLOGY 12 Hrs. Nernst equation - Potential difference across a membrane, Flow of ions due to diffusion, Flow of ions due to electrostatic interactions - Diffusion equation - Continuity equation, Diffusion equation, Mean-square position - Einstein’s relation - Mean displacement, Diffusion coefficient, Einstein's relation, Diffusion under external field

UNIT 4 PROBABILITY AND STATISTICS , FOURIER SERIES AND FOURIER TRANSFORM 12 Hrs. Introduction to distribution functions, Normal distribution, Examples from biology: End-to-end vector distribution of DNA, Concentration distribution - Fourier Series - Introduction to Fourier series, Fourier coefficients, Calculation of Fourier series for simple functions, Sum of periodic functions - Master equation: Polymerization dynamics, Molecular motor motion - Simple model for polymerization depolymerization dynamics, Simple model for molecular motor

UNIT 5 STATISTICAL THERMODYNAMICS OF BIOLOGICAL SYSTEMS 12 Hrs. Temperature, Energy and Entropy - Definition of temperature, Definition of internal energy, Definition of entropy, Calculation of entropy, entropy of a flexible protein - Partition function, Free energy - Definitions, Calculation of partition function, Calculation of Free energy, Thermal Equilibrium, Bending of DNA - Force-extension and looping of DNA- Force extension relation of single stranded DNA, Persistence length, Looping of DNA - Thermodynamics of protein organization along DNA - Proteins binding on DNA, Calculation of energy, entropy and free energy, Thought-experiment on DNA melting

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. M. Aitken, B. Broadhursts, S. Haldky, Mathematics for Biological Scientists, Garland Science, 2009 2. E. Batschelet, Springer Verlag, Introduction to Mathematics for Life Scientists, 3rd edition, 2003 3. R. De Sapio, W. H. Freeman, Calculus for Life Sciences, 1976 4. R Phillips, J Kondev, J. Theriot, Physical Biology of the Cell, Garland Science, 2009 5. H. C. Berg, Random Walks in Biology, Princeton university press, 1993

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 17 REGULATIONS 2015

SBI5114 TRANSLATOMICS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to identify the controlled measure to determine the rate of synthesis of mRNAs in proteins,

in regulating biological processes.

UNIT 1 INTRODUCTION TO COMPONENTS 12 Hrs. Analysing the components of living organisms. Translatiomics in cellular levels (RNA Splicing with Factors and Diseases occurring due to imbalance in PTM). Post-translational modifications and their biological functions. Basic correlation between Genotype to Phenotype.Basics of linear and non linear Principles in Machine Learning.

UNIT 2 INVITRO METHODS IN TRANSLATOMICS 12 Hrs. Tandem affinity purification-mass spectroscopy − Affinity chromatography−Co immunoprecipitation−Protein microarrays (H) −Protein-fragment complementation −Phage display−X-ray crystallography−NMR spectroscopy.

UNIT 3 INVIVO METHODS IN TRANSLATOMICS 12 Hrs. Yeast twp hybrid-screening a protein of interest against a random library of potential protein partners. Differential translation in genome wide studies Synthetic lethality-based on functional interactions rather than physical interaction.

UNIT 4 INSILICO METHODS IN TRANSLATOMICS 12 Hrs. Ortholog-based sequence approach−Domain-pairs-based sequence approach−Structure-based approaches−Gene neighborhood−Gene fusion−In silico 2 hybrid−Phylogenetic profile.

UNIT 5 CASE STUDIES IN TRNASLATOMICS 12 Hrs. Plastid Translatomics of Tomato−Chloroplast-to-Chromoplast Differentiation−The Translational Apparatus of Plastids and Its Role in Plant Development. Mitochondrial translatomics, Translatomics post-translational modifications. Future-translatomics & Translatomics in other cell organells. Translatomics of cancer. Translatomics and immune response.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Ahlert D., Ruf S., Bock R, Plastid protein synthesis is required for plant development in tobacco. Proc. Natl Acad. Sci. U S A.

100, 15730–15735, 2003 2. Zhang, Protein Interaction Networks-Computational Analysis, Cambridge University Press, New York, NY, USA, 2009. 3. C. Von Mering, R. Krause, B. Snel et al., Comparative assessment of large-scale data sets of protein-protein interactions,

Nature, vol. 417, no. 6887, pp. 399–403, 2002.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 65 REGULATIONS 2015

10. DNA / RNA Secondary Structure Evolution i) MFold ii) PlotFold

11. e-PCR, Gene Ontology 12. Sequence Submission in repository

MOLECULAR MODELING LAB 1. Construction of molecules 2. Secondary structure prediction 3. Molecular visualization – JMOL, VMD 4. Homology modelling – Insight II, Modeller 5. Docking- Autodock, Discovery Studio, Schrodinger 6. Molecular dynamics - AMBER 7. QSAR

SBI6533 SYSTEMS BIOLOGY LAB L T P C Total Marks 0 0 6 3 100

1. Modeling and Visualization 2. E cell 3. Gepasi 4. Copasi 5. Construction and Analysis of gene expression networks 6. Mat lab I 7. Mat Lab II 8. CellDesigner 9. Cytoscape

SBI6534 MAT LAB L T P C Total Marks 0 0 6 3 100

HIGH-THROUGHPUT SCREENING 1. Exploring Genome-wide Differences in DNA Methylation Profiles. 2. Identifying Differentially Expressed Genes from RNA-Seq Data. 3. Exploring Protein-DNA Binding Sites from Paired-End ChIP-Seq Data. 4. Visualize and integrate Short -read alignments.

SEQUENCE ANALYSIS 1. Calculating and Visualizing Sequence Statistics. 2. Aligning Pairs of Sequences. 3. Working with Whole Genome Data. 4. Comparing Whole Genomes. 5. Assessing the Significance of an Alignment. 6. Using Scoring Matrices to Measure Evolutionary Distance. 7. Nucleotide sequence analysis. 8. Protein and amino acid sequence analysis.

