BIOINFORMATICS

Course Structure

COURSE NO. COURSE TITLE CREDITS SEM

BIF 501 / 
@

FSC 604/
INTRODUCTION TO BIOINFORMATICS 2+1 I
MBB 555/
ABT 608
BIF 502@ ADVANCED BIOINFORMATICS 2+1 I
BIF 503@ TECHNIQUES IN BIOINFORMATICS 0+2 II
BIF 504**/ 
BASIC BIOCHEMISTRY 3+0 I, II
BIOCHEM 501
BIF 505**/ 
STATISTICS FOR BIOLOGICAL SCIENCES 2+1 I
STAT 532
BIF 506 CONCEPTS IN COMPUTING 2+2 I
PROGRAMMING LANGUAGES FOR
BIF 507* 2+2 I
BIOINFORMATICS
BIF 508**/ 
MBB 502/ FUNDAMENTALS OF MOLECULAR BIOLOGY 3+0 I
BIOCHEM 504
BIF 509**/ 
MATHEMATICS FOR BIOLOGICAL SCIENCES 2+0 I
STAT533
BIF 510/ 
MBB 512/ IMMUNOLOGY AND MOLECULAR DIAGNOSTICS 2+1 II
BIOCHEM 506
BIF 511 INTRODUCTION TO DATABASE SYSTEMS 2+1 II
BIF 512* COMPUTATIONAL AND SYSTEM BIOLOGY 2+2 II
BIF 513* BIOMOLECULAR SEQUENCE ANALYSIS 1+1 I
BIF 514 DYNAMIC WEB-DESIGN 1+2 I
BIF 515* BIOLOGICAL DATABANKS AND DATA MINING 1+2 II
BIF 516* MOLECULAR MODELLING AND DRUG DESIGN 2+2 I
BIF 517**/ 
GENOMICS AND PROTEOMICS 2+1 I
MBB508
BIF 518 PHARMACOGENOMICS AND IPR 2+1 II
BIF 591 MASTER’S SEMINAR 1 I, II

BIF 599 MASTER’S RESEARCH 20

* Compulsory for Master’s programme; ** May be taken as Minor/Supporting course

@
Courses open to all PG students of other departments/colleges only
Minor Subject for BIF students – Molecular Biology & Biotechnology or Biochemistry with
BIF 504/BIOCHEM 501 and BIF 517/ MBB 508
Supporting Subject for BIF students – STAT 532 and STAT 533
To be taught by:  Molecular Biology, Biotechnology & Bioinformatics;
 Biochemistry;  Statistics;  Bioinformatics, Biochemistry, Molecular Biology & Biotechnology;
 Veterinary Microbiology;  Bioinformatics, Molecular Biology & Biotechnology

1
 BIOINFORMATICS
Course Structure

BIF 501/ INTRODUCTION TO BIOINFORMATICS 2+1 SEM - I

MBB 555/ (To be taught jointly by Bioinformatics and Molecular
ABT 608 Biology & Biotechnology)
FSC 604
Objective
To impart an introductory knowledge about the subject of Bioinformatics to the students
studying any discipline of science.
Theory
UNIT-I: Introduction, biological databases – primary, secondary and structural, Protein
and Gene Information Resources – PIR, SWISSPROT, PDB, GenBank, DDBJ.
Specialized genomic resources.
UNIT-II: DNA sequence analysis, cDNA libraries and EST, EST analysis, pair wise
alignment techniques, database searching, multiple sequence alignment.
UNIT-III: Secondary database searching, building search protocol, computer aided drug
design – basic principles, docking, QSAR.
UNIT-IV: Analysis packages – commercial databases and packages, GPL software for
Bioinformatics, web-based analysis tools.
Practical
 Usage of NCBI resources
 Retrieval of sequence/structure from databases
 Visualization of structures
 Docking of ligand receptors
 BLAST exercises.
Suggested Readings
Attwood TK & Parry-Smith DJ. 2003. Introduction to Bioinformatics. Pearson Edu.
Rastogi SC, Mendiratta N & Rastogi P. 2004. Bioinformatics: Concepts, Skills and
Applications. CBS.

BIF 502 ADVANCED BIOINFORMATICS 2+1 SEM - I

Objective
To understand the usage of advanced techniques in Bioinformatics.
Theory
UNIT-I: Biological databases, database hierarchies, sequence and structure databases. Pair
wise sequence alignment and database similarity searching: global and local alignments,
matrices, gap penalties and statistical significance.
UNIT-II: Multiple sequence alignment and phylogenetic analysis, Microarray technology:
applications, analysis of data, clustering analysis. Pharmacogenomics: introduction,
applications, Genome for medicine, current and future perspectives.
UNIT-III: System modeling and metabolomics – concepts and principles. Nutrigenomics:
system biology in nutrition and health arena.
UNIT-IV: Genome annotation, EST clustering, protein modeling and design.
Practical
 Development of small database
 Phylogenetic analysis
 Microarray data analysis (sample data from open sources)
 Other practical exercises based on above topics
Suggested Readings
Baxevanis AD & Ouellette BFF. 2001. Bioinformatics: a Practical Guide to the Analysis
of Genes and Proteins. Wiley Interscience.
Mount DW Cold. 2001. Bioinformatics: Sequence and Genome Analysis. Spring Harbor.
Stekel D. 2003. Microarray Bioinformatics. Cambridge University Press.

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 Tomita M & Nishioka T. 2005. Metabolomics: The Frontier of Systems biology. Springer
Verlag.
Wong SHY. 2006. Pharmacogenomics and Proteomics: Enabling the Practice of
Personalized Medicine. American Association for Clinical Chemistry.

BIF 503 TECHNIQUES IN BIOINFORMATICS 0+2 SEM - II

Objective
To explore the usage of various Open source software for Bioinformatics applications
Practical
UNIT-I: Gene Information Resources: GenBank, EMBL, Protein Information Resources:
Swiss-Prot, BLOCKS, Gene Prediction Tools: GENSCAN, GRAIL.
UNIT-II: Structural Databases: PDB, CSD, RELIBASE, REBASE, File Format Converter
Tools: BABEL, ReadSeq, NCBI Resources.
UNIT-III: Visualization tools – RasMol, QMol, SwissPDB, Pymol, Modeling Tools:
MODELLER, SwissPDB, Geno3D, Docking Tools: Chimera, Dock, AutoDock,
GRAMM, Hex, Argus Lab.
UNIT-IV: Proteomics Tools: EXPASY, CDART, 3D-Structure Optimization Tools,
Sequence Analysis Tools: BLAST, FASTA, EMBOSS, TCOFFEE, Phylogenetic Analysis
Tools: Phylip, NTSYS, CLUSTALW/CLUSTALX, BIOEDIT.
Suggested Readings
Software Manuals and Help files.

BIF 504/ BASIC BIOCHEMISTRY 3+0 SEM - I, II

BIOCHEM 501 (To be taught by Biochemistry)
Objective
To provide elementary knowledge/overview of structure, functions and metabolism of
biomolecules.
Theory
UNIT-I: Scope and importance of biochemistry in agriculture; acid base concept and
buffers; pH; hydrogen bonding; hydrophobic, electrostatic and van der Waals forces;
General introduction to physical techniques for determination of structure of biopolymers.
UNIT-II: Classification, structure and function of carbohydrates, lipids, amino acids,
proteins, and nucleic acids; Biomembranes.
UNIT-III: Fundamentals of thermodynamics; Enzymes: classification, factors affecting
enzyme activity, enzyme kinetics, Structure and biological functions of vitamins and
hormones.
UNIT-IV: Metabolism of carbohydrates, lipids, proteins and nucleic acids. Mitochondrial
Electron transport chain and oxidative phosphorylation; DNA replication, transcription
and translation; recombinant DNA technology.
Suggested Readings
Conn EE & Stumpf PK. 1987. Outlines of Biochemistry. John Wiley.
Metzler DE. 2006. Biochemistry. Vols. I, II. Wiley International.
Nelson DL & Cox MM. 2004. Lehninger Principles of Biochemistry. 4th Ed. MacMillan.
Voet D, Voet JG & Pratt CW. 2007. Fundamentals of Biochemistry. John Wiley.

BIF 505/ STATISTICS FOR BIOLOGICAL SCIENCES 2+1 SEM - I

STAT 532 (To be taught by Statistics)
Objective
To understand the basic principles of statistics and mathematics and their applications in
relation to Biological system.
Theory
UNIT-I: Introduction to Statistical Bioinformatics, Principles of sampling from a
population; Random sampling.
UNIT-II: Frequency distributions: Graphical representations and Descriptive measures;
Standard Probability Distributions; Correlation and regression analysis.
UNIT-III: Hypothesis testing; Markov Models, Cluster Analysis: Hierarchical and Non-
Hierarchical methods.
UNIT-IV: Phylogenetic Analysis Tools: Maximum Likelihood, Parsimony methods.
Practical

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  Computational exercises on Random Sampling
 Construction and representation of frequency distributions
 Descriptive measures
 Probability distribution
Suggested Readings
Gupta SC & Kapoor VK. 2000. Fundamentals of Mathematical Statistics: A Modern
Approach. S. Chand & Co.
Warren JE & Gregory RG. 2005. Statistical Methods in Bioinformatics. Springer.

BIF 506 CONCEPTS IN COMPUTING 2+2 SEM - I

Objective
The objective of this course is to introduce the basic concepts of computing with
introduction to OS, graphics, networking and client-server technologies.
Theory
UNIT-I: Fundamentals of Computing; Introduction to Operating Systems: WINDOWS,
UNIX/Linux operating systems; Computer Security (hacking, cracking), Computer
Viruses.
UNIT-II: Computer Graphics: Visualization techniques - Software and Hardware,
Interactive Graphics; Viewing in three dimension; Raster algorithms; Rendering;
Animation; Image Processing with emphasis on biological systems.
UNIT-III: Computer Networking, Security of the network, Fire-walls, Network Goals,
Applications Network, Network architecture, Hierarchical networks, Ethernet and TCP/IP
family of protocols.
UNIT-IV: Use of INTERNET and WWW, Internet services.
Practical
 MS-Windows
 Linux, UNIX
 Network design
 Internet search
 Graphics and animation
Suggested Readings
David FR. 1997. Procedural Elements for Computer Graphics. WCB/McGraw-Hill.
Foley JD & Van Dam A. 1982. Fundamentals of Interactive Computer Graphics.
Addison-Wesley.
James FK & Keith WR. 2006. Computer Networking: A Top-Down Approach Featuring
the Internet. Prentice Hall.
Siever E. 2005. Linux in a Nutshell. O’Reilly.

