Plant Biotechnology – PG Courses – Centre for Plant Molecular Biology and Biotechnology

Brief details on PG programme on CPMB&B

In 1988 the Department of Biotechnology, Government of India, New Delhi sanctioned the “Postgraduate Education and Training Programme” leading to M.Sc., in Agricultural Biotechnology which gave a national colour to the biotechnology education at TNAU.

Name of the Program	Year of starting	Approved strength as on 2019
M.Sc., (Agriculture) in Biotechnology	1987	TNAU – 10 JNU – 15
Ph. D., (Plant Biotechnology)	1991	5

PG Courses offered:

M. Sc., (Ag.) in Biotechnology

Ph. D., (Plant Biotechnology)

Courses offered

M.Sc. (Ag.) Biotechnology (Semester System, 2019)

S. No.	Course No.	Course Title	Credit hours
1.	MBB 501	Principles of Biotechnology (also offered to M.Sc.(Ag.) Crop Physiology, M.Sc.(Ag.) Nano Science & Technology, Ph.D (Plant Pathology), Ph.D (Agrl. Entomology)	2+1
2.	MBB 502	Fundamentals of Molecular Biology	2+0
3.	MBB 503	Molecular Cell Biology	2+0
4.	MBB 504	Plant Tissue Culture and Genetic Transformation	2+1
5.	MBB 505	Techniques in Molecular Biology	0+3
6.	MBB 507	Molecular Breeding	2+0
7.	MBB 508	Genomics and Proteomics	2+0
8.	MBB 512	Immunology and Molecular Diagnostics	2+1
9.	PGS 504	Basic Concepts in Laboratory Techniques	0+1

Ph. D., (Ag.) Biotechnology (Semester System, 2019)

S. No.	Course No.	Course Title	Credit hours
1.	MBB 601	Advances In Plant Molecular Biology	3+0
2.	MBB 602	Advances In Genetic Engineering	3+0
3.	MBB 603	Advances In Microbial Biotechnology	3+0
4.	MBB 604	Advances In Crop Biotechnology	2+0
5.	MBB 605	Advances in Genomics and Bioinformatics	3+0
6.	MBB 606	Commercial Plant Tissue Culture	1+0

Programme Outcomes (PO) of M. Sc., (Ag.) in Biotechnology

PO1	Knowledge Development: Applying the mechanisms and principles learnt to solve the problems in agriculture by using biotechnological techniques and tools.
PO2	Understanding the problems and finding out solutions: Identifying the research gaps in the agricultural field by practical exposure and working out the methodology for solving the problems through literature collection and experimentation.
PO3	Conducting research for solving the problems: After identifying a research problem, formulation of a research proposal by collecting literature and deriving the methodologies for implementing the research through several experiments, collection of data, analysis of data and finally interpreting the data for getting a solution to the research problem.
PO4	Gaining knowledge on modern tools and techniques: While solving new research issues methodologies will be optimized, new tools may be developed, undergoing the usage of sophisticated equipments and valuable softwares / tools to attain the solutions scientifically.
PO5	Work efficiency: Students’ working efficiency will be improved either individually or working under team environment. Understanding the value of time and the productivity will be increased.
PO6	Professional Ethics: Apply ethical principles and commit to follow professional ethics and norms and guidelines in the practice of biotechnology.
PO7	Communication skills: Solutions found out for the research problems will be effectively communicated by way of writing research articles and presentations.
PO8	Biotechnology and society: Apply reasoning for the issues, informed by the contextual knowledge of the problems in hand and assess the risk associated with the societal, health, safety, legal and cultural issues of the problems and the consequent responsibilities relevant to the professional practice of the discipline.
PO9	Environment and sustainability: Understand the impact of the technological solutions developed through biotechnology in contexts of society and the environment, and demonstrate the knowledge need for sustainable development in judicious use of biotechnology tools and technique.
PO10	Life-long learning: Understanding the dynamism of biological sciences through change in technology besides developing positive attitude so as to prepare and engage in adapting to such recurring changes through the process of life-long learning.

M.Sc., (Ag.) in Biotechnology: Programme Specific Outcomes (PSO)

PSO1	Impart a high quality education in biotechnology among students to meet out future challenges in agriculture.
PSO2	Understand the nature and basic concepts of cell biology, Biochemistry, Molecular biology and bioinformatics.
PSO3	Analyze the complex problems of agriculture and address issues through use of modern tools and techniques in biotechnology.
PSO4	Perform experimental procedures as per the established laboratory standards in the areas of Biochemistry, Molecular biology, Plant Tissue Culture, Genetic Engineering, Molecular Ecology, Molecular Marker Technology and Bioinformatics.
PSO5	Understand the applications of biotechnology in all spheres of agriculture and develop crops with improved productivity thereby increasing farmers’ income, better human health and decreased environmental pollution.

Syllabus

M.Sc. (Ag.) Biotechnology (List of courses-Semester System, 2019)

S. No.	Course No.	Course Title	Credit hours
I. Major courses (20)
1.	MBB 501	Principles of Biotechnology	2+1
2.	MBB 502	Fundamentals of Molecular Biology	2+0
3.	MBB 503	Molecular Cell Biology	2+0
4.	MBB 504	Plant Tissue Culture and Genetic Transformation	2+1
5.	MBB 505	Techniques in Molecular Biology	0+3
6.	MBB 507	Molecular Breeding	2+0
7.	MBB 508	Genomics and Proteomics	2+0
8.	MBB 512	Immunology and Molecular Diagnostics	2+1
Total Credits			14+6
II. Minor courses (9)
1.	PLP 501	Principles of Plant Physiology	2+1
2.	BIC 510	Plant Biochemistry	2+1
3.	BIF 501	Introduction to Bioinformatics*	2+1
4.	GPB 503	Principles of Plant Breeding*	2+1
Total Credits			6+3
III. Supporting courses (5)
1.	STA 501	Applied Statistical methods	1+1
2.	STA 503	Design of Experiments	1+1
3.	STA 504	Computer applications in Statistics	0+1
Total Credits			2+3
IV. Seminar			1+0
V. Research			0+20
Total Credits			23+32=55

*Minor courses (Optional can be exercised for one course among the two)

Compulsory Non-credit courses

S. No.	Course No.	Course Title	Credit hours
1.	PGS 501	Library and Information Services	0+1
2.	PGS 502	Technical Writing and Communication Skills	0+1
3.	PGS 503	Intellectual Property and Its Management in Agriculture (E Course)	1+0
4.	PGS 504	Basic Concepts in Laboratory Techniques	0+1
5.	PGS 505	Agricultural Research, Research Ethics and Rural Development Programmes (E Course)	1+0
6.	PGS 506	Disaster Management (E Course)	1+0

M.Sc. (Ag.) Biotechnology

Course Contents

Major courses

MBB 501 Principles of Biotechnology (2+1)
OBJECTIVE
To familiarize the students with the fundamental principles of Biotechnology, various developments in Biotechnology and its potential applications.
THEORY
Unit I : Introduction & DNA structure
History, scope and importance; DNA structure, function and metabolism.
Unit II : Recombinant DNA technology
DNA modifying enzymes and vectors; Gene cloning- vectors, restriction enzymes; Methods of recombinant DNA technology; Nucleic acid hybridization; Gene libraries; PCR amplification; Applications of gene cloning in basic and applied research.
Unit III : Molecular Markers
Molecular markers and their applications; DNA sequencing; Genomics, transcriptomics and proteomics.
Unit IV : Plant Tissue culture and Plant Transformation
Plant cell and tissue culture techniques and their applications. Genetic Engineering and Transgenics.
Unit V : Applications of Biotechnology, Biosafety & IPR
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.
PRACTICALS
Isolation of genomic and plasmid DNA – Gel electrophoresis techniques – Restriction enzyme digestion, ligation, transformation and screening of transformants – PCR and molecular marker analysis – Plant tissue culture: media preparation, cell and explant culture, regeneration and transformation.
LECTURE SCHEDULE
1.	Introduction to biotechnology The concept of biotechnology and its definition
2.	History and the latest developments in biotechnology
3.	DNA structure, function and metabolism
4.	Central dogma of life- Replication, Transcription-Translation – protein synthesis.
5.	DNA modifying enzymes and vectors
6.	Recombinant DNA technology – plasmid and bacteriophage as cloning vectors.
7.	Vectors for large inserts, Probes, Expression vectors
8.	Reverse transcriptase and cDNA libraries
9.	Nucleic acid hybridization – methods and uses
10.	Gene libraries – construction and screening
11.	PCR amplification- principles
12.	Methods and applications of PCR
13.	Plant cell and tissue culture- introduction
14.	Plant cell culture- techniques and applications
15.	Plant cell and tissue culture success stories
16.	Animal cell culture – techniques and methods
17.	Mid Semester Examination
18.	Molecular markers – introduction
19.	Types of markers and their applications
20.	DNA sequencing- principles and methods
21.	Gene cloning – introduction and methods
22.	Applications of gene cloning in basic and applied research
23.	Genetic engineering and transgenics
24.	Direct gene transfer methods in plants – microinjection, electroporation and biolistic.
25.	Indirect method-Agrobacterium mediated gene transfer
26.	Gene transfer methods in animals – microinjection, PEG and viral mediated transfection
27.	Genomics- principles and applications
28.	Proteomics- principles and applications
29.	Transcriptomics- principles and applications
30.	Achievements and recent developments of genetic engineering in agriculture
31.	Achievements and recent developments of genetic engineering in medicine and animal husbandry
32.	Achievements and recent developments of genetic engineering in environmental remediation, energy production and forensics
33.	Public perception of biotechnology
34.	Biosafety and bioethics issues
PRACTICAL SCHEDULE
1.	Preparation of reagents of DNA extraction from plant tissue-leaf
2.	Isolation of genomic DNA from Plant
3.	Quantification of DNA (colorimetric/spectrophotometric) and Agarose Gel electrophoresis
4.	Restriction digestion of genomic DNA
5.	Isolation of plasmid DNA and electrophoresis
6.	Competent cell preparation
7.	Ligation, transformation and Screening of transformants
8.	Preparation of Crystal toxin protein from Bt
9.	SDS-PAGE for protein analysis
10.	DNA fingerprinting using PCR
11.	NTSys – analysis of diversity in crop plants
12.	Preparation of stock solutions for MS medium
13.	MS medium preparation
14.	Inoculation of explant-shoot tip, meristem tip and embryo
15.	Demonstration of biolistic and Agrobacterium mediated transformation
16.	Visit to commercial plant tissue culture laboratory
17.	Final Practical Examination
SUGGESTED READINGS
1.	Audric, G. and Ciel, D. 2010. Bioengineering: Principles, Methodologies and Applications (Biotechnology in Agriculture, Industry and Medicine), Nova Science Pub Inc.
2.	Becker JM, Coldwell GA & Zachgo EA. 2007. Biotechnology – A Laboratory Course.Academic Press.
3.	Bernard R. G., Jack J. P. and Cheryl L. P. 2009. Molecular Biotechnology: Principles and Applications of Recombinant DNA, American Society of Microbiology.
4.	Brown CM, Campbell I & Priest FG. 2005. Introduction to Biotechnology. Panima Pub.
5.	Brown TA. 2006. Gene Cloning and DNA Analysis. 5th Ed. Blackwell Publishing.
6.	Dale JW & von Schantz M. 2002. From Genes to Genomes: Concepts and Applications of DNA Technology. John Wiley & Sons.
7.	Gupta PK. 2004. Biotechnology and Genomics.Rastogi Publications.
8.	Rastogi, S. C. 2009. Biotechnology: Principles and Applications. Alpha Science Int’l Ltd.
9.	Sambrook J, Fritsch T &Maniatis T. 2001. Molecular Cloning – a Laboratory Manual. 2nd Ed. Cold Spring Harbour Laboratory Press.
10.	Singh BD. 2007. Biotechnology Expanding Horiozon. Kalyani Publishers.
SUGGESTED WEBSITES
1.	http://www.studentsguide.in/biotechnology/biotechnology-onlinetest.html
2.	http://www.123genomics.com/learning.html
3.	http://www.protocol-online.org/prot/Molecular_Biology
4.	http://askabiologist.asu.edu/expstuff/mamajis/index.html
5.	http://www.biotechnologyonline.gov.au/biotec/ethics.html