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 19 REGULATIONS 2015

SBI5202 NEXT GENERATION SEQUENCING L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE The student is given the exposure to the development of informatics tools able to assemble, map, and interpret

huge quantities of relatively or extremely short nucleotide sequence

UNIT 1 INTRODUCTION 12 Hrs. NGS - Platform overview - Biological applications - Basic concepts - Recent scientific breakthroughs using NGS technology – Data processing - Analysis workflow - Sequence quality evaluation - Alignment theories - Data formats - Data visualization - DNA sequencing - genetic variations - NGS and genetics of complex disease (etiology) - NGS and personal genome sequencing

UNIT 2 DNA SEQUENCING 12 Hrs. Experimental considerations - Whole genome sequencing - Target sequencing - Pool sequencing - Sequencing mappability - Refined alignment - Base quality recalibration - Variants identification for Diploid genome, Pooled DNA sequencing, Cancer genome - Variation recalibration - Pair-ends – identifying structure variants - Exome sequencing - Prioritizing genetic variants - Non-synonymous variants (SIFT, PolyPhen) - Synonymous variants - Regulatory variants - Statistical methods on rare variants. Next generation sequencing technologies (illumina, Ion Torrent / Ion Proton, SOLiD and Pac Bio) Short read assembly, alignment and applications - denovo sequencing, resequencing, gene expression,

UNIT 3 RNA SEQUENCING 12 Hrs. Biological theories on RNA-seq experiments - Experimental considerations - Published examples - Major scientific advance using RNA-seq – Alignment - Gene expression analysis - Differential expression analysis - Alternative splicing - Transcript variation - Allele-specific expression - RNA editing – smRNA

UNIT 4 ChIP – Seq 12 Hrs. Biological theories on ChIP-seq analysis - Published studies - Experimental considerations - DNA frament evaluation - Peak identification - Two condition comparison - Saturation analysis - Motif finding and related theories - DNA methylation - Experimental considerations - Statistical considerations - Bioinformatics tools - Histone modification - Experimental approaches - Statistical considerations - Hidden Markov model annotating histone Marks

UNIT 5 Analysis 12 Hrs. Using RNA-seq Data to Detect Differentially Expressed Genes.- Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR.- Analysis of Next Generation Sequencing Data Using Integrated Nested Laplace Approximation (INLA).- Design of RNA Sequencing Experiments.- Measurement, Summary, and Methodological Variation in RNA-sequencing small RNA sequencing.- Functional PCA for differential expression testing with RNA-seq data.- Isoform Expression Analysis Based on RNA-seq Data.- RNA Isoform Discovery Through Goodness of Fit Diagnostics.- Analysis of Metagenomic DataStatistical Considerations in the Analysis of Rare Variants. Epigenetics Next generation sequencing applications, in Agri Biotech, health care, metagenomics, GWAS and basic sciences.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Datta Somnath, Nettleton Dan (Eds.)Statistical Analysis of Next Generation Sequencing Data,2014. 2. Stuart M. Brown. Next-Generation DNA Sequencing Informatics, 2013. 3. Ali Masoudi-Nejad, Zahra Narimani, Nazanin Hosseinkhan. Next Generation Sequencing and Sequence Assembly:

Methodologies and Algorithms (SpringerBriefs in Systems Biology), ISBN-10: 1461477255, Springer; 2013

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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M.E. / M.Tech REGULAR 67 REGULATIONS 2015

SBI6536 STATISTICS USING R PACKAGE LAB L T P C Total Marks 0 0 6 3 100

1. Working with R and R Studio. 2. Built-in mathematical functions and Simple summary statistics. 3. Reading data from excel files. 4. Transformation of variables, subsets of datasets and merging datasets. 5. Basic High level plots and Modifications of scatterplots, histograms and parallel boxplots. 6. Simple and multiple linear regression. 7. One way analysis of variables: Psoriasis. 8. Matrix operations and Least squares estimates in linear regression.

SBM6531 BIOMEDICAL INSTRUMENTATION LAB L T P C Total Marks

0 0 6 3 100

1. Design of ECG Amplifier using Instrumentation Amplifier 2. Heart Rate Measurement using modules ad trainer kit 3. Identification of Heart Sounds -PCG 4. Defibrillator 5. Design of Cardiac Pacemaker. 6. Study of Heart Lung Machine. 7. Study of Haemodialysis. 8. Study of Short wave Diathermy. 9. Surgical Diathermy 10. Simulation of ECG waveforms using MATLAB.

SBM6532 ADVANCED MEDICAL SIGNAL & IMAGE PROCESSING LAB

L T P C Total Marks

0 0 6 3 100

MEDICAL IMAGE PROCESSING 1. Study of Basic commands in MATLAB 2. Image Linear Filtering and Transforms 3. Image Segmentation 4. Image Restoration techniques 5. Image registration 6. Image Enhancement 7. Morphological Operation 8. Finding the ROIs’

MEDICAL SIGNAL PROCESSING 1. Least Squares, Orthogonality, and Fourier series 2. Correlation, Fourier Spectra and the Sampling Theorem 3. Linear systems and Transfer Function 4. FIR Filter Design for Biomedical signal processing 5. IIR Filter Design for Biomedical signal processing 6. Study of ECG, EMG, EEG Signal Analysis 7. ECG noise cancellation 8. Biomedical Signal Compression

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M.E. / M.Tech REGULAR 33 REGULATIONS 2015

SBT5107 CELL BIOLOGY AND MOLECULAR GENETICS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Provides a comprehensive view on the basics of cell biology that includes about the cell structure and cell

organelles. This also details on the various cellular and molecular mechanisms involved in the cells and discusses at the genetic level.