BIF 507 PROGRAMMING LANGUAGES FOR 2+2 SEM - I

BIOINFORMATICS
Objective
Programming is a very significant area for bioinformatics and this course gives an
understanding for logics of programming and command-line and graphical GDIs.
Theory
UNIT-I: Programming in C: Pointers, pointers to functions, macro programming in C,
graphs, data structure - linked list, stack, queue, binary trees, threaded binary trees.
UNIT-II: File and exception handling in C, Programming in Visual Basic: Introduction to
Application Development using Visual Basic; Working with Code and Forms.
UNIT-III: Variables, Procedures and Controlling Program Executor; Standard Controls;
Data Access Using Data Control; Connecting to Database using VB.
UNIT-IV: Introduction to JAVA, variables, constants, control structures, input output,
classes. Jar and Java applets.
Practical
 Programming in C and Visual basic with special reference to database linking
 Small Java applets
Suggested Readings
Brian WK & Ritchie DM. 1988. C Programming Language. Prentice Hall.
Kanetkar. 2002. Let us C. BPB Publ.
Microsoft Developers Network (MSDN Digital Library). 2006. Microsoft.

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BIF 508/ FUNDAMENTALS OF MOLECULAR 3+0 SEM - I
MBB 502/ BIOLOGY
BIOCHEM 504 (To be taught jointly by Bioinformatics, Biochemistry and Molecular Biology &
Biotechnology)
Objective
To familiarize the students with the basic cellular processes at molecular level.
Theory
UNIT-I: Historical developments of molecular biology; nucleic acids as genetic material,
chemistry, structure and properties of DNA and RNA.
UNIT-II: Genome organization in prokaryotes and eukaryotes; repetitive and non-
repetitive DNA, satellite DNA; DNA replication, DNA polymerases, topoisomerases,
DNA ligase, reverse transcriptase, nucleases and restriction enzymes; site directed
mutagenesis, molecular mechanism of mutation, DNA repair mechanisms.
UNIT-III: Ribosomes structure and function, organization of ribosomal proteins and RNA
genes, transcription, RNA editing, RNA processing, etc; Genetic code, aminoacyl tRNA
synthases’ inhibitors of replication, transcription and translation.
UNIT-IV: Translation and post translational modifications; Regulation of gene expression
in prokaryotes and eukaryotes.
Suggested Readings
Lewin B. 2008. Gene IX. Peterson Publications/ Panima.
Malacinski GM & Freifelder D. 1998. Essentials of Molecular Biology. 3rd Ed. Jones &
Bartlett Publ.
Nelson DL & Cox MM. 2007. Lehninger’s Principles of Biochemistry. W.H. Freeman.
Primrose SB. 2001. Molecular Biotechnology. Panima.
Watson JD, Bakee TA, Bell SP, Gann A, Levine M & Losick R. 2008. Molecular Biology
of the Gene. 6th Ed. Pearson Edu. International.

BIF 509/ MATHEMATICS FOR BIOLOGICAL 2+0 SEM - I

STAT 533 SCIENCES
(To be taught by Statistics)
Objective
To understand and apply fundamental concepts of mathematics as applicable in Biology
and to acquaint about theoretical concepts of algebra and geometry and numerical
methods.
Theory
UNIT-I: Coordinate geometry with basic concepts of 2D and 3D geometry, Vector algebra
– Addition and subtraction of vectors, Dot and cross product, Scalar triple product.
UNIT-II: Matrix algebra: basic definitions, matrix operations, transpose of a matrix,
inverse of matrix, eigen values, Boolean algebra. Geometric and Arithmetic Progression.
UNIT-III: Solution of equation by bisection method, Iteration method, Newton Raphson
method, numerical differentiation.
UNIT-IV: Numerical integration- Trapezoidal rule, Simpson’s 1/3 and 3/8 rules, Runga
Kutta method of nth order. Fast Fourier transformation.
Suggested Readings
Babu CA & Seshan CR. 2006. New Engineering Mathematics. Narosa Publ.
Datta KB. 2002. Matrix and Linear Algebra. Prentice Hall.
Narayan S. 1980. Matrix Algebra. S. Chand & Co.
Rao S. 2006. Numerical Methods for Scientists and Engineers. Prentice Hall.

BIF 510/ IMMUNOLOGY ANDMOLECULAR DIAGNOSTICS 2+1 SEM - II

MBB 512/ (To be taught by Veterinary Microbiology)
BIOCHEM 506
Objective
To discuss the application of various immunological and molecular diagnostic tools.

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 Theory
UNIT-I: History and scope of immunology; Components of immune system: organs,
tissues and cells, Immunoglobulin structure and functions; Molecular organization of
immunoglobulins and classes of antibodies.
UNIT-II: Antibody diversity; antigens, haptens, antigen-antibody interactions;
immunoregulation and tolerance; Allergies and other hypersensitive responses;
Immunodeficiency; Vaccines.
UNIT-III: Application of immunology, immunological techniques, Principles of ELISA
and its applications; Monoclonal antibodies and their uses, molecular diagnostics;
Introduction to the basic principles of molecular technology and techniques used for
pathogen detection.
UNIT-IV: Basics and procedures of PCR, PCR based and hybridization based methods of
detection, microarrays based detection, multiplexing etc, detection of soil borne and seed
born infections, transgene detection in seed, planting material and processed food,
molecular detection of varietal impurities and seed admixtures in commercial
consignments.
Practical
 Preparation of buffers and reagents
 Serological tests such as bacterial slide agglutination, latex agglutination and agar gel
immunodiffusion
 Immunoassays including ELISA, western blotting, and fluorescent antibody test
 Hybridoma technique for production of monoclonal antibodies
 Recombinant protein antigen- production and immunization of laboratory animals
 Extraction of DNA/RNA from pathogenic microorganisms, PCR, genotyping,
diagnosis, etc.
Suggested Readings
Bloom BR & Lambert P-H. 2002. The Vaccine Book. Academic Press.
Elles R & Mountford R. 2004. Molecular Diagnosis of Genetic Disease. Humana Press.
Kindt TJ, Goldsby RA & Osbrne BA. 2007. Kuby’s Immunology. WH Freeman.
Levine MM, Kaper JB, Rappuoli R, Liu MA & Good MF. 2004. New Generation
Vaccines. 3rd Ed. Informa Healthcare.
Lowrie DB & Whalen R. 2000. DNA Vaccines. Humana Press.
Male D, Brostoff J, Roth DB & Roitt I. 2006. Immunology. Elsevier.
Rao JR, Fleming CC & Moore JE. 2006. Molecular Diagnostics. Horizon Bioscience.
Robinson A & Cranage MP. 2003. Vaccine Protocols. 2nd Ed. Humana Press.
Spinger TA, 1985. Hybridoma Technology in Biosciences and Medicine. Plenum Press.

BIF 511 INTRODUCTION TO DATABASE SYSTEMS 2+1 SEM - II

Objective
To familiarize the concept of RDBMS and to apply the database techniques to biological
databanks.
Theory
UNIT-I: Data Abstraction; Data Models; Instances and Schemes; E-R Model - Entity and
entity sets; Relations and relationship sets; E-R diagrams; Reducing E-R Diagrams to
tables; Network Data Model: Basic concepts; Hierarchical Data Model: Basic Concepts.
UNIT-II: Multimedia Databases - Basic Concepts and Applications; Indexing and
Hashing; Basic concepts (ISAM, B+ Tree indexed files, B Tree indexed files, Static Hash
functions, Dynamic Hash functions); Text Databases; Introduction to Distributed Database
Processing, Data Security.
UNIT-III: MySQL/MS-Access - Select Statements; Data Definition Statements; Data
Manipulation Statements; Data Control Statements; Other Database Objects (Views,
Sequences, Synonyms); Introduction to Application Development using Visual Basic;
Working with Code and Forms; Variables.
UNIT-IV: Procedures and Controlling Program Executor; Standard Controls; Data Access
Using Data Control; Connecting to Oracle Database using Visual Basic.
Practical
 Practical exercise using MySQL

6
  Design of database in MS-Access and MySQL
 Database linking
Suggested Readings
Date CJ. 1986. Introduction to Database Systems. Addison-Wesley.
Korth H & Silberschatz A. 2002. Database System Concepts. McGraw- Hill.
Martin D. 1986. Advanced Database Techniques. MIT Press.

BIF 512 COMPUTATIONAL AND SYSTEM BIOLOGY 2+2 SEM - II

Objective
To understand the computational aspects of structural biology; to familiarize the usage of
software for 3D structures of nucleic acids and proteins and to translate the sequence to
protein structure.
Theory
UNIT-I: Methods of single crystal X-ray Diffraction of macromolecules, NMR of
macromolecules Anatomy of Proteins - Ramachandran plot, Secondary structures, Motifs,
Domains, Tertiary and quaternary structures.
UNIT-II: Anatomy of DNA: A, B, Z DNA, DNA bending etc.; RNA structure; Structure
of Ribosome; Principles of Protein Folding; Structural data banks - Protein Data Bank,
Cambridge small molecular crystal structure data bank.
UNIT-III: Methods for Prediction of Secondary and Tertiary structures of Proteins, DNA,
RNA, Fold recognition, Ab initio methods for structure prediction; Homology modeling,
Methods for comparison of 3D structures of proteins.
UNIT-IV: Molecular interactions of Protein – Protein with special reference to signal
transduction and antigen-antibody interaction, Protein - DNA, Protein - carbohydrate,
DNA - small molecules. System modeling and metabolomics– concepts and principles.
Practical
 Usage of software for above topics
 Molecular Visualization tools: RasMol, QMol, Swiss PDB, Pymol
 Biomolecular Interaction Databases: BIND, DIP
 Structure Similarity Search Tools: CN3D, Vast Search
Suggested Readings
Fall CP. 2002. Computational Cell Biology. Springer.
Tsai CS. 2003. Computational Biochemistry. John Wiley & Sons.
Waterman MS. 1995. Introduction to Computational Biology: Maps, Sequences and
Genomes. CRC Press.