MBB 502 Fundamentals of Molecular Biology		(2+0)
OBJECTIVE
The objectives of this course are to make students understand how molecular machines are constructed and regulated so that they can accurately copy, repair, and interpret genomic information in prokaryotes and eukaryotic cells. Further, to appreciate the subject of molecular biology as a dynamic and ever-changing experimental science.
THEORY
Unit I : Chemistry of nucleic acids and its structure
Historical developments of molecular biology; Nucleic acids as genetic material; Chemistry; purines and pyrimidines-nucleosides and nucleotides; structure and properties of DNA and RNA; primary structure; secondary structure; tertiary structure.
Unit II : Genome organization and DNA replication
Genome organization in prokaryotes and eukaryotes; Genome packaging-Chromatin structure and function- Genome complexity-C value and C-value paradox; DNA re-association kinetics- Analysis of repetitive sequences. DNA replication- mode of replication; enzymology of DNA replication-initiation, elongation and termination in prokaryotes and eukaryotes. PCR-principles and applications. DNA damage-types and repair mechanisms-Recombination.
Unit III : Molecular events of transcription and RNA processing
Transcription process in prokaryotes; Promoters; RNA polymerase; RNA processing; Splicing; Reverse transcriptase; RNA editing; Eukaryotic transcription; eukaryotic promoters and enhancers. Nuclear export of mRNA-mRNA stability and degradation
Unit IV : Molecular events of translation
Ribosomes structure and function; Organization of ribosomal proteins and RNA genes; Genetic code – properties; Aminoacyl tRNA synthases. Translation and post-translational modifications; formation of initiation complex; elongation and termination; Protein stability- Protein turnover and degradation
Unit V : Gene Expression and its regulation
Gene regulation – Operon concept; molecular structure and regulation of lac Operon; Attenuation of trp operon; Small RNA mediated regulation (siRNA, miRNA, psi RNA etc.,). Important features of gene regulation in eukaryotes. Families of DNA binding transcription factors- Interaction of regulatory transcription factors with DNA: properties and mechanism of activation and repression.
LECTURE SCHEDULE
1.	Historical developments of molecular biology
2.	Nucleic acids as genetic material-experimental evidences
3.	Chemistry of nucleic acids- Sugars, purines and pyrimidines-nucleosides and nucleotides. Properties of DNA and RNA.
4.	Structure – primary structure; secondary structure; tertiary structure
5.	Genome organization in prokaryotes and eukaryotes
6.	Genome packaging-Chromatin structure and function
7.	Genome complexity-C value and C-value paradox; DNA re-association kinetics- Analysis of repetitive sequences
8.	DNA replication- classical experiments
9.	Models of replication; Mechanism of replication in prokaryotes
10.	DNA replication in eukaryotes
11.	PCR-principles and applications
12.	DNA damage-types and repair mechanisms
13.	Recombination: Chi sequences in prokaryotes; Homologous, non-homologous and site specific recombination
14.	Transcription-Prokaryotic RNA polymerase-sigma factors, promoters and consensus. Mechanism of transcription in prokaryotes
15. Transcription in eukaryotes-promoters, transcription factors, proximal elements and long range regulatory elements
16.	Mechanism of transcription in eukaryotes- initiation, elongation and termination
17.	Mid-semester examination
18.	Post transcriptional processing- Splicing, capping, cleavage and polyadenylation
19.	Post transcriptional processing of rRNA and tRNA
20.	RNA editing-insertion, deletion and base substitution
21.	Nuclear export of mRNA-mRNA stability and degradation
22.	Ribosome structure-function and characteristics. Translation-in prokaryotes
23.	Genetic code – properties; Aminoacyl tRNA synthases. pooling of charged tRNAs
24.	Translation in prokaryotes-30S and 70S initiation complex formation
25.	Translation in eukaryotes-40S and 80S initiation complex formation
26.	Elongation-translocation -transpeptidation and termination of translation
27.	Post translational modifications of proteins
28.	Protein stability- Protein turnover and degradation
29.	Regulation of gene expression and check points – overview
30.	Operon concept; molecular structure and regulation of lac Operon
31.	Gene regulation – Trp operon- repressible operon concept- Attenuation
32.	Important features of gene regulation in eukaryotes-regulatory RNA and RNA interference mechanisms, miRNA, non-coding RNA; Silencers and insulators, enhancers
33.	Families of DNA binding transcription factors- Interaction of regulatory transcription factors with DNA- Helix-turn-helix, helix-loop-helix, homeodomain; zinc fingers, basic DNA binding domains, nuclear receptors.
34.	Properties and mechanism of activation and repression- Ligand-mediated transcription regulation by nuclear receptors
SUGGESTED READINGS
1.	Allison, L.A. 2011. Fundamentals of Molecular Biology. (2nd Edition) John Wiley and Sons
2.	Krebs, J.E, Goldstein, E.S, Kilpatrick, S.T. 2017. Lewin’s Genes XII. Jones and Bartlett Publishers, Inc., p.838
3.	Malacinski, GM (2015) Essentials of Molecular Biology(4th Student edition) Jones and Bartlett Publishers, Inc.
4.	McLennan A, Bates A, Turner P and White, M (2012). BIOS Instant Notes in Molecular Biology, Taylor & Francis publishers.
5.	Nelson D.L and M.M. Cox. 2017. Lehninger Principles of Biochemistry, (7th Edn.) W. H. Freeman and Company, New York, USA. p.1328
6.	Weaver, RF (2012) Molecular Biology (5th edition). McGraw Hill Higher Education Inc.
7.	Watson JD, Baker TA, Bell SP, Gann A, Levine M &Losick R (2014) Molecular Biology of the Gene, 7th Edition, Cold Spring Harbor Laboratory Press, New York.
SUGGESTED WEBSITES
1.	www.dnalc.org
2.	www.hhmi.org/biointeractive/dna-collection
3.	www.johnkyrk.com
4.	www.dnatutorial.com

MBB 503 Molecular Cell Biology	(2+0)
OBJECTIVE
Students will understand structural and functional properties of cells and cell organelles, in addition to the properties of differentiated cell systems and tissues.
THEORY
Unit I : Basics of cell biology
Origin of life and hierarchy in life – Evolution of eukaryotic cell – Structure of basic cell and special features of prokaryotes, plant and animal cells – History of cell science
Unit II : Structure and function of cell organelles
Composition of Cells- Chemistry of a cell- – Biomembrane system- Basic structure of cytoplasmic cell organelles and their function – Cytoskeleton network – Chromosomes, variations in chromosome – Ultra structure and functions of Nucleus
Unit III : Cell Transport and Cell signalling
Transport of molecules between and within the cell- Endocytosis – Cell to cell communication- Cell receptors- overview of Cell signaling and Protein sorting in cells – Cell junctions
Unit IV : Cell cycle and Division
Cytoskeleton and Cell Movement – Cell cycle – Cell cycle checkpoints – Events of Mitosis, Meiosis and Fertilization-Basics of embryology – developmental biology of C. elegans and plants, Cell diversification in the early animal embryo, cell determination, Cell growth conditions and characteristics.
Unit V : Cell death, stem cell biology and Cancer
Programmed Cell Death – cell renewal – Stem Cells and its applications- Cancer: different types and stages and treatment- role of oncogenes and tumour suppressor genes

LECTURE SCHEDULE
1.		Origin of life and hierarchy in life- Evolution of eukaryotic cell
2.		Structure of basic cell and special features of prokaryotes
3.		Special features of animal and plant cells
4.		Different kinds of cells and their modifications in plants
5.		History of cell science
6.		Biomembrane system
7.		Structure and functions of plant cell wall
8.		Structure and function of ER, Golgi complex
9.		Structure and function of Mitochondria
10.		Structure and function of Choloplasts and other plastids
11.		Structure and function of Vacuoles, lysosomes, Cytoskeleton network
12.		Chromosomes and variations in chromosome
13.		Ultra structure and functions of Nucleus
14.		Transport of molecules between and within the cell
15.		Bulk transport mechanisms – Exocytosis and Endocytosis
16.		Cell junctions
17.		Mid-semester examination
18.		Cell to cell communication
19.		Types and functions of Cell receptors
20.		Overview of Cell signaling mechanisms: Autocrine, Paracrine and Endocrine
21.		Basics of Protein sorting in a cell
22.		Cell Movement
23.		Cell cycle and its check points
24.		Molecular basis of Mitosis and Meiosis
25.		Fertilization in plants and animals
26.		Basics of embryology
27.		Developmental biology of C. elegans
28.		Developmental biology of Arabidopsis and plants
29.		Cell diversification in the early animal embryo, cell determination
30.		Cell growth conditions and characteristics
31.		Programmed Cell Death (Apoptosis)
32.		Stem Cells and its applications
33.		Cancer: different types, stages and treatment
34.		Role of oncogenes and tumour suppressor genes in cancer development
SUGGESTED READINGS
1.	Harvey Lodish , Arnold Berk, Chris Kaiser, Monty Krieger, Anthony Bretscher, Hidde L.Ploegh, Angelika Amon , and Matthew P. Scott. 2012. Molecular Cell Biology Seventh Edition W. H. Freeman 973 p.
2.	Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D Watson 2007. Molecular Biology of the Cell Fifth Edition. Garland Scie nce New York
3.	Bruce Alberts, Dennis Bray, Karen Hopkin and Alexander D Johnson. 2013. Essential Cell Biology, 4th Edition, Garland Science; 4 edition 865p.
4.	Geoffrey M Cooper. 2000. The Cell – A Molecular Approach Boston University. Sunderland. (MA): Sinauer Associates; USA.
SUGGESTED WEBSITES
1.		http://www.cellbio.com/
2.		http://www.molbiolcell.org/
3.		http://www.nature.com/molcellbio/index.html
4.		http://www.cellbio.annualreviews.org/
5.		http://www.biology-questions-and-answers.com/cell-biology-review.html