UNIT 1 CELL STRUCTURE 12 Hrs. Comparison between plant and animal cells; Cell wall; Plasma membrane; Electrical properties of membrane, Modification of plasma membrane and intracellular junctions; Organization of plant cell wall. Cytoplasmic organelles - Protoplasm; Mitochondria; Chloroplast; ER; Golgi complex; Lysosome, endosome, Ribosome; Centriole; Nucleus. Cytoskeletal proteins and cell motility , surface antigens and determinants

UNIT 2 OVERVIEW OF CELL CYCLE 12 Hrs. Stages of cell cycle, components and checkpoints in cell cycle regulation.Mitotic and meiotic cell division; Distinction between mitosis in plant and animal .Chromosomes, chromatin and nucleosome: Chromosome structure in bacteria and eukaryotes, centromere, telomere, Hetero- and euchromatin, Nucleosome model and radial-loop scaffold model.

UNIT 3 BIOMEMBRANES 12 Hrs. Plasma membrane: structure-function relationship; Cell signaling: Cell surface, Hormone, receptors and signal transduction and second messengers. Cell differentiation, hormones and growth factors; Apoptosis- The transformed cell; Oncogenes, protooncogenes and etiology of cancer.

UNIT 4 HUMAN CHROMOSOMES 12 Hrs. Structure, number and classification, methods of chromosome preparation, banding patterns. Chromosome abnormalities, Autosomal abnormalities – syndromes, Sex chromosomal abnormalities – syndromes. Patterns of gene inheritance-Single gene pattern inheritance and Multifactorial pattern of inheritance .Autosomal and Sex chromosomal patterns of inheritance.Concept of genome and introduction to genomics.

UNIT 5 POPULATION&REPRODUCTION GENETICS 12 Hrs. Hardy-Weinberg law, Natural selection genetic drift, inbreeding, out breeding, genetic equilibrium.Male infertility, Female Infertility, assisted reproduction, Preimplantation genetics, Prenatal diagnosis, Genetic Counselling -Ethics and Genetics.

Max.60 Hours

TEXT / REFERENCE BOOKS 1. HaveryLodish, Arnold Berk, Lawrence Zipursky, Paul Matsudaira, David Baltimore, James Darnell, Molecular Cell Biology, 5th

Edition, Scientific American Books Inc. 2003. 2. J.D. Watson, N.H. Hopkins, J.W. Roberts, J.A. Steitz and A.M. Weiner, Molecular Biology of the Gene, 4th Edition, The

Benjamin / Cummings Publishers company Inc., California. 1987. 3. Eldon John Gardner, Michael J. Simmons, D. Peter Snustad, Principles of Genetics, 8th Edition, John Wiley & Sons Inc,

2005.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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M. E. / M. Tech REGULAR 80 REGULATIONS 2015

SBI5601 STRUCTURAL AND FUNCTIONAL GENOMICS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVES Students are allowed to acquire knowledge about the usage of high throughput tools for genome science. Students are allowed to comprehend, analyze, and evaluate the critical aspects of data interpretation in

genomics.

UNIT 1 INTRODUCTION 12 Hrs. Structure & Organization of Prokaryotic & Eukaryotic genome - Nucleotide and protein sequencing methods – Chemical, Enzymatic, high through put method – Automated sequencing methods – shotgun – chromosome walking, Contig assembly - Levels of structures in Biological macromolecules.

UNIT 2 CONFORMATIONAL ANALYSIS 12 Hrs. Biomolecules and their interactions - Forces that determine protein and nucleic acid structure, basic problems, polypeptide chains geometrics, potential energy calculations, observed values for rotation angles, hydrogen bonding, hydrophobic interactions and ionic interactions, disulphide bonds - Prediction of proteins structure - Nucleic acids, general characteristics of nucleic acid structure, geometrics, glycosidic bond rotational isomers - Ribose puckering -forces stabilizing ordered forms, base pairing, base stacking- tertiary structure of nucleic acids.

UNIT 3 STRUCTURAL ANALYSIS OF MACROMOLECULES 12 Hrs. Size and shape of macromolecules - methods of direct visualization - X-ray crystallography – X–ray diffraction, determination of molecular structures, electron microscopy, NMR. Protein structure databases - Protein Data Bank - SCOP - CATH - structure superposition - RMSD - TM-score- structure alignment - Different structure alignment algorithms - DALI, CE, VAST, TM-align - protein folds in PDB.

UNIT 4 STRUCTURE-FUNCTIONS RELATIONSHIP 12 Hrs. DNA binding proteins, Prokaryotic and Eukaryotic transcription factors - DNA polymerases, Helix-turn-Helix motif in DNA binding, Trp repressor, Zn fingers, helix-turn helix motifs in homeodomain, Leucine zippers - DNA polymerases,Membrane proteins and receptors, Trans-membrane segments, bacterio rhodopsin, photosynthetic centres, epidermal growth factor, insullin and PGDGF receptors and their interaction with effectors, protein phosphorylation, immunoglobulins, Serine proteases, ribonuclease, lysozyme.

UNIT 5 FUNCTIONAL GENOMICS 12 Hrs. Introduction to Functional Genomics - cytological maps - Hap Map - SNPs and variation- Genotyping, microarray- analysis and applications. Microarray oligo sets and fabrication - integrative genomics and Meta genomics. Quantitative Proteomics. Fluorescent imaging techniques. Quantitative RT-PCR analysis. High-throughput cloning and expression strategies. Next Generation Sequencing applications.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Cantor R., Schimmel P.R.,Biophysical Chemistry, Vol. I, II, W.H. Freeman & Co., 1985. 2. Kensal E. van Holde, W. Curtis Johnson and P. Shing Ho, Principle of Physical Biochemistry, Prentice Hall, New York, 1998. 3. Pennington SR, Dunn MJ, Proteomics from Protein Sequence to Function, Viva Books Ltd, 2002. 4. G. Gibson and M. V. Muse. A primer of Genome Science. Sinauer Associates Inc; 2 edition, December 2004.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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M. E. / M. Tech REGULAR 81 REGULATIONS 2015

SBI5602 MICROARRAY - TECHNIQUES AND APPLICATIONS

L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to understand the key concepts of class comparison and class discovery of genes.