BIF 513 BIOMOLECULAR SEQUENCE ANALYSIS 1+1 SEM - I

Objective
To understand the local and multiple alignment concepts and to carry out multiple
sequence alignment.
Theory
UNIT-I: Analysis of protein and nucleic acid sequences, multiple alignment programs.
UNIT-II: Development of programs for analysis of nucleic acid sequences, Use of
EMBOSS package.
UNIT-III: Phylogenetic analysis – Elements of phylogenetic analysis, tree interpretation,
tree data analysis, alignment – building data model.
UNIT-IV: Extraction of phylogenetics data sets, Distance and character based methods.
Practical
 EMBOSS
 File Format Converter Tools: BABEL, ReadSeq
 Phylogenetic Analysis Tools: Phylip, NTSYS, PAUP
 CLUSTALW/CLUSTALX
Suggested Readings
Baxevanis AD & Ouellettee BFF. 2001. Bioinformatics: a Practical Guide to the Analysis
of Genes and Proteins. Wiley Interscience.
Mount DW. 2001. Bioinformatics: Sequence and Genome Analysis. Spring Harbor, CSHL
Press.
Nei M & Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford Univ. Press.

7
 Salemi M & Vandamme AM. 2003. The Phylogenetic Handbook – A Practical Approach
to DNA and Protein Phylogeny. Oxford Univ. Press.

BIF 514 DYNAMIC WEB-DESIGN 1+2 SEM - I

Objective
This course teaches the basic principles and application of various technologies used in
creation of dynamic web content.
Theory
UNIT-I: PERL: Strings, Numbers, and Variables. Variable Interpolation, Basic Input and
Output, File handles, Making Decisions, Conditional Blocks, Loops, Combining Loops
with Input, Standard Input and Output, Finding the Length of a Sequence File.
UNIT-II: Pattern Matching, Extracting Patterns, Arrays, Arrays and Lists, Split and Join,
Hashes, A Real-World Example, BioPERL; Applications.
UNIT-III: Creation, hosting and maintenance of web-site using HTML, XML, ASP, JSP.
UNIT-IV: Creation, hosting and maintenance of web-site PHP, PERL and CGI.
Practical
 Creation of Web-based applications, interactive and dynamic webpages
 Connecting databases using CGI scripting
 Creation and maintenance of web-sites using HTML, XML, ASP, PHP, PERL and
CGI
 Retrieval of specific information from web-sites using CGI scripts
Suggested Readings
Moorhouse M & Barry P. 2004. Bioinformatics, Biocomputing and Perl: An Introduction
to Bioinformatics. John Wiley & Sons.
Tisdall JD. 2001. Beginning Perl for Bioinformatics. O'Reilly.

BIF 515 BIOLOGICALDATABANKSANDDATAMINING 1+2 SEM - II

Objective
To understand the biological databases – types and formats and to learn the retrieval,
deposition and analysis of sequences and structures from biological databanks.
Theory
UNIT-I: Data warehousing, data capture, data analysis; Introduction to Nucleic Acid and
Protein Data Banks; Nucleic acid sequence data banks: Genbank, EMBL nucleotide
sequence data bank.
UNIT-II: AIDS Virus sequence data bank, rRNA data bank, Protein sequence data banks:
NBRF-PIR, SWISSPROT, Signal peptide data bank; Database Similarity Searches.
UNIT-III: BLAST, FASTA, PSI-BLAST algorithms; Pair wise sequence alignment -
NEEDLEMAN and Wunsch, Smith Waterman algorithms; Multiple sequence alignments
- CLUSTAL, Patterns, motifs and Profiles in sequences.
UNIT-IV: Derivation and searching; Derived Databases of patterns, motifs and profiles:
Prosite, Blocks, Prints-S, Pfam, etc.; Primer Design.
Practical
 Gene Information Resources
 Protein Information Resources
 Structural Databases
 Sequence Analysis and Database Similarity Search Tools: BLAST, PHI-BLAST, PSI-
BLAST, FASTA, EMBOSS, CLUSTAL, TCOFFEE
 Use of similarity, homology and alignment tools
Suggested Readings
Letovsky S. (Ed).1999. Bioinformatics: Databases and Systems. Kluwer.
LeÛn D & Markel S. 2003. Sequence Analysis in a Nutshell: A Guide to Common Tools
and Databases. O’Reilly.
NCBI(www.ncbi.nlm.nih.gov).
PUBMED (www.pubmedcentral.nih.gov) and database web-sites.

BIF 516 MOLECULAR MODELLING AND DRUG 2+2 SEM - I

DESIGN
Objective

8
 To understand the Modelling of small molecules; to understand the computational
chemistry principles and to familiarize the role of computers in drug-discovery process.

Theory
UNIT-I: Concepts of Molecular Modelling, Molecular structure and internal energy,
Application of molecular graphics.
UNIT-II: Energy minimization of small molecules, Use of Force Fields and MM methods,
Local and global energy minima. Techniques in MD and Monte Carlo. Simulation for
conformational analysis, Ab initio, DFT and semiempirical methods.
UNIT-III: Design of ligands, Drug-receptor interactions, Classical SAR/QSAR, Docking
of Molecules.
UNIT-IV: Role of computers in chemical research; Structure representation, SMILES;
Chemical Databases, 2D and 3D structures, reaction databases, search techniques,
similarity searches; Chemoinformatics tools for drug discovery.
Practical
 Modelling Tools: MODELLER, Geno3D
 Docking Tools: Chimera, Dock, AutoDock Tools, GRAMM, Hex, ArgusLab
 3D-Structure Optimization Tools: CHEMSKETCH, CHEM 3D, ISIS Draw,
CHEMDRAW
Suggested Readings
Bunin BA. 2006. Chemoinformatics: Theory, Practice and Products. Springer.
Gasteiger J & Engel T. 2003. Chemoinformatics: A Textbook. Wiley-VCH.
Hinchliffe A. 2003. Molecular Modelling for Beginners. John Wiley & Sons.
Leach AR. 1996. Molecular Modelling: Principles and Applications. Longman.

BIF 517/ GENOMICS AND PROTEOMICS 2+1 SEM - I

MBB 508 (To be taught jointly by Bioinformatics and Molecular Biology & Biotechnology)
Objective
To familiarize the students about the genomic and proteomic concepts and usage of
various algorithms and programmes in analysis of genomic and proteomic data.
Theory
UNIT-I: Genomics: Whole genome analysis and comparative genomics, classical ways of
genome analysis, large fragment genomic libraries; Physical mapping of genomes;
Genome sequencing, sequence assembly and annotation.
UNIT-II: Functional genomics: Candidate gene identification, DNA chips, Mutants and
RNAi, Metabolomics for elucidating metabolic pathways, etc.
UNIT-III: Proteomics - Introduction to basic proteomics technology, Bio-informatics in
Proteomics, Gene to Protein Function: a Roundtrip, Proteome analysis.
UNIT-IV: Linkage analysis, genotyping analysis, pharmacogenomics, human/plant
genome and science after genomic era; Applications of genomics and proteomics in
agriculture, human health and industry.
Practical
 Gene Prediction Tools: GENSCAN, GRAIL, FGENESH
 NCBI Genomic Resources
 Proteomics Tools: EXPASY, CDART
Suggested Readings
Azuaje F & Dopazo J. 2005. Data Analysis and Visualization in Genomics and
Proteomics. John Wiley & Sons.
Brown TA. 2007. Genome III. Garland Science Publ.
Campbell AM & Heyer L. 2004. Discovery Genomics, Proteomics and Bioinformatics.
Pearson Edu.
Gibson G & Muse SV. 2004. A Primer of Genome Science. Sinauer Associates.
Jollès P & Jörnvall H. 2000. Proteomics in Functional Genomics: Protein Structure
Analysis. Birkhäuser.
Kamp RM. 2004. Methods in Proteome and Protein Analysis. Springer.
Primrose SB & Twyman RM. 2007. Principles of Genome Analysis and Genomics.
Blackwell.
Sensen CW. 2005. Handbook of Genome Research. Vols. I, II. Wiley CVH.
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BIF 518 PHARMACOGENOMICS AND IPR 2+1 SEM - II
Objective
To understand the translation of Bioinformatics into commercial gains; to familiarize the
concepts of microarray – data acquisition and analysis and learn the IPR issues in
Biological sciences with special emphasis on bioinformatics.
Theory
UNIT-I: Bioinformatics companies, Genomes, transcriptomes and proteomes – their
applications in medicine and agriculture, disease monitoring, profile for therapeutic
molecular targeting.
UNIT-II: Diagnostic drug discovery and genomics. Pharmacogenomics and its
application. SNPs and their applications. Microarray and genome wide expression
analysis: Introduction to basic microarray technology, Bioinformatics in microarrays,
Getting started – target selection.
UNIT-III: Customised microarray design, Image processing and quantification,
Normalization and filtering, Exploratory statistical analysis, Public Microarray data
resources.
UNIT-IV: Patenting and data generation from patent literature for commercial benefits.
IPR, and bioinformatics. Bioinformatics patents.
Practical
 Microarray Analysis Tools: MAGICTool
 Stanford Microarray Database
 Gene Expression Omnibus
 Creation of an On-line company
Suggested Readings
Blalock EM. 2003. A Beginner's Guide to Microarrays. Springer.
Catania M. 2006. An A-Z Guide to Pharmacogenomics. American Association for Clinical
Chemistry.
Chakraborty C & Bhattachary A. 2005. Pharmacogenomics. Biotech Books.
Stekel D. 2003. Microarray Bioinformatics. Cambridge University Press.