MBB 504 Plant Tissue Culture And Genetic Transformation (2+1)
OBJECTIVE
To familiarize the students and provide hands on training on various techniques of plant tissue culture, genetic engineering and transformation.
THEORY
Unit I : Concepts, methods of plant regeneration & techniques in plant tissue culture
History of plant tissue culture-concepts-Tissue culture media- components- plant growth regulators and their effects in vitro. In vitro morphogenesis– organogenesis and somatic embryogenesis. Molecular basis of cytodifferentiation, plant organ differentiation and somatic embryogenesis-synthetic seeds-callus and suspension culture- production of secondary metabolites.
Unit II : Plant tissue culture techniques for crop improvement
Micropropagation- Meristem tip culture and virus indexing Anther and microspore culture- Ovule, ovary and endosperm culture In vitro fertilization- Embryo rescue and wide hybridization- Protoplast culture and fusion techniques-application-Somaclonal variation- In vitro mutagenesis- In vitro germplasm conservation; TC industries
Unit III : Plant genetic transformation
Plant transformation methods – Agrobacterium mediated plant transformation, co-integrate and binary vector system – Direct gene transfer methods – biolistic gun, microinjection and electroporation. Chloroplast transformation. Transgene design-Promoters & Marker genes. Factors influencing transgene expression. Analysis of transgenic plants.
Unit IV : Engineering crops for stress tolerance and quality enhancement
Engineering for biotic stress resistance-Engineering for abiotic stress resistance – genes involved in biotic and abiotic stress resistance. Engineering for herbicide tolerance. Nutritional improvement – biofortification – vitamins, minerals, engineering seed storage proteins – cereals and pulses, manipulation of fatty acid and starch biosynthesis. Enhancement of shelf life – fruits and vegetables.
Unit V : Recent trends in transgenic technology
Molecular pharming – plant production of vaccines, antibodies and therapeutic proteins. Biosafety of transgenic plants – regulation of transgenic plants in India. Advanced technologies – cis genesis and intragenesis; Generation of marker free transgenic plants; Genome editing technology, CRISPR/Cas etc.
PRACTICALS
Tissue culture Laboratory set-up-Preparation of stock solutions and nutrient media- Handling and sterilization of plant material. Initiation of callus culture – shoot tip culture; Micropropagation-suspension culture- Synthetic seeds- anther culture-embryo culture. Regeneration, rooting and hardening of TC plants –In vitro selection for abiotic stress tolerance; Cloning gene of interest in a plant transformation vector – mobilization of transformation vector into Agrobacterium through triparental mating and electroporation. Confirmation of transconjugants and transformants; Agrobacterium mediated transformation – co-cultivation – selection of transformed tissues – regeneration of transformed tissues. Particle bombardment mediated transformation – bombardment – selection of bombarded tissues – regeneration of transformed tissues; Isolation of genomic DNA from transgenic plants – PCR, Southern hybridization analyses
LECTURE SCHEDULE
1.		Introduction–History of plant tissue culture- Concepts in plant tissue culture
2.		Tissue culture media-components-inorganic and organic additions
3.		Plant growth regulators and their effects in vitro
4.		In vitro morphogenesis – organogenesis and somatic embryogenesis
5.		Molecular basis of cytodifferentiation
6.		Molecular basis of plant organ differentiation
7.		Molecular basis of somatic embryogenesis-Synthetic seeds
8.		Callus and suspension culture- production of secondary metabolites
9.		Micro propagation-stages, micro propagation in banana and ornamental plants
10.		Meristem tip culture for virus elimination, virus indexing
11.		Anther and microspore culture
12.		Ovule, ovary and endosperm culture
13.		Embryo culture, embryo rescue and wide hybridization-In vitro fertilization
14.		Protoplast culture and fusion techniques- and applications
15.		Somaclonal variation-Causes-types-applications. In vitro mutagenesis
16.		In vitro germplasm conservation- normal, slow and rapid cryopreservation methods
17.		Mid Semester Examination
18.		Agrobacterium mediated plant transformation
19.		Direct gene transfer methods – Biolistic gun, microinjection and fusion
20.		Chloroplast transformation
21.		Transgene design-Promoters & Marker genes
22.		Factors influencing transgene expression
23.		Analysis of transgenic plants
24.		Engineering crops for biotic stress resistance
25.		Engineering crops for abiotic stress resistance.
26.		Engineering herbicilde tolerance
27.		Nutritional improvement – Biofortification – vitamins, minerals
28.		Engineering seed storage proteins in cereals and pulses
29.		Manipulation of fatty acid biosynthesis and starch biosynthesis
30.		Enhancement of shelf life in fruits and vegetables
31.		Molecular pharming – plant production of vaccines, antibodies and therapeutic proteins
32.		Biosafety of transgenic plants – regulation of transgenic plants in India
33.		Cis genesis and intragenesis, generation of marker free transgenic plants
34.		Genome editing technology – CRISPR/Cas
PRACTICAL SCHEDULE
1.		Tissue culture Laboratory set-up and preparation of stock solutions for medium preparation
2.		Preparation of nutrient media
3.		Callus culture in medicinal plant
4.		Nodal culture in chrysanthemum
5.		Micro propagation in banana
6.		Anther culture in Rice
7.		Embryo culture
8.		In vitro screening for abiotic stress tolerance
9.		Cloning gene of interest in a plant transformation vector -Restriction, Elution, ligation and bacterial transformation
10.		Mobilization of transformation vector into Agrobacterium through triparental mating
11.		Isolation of DNA from Agrobacterium strain &Restriction analysis of isolated binary vector
12.		Agrobacterium mediated transformation – preparation of explants
13.		Co-cultivation, Selection & Regeneration of transformed tissues
14.		Particle bombardment mediated transformation – preparation of target tissues
15.		Isolation of genomic DNA from transgenic plants and PCR
16.		Southern blotting & hybridization analysis
17.		Final Practical Examination
SUGGESTED READINGS
1.		Bhojwani and Dantu (2013). Plant Tissue Culture: an Introductory Text, Springer, New Delhi.
2.		Bhojwani, S.S and Razdan. M.K. (2009). Plant Tissue Culture-Theory and Practice. Elsevier India Pvt. Ltd.
3.		George, E. F., Hall, M. A. and De Klerk, G. J. (eds), Plant propagation by tissue culture.Volume 1. The background. 3rd edn. Springer, 2008, 501 p, ISBN 978-1-4020-5004-6
4.		Brown, T.A. 2006. Gene cloning and DNA analysis. An Introduction, (5th edn.) Blackwell publishing
5.		Adrian Slater, Nigel Scott and Mark Fowler. (2008). Plant Biotechnology – the Genetic Manipulation of Plants. Second Edition. Oxford University Press
6.		Lydiane Kyte, John Kleyn.2009. Plants from Test Tubes: An Introduction to Micropropagation. Timber Press
7.		Karl-Hermann Neumann, Ashwani Kumar, Jafargholi Imani. 2009. Plant Cell and Tissue Culture – A Tool in Biotechnology: Basics and Application . Springer-Verlag New York. ISBN: 3540938826
8.		Handbook of Plant Biotechnology, 2 volume set, Editors Paul Christou and Harry Klee. Wiley publisher, 2004, 1488 pages
9.		Molecular Farming- Plant made pharmaceuticals and technical proteins. Edited by Rainer Fischer and Stefan Schillberg, 2004, WILEY-VCH Verlag publisher
10.		Agrobacterium: From Biology to Biotechnology. 2008. Tzfira, Tzvi; Citovsky, Vitaly (Eds.). 750 pages. Springer publication. ISBN: 978-0-387-72289-4
SUGGESTED WEBSITES
1.				https://nptel.ac.in/courses/102103016
2.				http://www.phytotechlab.com
3.				http://www aggie-horticulture.tamu.edu/…/microprop.html – United States
4.				http://www.agbios.com/main.php
5.				http://cls.casa.colostate.edu/TransgenicCrops/what.html
6.				http://www.mcb.uct.ac.za/manual/MolBiolManual.htm
7.				http://www.web-books.com/MoBio/
8.				http://www.isaaa.org/
MBB 505 Techniques In Molecular Biology					(0+3)
OBJECTIVE
The objective of this course is to provide the students with experimental knowledge in molecular biology.
PRACTICALS
Biochemical techniques: Preparation of buffers and reagents, Chromatographic techniques (Gel Filtration Chromatography, Ion exchange Chromatography, Affinity Chromatography, HPLC); 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 DNA; Isolation of high molecular weight DNA and analysis; Metagenomics; Isolation of mRNA/total RNA. cDNA synthesis and RT-PCR. Gene cloning – Recombinant DNA construction, transformation and selection of transformants; PCR and optimization of factors affecting PCR. Real time polymerase chain reaction and data interpretation; Dot blot analysis; Southern hybridization; Northern hybridization; Radiation safety and non-radio isotopic procedure; Proteomics (2D gels, mass spectrometry, etc.); Molecular markers (SSR, SNP) and their analysis; Case study of SSR markers (linkage map, QTL analysis etc). Microarray studies and use of relevant software.
PRACTICAL SCHEDULE
1.	Preparation of buffers and reagents for chromatography
2.	Chromatographic techniques- Gel Filtration Chromatography
3.	Chromatographic techniques- Ion exchange Chromatography
4.	Chromatographic techniques – Affinity Chromatography
5.	Chromatographic techniques – HPLC
6.	Agarose gel electrophoresis – Nucleic acid
7.	Growth of bacterial culture and preparation of growth curve
8.	Isolation of Plasmid DNA from E.coli
9.	Restriction digestion of plasmid DNA
10.	Growth of lambda phage
11. Designing of gene specific primer and degenerate primer
12.			Isolation of total RNA from plant
13.			First strand cDNA synthesis
14.			Amplification of gene by RT-PCR
15.			Cloning of RT-PCR product into T/A vector
16.			Recombinant DNA construction – vector and insert DNA preparation
17.			Elution of DNA from agarose gel
18.			Competent cell preparation
19.			DNA ligation and transformation
20.			Screening for recombinant clones by PCR
21.			Confirmation of recombinant clones by restriction digestion
22.			PCR amplification and Factors affecting PCR amplification
23.			Real time PCR analysis
24.			Real time PCR data analysis
25.			Mid semester examination
26.			Isolation of DNA for metagenomic study
27.			Safety and non-radio isotopic procedure
28.			Isolation of high molecular weight DNA – Plant
29.			Dot blot analysis
30.			Southern transfer
31.			Southern hybridization
32.			Autoradiography and interpretation of result
33.			Northern transfer
34.			Northern hybridization
35.			Autoradiography and interpretation of result
36.			Microarray- labeling and hybridization
37.			Microarray- Scanning and data analysis
38.			Protein isolation SDS- PAGE
39.			Protein separation for SDS-PAGE
40.			Sample preparation for 2D-PAGE
41.			Protein isolation and quantification for 2D-PAGE
42.			First dimensional protein separation
43.			Second dimensional protein separation
44.			Staining and scanning of 2D gel
45.			Principles of MS-MALDI and 2D PAGE data analysis
46.			SSR genotyping-Parents, RILs
47.			SSR data scoring and data analysis
48.			QTL analysis
49.			Visit to DNA sequencing centre
50.			SNP analysis
51.			Final practical examination

SUGGESTED READINGS

1.	Sambrook and Green. (2012). Molecular Cloning: a Laboratory Manual (4th Edition). CSHL Press.
2.	Grotewold E. (2003). Methods in Molecular Biology. Vol. 236. Plant Functional Genomics: Humana Press Inc., Totowa, NJ, USA.
3.	Brownstein MJ and Khodursky AB. (2003). Methods in Molecular Biology. Vol. 224. Functional Genomics: Methods and Protocols. Humana Press Inc., Totowa, NJ, USA.
4.	Boopathi MN. (2013). Genetic Mapping and Marker Assisted Selection: Basics, Practice and Benefits. Springer Publications.
5.	Palanivelu P. (2016). Analytical Biochemistry and Separation Techniques. Twentyfirst Century Publications.

SUGGESTED WEBSITES

1.	https://www.nature.com/subjects/molecular-biology
2.	https://www.ascb.org/educationalresources/
3.	https://www.edx.org/learn/molecular-biology
4.	https://all-about-molecular-biology.jimdo.com/
MBB 507		Molecular Breeding (2+0)
OBJECTIVE
To introduces key principles of linkage and recombination for genetic map construction, and to develop expertise in the field of DNA markers for finger printing, genome mapping, Marker Assisted Breeding and genomics selection for practical plant breeding programme.
THEORY
Unit I : Introduction to molecular markers
Conventional plant breeding methods and its limitations; Complexity in genomes – Unique and Repeat sequences; Causes of sequence variations; Types of molecular markers – RAPD,RFLP, AFLP, SCARs, CAPS, SSRs, STMS and SNPs; Development of marker resources; Germplasm characterization using morphological and molecular markers.
Unit II : Mapping populations
Types of populations – F2 populations, RILs (recombinant inbred lines), Backcross lines, NILS (Near Isogenic Lines), Biparental mapping vs Multi-parent mapping, NAM (Nested Association mapping), MAGIC (Multi-parent advanced generation inter-cross).
Unit III : Genome mapping methods
Introduction to genome mapping- Construction of genetic linkage maps, Linkage mapping software packages; GWAS (Genome Wide Association Studies); Navigating from genetic to physical map; Targeting Induced Local Lesions in Genomes (TILLING), ECOTILLING and its application in crop breeding, Allele mining, Comparative/Synteny mapping.
Unit IV : Molecular mapping of complex traits and Marker Assisted Selection
Mapping simple and complex traits, QTL detection methods; Bulked Segregant Analysis; Fine mapping ; Map based cloning/ positional cloning for gene discovery;Strategies in molecular breeding – Marker Assisted Selection (MAS); Gene/QTL introgression; MABB (Marker Assisted Back cross breeding) – Foreground and back ground selection for introgression of QTL by SSR markers; Gene/QTL pyramiding strategies; MARS ( Marker Assisted Recurrent Selection).
Unit V : High throughput genotyping platforms and genomic selection
Linked markers vs gene based markers; Development of gene based markers – SNPs, InDels; Advances in SSR genotyping – capillary system and chip based; Principle of Association mapping – GWAS ;DARTseq, SNP genotyping – Illumina’s Golden Gate Technology, Fluidigm; GBS (genotyping by sequencing), Nano pore sequencing-Genomics Assisted Breeding ; Principles and methods of Genomic Selection.

LECTURE SCHEDULE
1.	Conventional plant breeding methods and its limitation
2.	Complexity in genomes – Unique and Repeat sequences, Causes of sequence variations
3.	Types of molecular markers – RAPD, RFLP, AFLP
4.	SCARs, CAPS, SSRs, STMS and SNPs
5.	Development of marker resources; Germplasm characterization
6.	Morphological and Molecular markers, diversity analysis
7.	Molecular markers in Plant variety protection
8.	IPR issues, hybrid purity testing
9.	Types of populations – F2 populations, RILs (recombinant inbred lines), Backcross lines, NILS (Near Isogenic Lines)
10.	Biparental mapping vs Multi-parent mapping, NAM (Nested Association mapping)
11.	MAGIC (Multi-parent advanced generation inter-cross)
12.	Introduction to genome mapping- Construction of genetic linkage maps
13.	Linkage mapping software packages; GWAS (Genome Wide Association Studies)
14.	Navigating from genetic to physical map
15.	Targeting Induced Local Lesions in Genomes (TILLING)
16.	ECOTILLING and its application in crop breeding, Allele mining
17.	Mid-semester examination
18.	Comparative/Synteny mapping
19.	Mapping simple and complex traits, QTL detection methods; Bulked Segregant Analysis
20.	Fine mapping
21.	Map based cloning/positional cloning for gene discovery
22.	Strategies in molecular breeding – Marker Assisted Selection (MAS); Genomics Assisted Breeding case studies
23.	Methods of Gene/QTL introgression
24.	MABB (Marker Assisted Back cross breeding) case studies
25.	Foreground and back ground selection for introgression of QTL by SSR markers
26.	Gene/QTL pyramiding strategies
27.	MARS (Marker Assisted Recurrent Selection)
28.	Linked markers vs gene based markers; Development of gene based markers – SNPs, InDels
29.	Advances in SSR genotyping – capillary system and chip based
30.	Principle of Association mapping – GWAS
31.	SNP genotyping methods- DART array sequencing
32.	Real Time PCR based methods, Illumina’s Golden Gate Technology
33.	Genotyping by sequencing methods-Fluidigm; GBS, Illumina Hi seq-Nano pore sequencing
34.	Principles and methods of Genomic Selection

SUGGESTED READINGS
1.	D.J. Somers, (2009), Plant Genomics – Methods and Protocols, Humana Press, Business Media.
2.	C. Kole, A.G. Abott, (2008), Principles and Practices of Plant Genomics, Science Publishers.
3.	R.K. Varshney, R. Tuberosa, (2008). Genomics Assisted Crop Improvement, Springer
4.	K. Meksem, G Kahl, (2005). The Handbook of Plant Genome Mapping: Genetic and Physical Mapping, Wiley-Blackwell.
5.	H.J. Newbury, (2003). Plant Molecular Breeding, CRC Press.
6.	A.F. Griffiths et al, (2000). An Introduction to Genetic Analysis,WH Freeman & Co.
SUGGESTED WEBSITES
1.	Plant Molecular Breeding – http://base.dnsgb.com.ua/files/book/Agriculture/PlantBreeding/Plant-Molecular-Breeding.pdf
2.	Molecular Plant Breeding – http://download.bioon.com.cn/ upload/201105/28152813_8350.pdf
3.	Molecular Markers and Marker-Assisted Breeding in Plants -http://cdn.intechopen.com/pdfs-wm/40178.pdf
4.	http://www.gramene.org/
5.	http://snp-seek.irri.org/
6.	http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp
7.	https://legumeinfo.org/