UNIT 1 GENE EXPRESSION 12 Hrs. Basics of Gene expression- definition , gene expression studies, gene expression patterns- Applications of gene expression studies- Microarrays – definition , discovery,technique, making microarrays, spotted microarrays, Insitu synthesized oligonucleotide arrays, inkjet array synthesis, affymetrix techniques, DNA CHIP technology, photolithography, spot quality, sample preparation and labeling, washing, image acquisition Sequencing by Hybridization Arrays- DNA MassArray™ Technology- Printing DNA Microarrays-Types of micorarrays-Designing a microarray experiment.

UNIT 2 IMAGE PROCESSING 12 Hrs. Image processing, feature extraction, identifying positions of features- Normalisation – data cleaning and transformation, within array normalization , between array normalization, measuring and quantifying microarray variability –variability between replicate features on an array-, variability between hybridizations to different arrays. Analysis of differentially expressed genes- significance analysis of microarrays.

UNIT 3 PREDICTION 12 Hrs. Prediction of cross hybridization to related genes, thermodynamics of nucleic acid duplexes, prediction of Tm- probe secondary structure. Analysis of relationships between genes ,tissues or treatments- similarity of gene or sample profiles –dimensionality reduction, principal component analysis ,hierarchial clustering, machine learning methods for cluster analysis.classification of tissues and samples – validation.

UNIT 4 CARBOHYDRATE MICROARRAYS 12 Hrs. Carbohydrate microarrays- Carbohydrate sources- Synthesis of oligosaccharides - Isolation of oligosaccharides from natural sources- Arrays of monosaccharides and disaccharides- Arrays of polysaccharides- Arrays of oligosaccharides- Perspectives- DNA micro array analysis-clustering-immunological applications.

UNIT 5 DATABASES AND TOOLS FOR MICROARRAYS 12 Hrs. Bioinformatics in Arrays- Databases and tools for microarrays- Bioconductor, expression profiler, EST databases- Assessing levels of gene expression using EST’s , TIGR gene indices, STACK, SAGE,CGAP, Xprofiler, ARRAY DB, cluster, treeview, Scanalyze, genecluster, informatics aspects of microarray production- MGED and gene-ontology, description of MIAME ((Minimum Information About a Microarray Experiment), Business Aspects of Biochip Technologies- Microarray Technology in Treating Disease.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Dov Stekel - Microarray bioinformatics, Cambridge, 2003. 2. Steen Knudsen - A Biologist's Guide to analysis of DNA microarraydata, second edition, John Wiley & Sons, Inc., 2004. 3. Andreas D Baxevanis and BF Francis Ouelette - Bioinformatics: A Practical Guide to the Analysis of Gene and Proteins ,

Wiley-Interscience, 1998 4. David W. Mount - Bioinformatics: Sequences and genome analyses, Cold Spring Harbor Laboratory press, 2000.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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M. E. / M. Tech REGULAR 82 REGULATIONS 2015

SBI5603 DATA MINING FOR BIOINFORMATICS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to develop, apply and analyze the statistical techniques for solving the annotation problems

in bioinformatics

UNIT 1 MINING FREQUENT PATTERNS, ASSOCIATIONS AND CORRELATIONS 12 Hrs. Basic Concepts, Efficient and Scalable Frequent Itemset Mining Methods, Mining various kinds of Association Rules, From Association Mining to Correlation Analysis, Constraint-Based Association Mining.

UNIT 2 CLASSIFICATION AND PREDICTION 12 Hrs. Issues Regarding Classification and Prediction, Comparison of classification and prediction methods Classification by Decision Tree Induction, Advantages of decision tree, Tree pruning approaches, Direct acayclic graph representation, IF-THEN-RULES :Rule extraction, Rule pruning. Bayesian Classification, Rule-Based Classification, Classification by Backpropagation, Support Vector Machines, Associative Classification, Lazy Learners, Other Classification Methods, Prediction, Accuracy and Error measures, Evaluating the accuracy of a Classifier or a Predictor, Ensemble Methods.

UNIT 3 CLUSTER ANALYSIS INTRODUCTION 12 Hrs. Cluster-definition-Application of cluster analysis,Types of Data in Cluster Analysis, A Categorization of Major Clustering Methods, Partitioning Methods, Hierarchical Methods, Density-Based Methods, Grid-Based Methods, Model-Based Clustering Methods, Clustering High-Dimensional Data, Constraint-Based Cluster Analysis, Outlier Analysis.

UNIT 4 MINING STREAMS, TIME SERIES AND SEQUENCE DATA 12 Hrs. Mining Data Streams, Mining Time-Series Data, Mining Sequence Patterns in Transactional Databases, Mining Sequence Patterns in Biological Data, Graph Mining, Social Network Analysis and Multirelational Data Mining.Challenges in web mining. Mining Object, Spatial, Multimedia, Text and Web Data: Multidimensional Analysis and Descriptive Mining of Complex Data Objects, Spatial Data Mining, Multimedia Data Mining, Text Mining, Mining the World Wide Web.

UNIT 5 APPLICATIONS AND TRENDS IN DATA MINING 12 Hrs. Mining Applications, Data Mining System Products and Research Prototypes, Additional Themes on Data Mining and Social Impacts of Data Mining. Trends in data mining (visual data mining, Biological data mining, web mining, Distributed data mining, Real time data mining, Multi database data mining, privacy protection and security in data mining).