10
 BIOINFORMATICS
List of Journals

 Bioinformatics - Oxford University Press

 BMC Bioinformatics - BioMed Central
 Briefings in Bioinformatics - Oxford University Press
 Briefings in Functional Genomics and Proteomics - Oxford University Press
 Computers in Biology and Medicine – Elsevier
 Journal of Bioinformatics and Computational Biology (JBCB) – World Scientific Publishers
 Journal of Biomedical Informatics – Elsevier
 Journal of Computational Biology - Mary Ann Liebert, Inc. publishers
 Journal of Molecular Modelling – Springer
 Nucleic Acids Research – Oxford Press
 Protein Engineering, Design and Selection (PEDS) – Oxford Press

e-Resources

 Bioinformatics.Org: The Open-Access Institute - http://bioinformatics.org/

 European Molecular Biology Network - http://www.embnet.org/
 European Bioinformatics Institute -http://www.ebi.ac.uk/
 The European Molecular Biology Laboratory - http://www.embl.org/
 International Society for Computational Biology - http://www.iscb.org/
 National Center for Biotechnology Information - http://www.ncbi.nlm.nih.gov/
 ExPASy Proteomics Server - http://us.expasy.org/
 Mouse Genome Informatics - http://www.informatics.jax.org/
 Center for Molecular Modeling - http://cmm.info.nih.gov/modeling/
 RCSB PDB - http://www.rcsb.org/pdb
 Bioinformatics resources -
http://www.biochem.ucl.ac.uk/bsm/BCSB/bioinfo_resources/bioinform_res.htm
 South African National Bioinformatics Institute - http://www.sanbi.ac.za/
 Swiss Institute of Bioinformatics - http://www.isb-sib.ch/
 Protein Structure Prediction Center - http://predictioncenter.llnl.gov/
 Programs for Genomic Applications -http://www.nhlbi.nih.gov/resources/pga/
 Computational Molecular Biology At NIH - http://molbio.info.nih.gov/molbio/
 Gene Ontology Home - http://www.geneontology.org/
 All About The Human Genome Project (HGP) - http://www.genome.gov/
 UCSC Genome Browser - http://genome.ucsc.edu/

11
 MOLECULAR BIOLOGY AND BIOTECHNOLOGY
Course Structure

COURSE NO. COURSE TITLE CREDITS SEM

MBB 501* PRINCIPLES OF BIOTECHNOLOGY 3+0 I
MBB 502*/  FUNDAMENTAL OF MOLECULAR BIOLOGY 3+0 I
BIOCHEM 504/
BIF 508
MBB 503 MOLECULAR CELL BIOLOGY 3+0 II
MBB 504 PLANT TISSUE CULTURE AND GENETIC 2+1 II
TRANSFORMATION
MBB 505* TECHNIQUES IN MOLECULAR BIOLOGY - I 0+3 I
MBB INDUSTRIAL BIOTECHNOLOGY 2+1 II
506/MICRO 505
MBB 507 MOLECULAR BREEDING 2+0 II
MBB 508/  GENOMICS & PROTEOMICS 2+1 I
BIF 517
MBB 509 TECHNIQUES IN MOLECULAR BIOLOGY - II 0+3 II
MBB 510 BIOSAFETY, IPR AND BIOETHICS 2+0 I
MBB 511/  ANIMAL BIOTECHNOLOGY 3+0 I
ABT 616
MBB 512/  IMMUNOLOGY AND MOLECULAR DIAGNOSTICS 2+1 II
BIOCHEM 506/
BIF 510
MBB 513 NANO-BIOTECHNOLOGY 3+0 I
MBB 514/  FOOD BIOTECHNOLOGY 2+1 I
FST 519
MBB 515/  BIOTECHNOLOGY OF HORTICULTURAL CROPS 2+1 II
FSC 509
MBB 553*/  BIOSTATISTICS AND COMPUTERS 2+1 I
STAT 534/
FST 531/
SOC 512
MBB 555/  INTRODUCTION TO BIOINFORMATICS 2+1 I
BIF 501/
ABT 608/
FSC 604
MBB 556 ENVIRONMENTAL BIOTECHNOLOGY 3+0 II
MMB 591 MASTER’S SEMINAR 1 I, II
MMB 599 MASTER’S RESEARCH 20 I, II
MBB 601 ADVANCES IN PLANT MOLECULAR BIOLOGY 3+0 I
MBB 602 ADVANCES IN GENETIC ENGINEERING 3+0 I
MBB 603 ADVANCES IN MICROBIAL BIOTECHNOLOGY 3+0 II
MBB 604/  ADVANCES IN CROP BIOTECHNOLOGY 3+0 I
VSC 604/
FLA 605
MBB 605/  ADVANCES IN FUNCTIONAL GENOMICS, 3+0 II
BIOCHEM 606/ PROTEOMICS AND METABOLOMICS
PP 602
MBB 606 COMMERCIAL PLANT TISSUE CULTURE 2+0 I
MBB 607/  ADVANCES IN ANIMAL BIOTECHNOLOGY 2+0 II
ABT 707
MBB 691 DOCTORAL SEMINAR I 1 I, II
12
 MBB 692 DOCTORAL SEMINAR II 1 I, II
MMB 699 DOCTORAL RESEARCH 45 I, II

SERVICE COURSE

PSMA 606 BIOTECHNOLOGY IN PLANTATION CROPS AND 1+1 II

SPICES
PP 603 MOLECULAR APPROACHES FOR IMPROVING 2+1 I
PHYSIOLOGICAL TRAITS (IN PART)
* Compulsory for Master’s programme; Compulsory for Doctoral programme - Any two courses of 600
series + Compulsory courses of M. Sc., if not studied earlier
To be taught by:  Bioinformatics, Biochemistry, Molecular Biology & Biotechnology;  Bioinformatics,
Molecular Biology & Biotechnology;  Animal Biotechnology;  Veterinary Microbiology;  Molecular
Biology & Biotechnology;  Molecular Biology & Biotechnology;  Statistics;  Bioinformatics,
Molecular Biology & Biotechnology;  Biochemistry, Molecular Biology & Biotechnology, Plant
Physiology

13
 MOLECULAR BIOLOGY AND BIOTECHNOLOGY
Course Contnts

MBB 501 PRINCIPLES OF BIOTECHNOLOGY 3+0 SEM - I

Objective
To familiarize the students with the fundamental principles of Biotechnology, various
developments in Biotechnology and its potential applications.
Theory
UNIT-I: History, scope and importance; DNA structure, function and metabolism.
UNIT-II: DNA modifying enzymes and vectors; Methods of recombinant DNA
technology; Nucleic acid hybridization; Gene libraries; PCR amplification; Plant and
animal cell and tissue culture techniques and their applications.
UNIT-III: Molecular markers and their applications; DNA sequencing; Applications of
gene cloning in basic and applied research; Genetic engineering and transgenics;
Introduction to Genomics, transcriptomics and proteomics.
UNIT-IV: General application of biotechnology in Agriculture, Medicine, Animal
husbandry, Environmental remediation, Energy production and Forensics; Public
perception of biotechnology; Bio-safety and bioethics issues; Intellectual property rights
in biotechnology.
Suggested Readings
Becker JM, Coldwell GA & Zachgo EA. 2007. Biotechnology – a Laboratory Course.
Academic Press.
Brown CM, Campbell I & Priest FG. 2005. Introduction to Biotechnology. Panima Publ.
Brown TA. Gene Cloning and DNA Analysis. 5th Ed. Blackwell Publ.
Dale JW & von Schantz M. 2002. From Genes to Genomes: Concepts and Applications of
DNA Technology. John Wiley & Sons.
Gupta PK. 2004. Biotechnology and Genomics. Rastogi Publ.
Sambrook J, Fritsch T & Maniatis T. 2001. Molecular Cloning – a Laboratory Manual.
2nd Ed. Cold Spring Harbour Laboratory Press.
Singh BD. 2007. Biotechnology Expanding Horiozon. Kalyani Publ.

MBB 502/ FUNDAMENTALSOFMOLECULARBIOLOGY 3+0 SEM - I

BIOCHEM 504/ (To be taught jointly by Molecular Biology & Biotechnology, Biochemistry and
BIF508 Bioinformatics)
Objective
To familiarize the students with the basic cellular processes at molecular level.
Theory
UNIT-I: Historical developments of molecular biology; nucleic acids as genetic material,
chemistry, structure and properties of DNA and RNA.
UNIT-II: Genome organization in prokaryotes and eukaryotes; repetitive and non-
repetitive DNA, satellite DNA; DNA replication, DNA polymerases, topoisomerases,
DNA ligase, reverse transcriptase, nucleases and restriction enzymes; site directed
mutagenesis, molecular mechanism of mutation, DNA repair mechanisms.
UNIT-III: Ribosomes structure and function, organization of ribosomal proteins and RNA
genes, transcription, RNA editing, RNA processing, etc; Genetic code, aminoacyl tRNA
synthases’ inhibitors of replication, transcription and translation.
UNIT-IV: Translation and post translational modifications; Regulation of gene expression
in prokaryotes and eukaryotes.
Suggested Readings
Lewin B. 2008. Gene IX. Peterson Publ. / Panima.
Malacinski GM & Freifelder D. 1998. Essentials of Molecular Biology. 3rd Ed. Jones &
Bartlett.
Nelson DL & Cox MM. 2007. Lehninger’s Principles of Biochemistry. W.H. Freeman.
Primrose SB. 2001. Molecular Biotechnology. Panima.
Watson JD, Bakee TA, Bell SP, Gann A, Levine M & Losick R. 2008.Molecular Biology
of the Gene. 6th Ed. Pearson Edu.

14
MBB 503 MOLECULAR CELL BIOLOGY 3+0 SEM - II
Objective
To familiarize the students with the cell biology at molecular level.
Theory
UNIT-I: General structure and constituents of cell; Similarities and distinction between
plant and animal cells; Cell wall, cell membrane, structure and composition of
biomembranes, cell surface related functions.
UNIT-II: Structure and function of major organelles: Nucleus, Chloroplasts,
Mitochondria, Ribosomes, Lysosomes, Peroxisomes, Endoplasmic reticulum,
Microbodies, Golgi apparatus, Vacuoles, etc.
UNIT-III: Organellar genomes and their manipulation; Ribosomes in relation to cell
growth and division; Cyto-skeletal elements.
UNIT-IV: Cell division and regulation of cell cycle; Membrane transport; Transport of
water, ion and biomolecules; Signal transduction mechanisms; Protein targeting.
Suggested Readings
Gupta PK. 2003. Cell and Molecular Biology. 2nd Ed. Rastogi Publ.
Lodish H. 2003. Molecular Cell Biology. 5th Ed. W.H. Freeman & Co.
Primrose SB. 2001. Molecular Biotechnology. Panima.