MBB	508 Genomics And Proteomics (2+0)
OBJECTIVE
The overall aim of the course is to provide introductory knowledge concerning genomics and proteomics, and their applications.
THEORY
Unit I : Genome organization
Brief overview of genome organization, gene structure and gene expression in Prokaryotic and Eukaryotic organization; Extra-chromosomal DNA: bacterial plasmids, mitochondria and chloroplast; Introduction to genomics, transcriptomics, proteomics and assigning gene functions.
Unit II : Structural Genomics
Genome analysis – genome maps – genetic maps; physical maps; Physical mapping (BAC libraries), cytogenetic techniques, FISH technique in gene mapping, somatic cell hybridization, radiation hybrid maps, in-situ hybridization; Genetic mapping – Introduction to Molecular markers; types of markers; linkage map construction; QTL mapping; Bi-parental, Multi-parental mapping; Marker Assisted selection – MAS, MABB, QTL Pyramiding; Advances in MAS.
Unit III : Genome sequencing
Introduction to DNA sequencing, methods of DNA sequencing (Sanger, Maxam & Gilbert, Pyrosequencing, Nanopore, Illuumina, PacBio etc); Metagenomics; 16S rRNA typing/sequencing; Genome sequencing – strategies; Whole genome sequence assembly and annotation; Genome sequencing projects – human, microbes, plants and animals genomes. Accessing WGS information – Genome re-sequencing projects – rice 3K and Arabidopsis 1K genome projects
Unit IV : Functional Genomics
Forward and reverse genetics: Gene expression profiling; Transcriptomics – RT-PCR, Northern, cDNA library, SSH, DD-RT-PCR, cDNA-AFLP, SAGE, MPSS, Microarrays, RNA-Seq etc., miRNAs and siRNAs; Assigning gene functions – mutagenesis; Over expression and knock out mutants; RNAi technology; Genome editing.
Unit V : Proteomics
Aims, strategies and challenges in proteomics; Proteomics technologies: 2D-PAGE, Mass spectrometry, Proteome databases. Protein-protein and protein-DNA interactions; Protein chips and functional
proteomics; Yeast 2-hybrid system, Designing novel agrochemicals; Introduction to metabolomics, Lipidomics, ionomics etc.

LECTURE SCHEDULE
1.	Introduction to Genomics – Proteomics; Genomes – Organization in prokaryotes and eukaryotes; Physio-chemical properties of a genome
2.	Gene structure and Gene expression in prokaryotes and eukaryotes
3.	Genetic exchange in prokaryotes and eukaryotes – principles; Introduction to genome maps – types of genome maps – Genetic and physical maps
4.	Genetic mapping – Linkage mapping; QTL mapping – principles & methods
5.	Marker Assisted Selection – Principles, methods and applications
6.	Marker Assisted Back cross breeding – principles, methods and applications
7.	Advancements in MAS – NAM, MAGIC and Genomic Selection
8.	Introduction to Physical mapping – types of physical maps
9.	Methods of sequencing
10.	Methods of Sequencing
11.	Metagenomics – 16s rRNA/shot gun
12.	Genome sequencing strategies, tools and techniques
13.	Genome sequencing assembly and annotation
14.	Genome databases – humans, plants, microbes and animals
15.	Genome databases – Resequencing of plant genomes (Rice, Arabidopsis)
16.	Introduction to Functional genomics – Tools and techniques in gene expression profiling
17.	Mid-semester examination
18.	Transcriptomics – RT-PCR , Northern analysis
19.	cDNA library screening – ESTs; DD-RT-PCR , cDNA AFLP – SAGE
20.	Microarrays – Principle, methodology
21.	Microarrays – data analysis and case studies
22.	RNA sequencing – tools and techniques
23.	Introduction to Proteomics – need for proteomics, Definition and types of proteomics; 2D PAGE
24.	Mass spectrometry and applications in proteomics
25.	Applications of proteomics in Agriculture, Designing novel agrochemicals
26.	Metabolomics, Ionomics, Lipidomics, Glycomics, Phenomics
27.	Assigning functions of a gene – Mutagenesis – Over-Expression Mutants
28.	Knock-out mutants – RNAi approach
29.	Genome editing
30.	Allele mining in crop improvement
31.	Introduction to Gene traps, Yeast two hybrid system etc.,
32.	Case studies in Genomics, Functional genomics and Proteomics
33.	Case studies in Genomics, Functional genomics and Proteomics
34.	Case studies

SUGGESTED READINGS

1.	Stephen P. Hunt, Rick Livesey. 2009. Functional Genomics: A Practical Approach.
2.	TA Brown, Genomes 3, Garland Sciences.
3.	Primrose S & Twyman R, (2006), Principles of Gene Manipulation and Genomics, 7th Edition, Blackwell.
4.	Christopher A. Cullis. 2005. Plant Genomics and Proteomics.
5.	Liebler, Daniel C, (2002), Introduction to proteomics- tools for the new biology, Humana Press,Totowa, NJ.
6.	Campbell AM &Heyer LJ, (2007), Discovering Genomics, Proteomics and Bioinformatics, 2nd Edition. CSHL Press.
7.	Primrose. S. B. and Twyman. R. 2004. Principles of Genome Analysis and Genomics. Third edition University of York.

SUGGESTED WEBSITES

1.	Proteomics and Genomics- http://nptel.ac.in/courses/102103017/
2.	Introduction to Proteomics – Principles and Applications – http://onlinelibrary.wiley.com/book/10.1002/9780470603871
3.	Introduction to Proteomics, Tools for the New Biology – http://fie.zums.ac.ir/ebook/38Introduction to Proteomics, Tools for the New Biology-Daniel Liebler- 0896039919-Humana Pres.pdf
4.	Genomics, Proteomics and Bioinformatics – https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2347366/
5.	Online textbook-Proteomics: – https://learner.org/courses/biology/textbook/proteo/index.html
MBB 512 Immunology and Molecular Diagnostics (2+1)
OBJECTIVE
To understand the immunological system in human beings, various diseases of human beings and to know about the diagnostic kits/tools available for detection of diseases.
THEORY
Unit I : Immune system and Immunity
Introduction and history of Immunology. Organs of immune system – primary and secondary lymphoid organs – bone marrow, thymus, spleen, lymph node, mucosa / cutaneous / gut associated lymphoid tissues. Cells of the immune system – hematopoietic stem cells, hematopoiesis, B lymphocytes, T lymphocytes, natural killer (NK) cells, macrophages, dendritic
cells and their roles. Blood – plasma, red blood cells, white blood cells, platelets. Immunity – Innate immunity – anatomical barriers, cells and receptors of innate immune system – acquired immunity – humoral and cell mediated immunity.
Unit II : Antigen-antibody (Ag-Ab) interactions: Principles and applications
Antigens – types, properties and immunogenicity. Antibodies – immunoglobulins (Ig) – structure, classification, biological properties and functions – isotype, allotype and idiotype. Organization and expression of Ig genes, antibody class switching and diversity. Ag-Ab interactions – affinity, avidity, specificity and cross reactivity. Precipitation and agglutination reactions.
Unit III : Immune responses and effector mechanisms
Maturation, activation and differentiation of B cells and T cells. B cell and T cell receptors.Major histocompatibility complex (MHC) in human – structure and function of MHC I and II – antigen processing and presentation – MHC restriction. Complement system – complement proteins – classical, alternative and lectin pathways – lytic attack complex – role in defense mechanism. Cytokines –interleukins, interferons and their role. Hypersensitivity – allergens and types of hypersensitivity reactions. Immunological tolerance, immunoregulation, immunodeficiency – inherited and acquired immunodeficiency diseases.
Unit IV : Immune system in health, vaccines and monoclonal antibodies
Auto immunity and auto immune diseases. Transplantation immunology – types of grafts, human leukocyte antigen (HLA) typing, mixed lymphocyte reaction, organ transplants, graft rejection, xenotransplantation. Tumor immunology – types of tumors, metastasis, tumor antigens, immune responses, mechanisms of tumor evasion from immune system, immunotherapy. Immune responses to infectious diseases – bacterial (leprosy and pneumonia), viral (influenza and HIV) and parasitic (malaria and filariasis) diseases. Vaccines – principle of vaccination, active and passive vaccination, immunoprophylaxis, vaccination schedule. Types of vaccines – live, killed, polysaccharide, conjugate, subunit, split, multivalent, DNA vaccines, recombinant vaccines and edible vaccines. Monoclonal and polyclonal antibodies. Production of monoclonal antibodies – hybridoma technology – phage display technology – applications of monoclonal antibodies.
Unit V : Molecular diagnostic tools/kits for detection of various diseases in medicine and agriculture
Principles and applications of PCR, RT-PCR, qRT-PCR and hybridization based methods of detection, microarrays based detection, FISH, DNA sequencing, NGS, Radio immunosorbent assay, ELISA, Chemiluminescent immunoassay, dot blot immunoassay, Lateral flow immunoassay strips, Western blotting, immunofluorescence, flow cytometry assays, Immunoelectron microscopy, hyperspectral techniques and biosensors in detection of human and plant diseases. 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.

PRACTICALS

Blood grouping by hemagglutination technique. RBC and WBC counting through haemocytometer; Isolation, purification and estimation of antigenic proteins.Selection of animals and rearing – immunization – raising antibodies – blood collection methods – purification of antibodies; Immunodiffusion techniques – Ouchterlony double immunodiffusion and radial immunodiffusion; SDS-PAGE analysis of antigenic proteins; Antigen-antibody interactions by ELISA and Lateral flow immunoassay strips; Genomic DNA isolation from blood sample; Extraction of DNA/RNA from plant samples and detection of bacterial/viral plant diseases using diagnostic kits.

	LECTURE SCHEDULE
	1.		Introduction and history of Immunology
	2.		Organs of immune system
	3.		Cells of immune system
	4.		Blood – components and functions
	5.		Innate and acquired immunity
	6.		Cell mediated and humoral immunity
	7.		Antigens-types and properties and immunogenecity
	8.		Immunoglobulins – structure, classification, biological properties and functions
	9.		Organization of expression of Ig genes, antibody class switching and diversity
	10.		Ag-Ab interactions – affinity, avidity, specificity and cross reactivity, Agglutination and Precipitation tests
	11.		Maturation, activation and differentiation of B cells and T cells, B cell receptors and T cell receptors
	12.		Structure and function of MHC I and II
	13.		Antigen processing and presentation and MHC restriction
	14.		Complement system – classical, alternative and lectin pathways
	15.		Hypersensitivity reactions – Type I and Type II
	16.		Hypersensitivity reactions – Type III and Type IV
	17.		Mid Semester Examination
	18.		Cytokines – interleukins and interferons and their role
	19.		Immunological tolerance and regulation
	20.		Immunodeficiency – inherited and acquired immunodeficiency diseases
	21.		Autoimmunity and autoimmune diseases
	22.		Transplantation immunology
	23.		Tumor immunology
	24.		Immunology of bacterial and viral diseases
	25.		Immunology of parasitic diseases
	26.		Monoclonal Vs polyclonal antibodies and hybridoma technology
	27.		Phage display technology
	28.		Vaccination – principle, immunoprophylaxis, vaccination schedule and different types of vaccines
	29.		Principles and applications of PCR, RT-PCR, qRT-PCR, hybridization based methods of detection of human and plant diseases
	30.		Microarrays based detection, FISH, DNA sequencing, NGS based methods for detection
of human and plant diseases
31.		Radio immunosorbent assay, ELISA, Dot blot immunoassay, Lateral flow immunoassay strips, Western blotting, immunofluorescence, flow cytometry assays and Immunoelectron microscopy
32.		Hyperspectral techniques and biosensors for detection of human and plant diseases
33.		Detection of soil borne and seed born infections and transgene detection in seed and planting material and processed food
34.		Molecular detection of varietal impurities and seed admixtures in commercial consignments

PRACTICAL SCHEDULE

1.	Blood grouping of human beings – agglutination test
2.	RBC and WBC counting through haemocytometer
3.	Isolation of antigenic protein by ammonium sulphate precipitation method
4.	Purification of antigenic protein by dialysis method
5.	Estimation of antigenic protein concentration by Lowry’s method
6.	Selection of animals and rearing
7.	Blood collection from rabbit and pre-immune serum separation
8.	Immunization of animals
9.	Separation of antibodies from antiserum and purification of Ab
10.	Ouchterlony double immunodiffusion technique
11.	Analysis of Antigen/Antibody through SDS PAGE electrophoresis
12.	ELISA Lateral flow immunoassay strips – Pregnancy detection kit
13.	Lateral flow immunoassay strips – Pregnancy detection kit
14.	Genomic DNA isolation from blood sample and quantification
15.	Extraction of DNA/RNA from bacteria/virus diseases infected plant samples
16.	Detection of bacterial/viral plant diseases using diagnostic kits
17.	Final Practical Examination