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Data Mining Techniques – Arun K Pujari,2nd edition, Universities Press,2001. 2. Insight into Data Mining,K.P.Soman,S.Diwakar,V.Ajay,PHI,2008. 3. Data Mining – Concepts and Techniques - Jiawei Han & Micheline Kamber, Morgan Kaufmann Publishers, Elsevier,2nd

Edition, 2006. 4. Introduction to Data Mining – Pang-Ning Tan, Michael Steinbach and Vipin Kumar, Pearson education,2014.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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M. E. / M. Tech REGULAR 84 REGULATIONS 2015

SBI5605 MACHINE LEARNING FOR BIOINFORMATICS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to understand the modeling methods, such as supervised classification and clustering along

with the application of probabilistic graphical models for knowledge discovery, as well as deterministic and stochastic heuristics for optimization.

UNIT 1 MACHINE LEARNING 12 Hrs. Machine-Learning Foundations: The Probabilistic Framework -Introduction: Bayesian modeling -The Cox Jaynes axioms - Bayesian inference & induction -Model structures: graphical models & other tricks - Probabilistic Modeling & Inference: Examples -The simplest sequence models - Statistical mechanics Machine Learning Algorithms - Introduction -Dynamic programming -Gradient descent -EM/GEM algorithms –Markov chain Monte-Carlo methods - Simulated annealing – Evolutionary & genetic algorithms. Learning algorithms: miscellaneous aspects.

UNIT 2 SUPPORT VECTOR MACHINE (SVM) 12 Hrs. SVM: introduction – architecture – kernel - ROC – feature selection – sensitivity – specificity – accuracy – implementation - svm applications in sequence analysis, structure prediction , drug design –svm light - libsvm – weka.

UNIT 3 NEURAL NETWORKS 12 Hrs. Neural Networks: The Theory -Introduction - Universal approximation properties – Priors & likelihoods - Learning algorithms: backpropagation - Neural Networks: Applications - Sequence encoding & output interpretation- Sequence correlations & neural networks – Prediction of protein secondary structure - Prediction of signal peptides & their cleavage sites - Applications for DNA & RNA nucleotide sequences - Prediction performance evaluation - Different performance measures -Perceptrons and Multilayer Perceptrons -Neural Networks in Drug Design.

UNIT 4 HIDDEN MARKOV MODELS 12 Hrs. Hidden Markov Models: The Theory - Introduction -Prior information & initialization -Likelihood & basic algorithms - Learning algorithms -Applications of HMMs: general aspects -Protein applications - DNA & RNA applications - Advantages & limitations of HMMs – tools.

UNIT 5 PROBABILISTIC GRAPHICAL MODELS 12 Hrs. Probabilistic Graphical Models in Bioinformatics - Markov models & DNA symmetries - Markov models & gene finders - Hybrid models & neural network parameterization of graphical models -The single-model case - Bi-directional recurrent neural networks for protein secondary structure prediction

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Pierre Baldi and Soren Brunak, Bioinformatics: the Machine Learning Approach – Publisher: MIT Press, 1998. 2. David W Mount, Bioinformatics: sequence and genome analysis, 2nd edition, CBS publishers, 2004. 3. Zupan J., Gasteiger J.- Neural Networks in Chemistry and Drug Design. Wiley-VCH, 2000.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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M. E. / M. Tech REGULAR 89 REGULATIONS 2015

SBI5610 COMPUTATIONAL CHEMISTRY L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to apply various mathematical models to solve the chemical and physical problems with the

help of scientific programming.

UNIT 1 FOUNDATIONS OF MOLECULAR ORBITAL THEORY 12 Hrs. Quantum Mechanics and the Wave Function - The Hamiltonian Operator - General Features- The Variational Principle - The Born–Oppenheimer Approximation - Construction of Trial Wave Functions - The LCAO Basis Set Approach - The Secular Equation.

UNIT 2 HUCKEL THEORY 12 Hrs. Fundamental Principles - Application to the Allyl System Many-electron Wave Functions - Hartree-product Wave Functions -The Hartree Hamiltonian - Electron Spin and Antisymmetry - Slater Determinants - The Hartree-Fock Self-consistent Field Method.

UNIT 3 SEMIEMPIRICAL METHODS 12 Hrs. . Introduction - The basic principles of SCF SE methods - the Neglect of DifferentialOverlapMethod -Complete Neglect of Differential Overlap Method- Modified Neglect of the Diatomic Overlap Method- AustinModel 1 Method Parametric Method 3 Model - The Pairwize Distance Directed Gaussian Method - The Zero Differential Overlap Approximation Method- Software Used for Semiempirical Calculations.

UNIT 4 BASIS SETS 12 Hrs. Introduction -The Energy Calculation from the STO Function - The Energy Calculation of Multielectron - Gaussian -Differences Between STOs and GTOs -Classification of Basis Sets-Minimal Basis -A Comparison of Energy Calculations of the Hydrogen Atom Based on STO-nGBasis Sets -STO-2G - STO-3G - STO-6G – Contracted Gaussian Type Orbitals - Double- and Triple-Zeta Basis Sets and the Split-Valence Basis Sets -Polarized Basis Sets -Basis Set Truncation Errors - Basis Set Superposition Error - Methods to Overcome -The Chemical Hamiltonian Approach -The Counterpoise Method -The Intermolecular Interaction Energy of Ion Water Clusters - A List of Commonly Available Basis Sets -Internet Resources for Generating Basis Sets.

UNIT 5 DENSITY FUNCTIONAL THEORY 12 Hrs. Introduction - The basic principles of density functional theory – electron Density -Pair Density -The Development of DFT- The Functional - The Hohenberg and Kohn Theorem -The Kohn and Sham Method - Density Functionals -The Dirac-Slater Exchange Energy Functional and the Potential -DFT Methods - Applications of -The Performance of DFT - Advantages of DFT in Biological Chemistry.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Ramachandran K. I., Deepa G., Namboori K.- Computational Chemistry and Molecular Modeling Principles and Applications

-, Springer-Verlag Berlin Heidelberg, 2008. 2. Jensen F., Introduction to Computational Chemistry, Wiley, New York, 1999. 3. Errol Lewars - Computational chemistry, Kluwer Academic Publishers, 2003

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M. E. / M. Tech REGULAR 90 REGULATIONS 2015

SBI5611 IMMUNOINFORMATICS & COMPUTATIONAL VACCINOLOGY

L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to understand the immunological foundations of a biological system with the help of

computational techniques.