MBB 504 PLANT TISSUE CULTURE AND GENETIC 2+1 SEM - II

TRANSFORMATION
Objective
To familiarize the students and provide hands on training on various techniques of plant
tissue culture, genetic engineering and transformation.
Theory
UNIT-I: History of plant cell and tissue culture; Culture media; Various types of culture;
callus, suspension, nurse, root, meristem, etc.; In vitro differentiation: organogenesis and
somatic embryogenesis; Plant growth regulators: mode of action, effects on in vitro
culture and regeneration; Molecular basis of plant organ differentiation.
UNIT-II: Micropropagation; Anther and microspore culture; Somaclonal variation; In
vitro mutagenesis; In vitro fertilization; In vitro germplasm conservation; Production of
secondary metabolites; Synthetic seeds.
UNIT-III: Embryo rescue and wide hybridization; Protoplast culture and regeneration;
Somatic hybridization: protoplast fusion, cybrids, asymmetric hybrids, etc.
UNIT-IV: Methods of plant transformation; Vectors for plant transformation; Genetic and
molecular analyses of transgenics; Target traits and transgenic crops; Biosafety issues,
testing of transgenics, regulatory procedures for commercial approval.
Practical
 Laboratory set-up.
 Preparation of nutrient media; handling and sterilization of plant material;
inoculation, subculturing and plant regeneration.
 Anther and pollen culture.
 Embryo rescue.
 Suspension cultures and production of secondary metabolites.
 Protoplast isolation, culture and fusion.
 Gene transfer using different methods, reporter gene expression, selection of
transformed tissues/plants, molecular analysis.
Suggested Readings
Bhojwani SS. 1983. Plant Tissue Culture: Theory and Practice. Elsevier.
Christou P & Klee H. 2004. Handbook of Plant Biotechnology. John Wiley & Sons.
Dixon RA. 2003. Plant Cell Culture. IRL Press.
George EF, Hall MA & De Klerk GJ. 2008. Plant Propagation by Tissue Culture.
Agritech Publ.
Gupta PK. 2004. Biotechnology and Genomics. Rastogi Publ.
Herman EB. 2005-08. Media and Techniques for Growth, Regeneration and Storage.
Agritech Publ.
Pena L. 2004. Transgenic Plants: Methods and Protocols. Humana Press.

15
 Pierik RLM. 1997. In vitro Culture of Higher Plants. Kluwer.
Singh BD. 2007. Biotechnology: Expanding Horiozon. Kalyani.
MBB 505 TECHNIQUES IN MOLECULAR 0+3 SEM - I
BIOLOGY-I
(Pre-requisite MBB 501)
Objective
To provide hands-on training on basic molecular biology techniques.
Practical
UNIT-I: Good lab practices; Biochemical techniques: Preparation of buffers and reagents,
Principle of centrifugation, Chromatographic techniques (TLC, Gel Filtration
Chromatography, Ion exchange Chromatography, Affinity Chromatography).
UNIT-II: Gel electrophoresis- agarose and PAGE (nucleic acids and proteins); Growth of
bacterial culture and preparation of growth curve; Isolation of plasmid DNA from
bacteria; Growth of lambda phage and isolation of phage DNA; Restriction digestion of
plasmid and phage DNA; Isolation of high molecular weight DNA and analysis.
UNIT-III: Gene cloning – Recombinant DNA construction, transformation and selection
of transformants; PCR and optimization of factors affecting PCR.
UNIT-IV: Dot blot analysis; Southern hybridization; Northern hybridization; Western
blotting and ELISA; Radiation safety and non-radio isotopic procedure.
Suggested Readings
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA & Struhl K. 2002.
Short Protocols in Molecular Biology. John Wiley.
Kun LY. 2006. Microbial Biotechnology. World Scientific.
Sambrook J, Russel DW & Maniatis T. 2001. Molecular Cloning: A Laboratory Manual.
Cold Spring Harbour Laboratory Press.

MBB 506/MICRO 505 INDUSTRIAL BIOTECHNOLOGY 2+1 SEM - II

( To be taught jointly byMBB&B & Microbiology)
Objective
To familiarize students about microbial processes/systems/activities for the development
of industrially important products/ processes.
Theory
UNIT-I: Introduction, scope and historical developments; Isolation, screening and genetic
improvement and maintenance of industrially important organisms.
UNIT-II: Types fermentation systems; Bioreactor designs and operations; Production of
primary and secondary metabolites e.g alcohol, organic acids, organic solvents, amino
acids, enzymes, antibiotics.
UNIT-III: Production of fermented beverages, single cell protein; Recombinant DNA
technology based products, Biotransformation.
UNIT-IV: Overproduction of metabolites; Metabolic engineering of microbes for
production of novel products for industry; Downstream processing; Immobilization of
cells/enzymes.
UNIT-V: Industrial biotechnology for pollution control, treatment of industrial and other
wastes, Production of eco-friendly chemicals e.g biopesticides, bio-insecticides, bio-
fertilizers, bio-fuels, etc.
Practical
 Isolation of industrially important microorganisms, their maintenance and
improvement.
 Production of industrial compounds such as alcohol, beer, citric acid, lactic acid and
their recovery.
 Study of bio-reactors and their operations.
 Production of biofertilizers.
 Immobilization of cells and enzymes, studies on its kinetic behavior.
Suggested Readings
Cruger W & Cruger A. 2004. Biotechnology – A Textbook of Industrial Microbiology,
Panima.
Huffnagle GB & Wernick S. 2007. The Probiotics Revolution: The Definitive Guide to
Safe, Natural Health. Bantam Books.
Kun LY. 2006. Microbial Biotechnology. World Scientific.

16
 Primrose SB. 2001. Molecular Biotechnology. Panima.
Ward OP. 1989. Fermentation Biotechnology, Prentice Hall.

MBB 507 MOLECULAR BREEDING 2+0 SEM - II

Objective
To familiarize the students about the use of molecular biology tools in plant breeding.
Theory
UNIT-I: Principles of plant breeding; Breeding methods for self and cross pollinated
crops; Heterosis breeding; Limitations of conventional breeding; Aspects of molecular
breeding.
UNIT-II: Development of sequence based molecular markers - SSRs and SNPs; Advanced
methods of genotyping; Mapping genes for qualitative and quantitative traits.
UNIT-III: QTL mapping using structured populations; AB-QTL analysis; Association
mapping of QTL; Fine mapping of genes/QTL; Map based gene/QTL isolation and
development of gene based markers; Allele mining by TILLING and Eco-TILLING; Use
of markers in plant breeding.
UNIT-IV: Marker assisted selection (MAS) in backcross and heterosis breeding;
Transgenic breeding; Foreground and background selection; MAS for gene introgression
and pyramiding: MAS for specific traits with examples.
Suggested Readings
Chittaranjan K. 2006-07. Genome Mapping and Molecular Breeding in Plants. Vols. I-
VII. Springer.
Newbury HJ. 2003. Plant Molecular Breeding. Blackwell Publ.
Weising K, Nybom H, Wolff K & Kahl G. 2005. DNA Fingerprinting in Plants:
Principles, Methods and Applications. Taylor & Francis.

MBB 508/ GENOMICS AND PROTEOMICS 2+1 SEM - I

BIF 517 (To be taught jointly by Molecular Biology & Biotechnology and Bioinformatics)
Objective
To familiarize the students about the genomic and proteomic concepts and usage of
various algorithms and programmes in analysis of genomic and proteomic data.
Theory
UNIT-I: Genomics: Whole genome analysis and comparative genomics, classical ways of
genome analysis, large fragment genomic libraries; Physical mapping of genomes;
Genome sequencing, sequence assembly and annotation.
UNIT-II: Functional genomics: Candidate gene identification, DNA chips, Mutants and
RNAi, Metabolomics for elucidating metabolic pathways, etc.
UNIT-III: Proteomics - Introduction to basic proteomics technology, Bio-informatics in
Proteomics, Gene to Protein Function: a Roundtrip, Proteome analysis.
UNIT-IV: Linkage analysis, genotyping analysis, pharmacogenomics, human/plant
genome and science after genomic era; Applications of genomics and proteomics in
agriculture, human health and industry.
Practical
 Gene Prediction Tools: GENSCAN, GRAIL, FGENESH
 NCBI Genomic Resources
 Proteomics Tools: EXPASY, CDART
Suggested Readings
Azuaje F & Dopazo J. 2005. Data Analysis and Visualization in Genomics and
Proteomics. John Wiley & Sons.
Brown TA. 2007. Genome III. Garland Science Publ.
Campbell AM & Heyer L. 2004. Discovery Genomics, Proteomics and Bioinformatics.
Pearson Edu.
Gibson G & Muse SV. 2004. A Primer of Genome Science. Sinauer Associates.
Jollès P & Jörnvall H. 2000. Proteomics in Functional Genomics: Protein Structure
Analysis. Birkhäuser.
Kamp RM. 2004. Methods in Proteome and Protein Analysis. Springer.
Primrose SB & Twyman RM. 2007. Principles of Genome Analysis and Genomics.
Blackwell.
Sensen CW. 2005. Handbook of Genome Research. Vols. I, II. Wiley CVH.

17
MBB 509 TECHNIQUES IN MOLECULAR 0+3 SEM - II
BIOLOGY -II
(Pre-requisite MBB 505)
Objective
To provide hands-on training on various molecular techniques used in molecular breeding
and genomics.
Practical
UNIT-I: Construction of gene libraries; Synthesis and cloning of cDNA and RTPCR
analysis; Real time PCR and interpretation of data.
UNIT-II: Molecular markers (RAPD, SSR, AFLP etc) and their analysis; Case study of
SSR markers (linkage map, QTL analysis etc); SNP identification and analysis;
Microarray studies and use of relevant software.
UNIT-III: Proteomics (2D gels, mass spectrometry, etc.); RNAi (right from designing of
construct to the phenotyping of the plant); Yeast 1 and 2-hybrid interaction.
UNIT-IV: Generation and screening of mutants; Transposon mediated mutagenesis.
Suggested Readings
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA & Struhl K. 2002.
Short Protocols in Molecular Biology. Wiley.
Caldwell G, Williams SN & Caldwell K. 2006. Integrated Genomics: A Discovery-Based
Laboratory Course. John Wiley.
Sambrook J, Russel DW & Maniatis T. 2001. Molecular Cloning: a Laboratory Manual.
Cold Spring Harbour Laboratory Press.