SUGGESTED READINGS

1.	Abbas, A.K., Lichtman, A.H., Shiv Pillai. 2015. Basic immunology – Functions and disorders of the immune system, 5th Edition, ISBN: 9780323390828, USA, 352p.
2.	David Male, Jonathan Brostoff, David Roth and Ivan Roitt. 2013. Immunology, 8th Edition, ISBN: 978-0-323-08058-3, Saunders Publications, USA, 464p.
3.	Delves, P.J., Martin, S.J., Burton, D.R., Roitt, I.M. 2017. Roitt’s Essential Immunology, 13th Edition, ISBN : 978-1-118-41577-1, Wiley Blackwell Publications, New York, 576p.
4.	Elles R & Mountford R. 2004. Molecular Diagnosis of Genetic Disease. Humana Press.
5.	Judy Owen, Jenni Punt, Sharon Stranford. 2012. Kuby Immunology. Seventh edition, W.H. Freeman Publishers, ISBN-13: 978-1-4292-1919-8, 574 p.
6.	Juluri R. Rao, Fleming, C. C. and J. E. Moore. 2006. Molecular Diagnostics: Current Technology and Applications, ISBN: 978-1-904933-19-9, Horizon Scientific Press, Norfolk, UK, 380p.
7.	Lela, Buckingham, Maribeth L. Flaws 2009. Molecular Diagnostics: Fundamentals, Methods and clinical applications.360 p, Publisher: F. A. Davis Company.
8.	Lydyard P, Whelan A, Fanger, M. 2012. BIOS Instant Notes in Immunology, 3rd Edition, ISBN-10: 0415607531, Garland science Publishers, New York, 327p.
9.	Murphy K. 2017. Janeway’s Immunobiology, 9th Edition, ISBN: 9780815345053, Garland Science Publishers, New York, USA, 904p.
10.	Nader Rifai, Horvath, A.R. and Wittwer, C.T. 2018. Tietz Text book of Clinical Chemistry and Molecular Diagnostics.
11.	Nandhini Shetty. 2005. Immunology-Introductory text book. New Age International (P) Limited Publishers, New Delhi.
12.	Rao JR, Fleming CC & Moore JE. 2006. Molecular Diagnostics. Horizon Bioscience
12.	Rao, C.V. 2008. Immunology- A textbook. Narosa Publishing house, New Delhi.
13.	Sudha Gangal and Shubhangi Sontakke. 2013. Text book of basic and clinical immunology. University press, Hyderabad. 532 p.
14.	Sulabha Pathak. 2010. Immunology: Essential and Fundamental, (III Edn) Blackwell Publishers, p400.

SUGGESTED WEBSITES

1.	Immunology by Kuby – www.whfreeman.com/kuby/
2.	Immunology – http://en.wikipedia.org/wiki/Immunology
3.	Immunology – http://en.wikibooks.org/wiki/Immunology
4.	Annual Review of Immunology – http://www.annualreviews.org/journal/immunol
5.	Immunology Notes – http://www.mednotes.net/notes/immunology/
6.	http://www.mi.interhealth.info/
7.	http://artandersonmd.com/
8.	Lecture Notes, Cellular and Molecular Immunology, MIT – http://ocw.mit.edu/ courses/health-sciences-and-technology/hst-176-cellular-and-molecular-immunology-fall-2005/lecture-notes/
9.	http://www.roitt.com/glossary.asp

Minor courses

PLP 501 Principles of Plant Physiology (2+1)

OBJECTIVE

The main objective of the course is to understand the basic principles of important physiological processes in plants; To study the role and functions of nutrients and Plant Growth Regulators on crop production.

THEORY

Unit I : Plant Water Relations

Introduction and role of plant physiology in Agriculture – Structure of Cell organelles and their physiological functions. Soil and plant water relations: properties and role of water in plants -water potential of plant and soil – Mechanism of water uptake and movement in plants. Water loss from plant – role of light – Stomatal structure and function – mechanism of stomata movement. Evapotranspiration: Evaporation – transpiration –- factors influencing transpiration rate – antitranspirants.

Unit II : Mineral Nutrition

Essential and Beneficial elements – classification and function of elements in plants – macro and micro elements-critical levels – hidden hunger – Uptake of mineral elements in plants –Mechanisms of absorption and translocation in plants – Chelates – nutrient deficiency symptoms and their management – Foliar nutrition.

Unit III : Photosynthesis and Respiration

Photosynthesis and its importance in crop yield. Photochemical reactions – reduction of CO2 in C3, C4 and CAM pathways – Comparison and difference in their photosynthetic efficiency. Photorespiration and its significance. Factors affecting photosynthesis – Translocation of photosynthates and its importance in sink development. Respiration – Glycolysis, TCA and Pentose Phosphate Pathway – Oxidative Phosphorylation – differences between Oxidative

Phosphorylation and Photophosphorylation – Respiratory quotient and energy budgeting in respiration – Nitrogen metabolism – Inorganic nitrogen species (N2, NO3 and NH3) and their reduction to amino acids – secondary metabolites and their significance in plant defense mechanism.

Unit IV : Growth and Development

Growth, differentiation and development – definitions, phases of growth – analysis of growth components. Plant growth hormones – physiological role and application in crop production – synthetic growth regulators, growth retardants and inhibitors. Abscission – Senescence – classification, physiological and biochemical mechanism and its significance in crop production. Physiology of flowering – Photo morphogenesis – Photoreceptors: phytochrome and cryptochrome – photoperiodism and vernalization – regulation of flowering in crops. Seed physiology – germination – physiological basis of germination. Dormancy – types and mechanisms of dormancy – breaking and induction of dormancy.

Unit V : Stress Physiology

Physiology of abiotic stresses in plants – water, temperature, light and salt stress- Influence of different stresses at plant levels– Resistance/tolerance mechanism-mitigation – Global warming and its impact on physiological basis of crop productivity.

PRACTICALS

Estimation of Relative Water Content and Leaf water potential -Measurement of transpiration rate and Gas Exchange measurements using IRGA -Stomatal Index and Frequency – Influence of ABA on stomatal regulation -Assessment of Light Use Efficiency -Estimation of soluble protein content Separation and estimation of chlorophylls and carotenoid pigments -Diagnosis of nutritional disorders -Qualitative estimation of Nutrients – Rapid tissue test – Estimation of Nitrate Reductase activity – Leaf Area measurement and Growth analysis – Assessment of Drought tolerance: CSI -Quantification of osmolyte: Proline – Bio-assay for Cytokinin-Estimation of anti oxidant enzymes activity: Peroxidase / Catalase – Estimation of Total Phenolics.

LECTURE SCHEDULE

Introduction and role of plant physiology in Agriculture Structure of Cell organelles and their physiological functions.

Soil and plant water relations: properties and role of water in plants – cell water terminologies, water potential of plant and soil

Mechanism of water uptake and movement in plants
Water loss from plant – role of light – Stomatal structure and function – mechanism of stomata movement.

Evapotranspiration: Evaporation – transpiration – Driving forces of transpiration –factors influencing transpiration rate – antitranspirants.

Essential and Beneficial elements – classification and function of elements in plants –critical levels – hidden hunger

Uptake of mineral elements in plants – Mechanisms of absorption and translocation in plants – Chelates

Nutrient deficiency symptoms and their management – Foliar nutrition
Photosynthesis and its importance in crop yield; photochemical reactions
Reduction of CO2 in C3, C4 and CAM pathways
Comparison and difference in their photosynthetic efficiency. Photorespiration and its significance.

Translocation of photosynthates and its importance in sink development
Respiration – Glycolysis, TCA cycle and Pentose Phosphate Pathway
Oxidative Phosphorylation – differences between Oxidative Phosphorylation and Photophosphorylation

Respiratory quotient and energy budgeting in respiration
Nitrogen metabolism – Inorganic nitrogen species (N2, NO3 and NH3) and their reduction to amino acids

Mid Semester Examination
Secondary metabolites and their significance in plant defense mechanism.
Growth, differentiation and development – definitions, phases of growth – analysis of growth components.

Plant growth hormones – physiological role and application of Auxins in crop production

Physiological role and application of Gibberellins and Cytokinins in crop production
Physiological role and application of Ethylene and ABA in crop production
Synthetic growth regulators, growth retardants and inhibitors.
Abscission – classification, physiological and biochemical mechanism and its significance in crop production.
Senescence – classification, physiological and biochemical mechanism and its significance in crop production.

Physiology of flowering – Photo morphogenesis – Photoreceptors: phytochrome and cryptochrome

Photoperiodism and vernalization – regulation of flowering in crops.
Seed physiology – germination – physiological basis of germination.
Dormancy – types and mechanisms of dormancy – breaking and induction of dormancy.
Physiology of water stress in plants – Influence at plant levels – resistance / tolerance mechanism– mitigation

Physiology of temperature stress in plants – Influence at plant levels – resistance /tolerance mechanism– mitigation

Physiology of light stress in plants – Influence at plant levels – resistance /tolerance mechanism– mitigation

Physiology of salt stress in plants – Influence at plant levels resistance /tolerance mechanism– mitigation

Global warming and its impact on physiological basis of crop productivity

PRACTICAL SCHEDULE

Estimation of Relative Water Content and Leaf water potential
Measurement of transpiration rate and Gas exchange measurements using IRGA/PPS
Determination of Stomatal Index and Frequency
Assessment of Light Use Efficiency
Separation and estimation of chlorophylls and carotenoid pigments
Estimation of soluble protein content
Diagnosis of nutritional disorders
Qualitative estimation of Nutrients – Rapid tissue test
Estimation of Nitrate Reductase activity
Leaf Area measurement and Growth analysis
Assessment of Drought tolerance: Chlorophyll Stability Index (CSI)
Quantification of osmolyte: Proline
Bio-assay for Cytokinin
Estimation of anti oxidant enzyme activity: Catalase
Estimation of anti oxidant enzyme activity: Peroxidase
Estimation of Total Phenolics
Final Practical Examination

SUGGESTED READINGS

Taiz. L. and Zeiger. E., 2010 (Fifth edition). Plant Physiology. Publishers: Sinauer Associates, Inc., Massachusetts, USA

Salisbury FB & Ross C. 1992. Plant physiology. Wadsworth Publishing Company, USA.
Jain, V.K. 2007. Fundamentals of plant physiology, S.Chand & Company Ltd., New Delhi.

SUGGESTED WEBSITES

http://www.plantphys.org
http://4e.plantphys.net
https://books.google.co.in/books/about/Plant_Physiology.html

BIC 501 Plant Biochemistry (2+1)

OBJECTIVE

To provide detailed information about biochemical and molecular basis of various plant processes and plant growth regulatory substances.

THEORY

Unit I : Biosynthesis of primary metabolites

Biosynthesis of storage and structural carbohydrates, Sucrose – starch interconversion; Storage proteins – post translational modification, folding and stability ; Storage lipids. Biochemistry of seed germination and development. Biochemistry of fruit ripening.

Unit II : Stress biochemistry

Abiotic stresses, ROS. Enzymic and non – enzymic antioxidants.Biosynthesis and mechanism of action of osmoprotectants – glycine-betaine, proline; polyamines; heat shock proteins.

Unit III : Plant defense system

PR proteins, phytoalexins, cinnamic acid, salicylates, jasmonic acid, toxic aminoacids – mode of action.Anti-nutritional factors in pulses, cereals, oil seeds, fruits and vegetables.

Unit IV : Biochemistry and significance of secondary metabolites

Shikimate pathway, Acetate-mevalonate pathway.Biochemistry and significance of cyanogenic glycosides, glucosinolates, phenolic compounds, terpenoids, alkaloids.

PRACTICALS

Estimation of Proline, starch by anthrone method, total free aminoacids, protein by Lowry’s method, total phenols, tannins, Extraction of alkaloids, Extraction and estimation of lycopene and carotenoids – Enzyme extraction methods — Assay of peroxidase – Assay of polyphenol oxidase.

SUGGESTED READINGS

Buchanan, B.B., W. Gruissem and R.L. Jones. 2000. Biochemistry and Molecular Biology of Plants.2nd Ed. John Wiley.

Dey, P.M. and J.B.Harborne. 1997. Plant Biochemistry, Academic Press, New York.
Goodwin, T.W. and E.I. Mercer. 1983. Introduction to Plant Biochemistry. Pergamon Press.

Heldt, H.S. 1997. Plant Biochemistry and Molecular Biology.Oxford Univ Press
Lea, P.J and R.C. Leegood. 1993. Plant Biochemistry and Molecular Biology. 2nd Ed.John Wiley.

SUGGESTED WEBSITES

http://www.ncbi.nlm.nih.gov
http://us.expasy.org
http://www.worthington-biochem.com
http://www.biochemist.org
http://www.gwu.edu/~mpb

BIF 501 Introduction to Bioinformatics 2+1

OBJECTIVE

To impart an introductory knowledge about the subject of bioinformatics to the students studying any discipline of science.

THEORY

Unit I : Introduction and Biological databases

Introduction, history and evolution, scope and importance of bioinformatics, Biological database – Introduction, classification, Primary, secondary database, structure databases. Gene Information Resources – Genebank, DDBJ, EMBL. Protein primary database-PIR, SWISSPROT, Protein secondary databases – PROSITE, Pfam. Protein secondary structure database- CATH, SCOP, Protein 3D structure database-PDB, Specialized genomic resources.

Unit II : Sequence analysis

DNA sequence analysis, cDNA libraries and EST, Alignment-Global and local alignment, Pairwise alignment techniques, Algorithms – Smith and Waterman, Needlemann and Wunsch

Unit III : Sequence alignment

Database search tools-BLAST and its Variants, Multiple sequence alignment-Introduction, applications, and tools.

Unit IV : Phylogenetic analysis

Phylogenetics – analysis- terminology, tree construction methods and evaluation of tree. Phylogenetic packages – PHYLIP, Primer designing.