UNIT 1 INTRODUCTION TO IMMUNOINFORMATICS 12 Hrs. Definition of Immunoinformatics – overview of the Immune system- Brief introduction to immunoformatics and computational vaccinology-Immunogenecity a brief primer-Epitopes and Epitology – Immunoinformatics databases-IMGT – IMGT-GENE-DB– IMGT-HLA ,IMGT/LIGM-DB - HaptenDB – EPITOME – dbMHC – JenPep. Monoclonal antibodies database.

UNIT 2 GENOTYPING METHODS AND DISEASE ASSOCIATION 12 Hrs. Genotyping of SNPs, classical HLA typing, MHV haplotypes, Molecular haplotyping, microhaplotyping. HLA and disease associations, Identifying Major Histocompatibility Complex Supertypes.

UNIT 3 ALLERGEN BIOINFORMATICS 12 Hrs. Introduction- allergen database-need for allergen database-existing allergen database: IUIS, UniProt, SDAP, ALLERGOME, Allergenicity prediction-sequence similarity search, FAO and WHO guidelines, current status of allergenicity prediction.

UNIT 4 COMPUTATIONAL VACCINOLOGY 12 Hrs. Vaccines –types- Conventional methods used for Preparation of vaccines -From immunome to vaccine- epitope mapping,-vaccine design tools-Prediction of cytotoxic T cells (MHC CLASS I) epitopes-Antigen processing in the MHC –I pathway, Prediction of T helper cells(MHC-II) epitopes-processing of MHC-II epitopes.B cell Epitopes. B cell epitope prediction tools , Tools in immunoinformatics for the prediction binding affinity between peptide: TAP: MHC: TCR- MHC:Peptide Binding Prediction - SYFPEITHI, BIMAS, MHCPred, TEPITOPE, NetMHC, BLEEP Proteasomal Cleavage Prediction : PAProC, NetChop - TAP Binding:TAPPred T-cell Binding: EpiJen.

UNIT 5 IMMUNOGENETICS TO IMMUNOMICS 12 Hrs. Biomolecular structure prediction using Immune inspired algorithsm- overview of discrete models-discrete models for HIV infection-simulation of HIV-1 infections-simulation of HIV -1 Molecular evolution in response to chemokine receptors and antibodies- Integration of immune models using Petri Nets.

Max. 60 Hours TEXT / REFERENCE BOOKS 1. Darren R. Flower, Immunoinformatics: Predicting Immunogenicity In Silico (Methods in Molecular Biology), 2010. 2. Flower, Darren D.R., Timmis, In Silico Immunology, Jon (Eds.) XVIII, 450 pages.In Silico Immunology, 2007 3. Immunoinformatics: Bioinformatic Strategies for Better Understanding of Immune Function, No. 254 -Novartis

Foundation,2011.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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M. E. / M. Tech REGULAR 92 REGULATIONS 2015

SBI56013 PHENOMICS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to analyze the rate of translation of genetic instructions from a single gene or the whole

genome into the full set of phenotypic traits of an organism

UNIT 1 INTRODUCTION TO EVOLUTION 12 Hrs. Basics of Natural Selection-Introduction to Hardey Weinberg. Basics of evolutionary theory, Pre Darwinian theory-Darwin’s theory –Lamarck’s theory-Modern evolution theory, molecule genetics, population genetics, Linkage and Recombination.

UNIT 2 MECHANISM OF GENOME EVOLUTION 12 Hrs. Endosymbiosis and lateral gene transfer. Translocation, Transposition, retroposition, and junk DNA. Chromosomal evolution: genome projects and comparative mapping.Horizontal gene transfer, Tandem repeat evolution Introduction to genome duplications -whole genome duplication-Subchromosomal duplication and evolution of introns.

UNIT 3 EVOLUTION OF GENE FAMILIES 12 Hrs. Introduction to orthologs and paralogs, XenologsEmbedded trees-Inference of gene duplication and losses. Positive selection. Endogenous retroviral elements. Rooting the tree of life with gene families. Reconstructing the evolution of function. Domain shuffling and concerted evolution.

UNIT 4 EVOLUTION & DEVELOPMENT OF A GENE FUNCTION 12 Hrs. Role of gene family evolution in morphological innovations- Neofunctionalization and subfunctionalization. The Line-1 family,The major Sine families –B1 and B2-General comments on SINES and LINES, Genomic stutters-microsatellites-minisattelites-macrosatellites. Changes in the expression of developmental control- genes as a cause of morphological changes- homology concepts. Complexity and canalization in development.

UNIT 5 STATISTICAL ANALYSIS OF MOLECULAR EVOLUTION 12 Hrs. Advanced models of nucleotide substitution- gamma-distributed mutation rates, codon models and analysis of selective pressure. Statistical analysis of biological hypotheses- likelihood ratio tests, Akaike Information Criterion, Bayesian statistics. Reconstruction of phylogenetic trees -parsimony, distance based methods, maximum likelihood, and Bayesian techniques. Simulating molecular evolution. Neutral and adaptive protein evolution. Molecular clock and estimation of species divergence times. Software for evolution analysis-MEGA.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. T. Ohta. The current significance and standing of neutral and nearly neutral theories. Bioessays 18:673, 1996. 2. M Kreitman. The neutral theory is dead; long live the neutral theory. Bioessays 18:678, 1996. 3. Lahn BT, Page DC. Four evolution strata on the human X chromosome. Science 286:964-967, 1999. 4. Ayala FJ. Molecular clock mirages. Bioessays 21:71-75, 1999. 5. Wray GA, Levinton JS, Shapiro LH. Molecular evidence for deep precambrian divergences among metazoan phyla. Science

274:568-573, 1996. 6. Doolittle WF. Phylogenetic classification and the universal tree. Science 284:2124-2128, 1999. 7. Fryxell KJ. The coevolution of gene family trees. Trends in Genetics 12:364-369, 1996.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks .

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M. E. / M. Tech REGULAR 93 REGULATIONS 2015

SBI5614 GENE VARIATION AND DISEASES L T P Credits Total Marks 3 1 0 4 100

COURSE OBJECTIVE It deals with Basic concepts of Drug metabolism and influence of genetic variation on drug response in individuals

UNIT 1 BASICS OF GENE VARIATION 12 Hrs. Introduction- Mendal to Molecules. Nucleic acids and Central dogma. Comparison of eukaryotic, prokaryotic and viral genetic materials, Introduction-Recombinant DNA technology and Genetic Nomenclature.

UNIT 2 REPLICATION AND RECOMBINATION 12 Hrs. Introduction - Replication and Mutagenesis. Mutagenes.DNA Damage and Repair. Meosis and Reproduction. Homologus Recombination. Crossing-over

UNIT 3 TRANSCRIPTIONAL MACHINERY AND GENOME VARIENTS 12 Hrs. Regulatory Transcriptional Machinery I: Gene promoters, enhancers and silencers. Regulatory Transcriptional Machinery II: Transcription factors and transcriptional control. Gene regulatory model (Lac operon and Tryptophan operon concept). Comparative genomics. Patterns of human genetic variation. Structural and copy-number variation.

UNIT 4 EPIGENETICS AND RNA PROCESSING 12 Hrs. Memory of transcriptional states through epigenetic regulation. Epigenetics of non-coding RNA, DNA methylation and Histone Modifications. Splicing and Translation. piRNAs/endosiRNAs in genome integrity and inheritance. Introduction to Long non-coding RNAs.

UNIT 5 GENETIC NETWORKS AND CASE STUDY 12 Hrs. Introduction to Regulatory circuits from Genetics to Genomics.Basic concept of networks and it impact in Systems Biology. Case study of a autosomal and an auto immune disease in Hapmap and GWAS.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Kenneth M. Weiss, Genetic Variation and Human Disease: Principles and Evolutionary Approaches (Cambridge Studies in

Biological and Evolutionary Anthropology), Cambridge University Press; Reprint edition 1995. 2. Lucio G. Costa, David L. Eaton, Gene-Environment Interactions: Fundamentals of Ecogenetics, Wiley-Blackwell, April 2006. 3. Mark Steven Miller (Editor), Maureen Cronin, Genetic Polymorphisms and Susceptibility to Disease (Taylor & Francis Series

in Pharmaceutical Sciences), CRC Press, 2000. 4. Michael Weiner, Stacey Gabriel, Genetic Variation: A Laboratory Manual, Cold Spring Harbor Laboratory Press,U.S.; Lab

Manual edition, 2007. 5. Michael Montoya , Making the Mexican Diabetic - Race, Science and the Genetics of Inequality, University of California,

Press, 1st Edition, 2011.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M. E. / M. Tech REGULAR 94 REGULATIONS 2015

SBI5615 METABOLOMICS L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Students are allowed to investigate the metabolic profile of an organism to understand the molecular basis of a

disease from the experimental data.

UNIT 1 INTRODUCTION AND TERMINOLOGY 12 Hrs. Introduction and brief descriptions: Metabolome, metabolomics and metabonomics - Concepts and few applications of metabolomics and Toxicogenomics- Human Metabolome Project – Interactomics-metabolic network.

UNIT 2 DRUG METABOLOMICS 12 Hrs. Metabolic activity and Interactions of Drugs: Drug administration & drug action and its complexicity- Drug Metabolism and Biological activities and dynamics of homologous series of drugs - drug receptor interaction, forces involved and theories of interaction. Protein –Protein interactions, Protein –lipid intercations and protein-carbohydrate interactions-kinetics and factors affecting protein binding.

UNIT 3 METABOLOMICS OF BIOMOLECULES 12 Hrs. Metabolism of Biomolecules: Introduction to metabolism, Bioenergetics. Biosynthesis of fatty acid, Regulation of amino acid biosynthesis.Carbohydrate metabolism, Lipid metabolism, Protein metabolism, Nucleic acid metabolism,

UNIT 4 METABOLOMIC DATABASES 12 Hrs. Metabolic pathway databases: PubChem- ChEBI- KNApSAcK- ExPaSy Pathways- BioCyc, EcoCyc, AraCyc and MetaCyc - Plant Metabolic Network (PMN)-Databases for Si RNA, MiRNA, KEGG, Nutrigenomics.

UNIT 5 METABOLOMICS ANALYSIS TOOLS 12 Hrs. Tools and servers for metabolic data analysis: Brief introduction and applications - Pathway Tools Omics Viewer – Genostar- metaSHARK -Pathway Explorer -Pathway Browser -KDB Explorer. Imat (integrative metabolic analysis tool), NeAT (Network analysis tools), Ipath (Intercative pathway explorer), HumanCyc, Katsura.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. William J Griffiths and Stephen Neidle, Metabolomics, Metabonomics and Metabolite Profiling: RSC (RSC Biomolecular

Sciences, Royal Society of Chemistry; 1st edition, 2007. 2. Michael Lammerhofer, Wolfram Weckwerth, Metabolomics in Practice: Successful Strategies to Generate and Analyze

Metabolic Data, Wiley-VCH; 1st edition, 2013. 3. Haleem J Issaq, Timothy D. Veenstra, Proteomic and Metabolomic Approaches to Biomarker Discovery, Academic Press;

1st edition, 2013. 4. John C. Lindon, Jeremy K. Nicholson, The Handbook of Metabonomics and Metabolomics, Elsevier Science; 1st edition,

2007. 5. Norbert W. Lutz, Methodologies for Metabolomics: Experimental Strategies and Techniques, Cambridge University Press;

1st edition, 2013.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M. E. / M. Tech REGULAR 114 REGULATIONS 2015

SBT 5606 STEM CELL RESEARCH (For M.Tech)

L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVE Stem cells are the pluripotent cells having gained recent attention. The course introduces the various concepts of

stem cell research

UNIT 1 FUNDAMENTALS OF STEM CELL BIOLOGY 12 Hrs. Embryogenesis - Developmental stages - properties of stem cells – pluripotency, totipotency. Definitions and molecular mechanisms factors that dictate stem cell behaviour. Identification and characteristic of pluripotent stem cells in animal and humans; sources of pluripotentcells - blastocysts, parthenogenesis, nuclear transfer, IPS, stem cell markers.