MBB 510 BIOSAFETY, IPR AND BIOETHICS 2+0 SEM - I

Objective
To discuss about various aspects of biosafety regulations, IPR and bioethic concerns
arising from the commercialization of biotech products.
Theory
UNIT-I: Biosafety and risk assessment issues; Regulatory framework; National biosafety
policies and law, The Cartagena protocol on biosafety, WTO and other international
agreements related to biosafety, Cross border movement of germplasm; Risk management
issues - containment.
UNIT-II: General principles for the laboratory and environmental biosafety; Health
aspects; toxicology, allergenicity, antibiotic resistance, etc; Impact on environment: gene
flow in natural and artificial ecologies; Sources of gene escape, tolerance of target
organisms, creation of superweeds/superviruses, etc.
UNIT-III: Ecological aspects of GMOs and impact on biodiversity; Monitoring strategies
and methods for detecting transgenics; Radiation safety and nonradio isotopic procedure;
Benefits of transgenics to human health, society and the environment.
UNIT-IV: The WTO and other international agreements; Intellectual properties,
copyrights, trademarks, trade secrets, patents, geographical indications, etc; Protection of
plant variety and farmers right act; Indian patent act and amendments, patent filing;
Convention on biological diversity; Implications of intellectual property rights on the
commercialization of biotechnology products.
Suggested Readings
Singh BD. 2007. Biotechnology: Expanding Horizon. Kalyani.
http://patentoffice.nic.in
www.wipo.org
www.dbtindia.nic.in
www.dbtbiosafety.nic.in

MBB 511/ ANIMAL BIOTECHNOLOGY 3+0 SEM - I

ABT 616 (To be taught by Animal Biotechnology)
Objective
Intended to provide an overview and current developments in different areas of animal
biotechnology.
Theory

18
 UNIT-I: Structure of animal cell; History of animal cell culture; Cell culture media and
reagents, culture of mammalian cells, tissues and organs, primary culture, secondary
culture, continuous cell lines, suspension cultures, somatic cell cloning and hybridization,
transfection and transformation of cells, commercial scale production of animal cells,
application of animal cell culture for in vitro testing of drugs, testing of toxicity of
environmental pollutants in cell culture, application of cell culture technology in
production of human and animal viral vaccines and pharmaceutical proteins.
UNIT-II: Introduction to immune system, cellular and hormonal immune response, history
of development of vaccines, introduction to the concept of vaccines,conventional methods
of animal vaccine production, recombinant approaches to vaccine production, hybridoma
technology, phage display technology for production of antibodies, antigen-antibody
based diagnostic assays including radioimmunoassays and enzyme immunoassays,
immunoblotting, nucleic acid based diagnostic methods, commercial scale production of
diagnostic antigens and antisera, animal disease diagnostic kits, probiotics.
UNIT-III: Structure of sperms and ovum, cryopreservation of sperms and ova of livestock,
artificial insemination, super ovulation, in vitro fertilization, culture of embryos,
cryopreservation of embryos, embryo transfer, embryo-spliting, embryo sexing, transgenic
manipulation of animal embryos, different applications of transgenic animal technology,
animal viral vectors, animal cloning basic concept, cloning from- embryonic cells and
adult cells, cloning of different animals, cloning for conservation for conservation
endangered species, ethical, social and moral issues related to cloning, in situ and ex situ
preservation of germplasm, in utero testing of foetus for genetic defects, pregnancy
diagnostic kits, anti-fertility animal vaccines, gene knock out technology and animal
models for human genetic disorders.
UNIT-IV: Introduction to different breeds of cattle, buffalo, sheep, goats, pigs, camels,
horses, canines and poultry, genetic characterization of livestock breeds, marker assisted
breeding of livestock, introduction to animal genomics, different methods for
characterization of animal genomes, SNP, STR, QTL, RFLP, RAPD, genetic basis for
disease resistance, Transgenic animal production and application in expression of
therapeutic proteins. Immunological and nucleic acid based methods for identification of
animal species, detection of meat adulteration using DNA based methods, detection
food/feed adulteration with animal protein, identification of wild animal species using
DNA based methods using different parts including bones, hair, blood, skin and other
parts confiscated by anti-poaching agencies.
Suggested Readings
Gordon I. 2005. Reproductive Techniques in Farm Animals. CABI.
Kindt TJ, Goldsby RA & Osbrne BA. 2007. Kuby Immunology. WH Freeman.
Kun LY. 2006. Microbial Biotechnology. World Scientific.
Levine MM, Kaper JB, Rappuoli R, Liu MA, Good MF. 2004. New Generation Vaccines.
3rd Ed. Informa Healthcare.
Lincoln PJ & Thomson J. 1998. Forensic DNA Profiling Protocols. Humana Press.
Portner R. 2007. Animal Cell Biotechnology. Humana Press.
Spinger TA. 1985. Hybridoma Technology in Biosciences and Medicine. Plenum Press.
Twyman RM. 2003. Advanced Molecular Biology. Bios Scientific.

MBB 512/ IMMUNOLOGY AND 2+1 SEM - II

BIOCHEM 506/ MOLECULAR DIAGNOSTICS
BIF 510 (To be taught by Veterinary Microbiology)
Objective
To discuss the application of various immunological and molecular diagnostic tools.
Theory
UNIT-I: History and scope of immunology; Components of immune system: organs,
tissues and cells, Immunoglobulin structure and functions; Molecular organization of
immunoglobulins and classes of antibodies.
UNIT-II: Antibody diversity; antigens, haptens, antigens- antibody interactions;
immunoregulation and tolerance; Allergies and other hypersensitive responses;
Immunodeficiency; Vaccines.
UNIT-III: Application of immunology, immunological techniques, Principles of ELISA
and its applications; Monoclonal antibodies and their uses, molecular diagnostics;

19
 Introduction to the basic principles of molecular technology and techniques used for
pathogen detection.
UNIT-IV: Basics and procedures of PCR, PCR based and hybridization based methods of
detection, microarrays based detection, multiplexing etc, detection of soil borne and seed
born infections, transgene detection in seed, planting material and processed food,
molecular detection of varietal impurities and seed admixtures in commercial
consignments.
Practical
 Preparation of buffers and reagents.
 Serological tests such as bacterial slide agglutination, latex agglutination and agar gel
immunodiffusion.
 Immunoassays including ELISA, western blotting, and fluorescent antibody test.
 Hybridoma technique for production of monoclonal antibodies.
 Recombinant protein antigen- production and immunization of laboratory animals.
 Extraction of DNA/RNA from pathogenic microorganisms, PCR, genotyping,
diagnosis, etc.
Suggested Readings
Bloom BR & Lambert P-H. 2002. The Vaccine Book. Academic Press.
Elles R & Mountford R. 2004. Molecular Diagnosis of Genetic Disease. Humana Press.
Kindt TJ, Goldsby RA & Osbrne BA. 2007. Kuby’s Immunology. WH Freeman.
Levine MM, Kaper JB, Rappuoli R, Liu MA & Good MF. 2004. New Generation
Vaccines. 3rd Ed. Informa Healthcare.
Lowrie DB & Whalen R. 2000. DNA Vaccines. Humana Press.
Male D, Brostoff J, Roth DB & Roitt I. 2006. Immunology. Elsevier.
Rao JR, Fleming CC & Moore JE. 2006. Molecular Diagnostics. Horizon Bioscience.
Robinson A & Cranage MP. 2003. Vaccine Protocols. 2nd Ed. Humana Press.
Spinger TA, 1985. Hybridoma Technology in Biosciences and Medicine. Plenum Press.

MBB 513 NANO-BIOTECHNOLOGY 3+0 SEM - I

Objective
Understanding the molecular techniques involved in structure and functions of nano-
biomolecules in cells such as DNA, RNA and proteins.
Theory
UNIT-I: Introduction to Biomacromolecules: The modern concepts to describe the
conformation and dynamics of biological macromolecules: scattering techniques,
micromanipulation techniques, drug delivery applications etc.
UNIT-II: Cellular engineering: signal transduction in biological systems, feedback control
signaling pathways, cell-cell interactions etc. Effects of physical, chemical and electrical
stimuli on cell function and gene regulation.
UNIT-III: Chemical, physical and biological properties of biomaterials and bioresponse:
biomineralization, biosynthesis, and properties of natural materials (proteins, DNA, and
polysaccharides), structure-property relationships in polymeric materials (synthetic
polymers and structural proteins); Aerosol properties, application and dynamics;
Statistical Mechanics in Biological Systems.
UNIT-IV: Preparation and characterization of nanoparticles; Nanoparticular carrier
systems; Micro- and Nano-fluidics; Drug and gene delivery system; Microfabrication,
Biosensors, Chip technologies, Nano- imaging, Metabolic engineering and Gene therapy.
Suggested Readings
Nalwa HS. 2005. Handbook of Nanostructured Biomaterials and their Applications in
Nanobiotechnology. American Scientific Publ.
Niemeyer CM & Mirkin CA. 2005. Nanobiotechnology. Wiley Interscience.

MBB 514/ FOOD BIOTECHNOLOGY 2+1 SEM - I

FST 519 (To be taught by Molecular Biology & Biotechnology)
Objective
This is a special course designed for students of FST to acquaint with the fundamentals
and application of biotechnology in relation to raw materials for food processing,
nutrition, food fermentations, waste utilization and better use of genetic resources.
Theory

20
 UNIT-I: Prospects of biotechnology- definition, history, scope and applications,
Application of biotechnology in food (food industries), pharmaceuticals and agriculture,
food/plant waste utilization, biogas plants; organisms and their utilization for the
production of fermented foods and beverages.
UNIT-II: Structure and function of nucleic acids; Recombinant DNA technology:
restriction and other DNA modifying enzymes, vectors, DNA libraries, gene cloning,
PCR, gene expression, etc.
UNIT-III: Applications of genetical control mechanism in industrial fermentation process,
(induction, manipulation and recombination); Biomass production by using various
microorganisms; Cell and tissue culture, Secondary metabolites synthesis; Transgenic
organisms (GMOs): methods, applications, safety aspects, etc.
UNIT-IV: Biotechnology for enhancing quality attributes of food; Enzyme biotechnology;
Enzyme immobilization techniques and their applications in food industry; Microbial
transformations; Potential impact and future aspects of biotechnology in food industry.
Practical
Study of auxotroph, Micropropogation through tissue culture, Strain improvement through
U.V. mutation, Mutagenesis using chemical mutagens (ethidium bromide), Isolation and
analysis of genomic DNA from E.coli and Bacillus cereus, Isolation of protoplasts,
Introduction to the techniques of ELISA / Southern blot / DNA fingerprinting / Agarose
gel electrophoresis, etc.
Suggested Readings
Bains W. 1993. Biotechnology from A to Z. Oxford Univ. Press.
Joshi VK & Pandey A.1999. Biotechnology: Food Fermentation. Vols. I, II. Education
Publ.
Knorr D.1982. Food Biotechnology. Marcel Dekker.
Lee BH. 1996. Fundamentals of Food Biotechnology. VCH.
Perlman D. 1977-1979. Annual Reports of Fermentation Processes.
Prescott SC & Dunn CG. 1959. Industrial Microbiology. McGraw Hill.
Ward OP. 1989. Fermentation Biotechnology. Prentice Hall.