Unit V : Protein modeling and docking

Introduction to computational methods for protein structure prediction, Homology modeling, Virtual Screening, Docking. Analysis packages – commercial packages and online resources for analysis of protein and DNA sequences.

PRACTICALS

Usage of NCBI resources, Retrieval of nucleotide sequence from databases- NCBI, EMBL, DDBJ, Retrieval of nucleotide sequence from Protein- UNIPROT, Retrieval of protein tertiary structure- PDB, BLAST and its variants – BLASTn, BLASTp, BLASTX, tBLASTN, tBLASTX, PSI BLAST, PHIBLAST, Multiple Sequence Alignment- CLUSTAL, MEGA, Phylogenetic Tree analysis-PHYLIP, Primer Designing, Protein sequence analysis- primary, secondary structure prediction, Visualization of structures- Rasmol, SwissPDBViewer, Protein structure prediction- Homology modeling, Docking of ligand receptors

LECTURE SCHEDULE

Bioinformatics-definition, the evolution of bioinformatics as separate discipline
Applications of Bioinformatics in various fields.
Scope and importance of biological data – Types and characteristics
Biological databases -Introduction, classification-primary, secondary and tertiary
Nucleic acid primary sequence database – GenBank, DDBJ and EMBL
Protein primary database – PIR, UNIPROT
Protein secondary databases – PROSITE, Pfam
Protein Secondary structure database- CATH, SCOP
Protein 3D structure database- PDB
Specialized genomic resources
DNA sequence analysis
cDNA libraries
EST database
Pair wise alignment – The dotplot
Sequence alignment – dynamic programming- globalalignment
Dynamic programming-local alignment
Mid Semester Examination
Database search tools–BLAST
Variants of BLAST
PHIBLAST, PSIBLAST
Multiple sequence alignment – Introduction and applications
Phylogenetics- analysis- terminology
Tree construction methods-character based
Tree construction methods-Distance based
Phylogenetic package –PHYLIP
Primer designing
Introduction to computational methods for protein structure prediction
Protein structure determination by homology modeling
Evaluation and Validation of the computational modeling
Computer aided drug discovery – Introduction and basic principles
Drug design-Ligand based
Drug design -Receptor based
Web-based analysis tools for protein sequences
Web-based analysis tools for nucleic acid sequences

PRACTICAL SCHEDULE

Resources of NCBI
DNA databases – NCBI, EMBL, DDBJ
Protein databases – UNIPROT
Structure databases – PDB
Variants of BLAST – Blastp, Blastn
Variants of BLAST – Blastx, tbalstn, tblastx
Variants of BLAST – PHIBlast , PSIBlast
Multiple sequence alignment
Phylogenetic Tree analysis-PHYLIP
Primer Designing
Protein sequence analysis- primary, secondary structure prediction
Molecular visualization tool – Rasmol
Molecular visualization tool – SPDBV
Homology Modeling
Validation and refinement
Docking of ligand interaction
Final Practical Examination

SUGGESTED READINGS

Bioinformatics for DNA sequence analysis, 2009, David posada, Humana Press Inc.
Bioinformatics, ShubaGopal, 2010, Tata McGraw hill Education private limited, New Delhi.

Applied Bioinformatics – An Introduction, Selzer, P.M., Marhöfer, R.J., Rohwer, A,2008. Springer Publications.

Hooman Rashidi, Lukas K. Buehler, 2005. Bioinformatics Basics: Applications in Biological Science and Medicine Edition: 2nd edition, CRC Publisher,

Andreas D. Baxevanis B. F. Francis Ouellette, 2004 , Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins , 3rd edition, Wiley, John & Sons publishers,

Attwood TK & Parry-Smith DJ. 2003. Introduction to Bioinformatics. Pearson Education.
Rastogi SC, Mendiratta N & Rastogi P. 2004. Bioinformatics: Concepts,Skills and Applications. CBS.

Baxevanis. A. D. and Ouellette. B. F. F. (Eds). 2001. Bioinformatics: A practical guide to the analysis of genes and proteins. Wiley Interscience. New York.

Bioinformatics Basics: Applications in Biological Science and Medicine, Hooman Rashidi, Lukas K. Buehler, Edition: 2nd edition, May 2005, Publisher: CRC Press/Taylor & Francis Group.

SUGGESTED WEBSITES

www.bioinformatics-india.com
www.bioinformatics.org
www.ibioinformatics.org
www.ebi.ac.uk/Databases
www.ncbi.nlm.nih.gov

GPB 501 Principles of Genetics (1+1)

OBJECTIVE

This course is aimed at understanding the basic concepts of classical and developmental genetics, helping students to develop their analytical and problem solving skills. Will improve the students understanding on applied aspects of genetics, principally plant breeding science and molecular biology.

THEORY

Unit I :

Beginning of genetics, early concepts of inheritance, Review of Medelian Concepts of Inheritance- Deviation from Mendelian Inheritance-Gene interaction– Intra allelic and inter allelic–Multiple Factor Hypothesis. Chromosomal theory of Inheritance-Sex linked and Sex influenced genes and their inheritance–Sex determination and Sex chromosomes–Environmental Influence of sex determination

Unit II :

Genetic Linkage and Crossing over–Linkage analysis–Detection–Linkage phases–Linkage and recombination-Two factor analysis-Three factor analysis– Factors affecting recombination-Measurement of Genetic Recombination– Recombination fraction–Interference–Mapping functions-Linkage/Genetic map construction-Extra chromosomal inheritance-Genetic inheritance in other than diploids. Complementation analysis-Fine structure of gene-bar locus, complex loci, rII locus-Split genes-Overlapping genes–Pseudogenes-Transposable genetic elements-Gene families and clusters- Gene function: inborn errors of metabolism- One gene/one enzyme hypothesis, pathways of gene action – Genes at population level.

Unit III :

DNA is the genetic material-Nucleic acids and their chemistry- DNA and RNA- DNA as the genetic material-Types of DNA: double helix, Z-DNA, B-DNA, A-DNA – DNA the central dogma of molecular biology. Genetic control of development – Gene interaction at celluar level – Genes in cell differentiation – Role of nucleus in ontogenic regulation – Differential gene activity at transcriptional level – Gene amplification – redundancy – dosage compensation – Differential gene activity during ontogenesis.

Unit IV :

Genes in developmental adaptations – Polymorphism during ontogeny: variations in isozymes and proteins – Gene modifiers on phenotypic expression: phenocopy, allelic exclusion – Maternal effect and extra-chromosomal inheritance – Nuclear and cytoplasmic interactions- Genome imprinting and its implications.

Unit V :

Intergenome interaction and developmental regulation – Gene interaction at tissue level – Gene mosaicism – Time factors in genetic regulation – Genetic heterogenity and tissue system development. Epigenetics – Genetic regulation of differentiation at organism level – Organisation systems controlling differential gene expression – Apotopsis – Cell aging and death

PRACTICALS

Basic Genetics-Problems in Mendelian inheritances – Mono and dihybrid ratios – Basic Genetics -problems in Mendelian inheritances: Trihybrid ratios – Modifications of monohybrid ratios -Modifications of dihybrid ratios – Linkage analysis – two point and three point test – Multipoint analysis-linkage estimation – recombination frequency – Mapping functions used in linkage analysis.

LECTURE SCHEDULE

History of Genetics – Pre Mendelian, Mendelian and Post Mendelian periods.
Gene interactions: intra and inter allelic interactions
Multiple alleles, pseudo alleles and pseudogenes, pleiotropy
Sex determination- Sex linked, sex influenced and sex limited genes
Chromosomes and heredity- Linkage and linkage groups and Stern’s experiment
Linkage and crossing over-Phases of linkage-Interference and coefficient of coincidence
Recombination fraction and Mapping functions
Mid Semester Examination
Gene: gene concept, unit of function, replication, recombination and mutation
Complementation analysis; Fine structure of gene – bar locus, complex loci, rII locus
Gene function: inborn errors of metabolism; One gene/one enzyme hypothesis, pathways of gene action

Genetic control of development- Gene interaction at celluar level –tissue level
Maternal effect and extra-chromosomal inheritance – Nuclear and cytoplasmic interactions
Genome imprinting and its implications
Genetic regulation and development
Epigenetics in biological systems
Gene: gene concept, unit of function, replication, recombination and mutation

PRACTICAL SCHEDULE

Mendelian inheritance of single gene and two genes
Mendelian inheritance of three genes
Deviations in single gene inheritance – Co-dominance and Incomplete dominance
Multiple alleles and their inheritance
Deviations in the inheritance of two genes – Gene interactions
Deviations in the inheritance of two genes – Gene interactions
Detection of linkage in various biological systems
Genetic linkage – Linkage analysis – two point and three point analysis
Phases of linkage
Estimation of recombination fraction -Various methods
Mapping function- Various mapping functions
Sex linked genes and their inheritance- Drosophila
Sex linked genes and their inheritance- Humans
Multiple factor hypothesis and inheritance of multiple genes
Genetics and its implications in understanding major diseases
Genes at population level- Gene frequency and genotypic frequency
Final Practical Examination

SUGGESTED READINGS

Browder, L.W. 1980. Developmental Biology. Saunders College, Philadelphia. 602p.
Diwan, A.P and N.K.Dhakad .1996. Principles of Developmental Biology. Anmol Publications Private Limited, New Delhi.562p

Diwan,A.P and N.K.Dhakad. 1996.Genetics and Development. Anmol Publications Private Limited ,New Delhi.398p

Gardner, E.J, M.J. Simmons and D.P.Snustad. 1991. Principles of Genetics. John Wiley & Sons, Inc New York. 649p

Gillham, N.W. 1994. Organelle genes and Genomes. Oxford University Press, Oxford. 424p
Hartl, D.L. 1994. Genetics. Jones and Bartlett Publishers, London. 584p.
Hartwell, L.H., Hood, L., Goldberg, M.L., Reynolds, A.E., Silver, L.M. and Veres, R.C. 2004. Genetics: From Genes to Genomes, 2nd edn., McGraw-Hill, New York

Hawkins, J. D.1991.Gene structure and expression (Third edition). Cambridge University. Press, Cambridge. 212p.

Kevles, D.J. 1985. In the Name of Eugenics: Genetics and the Uses of Human Heredity, Knopf, New York

Klug, W.S. and Cummings, M.R. 2003. Concepts of Genetics, 7th edn., Prentice-Hall/Pearson Education, Upper Saddle River, NJ

Korochkin, L. I. 1981. Gene interactions and Development. Springer-Verlag, Berlin.
Lewin B. 2008. Genes IX. Jones & Bartlett Publ.
Maclean, N. 1979. Differentiation of Cells. Edward Arnold (Publishers) Limited, London.
Pierce, B.A. 2003. Genetics: A Conceptual Approach, W.H. Freeman, New York
Russell P.J. 1998. Genetics. The Benzamin/Cummings Publ. Co.
Sang, J. H. 1984. Genetics and Development. Longman, London
Snustad, D. P., M. J. Simmons and J. B. Jenkins. 1997. Principles of Genetics. John Wiley & Sons, Inc New York. 829p

Stansfield. W. D. 1969. Schaum’s Outline of Theory and Problems of Genetics. McGraw-Hill Book Company

Strickberger M.W. 2005. Genetics (III Ed). Prentice Hall, New Delhi, India
Tamarin RH. 1999. Principles of Genetics. Wm. C. Brown Publishers.
Watson, J. D., N. H. Hopkins, J. W. Roberts, J. A. Steitz and A. M. Weiner. 1987. Molecular Biology of the Gene. The Benjamin/Cummings Publishing Co.Inc. Menlo Park. 1163p.

Weaver, R. F and P. W. Hedrick. 1995. Basic Genetics. Wm.C.Brown Publishers, London. 498p.

SUGGESTED WEBSITES

http://www.dnaftb.org/dnaftb/1/concept/
http://faculty.mwsu.edu/biology/jon.scales/Courses/Genetics/gen_notes.htm
http://www.wiley.com/college/math/biol/genlink/topics1.html
http://anthro.palomar.edu/mendel/Default.htm
http://users.iab.uaf.edu/~kevin_mccracken/genetics/
http://www.nature.com/scitable/topicpage/gregor-mendel-and-the-principles-ofinheritance-
http://nitro.biosci.arizona.edu/courses/EEB320-2005/EEB320.html
http://bcs.whfreeman.com/mga2e/default.asp?s=&n=&i=&v=&o=&ns=0&t=&uid=0&rau=0
http://www.biology-online.org/2/5_mendelian_genetics.htm
http://www.ashg.org/education/genbooks.shtml
http://biology.jbpub.com/book/genes/flashcards.cfm?chapter=1&step=2&resource=

Flashcard

III. Supporting courses

STA 501 Applied Statistical Methods (1+1)

OBJECTIVE

The students would be exposed to concepts of statistical methods and statistical inference that would help them in understanding the importance of statistics. It would also help them in understanding the concepts involved in computation, analysis and interpretation. The students would get an exposure to selection of sampling procedure, parameter estimation, tests of significance, correlation, regression and multiple linear regression techniques for analysis of thesis data.

THEORY

Unit I : Sampling Theory and Estimation

Sampling theory – population – finite and infinite population – parameter – sample – statistic – sampling – need for sampling – probability sampling – simple random sampling (SRS) – methods of selection of SRS – lottery method and random number table method – non–probability sampling – purposive and judgment sampling – sampling distributions – standard error and its uses Estimation theory – estimate – estimator – types of estimation – point estimation – properties of good estimators – unbiasedness, consistency, efficiency and sufficiency – interval estimation –confidence limits – confidence interval.