UNIT 2 TYPES OF STEM CELLS 12 Hrs. Germ Line Stem Cell, Determination of the Germ Line; Identification, Characterization and Purification of Germ Line Stem cells; Germ Line Stem cell Niche; Establishment of Germ Line cells in vitro - Properties of Germ Line Stem cells.Embryonic Stem Cells In vitro fertilization - culturing of embryos - isolation of human embryonic stem cells - growing ES cells in labs - stimulation ES cells for differentiation - identification –properties of ES cells.Adult stem cell Somatic stem cells - test for identication of adult stem cells - adult stem cell differentiation – transdifferentiation - plasticity - different types of adult stem cells - properties of adult stem cell

UNIT 3 REPRESENTATIVES OF STEM CELL 12 Hrs. Neuronal stem cells, mesenchymal and cardiac stem cells Hematopoietic stem cells, Epithelial stem cells (Skin,intestine, breast) and cancer stem cells

UNIT 4 GENE THERAPY, APPLICATION AND REPARATIVE MEDICINE 12 Hrs. Gene therapy - stem cells and animal cloning, introduction to modeling cell behaviour unique characteristic of stem cell and modeling of signal transduction. Mechanisms for stem cell manipulation in controlled microenvironments.Therapeutic applications and reparative medicine - parkinson disease - neurological disorder - limb amputation – heart disease - spinal cord injuries - diabetes - burns-HLA typing - Alzheimer’s Disease

UNIT 5 STEM CELL – BASED TISSUE REGENERATION AND ETHICAL ISSUE 12 Hrs. Tissue engineering application - production of complete organ - kidney - eyes - heart - brain. Establishment of human stem cell bank. Stem cell policy and ethics, stem cell research: Hype, hope and controversy.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Kursad Turksen, Embryonic Stem cells - Protocols, 2nd Edition, Humana Press, 2002. 2. Stem cell and future of regenerative medicine. By committee on the Biological and Biomedical applications of Stem cell

Research.National Academic press, 2002.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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SATHYABAMA UNIVERSITY FACULTY OF BIO AND CHEMICAL ENGINEERING

M. E. / M. Tech REGULAR 118 REGULATIONS 2015

SBT 5610 BIOETHICS, BIOSAFETY AND IPR (For M.Tech)

L T P Credits Total Marks

3 1 0 4 100

COURSE OBJECTIVES The ethical and safety concerns in the Biotechnology field with respect to Global and Indian standards are

discussed. The current trends and issues of intellectual property rights are highlighted

UNIT 1 BIOSAFETY 12 Hrs. Introduction, Biosafety Issues in Biotechnology – Historical Background; Introduction to Biological Safety Cabinets; Biosafety levels, Primary containment for Biohazards. Biosafety levels of specific Microorganisms; Recommended Biosafety levels for Infectious agents and Infected animals.

UNIT 2 BIOSAFETY GUIDELINES 12 Hrs. Biosafety guidelines and regulations (National and International) – Operation of Biosafety Guidelines and Regulations of Government of India; Definition of GMO’s and LMO’s; Roles of Institutional Biosafety Committee, RCGM, GEAC, etc., for GMO applications in Food and Agriculture. Environmental release of GMO’s, Risk analysis, Risk assessment, Risk management and Communication.

UNIT 3 INTELLECTUAL PROPERTY RIGHTS 12 Hrs. Types of IP; Patents, TradeMarks, Copyright & related rights, Industrial design, Traditional knowledge, Geographical indications – Importance of IPR. Patent filing procedures – National and PCT filing procedure. Intellectual properties of relevance to Biotechnology.

UNIT 4 GREEMENTS AND TREATIES 12 Hrs. History of GATT and TRIPS agreement; Madrid agreement; Hague agreement; WIPO treaties; Budapest treaty; PCT; Indian patent Act 11270 and Recent amendments. Role of a Country Patent Office. Patent infringement – meaning, scope, litigation.

UNIT 5 ENGINEERING ETHICS AND BIOETHICS 12 Hrs. Engineering ethics – Professional ideals and virtues – Engineers as responsible experimenters – Research ethics. Framework for Ethical decision making; Biotechnology and Ethics, Biowarfare and Biopiracy. Introduction to Animal Ethics, Animal Rights and use of animals.

Max. 60 Hours

TEXT / REFERENCE BOOKS 1. Mike Martin and Roland Schinzinger, Ethics in Engineering, McGraw Hill, 2005. 2. Kankanala C, Genetic Patent law and Strategy, First edition, Manupatra Information solution Pvt.Ltd.,2007. 3. Sasson A, Biotechnologies in developing countries present and future, UNESCO Publishers, 1993. 4. Singh K, Intellectual Property Rights on Biotechnology, Kalyani Publication, 2nd Edition, 2008. 5. Edmund G Seebauer and Robert L Barry, “Fundamentals of Ethics for Scientists and Engineers”, Oxford University Press,

2001.

END SEMESTER EXAMINATION QUESTION PAPER PATTERN Max. Marks : 80 Exam Duration : 3 Hrs. PART A : 6 Questions of 5 Marks each – No Choice 30 Marks PART B : 2 Questions from each unit of internal choice, carrying 10 Marks each 50 Marks

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