MBB 515/ BIOTECHNOLOGY OF HORTICULTURAL 2+1 SEM - II

FSC 509 CROPS
(To be taught by Molecular Biology & Biotechnology)
Objective
Understanding the principles, theoretical aspects and developing skills in biotechnology of
horticultural crops.
Theory
UNIT-I : Harnessing bio-technology in horticultural crops, influence of plant materials,
physical, chemical factors and growth regulators on growth and development of plant cell,
tissue and organ culture.
UNIT-II: Callus culture – types, cell division, differentiation, morphogenesis,
organogenesis, embryogenesis, artificial seeds.
UNIT-III: Use of bioreactors and in vitro methods for production of secondary
metabolites, suspension culture, nutrition of tissues and cells, regeneration of tissues, ex
vitro, establishment of tissue cultured plants, rapid clonal propagation.
UNIT-IV: Physiology of hardening - hardening and field transfer, organ culture –
meristem, embryo, anther, ovule culture, embryo rescue, somaclonal variation, haploids,
in vitro mutation, , cryopreservation.
UNIT-V: Wide hybridization, in vitro pollination and fertilization, protoplast culture and
fusion, identification of somatic hybrids and cybrids, genetic engineering and
transformation, use of molecular markers, achievements of biotechnology in horticultural
crops.
Practical
An exposure to low cost, commercial and homestead tissue culture laboratories, media
preparation, inoculation of explants for clonal propagation, callus induction and culture,
regeneration of plantlets from callus, sub-culturing, techniques on anther, ovule, embryo
culture, somaclonal variation, protoplast isolation and culture, genetic transformation.
Suggested Readings
Bajaj YPS. (Ed.). 1989. Biotechnology in Agriculture and Forestry. Vol. V, Fruits.
Springer.

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 Brown TA. 2001. Gene Cloning and DNA Analysis and Introduction. Blackwell Publ.
Chopra VL & Nasim A. 1990. Genetic Engineering and Biotechnology – Concepts,
Methods and Applications. Oxford & IBH.
Gorden H & Rubsell S. 1960. Hormones and Cell Culture. AB Book Publ.
Keshavachandran R & Peter KV. 2008. Plant Biotechnology: Tissue Culture and Gene
Transfer. Orient & Longman (Universal Press).
Keshavachandran R, Nazeem PA, Girija D, John PS & Peter KV. 2007. Recent Trends in
Biotechnology of Horticultural Crops. Vols. I, II. New India Publ. Agency.
Parthasarathy VA, Bose TK, Deka PC, Das P, Mitra SK & Mohanadas S. 2001.
Biotechnology of Horticultural Crops. Vols. I-III. Naya Prokash.
Pierik RLM. 1987. In vitro Culture of Higher Plants. Martinus Nijhoff Publ.
Skoog F & Miller CO. 1957. Chemical Regulation of Growth and Formation in Plant
Tissue Culture in vitro. Symp. Soc. Exp. Biol. 11: 118-131.
Vasil TK, Vasi M, While DNR & Bery HR.1979. Somatic Hybridization and Genetic
Manipulation in Plants. Plant Regulation and World Agriculture. Planum Press.
Williamson R. 1981-86. Genetic Engineering. Vols. I-V. Academic Press.

MBB 553/ BIOSTATISTICS AND COMPUTERS 2+1 SEM - I

STAT534/ (To be taught by Statistics)
FST531/
SOC512
Objective
This is a course of applied Statistics to be taken by M.Sc. students of Biotechnology, FST
and Sociology departments of CoBS&H. They are exposed to various statistical methods
to analyze their experimental data.
Theory
UNIT-I: Aims, scope and idea of elementary statistics; Measures of central tendency and
dispersion, skewness and kurtosis.
UNIT-II: Concept of probability and probability laws, mathematical expectation,
moments, moments generating function; Standard probability distributions- Binomial,
Poisson and Normal distributions.
UNIT-III: Tests of significance based on Z, ᵡ2, t and F statistics; Correlation and
regression, curve fitting by least squares methods.
UNIT-IV: Basic principles, organization and operational aspects of computers, operating
systems. Introduction to MS-Office, MS-Word, MS-Excel. Statistical Data analysis based
on above topics through MS-Excel.
Practical
 Data analysis using probability, test of significance
 Correlation and regression analysis
 Usage of MS-Windows
 Exercises on test processing, spreadsheet and DBMS
 SPSS
Suggested Readings
Agarwal BL. 2003. Basic Statistics. New Age.
Gupta SP. 2004. Statistical Methods. S. Chand & Sons.
Dutta NK. 2002. Fundamentals of Bio-Statistics. Kanishka Publ.,Wiley Eastern.

MBB 555/ INTRODUCTION TO BIOINFORMATICS 2+1 SEM - I

BIF 501/ (To be taught jointly by Molecular Biology & Biotechnology,
ABT 608/ Bioinformatics)
FSC 604
Objective
To impart an introductory knowledge about the subject of bioinformatics to the students
studying any discipline of science.
Theory
UNIT-I: Introduction, biological databases – primary, secondary and structural, Protein
and Gene Information Resources – PIR, SWISSPROT, PDB, genebank, DDBJ.
Specialized genomic resources.

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 UNIT-II: DNA sequence analysis, cDNA libraries and EST, EST analysis, pairwise
alignment techniques, database searching, multiple sequence alignment.
UNIT-III: Secondary database searching, building search protocol, computer aided drug
design – basic principles, docking, QSAR.
UNIT-IV: Analysis packages – commercial databases and packages, GPL software for
Bioinformatics, web-based analysis tools.
Practical
 Usage of NCBI resources
 Retrival of sequence/structure from databases
 Visualization of structures
 Docking of ligand receptors
 BLAST exercises.
Suggested Readings
Attwood TK & Parry-Smith DJ. 2003. Introduction to Bioinformatics. Pearson Edu.
Rastogi SC, Mendiratta N & Rastogi P. 2004. Bioinformatics: Concepts, Skills and
Applications. CBS.

MBB 556 ENVIRONMENTAL BIOTECHNOLOGY 3+0 SEM - II

Objective
To apprise the students about the role of biotechnology in environment management for
sustainable eco-system and human welfare.
Theory
UNIT-I: Basic concepts and environmental issues; types of environmental pollution;
problems arising from high-input agriculture; methodology of environmental
management; air and water pollution and its control; waste water treatment - physical,
chemical and biological processes; need for water and natural resource management.
UNIT-II: Microbiology and use of micro-organisms in waste treatment; biodegradation;
degradation of Xenobiotic, surfactants; bioremediation of soil & water contaminated with
oils, pesticides & toxic chemicals, detergents etc; aerobic processes (activated sludge,
oxidation ditches, trickling filter, rotating drums, etc); anaerobic processes: digestion,
filteration, etc.
UNIT-III: Renewable and non-Renewable resources of energy; energy from solid waste;
conventional fuels and their environmental impact; biogas; microbial hydrogen
production; conversion of sugar to alcohol; gasohol; biodegradation of lignin and
cellulose; biopesticides; biofertilizers; composting; vermiculture, etc.
UNIT-IV: Treatment schemes of domestic waste and industrial effluents; food, feed and
energy from solid waste; bioleaching; enrichment of ores by microorganisms; global
environmental problems: ozone depletion, UV-B, greenhouse effects, and acid rain;
biodiversity and its conservation; biotechnological approaches for the management
environmental problems.
Suggested Readings
Evans GM & Furlong JC. 2002. Environmental Biotechnology: Theory and Application.
Wiley International.
Jordening H-J & Winter J. 2006. Environmental Biotechnology: Concepts and
Applications. Wiley-VCH Verlag.

MBB 601 ADVANCES IN PLANT 3+0 SEM - I

MOLECULAR BIOLOGY
(Pre-requisite MBB 501)
Objective

To discuss the specialized topics and recent advances in the field of plant molecular
biology.
Theory
UNIT-I: Arabidopsis in molecular biology, Forward and Reverse Genetic Approaches,
Transcriptional and post-transcriptional regulation of gene expression, isolation of
promoters and other regulatory elements.
UNIT-II: RNA interference, Transcriptional gene silencing, Transcript and protein
analysis, use of transcript profiling to study biological systems.

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 UNIT-III: Hormone regulatory pathways: Ethylene, Cytokinin, Auxin and ABA, SA and
JA; ABC Model of Floral Development, Molecular basis of self incompatibility,
Regulation of flowering: photoperiod, vernalization, circadian rhythms.
UNIT-IV: Molecular biology of abiotic stress responses: Cold, high temperature,
submergence, salinity and drought; Molecular Biology of plant-pathogen interactions,
molecular biology of Agrobacterium Infection, Molecular biology of Rhizobium infection
(molecular mechanisms in symbiosis), Programmed cell death in development and
defense.
Suggested Readings
Buchanan B, Gruissen W & Jones R. 2000. Biochemistry and Molecular Biology of
Plants. American Society of Plant Physiologists, USA.
Lewin B. 2008. Gene IX. Peterson Publications/ Panima.
Malacinski GM & Freifelder D. 1998. Essentials of Molecular Biology. 3rd Ed. Jones &
Bartlett Publ.
Nelson DL & Cox MM. 2007. Lehninger’s Principles of Biochemistry. WH Freeman &
Co.
Watson JD, Bakee TA, Bell SP, Gann A, Levine M & Losick R. 2008. Molecular Biology
of the Gene. 6th Ed. Pearson Edu.