Unit II : Test of Hypothesis

Test of significance – null and alternative hypothesis – Type I and Type II errors – critical region –level of significance – degrees of freedom – large sample test – tests for significance of means and proportions for large samples – small sample test – t–test – testing the significance of single mean – testing the significance of two means for independent and paired samples – F–test for equality of two variances – 2 test for goodness of fit a and test for independence of attributes – test for equality of several variances (Bartlett’s test).

Unit III : Correlation Analysis

Bivariate distribution – simple correlation – meaning – assumptions – positive and negative correlation – scatter diagram – computation of correlation coefficient – properties of correlation coefficient – testing and interpretation of correlation coefficient – coefficient of determination – Fisher’s Z–transformation – testing several correlation coefficients – Spearman’s rank correlation (with and without ties).

Unit IV : Simple Linear Regression Analysis

Regression – simple linear regression – meaning – assumptions – fitting of simple linear regression equation of y on x – properties of regression coefficient – testing and interpretation of regression coefficient and intercept.

Unit V : Multiple Linear Regression Analysis

Multiple linear regression – assumptions – difference between simple and multiple linear regression – standardised and partial regression coefficients – fitting of multiple linear regression equation – testing the regression coefficients – interpretation of regression coefficients – multiple correlation – coefficient of multiple determination (R2) – interpretation of R2 – selection of variables – stepwise regression approach – multicollinearity – applications of dummy variables.

PRACTICALS

Interval estimation for means and proportion – large sample test – Z test – tests for significance of means and proportions for large samples – small sample test – t–test – testing the significance of single mean – testing the significance of two means for independent and paired samples – F–test for equality of two variances – chi square test for goodness of fit and test for independence of attributes – test for equality of several variances (Bartlett’s test) – Simple correlation – computation of correlation coefficient – properties of correlation coefficient – testing and interpretation of correlation coefficient – coefficient of determination – Fisher’s Z–transformation – testing several correlation coefficients – Spearman’s rank correlation (with and without ties) – Simple linear regression – fitting of simple linear regression equation of y on x – testing and interpretation of regression coefficient and intercept – Multiple linear regression – fitting of multiple linear regression equation – testing the partial regression coefficients – interpretation of regression coefficients.

LECTURE SCHEDULE

Sampling theory – population – finite and infinite population – parameter – sample – statistic – Sampling – need for sampling – probability sampling – simple random sampling (SRS) – SRSWR and SRSWOR

Methods of selection of SRS – lottery method and random number table method – non–probability sampling – purposive and judgment sampling

Sampling distributions – large and small sampling distributions – Z, t, F and 2 distributions – standard error and its uses

Estimation theory – estimate – estimator – types of estimation – point estimation – properties of good estimators – unbiasedness, consistency, efficiency and sufficiency –interval estimation – confidence limits – confidence interval

Test of significance – null and alternative hypothesis – Type I and Type II errors – critical region – level of significance – degrees of freedom – Large sample test (Z–test) – assumptions – tests for significance of means and proportions for large samples

Small sample test – t–test – assumptions – testing the significance of single mean –Testing the significance of two means for independent – paired t–test for dependent samples

F–test for equality of two variances – 2 test for goodness of fit
Mid Semester Examination
t test for independence of attributes – m x n contingency table – 2 x 2 contingency table – Yates correction for continuity – test for equality of several variances (Bartlett’s test)

Bivariate distribution – simple correlation – meaning – assumptions – positive and negative correlation – scatter diagram – computation of correlation coefficient – properties of correlation coefficient – testing and interpretation of correlation coefficient – coefficient of determination

Fisher’s Z–transformation – testing several correlation coefficients – Spearman’s rank correlation (with and without ties)

Regression – simple linear regression – meaning – assumptions – fitting of simple linear regression equation of y on x – properties of regression coefficient

Testing and interpretation of regression coefficient and intercept
Multiple linear regression – assumptions – difference between simple and multiple linear regression – standardised and partial regression coefficients – testing and interpretation of the partial regression coefficients

Multiple correlation – coefficient of multiple determination (R2) – interpretation of R2
Selection of variables – stepwise regression approach
Multicollinearity – meaning – its applications – applications of dummy variables

PRACTICAL SCHEDULE

Interval Estimation – confidence interval for population proportion – confidence interval for population mean

Large sample test – Z test – sampling of attributes – test for single proportion – test for equality of two proportions

Large sample test – sampling of variables – test for single mean – test for equality of two means

Small sample test – t test – test for single mean
Test for equality of two means (independent samples)
Paired – t – test – dependent samples
F – test – test for equality of two variances
χ2 – test for goodness of fit
χ2 – test for independence of attributes – m x n contingency table – 2 x 2 contingency table – Yates correction for continuity

χ 2 – test for homogeneity of several variances (or) Bartlett’s test
Correlation – correlation coefficient and testing its significance
χ 2 – test for homogeneity of several correlation coefficients
Spearman’s rank correlation (with and without ties)
Simple linear regression – regression coefficient and testing its significance – intercept and testing its significance

Fitting of multiple linear regression
Estimation of multiple linear regression using MS Excel.
Final Practical Examination

SUGGESTED READINGS

Rangaswamy, R, 2009, A text book of Agricultural Statistics, New Age International (P) Ltd., New Delhi.

Gupta. S.P, 2005, Statistical Methods, Sultan Chand & Sons, New Delhi.
K.P. Dhamu and K. Ramamoorthy, 2007, Statistical Methods, Agrobios (India), Jodhpur.
S.C. Gupta & V.K. Kapoor, 2006, Fundamentals of Mathematical Statistics, Sultan Chand & Sons, New Delhi.

Sahu P.K, 2007, Agriculture and Applied Statistics-I, Kalyani Publishers, Ludhiana. D.C. Sanchetti & V.K. Kapoor, 2007, Statistics (Theory, Methods and Application), Sultan Chand & Sons, New Delhi.

G. Nageswara Rao, 2007, Statistics for agricultural sciences, BS Publications, Hyderabad E.V. Divakara Sastry, 2007, Essentials of Agricultural Statistics, Pointer Publishers, Jaipur.

Murray R. Spiegel and Larry J. Stephens, 2007, Schaum’s Outline of Theory and Problems of Statistics, McGraw–Hill, New Delhi.

SUGGESTED WEBSITES

http://www.statistics.com/resources/glo.ssary/
www.statsoft.com
http://www.iasri.res.in/ebook/EB_SMAR/index.htm
www.stats.gla.ac.uk/steps/glossary/index.html
http://davidmlane.com/hyperstat/
http://www.stattrek.com/
http://www.businessbookmall.com/Statistics Internet Library.htm
http://www.stat-help.com

STA 503 Computer Applications in Statistics (0+1)

OBJECTIVE

This course is meant for exposing the students in the usage of various statistical packages like Ms.Excel, SYSTAT and SAS for analysis of data. It would provide the students hands on experience in the analysis of their research data. This course is useful to the students of all disciplines.

PRACTICALS

Operating system – windows – MS Excel – statistical functions – measures of central tendency – mean, median, mode, geometric mean, harmonic mean – quartiles and percentiles – measures of dispersion – range, quartile deviation, mean deviation, standard deviation, variance and coefficient of variation – skewness and kurtosis – finding critical values of t, F and 2.

Statistical data analysis using MS Excel – descriptive statistics – independent and paired t–tests –F test for testing the equality of variances – large sample test for comparing two means –correlation coefficient – simple linear regression analysis – multiple linear regression analysis.

For Social Science students

One way ANOVA – two way ANOVA – cross tabulation – goodness of fit – contingency table –Kolmogrov Smirnov test – Mann Whitney U–test – Wilcoxon matched pairs signed rank test –Kruskal Wallis one–way analysis – Friedman two–way analysis – Spearman rank correlation –Kendall’s rank correlation – Kendall’s coefficient of concordance. Time series analysis – moving average – exponential smoothing.

For Plant Science Students

Design of experiments – using AGRES / IRRISTAT – Completely Randomised Design (CRD) –Randomised Block Design (RBD) – factorial experiments – symmetrical and asymmetrical series –split plot design – split– split plot design – data transformation – log transformation – square root transformation – angular transformation.

PRACTICAL SCHEDULE

Introduction to operating system – windows
Introduction to SYSTAT and SAS packages.
MS Excel – Statistical functions for measures of central tendency and dispersion – skewness and kurtosis

Finding critical values of t, F and 2 – correlation coefficient – coefficient of determination – intercept and slope

MS Excel – Data analysis – Descriptive statistics – F-test for testing equality of two variances

Independent and paired t-tests- Large sample test for equality of two means Correlation analysis and its test of significance – simple linear regression analysis
Multiple regression analysis
Mid Semester Examination

For Social Science students (using SYSTAT and SAS)

Analysis of Variance – one way ANOVA and two way ANOVA
2 test – cross tabulation – test for goodness of fit – test for independence of attributes
Non-parametric test – Kolmogorov Smirnov test – Mann-Whitney U-test Wilcoxon matched pairs signed rank test – Kruskal Wallis One way Analysis
Friedman two way analysis – Spearman’s rank correlation
Kendall’s rank correlation – Kendall’s coefficient of concordance
Time series – moving average – exponential smoothing
Final Practical Examination

For Plant Science Students (using AGRES)

Completely Randomised Design (CRD)
Randomised Block Design (RBD)
Symmetrical Factorial Experiments
Asymmetrical Factorial Experiments
Split plot Design
Split-split plot Design
Data Transformations – log transformation – square root transformation – angular transformation

Final Practical Examination

SUGGESTED READINGS

Sharma. K.V.S., 2010, Statistics Made Simple: Do it yourself on PC, Prentice Hall of India, New Delhi.

Sanjay Saxena, 2003, A first course in Computers, Vikas Publishing House (P) Ltd., New Delhi.

Gene Weisskopf, 2000, ABC’s of Excel.
Ramesh Babu and Samyuktha, 2003, Computer Practice – I, V.R.B. Publications.
SYSTAT User’s guide and User’s manual.
SAS User’s guide and User’s manual.

SUGGESTED WEBSITES

http://www.iasri.res.in/ebook/EBADAT/index.htm
http://www.iasri.res.in/ebook/EB_SMAR/index.htm
http://www.statistics.com/resources/glossary/
www.statsoft.com
http://www.exceltip.com/
http://www.baycongroup.com/el0.htm
http://office.microsoft.com/training/training.aspx?AssetID=RC100620751033

STA 504 Statistical Methods For Social Sciences (1+1)

OBJECTIVE

The students would be exposed to the concepts of statistical methods and statistical inference that would help them in understanding the importance of statistics. It would also help them in understanding the concepts involved in computation, analysis and interpretation. The students would get an exposure to selection of sampling procedure, parameter estimation, test of significance, correlation, regression and multiple linear regression techniques.

THEORY

Unit I : Sampling Theory

Sampling theory – population – finite and infinite population – sample – parameter and statistic –census – sample survey – sampling – need for sampling – sampling unit and sampling frame –random sample – sampling vs complete enumeration – non–probability sampling methods –probability sampling methods – simple random sampling (SRS) – SRSWR and SRSWOR – methods of selection of SRS – lottery method and random number table method – systematic sampling – stratified random sampling – stratification – types of allocation – equal, proportional, Neyman optimum allocation – cluster sampling – determination of sample size in SRS, stratified random sampling, systematic and cluster sampling – probability proportional to size (PPS) sampling – sampling and non–sampling errors.

Unit II : Test of Hypothesis

Unit III : Correlation Analysis

Unit IV : Simple Linear Regression Analysis

Unit V : Multiple Linear Regression Analysis

Multiple linear regression – assumptions – difference between simple and multiple linear regression – standardized and partial regression coefficients – fitting of multiple linear regression equation – testing the regression coefficients – interpretation of regression coefficients – multiple correlation – coefficient of multiple determination (R2) – interpretation of R2 – selection of variables – stepwise regression approach.

PRACTICALS

Selection of simple random sample ( SRS) – estimation of parameters and sample size in SRS – selection and estimation in systematic sampling and stratified sampling – determination of sample size in stratified random sampling – selection of clusters and parameter estimation in cluster sampling – large sample test – Z test – tests for significance of means and proportions for large samples – small sample test – t–test – testing the significance of single mean – testing the significance of two means for independent and paired samples – F–test for equality of two variances – Simple correlation – computation of correlation coefficient – testing and interpretation of correlation coefficient – coefficient of determination – Simple linear regression – fitting of simple linear regression equation of y on x – testing and interpretation of regression coefficient and intercept – Multiple linear regression – fitting of multiple linear regression equation – testing the partial regression coefficients – interpretation of regression coefficients.