MBB 602 ADVANCES IN GENETIC ENGINEERING 3+0 SEM – I

(Pre-requisite MBB 501)
Objective
To discuss the specialized topics and advances in field of genetic engineering and their
application in plant improvement.
Theory
UNIT-I: General overview of transgenic plants; Case studies: Genetic engineering of
herbicide resistance, Transgenic plants resistant to insects/pests, Genetic engineering of
abiotic stress tolerance, Engineering food crops for quality, Genetically engineered
pollination control, Induction of male sterility in plants.
UNIT-II: Molecular farming of plants for applications in veterinary and human medicine
systems: Boosting heterologous protein production in transgenics, Rapid production of
specific vaccines, High-yield production of therapeutic proteins in chloroplasts.
UNIT-III: Recent developments in plant transformation strategies; Role of antisense and
RNAi-based gene silencing in crop improvement; Regulated and tissue-specific
expression of transgenes for crop improvement; Gene stacking; Pathway engineering;
Marker-free transgenic development strategies; High throughput phenotyping of
transgenic plants.
UNIT-IV: Field studies with transgenic crops; Environmental issues associated with
transgenic crops; Food and feed safety issues associated with transgenic crops; Risk
assessment of transgenic food crops.
Suggested Readings
Christou P & Klee H. 2004. Handbook of Plant Biotechnology. John Wiley & Sons.
Specific journals mentioned later.

MBB 603 ADVANCES IN MICROBIAL 3+0 SEM - II

BIOTECHNOLOGY
(Pre-requisite MBB 501)
Objective
To discuss specialized topics about industrially important microorganisms.
Theory
UNIT-I: Fermentative metabolism and development of bioprocessing technology,
processing and production of recombinant products; isolation, preservation and
improvement of industrially important microorganisms.
UNIT-II: Immobilization of enzymes and cells; Batch, plug flow and chemostate cultures;
Computer simulations; Fed-batch and mixed cultures; Scale-up principles; Down stream
processing etc.
UNIT-III: Current advances in production of antibiotics, vaccines, and biocides; Steroid
transformation; Bioreactors; Bioprocess engineering; Production of non-microbial origin
products by genetically engineered microorganisms.

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 UNIT-IV: Concept of probiotics and applications of new tools of biotechnology for
quality feed/food production; Microorganisms and proteins used in probiotics; Lactic acid
bacteria as live vaccines; Factors affecting delignification; Bioconversion of substrates,
anti-nutritional factors present in feeds; Microbial detoxification of aflatoxins; Single cell
protein, Bioinsecticides; Biofertilizers; Recent advances in microbial biotechnology.
Suggested Readings
Specific journals and published references.

MBB 604/ ADVANCES IN CROP BIOTECHNOLOGY 3+0 SEM – I

(Pre-requisite MBB 501)
VSC604/
FLA 605
Objective
To discuss specialized topics on the application of molecular tools in breeding of specific
crops.
Theory
UNIT-I: Conventional versus non-conventional methods for crop improvement; Present
status and recent developments on available tissue culture, transformation, molecular
marker and genomic tools for crop improvement.
UNIT-II: Genetic engineering for resistance against abiotic (drought, salinity, flooding,
temperature, etc) and biotic (insect pests, fungal, viral and bacterial diseases, weeds, etc)
stresses; Genetic Engineering for increasing crop productivity by manipulation of
photosynthesis, nitrogen fixation and nutrient uptake efficiency; Genetic engineering for
quality improvement (protein, essential amino acids, vitamins, mineral nutrients, etc);
edible vaccines, etc.
UNIT-III: Molecular breeding: constructing molecular maps; integrating genetic, physical
and molecular maps; diversity assessment and phylogenetic analysis; molecular tagging of
genes/traits; selected examples on marker assisted selection of qualitative and quantitative
traits.
UNIT-IV: Discussion on application of molecular, transformation and genomic tools for
the genetic enhancement in some major cereal, legume, oilseed, vegetable and
horticultural crops.
Suggested Readings
Specific journals and published references.

MBB 605/ ADVANCES IN FUNCTIONAL GENOMICS, 3+0 SEM - II

BIOCHEM 606/ PROTEOMICS AND METABOLOMICS
PP 602 (Pre-requisite MBB 501)
(To be taught jointly by Molecular Biology & Biotechnology,
Biochemistry, Plant Physiology)
Objective
To discuss recent advances and applications of functional genomics and proteomics in
agriculture, medicine and industry.
Theory
UNIT-I: Genome sequencing and functional genomics; Human, animal, plant, bacterial
and yeast genome projects; genome annotation; ab initio gene discovery; functional
annotation and gene family clusters; etc.
UNIT-II: Functional analysis of genes; RNA-mediated interference; gene knockoffs; Gene
traps/ T-DNA insertion lines; homologous recombination; microarray profiling; SAGE;
SNPs/variation; yeast-two hybrid screening; gene expression and transcript profiling; EST
contigs; EcoTILLING; allele/gene mining; synteny and comparative genomics; Genome
evolution, speciation and domestication etc.
UNIT-III: Proteomics: protein annotation; protein separation and 2D PAGE; mass
spectroscopy; protein microarrays; protein interactive maps; structural proteomics: protein
structure determination, prediction and threading, software and data analysis/
management, etc.
UNIT-IV: Metabolic pathway engineering, Discussion on selected papers on functional
genomics, metabolomics, proteomics, integrative genomics etc.
Suggested Readings

25
 Specific journals and published references.

MBB 606 COMMERCIAL PLANT TISSUE CULTURE 2+0 SEM – I

(Pre-requisite MBB 501)
Objective
To discuss the commercial applications of plant tissue culture in agriculture, medicine and
industry.
Theory
UNIT-I: Micropropagation of commercially important plant species; plant multiplication,
hardening, and transplantation; genetic fidelity; scaling up and cost reduction; bioreactors;
synthetic seeds; management and marketing.
UNIT-II: Production of useful compounds via biotransformation and secondary metabolite
production: suspension cultures, immobilization, examples of chemicals being produced
for use in pharmacy, medicine and industry.
UNIT-III: Value-addition by transformation; development, production and release of
transgenic plants; patent, bio-safety, regulatory, environmental and ethic issues;
management and commercialization.
UNIT-IV: Some case studies on success stories on commercial applications of plant tissue
culture. Visits to some tissue culture based commercial units/industries.
Suggested Readings
Specific journals and published references.

MBB 607/ ADVANCES IN ANIMAL BIOTECHNOLOGY 2+0 SEM - II

ABT707 (To be taught by Animal Biotechnology)
(Pre-requisite MBB 501)
Objective
Intended to provide cutting edge knowledge on advances in different areas of animal
biotechnology.
Theory
UNIT-I: Advances in animal cell culture technology, suspension culture technology,
advances in commercial scale productions of mammalian cells.
UNIT-II: Advances in cell cloning and cell hybridization, advances in monoclonal
antibody production technology, Advances in diagnostic technology, Computational
vaccinology, reverse genetics based vaccines.
UNIT-III: Advances in embryo manipulation, knock out and knock in technology,
advances in animal cloning technology, stem cell technology, Advances in development of
animal models for human diseases using transgenic animal technology.
UNIT-IV: Advances in genetic basis for animal disease resistance, Molecular methods for
animal forensics, Advances in animal genomics, proteomics.
Suggested Readings
Selected articles from journals.

26
PLANT MOLECULAR BIOLOGY & BIOTECHNOLOGY
List of Journals

 Advances in Botanical Research

 Advances in Enzyme Regulation
 Advances in Enzymology
 Advances in Genetics
 Agricultural and Biological Research
 Analytical Biochemistry
 Annals of Botany
 Archives of Biochemistry and Biophysics
 Archives of Microbiology
 Biochemical and Biophysical Research Communication
 Biochemical Genetics
 Biochemistry
 Biotechnology and Bioengineering
 Critical Reviews in Plant Sciences
 Crop Science
 EMBO Journal
 Euphytica
 Genetic and Plant Breeding
 Genome
 Indian Journal of Genetics and Plant Breeding
 Journal of Biotechnology
 Journal of Experimental Botany
 Journal of General Microbiology
 Journal of Heredity
 Journal of Plant Biochemistry and Biotechnology
 Journal of Plant Biology
 Molecular and Cellular Biochemistry
 Molecular Breeding
 Molecular Genetics and Genomics
 Nature
 Nature Biotechnology
 Plant Cell
 Plant Molecular Biology
 Plant Physiology
 Plant Physiology and Biochemistry
 Proceedings of The National Academy of Sciences (USA)
 Science
 Trends in Biochemical Sciences
 Trends in Biotechnology
 Trends in Cell Biology
 Trends in Food Science and Technology
 Trends in Genetics
 Trends in Microbiology
 Trends in Plant Sciences
e-Resources

 National Center for Biotechnology Information

o http://www.ncbi.nlm.nih.gov/
 The World Wide Web Virtual Library: Biotechnology.
o http://www.cato.com/biotech/

27
 The Transgenic/Targeted Mutation Database (TBASE)
o http://www.bis.med.jhmi.edu/Dan/tbase/tbase.html
 Primer on Molecular Genetics
o http://www.bis.med.jhmi.edu/Dan/DOE/intro.html.
 Bioportal
o http://bioportal.gc.ca/english/BioPortalHome.asp
 Access Excellence
o http://www.gene.com/ae
 BioTech Biosources Database: Indiana University
o http://biotech.chem.indiana.edu/
 Information Systems for Biotechnology
o http://gophisb.biochem.vt.edu/
 All About The Human Genome Project (HGP)
o http://www.genome.gov/
 Human Genome Project at the Sanger Institute
o http://www.sanger.ac.uk/HGP/
 UCSC Genome Browser
o http://genome.ucsc.edu/
 Gramene
o www.gramene.org/
 The Institute for Genomic Research
o www.tigr.org

Suggested Broad Topics for Master’s and Doctoral Research

 Micropropagation of important crop plants, cash crops, ornamentals, forest and horticultural
trees, medicinal and aromatic plants.
 Development of transgenics in field crops for resistance against biotic and abiotic stresses, and
to improve the nutritional quality, etc.
 DNA fingerprinting of important plant species and germplasm.
 Development of molecular markers (SNP, SSR, transposable elements, etc) and their
utilization for genetic diversity and phylogenetic analysis.
 Molecular mapping and marker-assisted selection for major-gene traits in crop species.
 Value-addition including biopesticides, biofertilizers, biofuels, biodegradable plastics,
secondary metabolites, etc.
 Genome sequencing and functional analysis of genes of important organisms.
 Allele mining, proteomics, genomics and metabolic engineering for crop improvement.
 Immobilization of enzymes/microorganisms.
 Protein engineering.
 To develop crops with improved mineral (Fe, Zn, Vitamin A, etc) bioavailbility.
 Biodiversity and conservation of endangered plant species.
 Bioprocess engineering and down stream processing.

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