LECTURE SCHEDULE

Sampling theory – population – finite and infinite population – sample – parameter and statistic – census – sample survey – sampling – need for sampling Sampling unit and sampling frame – random sample – sampling vs complete enumeration

Sampling methods – non–probability sampling methods
Probability sampling methods – simple random sampling (SRS) – SRSWR and SRSWOR – methods of selection of SRS – lottery method and random number table method – determination of sample size in SRS

Systematic sampling – stratified random sampling – stratification – types of allocation – equal, proportional, Neyman optimum allocation – determination of sample size in stratified random sampling and systematic sampling

Cluster sampling – application of cluster sampling in social sciences – determination of sample size in cluster sampling

Probability proportional to size (PPS) sampling – sampling and non–sampling errors
Mid Semester Examination
Test of significance – null and alternative hypothesis – Type I and Type II errors – critical region – level of significance – degrees of freedom – Large sample test (Z–test) – assumptions – tests for significance of means and proportions for large samples

Small sample test – t–test – assumptions – testing the significance of single mean –testing the significance of two means for independent samples

Paired t–test for dependent samples – F–test for equality of two variances
Bivariate distribution – simple correlation – meaning – assumptions – positive and negative correlation – scatter diagram – computation of correlation coefficient – properties of correlation coefficient – testing and interpretation of correlation coefficient – coefficient of determination

Regression – simple linear regression – meaning – assumptions – fitting of simple linear regression equation of y on x – properties of regression coefficient

Testing and interpretation of regression coefficient and intercept
Multiple linear regression – assumptions – difference between simple and multiple linear regression – standardized and partial regression coefficients – testing and interpretation of the partial regression coefficients

Multiple correlation – coefficient of multiple determination (R2) – interpretation of R2 Selection of variables – stepwise regression approach

PRACTICAL SCHEDULE

Selection of simple random sample (SRS) – determination of sample size in SRS
Parameter estimation in SRS
Selection and estimation in systematic sampling – determination of sample size in systematic sampling

Selection of stratified random sample – estimation of parameters in stratified random sampling

Determination of sample size in stratified random sampling under each allocation
Selection of clusters in cluster sampling – estimation of parameters in cluster sampling – determination of sample size in cluster sampling

Large sample test – Z test – sampling of attributes – test for single proportion – test for equality of two proportions

Large sample test – sampling of variables – test for single mean
Large sample test – sampling of variables – test for equality of two means
Small sample test – t test – test for single mean
Test for equality of two means (independent samples)
Paired t – test for dependent samples
F – test – test for equality of two variances
Correlation – computation of correlation coefficient and testing its significance
Simple linear regression – regression coefficient and testing its significance – intercept and testing its significance

Fitting of multiple linear regression
Final Practical Examination

SUGGESTED READINGS

Rangaswamy, R, 2009, A text book of Agricultural Statistics, New Age International (P) Ltd., New Delhi.

Gupta. S.P, 2005, Statistical Methods, Sultan Chand & Sons, New Delhi.
Sahu P.K, 2007, Agriculture and Applied Statistics-I, Kalyani Publishers, Ludhiana.
K.P. Dhamu and K. Ramamoorthy, 2007, Statistical Methods, Agrobios (India), Jodhpur.
S.C. Gupta & V.K. Kapoor, 2006, Fundamentals of Mathematical Statistics, Sultan Chand & Sons, New Delhi.

A.K.P.C. Swain, 2003, Finite Population Sampling, South Asian Publishers, New Delhi.
G. Nageswara Rao, 2007, Statistics for agricultural sciences, BS Publications, Hyderabad

E.V. Divakara Sastry, 2007, Essentials of Agricultural Statistics, 2007, Pointer Publishers, Jaipur.

Murray R. Spiegel and Larry J. Stephens, 2007, Schaum’s Outline of Theory and Problems of Statistics, McGraw–Hill, New Delhi.

Cochran, W.G., 1989, Sampling Techniques, Oxford and IBH Publishing Co.

SUGGESTED WEBSITES

http://www.statistics.com/resources/glo.ssary/
www.statsoft.com
http://www.iasri.res.in/ebook/EB_SMAR/index.htm
www.stats.gla.ac.uk/steps/glossary/index.html
http://davidmlane.com/hyperstat/
http://www.stattrek.com/
http://www.businessbookmall.com/Statistics Internet Library.htm
http://www.stat-help.com/

Compulsory Non-credit courses PGS 501 Library and Information Services (0+1)
OBJECTIVE
To equip the library users with skills to trace information from libraries efficiently, to apprise them of information and knowledge resources, to carry out literature survey, to formulate information search strategies, and to use modern tools (Internet, OPAC, search engines etc.) of information search.
PRACTICALS
Introduction to library and its services; Role of libraries in education, research and technology transfer; Classification systems and organization of library; Sources of information- Primary Sources, Secondary Sources and Tertiary Sources; Intricacies of abstracting and indexing services (Science Citation Index, Biological Abstracts, Chemical Abstracts, CABI Abstracts, etc.); Tracing information from reference sources; Literature survey; Citation techniques/Preparation of bibliography; Use of CD-ROM Databases, Online Public Access Catalogue and other computerized library services; Use of Internet including search engines and its resources; e-Resources access methods.
SUGGESTED READINGS
1.		Ranganathan S.R. 2006. Colon Classification 6th ed .Ess Ess Publications, New Delhi
2.		Renuka, P. 2009. Library and information services in Agriculturaleducation, Research and Extension, Akansha publishing house , New Delhi.
3.		Veeranjaneyulu, Mahapatra and Visakhi, 2012. Library Services in the knowledge web, New India Publishing Agency, New Delhi.
SUGGESTED WEBSITES
1.		http://www.icar.org.in
2.		http://egranth.ac.in/
3.		http://nopr.niscair.res.in/
4.		http://krishikosh.egranth.ac.in/
5.		http://14.139.232.167:8080/equestthesis/
PGS 502 Technical Writing and Communication Skills (0+1)
OBJECTIVE
This course is intended to expose the students about the basics skills needed for writing, reporting scientific data in the form of reports, research papers, manuals etc., and develop skill in preparing appropriate graphics to be used in such documents and presentations.
THEORY
Unit I :
Basics of writing, writing style, art of clear writing: Readability and comprehension testing procedures, Principles of technical writing, purpose of technical reports, Preparing a documentation plan, Understanding information types, Gathering the data, Analyzing and sorting the results, Outlining the report
Unit II :
Use of charts, graphs, tables, diagrams and photographs, scientific photography, Graphic formats, typology, Presentation of scientific data, general and exact data, Editing, Proof reading, Bibliography
Unit III :
Role of visuals in Communication; Characteristics of visuals, functions of visuals and graphics; Theories of visual perception; Classification of visuals, visual formats, Selection of visuals, Preparing lecture slides – content, limitation and layout; its utility in preparing presentations for research papers and other publications, Public speaking.
PRACTICALS
Writing technical reports, research papers, preparing graphics, preparing computer based presentations.
SUGGESTED READINGS
1.	Day, Robert A. and Gastel, Barbara. 2006. How to Write and Publish a Scientific Paper. 6th Edition, Cambridge University Press, U.K.
2.	James W.B., Richard B.L., Fried F. Harcleroad. 1952. A.V. Instructional Material and Methods. McGraw Hill.
3.	Lucas, S.E. 2007. The Art of Public Speaking, 10th Edition; New York: McGraw-Hill.
4.	Matthews, Janice R. and Robert W. Matthews. 2008. Successful Scientific Writing. 3rd Edition, Cambridge University Press, U.K.
5.	Turk, Christopher and Kirkman, John. 1994. Effective Writing. Second Edition, EandFN Spon, London
PGS 503 Intellectual Property and Its Management In Agriculture (E-Course) (1+0) OBJECTIVE
The main objective of this course is to equip students and stakeholders with knowledge of intellectual property rights (IPR) related protection systems, their significance and use of IPR as a tool for wealth and value creation in a knowledge-based economy.

THEORY

Historical perspectives and need for the introduction of Intellectual Property Right regime; TRIPs and various provisions in TRIPS Agreement; Intellectual Property and Intellectual Property Rights (IPR), benefits of securing IPRs; Indian Legislations for the protection of various types of Intellectual Properties; Fundamentals of patents, copyrights, geographical indications, designs and layout, trade secrets and traditional knowledge, trademarks, protection of plant varieties and farmers’ rights and biodiversity protection; Protectable subject matters, protection in biotechnology, protection of other biological materials, ownership and period of protection; National Biodiversity protection initiatives; Convention on Biological Diversity; International Treaty on Plant Genetic Resources for Food and Agriculture; Licensing of technologies, Material transfer agreements, Research collaboration Agreement, License Agreement.

SUGGESTED READINGS

Erbisch, F.H. and K. Maredia.1998.Intellectual Property Rights in Agricultural Biotechnology.CABI.

Ganguli, P. 2001. Intellectual Property Rights: Unleashing Knowledge Economy. McGraw-Hill.

Intellectual Property Rights: Key to New Wealth Generation. 2001. NRDC and Aesthetic Technologies

Ministry of Agriculture, Government of India. 2004. State of Indian Farmer. Vol. V.

Layout Design Act, 2000

Ministry of Agriculture, Government of India. 2004. State of Indian Farmer. Vol. V.

National Biological Diversity Act, 2003.

PPV and FR Act, 2001, and Rules 2003

Rothschild, M and N. Scott. 2003. Intellectual Property Rights in Animal Breeding and Genetics. CABI.

Saha, R. 2006. Intellectual Property Rights in NAM and Other Developing Countries: A Compendium on Law and Policies. Daya Publ. House.

Technology Generation and IPR Issues.Academic Foundation.

The Copyright Act, 1957 and amendments

The Indian Acts – Patents Act, 1970 and amendments; Design Act, 2000

Trademarks Act, 1999

SUGGESTED WEBSITES

1. World Intellectual Property Organization (http://www.wipo.int/portal/index.html.en)

2. World Trade Organization (http://www.wto.org/)

3. United States Patent and Trademark Office (www.uspto.gov)

4. International Union for the Protection of New Varieties of Plants (http://www.upov.int/)

5. Convention on Biological Diversity (www.cbd.int)

6. Indian Patent Office (http://www.patentoffice.nic.in/)

7. National Institute for Intellectual Property Management

8. (http://ipindia.nic.in/Niipm/index.htm)

9. PPV and FR Authority (http://plantauthority.gov.in/)

10. National Innovation Foundation (www.nif.org.in)

11. National Biodidiversity Authority (http://nbaindia.org/)

12. ICAR guide on IP management (www.icar.org.in/files/reports/other-reports/icar-ipmttcguide.pdf)

13. Journal of Intellectual Property Rights (http://www.niscair.res.in/sciencecommunication/

14. ResearchJournals/rejour/jipr/jipr0.asp)

PGS 504 Basic Concepts In Laboratory Techniques (0+1)

OBJECTIVE

To acquaint the students about the basics of commonly used techniques in laboratory. The techniques furnished here will vary based on the scope and needs of each discipline. Accordingly, the syllabi could be modified.

PRACTICALS

Safety measures while in Lab; Handling of chemical substances; Use of burettes, pipettes, measuring cylinders, flasks, separator funnel, condensers, micropipettes and vaccupets; washing, drying and sterilization of glassware; Drying of solvents/chemicals. Weighing and preparation of solutions of different strengths and their dilution; Handling techniques of solutions; Preparation of different agro-chemical doses in field and pot applications; Preparation of solutions of acids; Neutralisation of acid and bases; Preparation of buffers of different strengths and pH values. Use and handling of microscope, laminar flow, vacuum pumps, viscometer, thermometer, magnetic stirrer, micro-ovens, incubators, sand bath, water bath, oil bath; Electric wiring and earthing. Preparation of media and methods of sterilization; Seed viability testing, testing of pollen viability; Tissue culture of crop plants; Description of flowering plants in botanical terms in relation to taxonomy. Specific methodologies concerning each discipline

SUGGESTED READINGS

Furr, A.K. 2000.CRC Hand Book of Laboratory Safety.CRC Press.
Gabb, M.H. and W.E. Latchem. 1968. A Handbook of Laboratory Solutions. Chemical Publ. Co.

PGS 505 Agricultural Research, Research Ethics And Rural Development Programmes (e-course) (1+0)

OBJECTIVE

The course intends to sensitize the scholars about the basic issues related with agricultural research, ethics in research as well as rural development. The scholars will be also educated about principles and philosophy of rural development and motivated towards practicing and promoting ethics in research and developmental endeavours.
THEORY
	Unit I :
	History of agriculture in brief; Global agricultural research system: need, scope, opportunities; Role in promoting food security, reducing poverty and protecting the environment; National Agricultural Research Systems (NARS) and Regional Agricultural Research Institutions; Consultative Group on International Agricultural Research (CGIAR): International Agricultural Research Centres (IARC), partnership with NARS, role as a partner in the global agricultural research system, strengthening capacities at national and regional levels; International fellowships for scientific mobility.
	Unit II :
	Research ethics: research integrity, research safety in laboratories, welfare of animals used in research, computer ethics, standards and problems in research ethics.

Unit III :

Concept and connotations of rural development, rural development policies and strategies. Rural development programmes: Community Development Programme, Intensive Agricultural District Programme, Special group –Area Specific Programme, Integrated Rural Development Programme (IRDP), Panchayati Raj Institutions, Co-operatives, Voluntary Agencies/Non Governmental Organisations. Critical evaluation of rural development policies and programmes.Constraints in implementation of rural policies and programmes.
SUGGESTED READINGS
	1.	Ableman, M. 2005. Fields of plenty: A farmer’s journey in search of real food and the people who produce it. San Francisco: Chronicle Books.
	2.	Agarwal, A. 2005. Environmentality: Technologies of government and the making of subjects. Durham, NC: Duke University Press
	3.	Gadgil, M. and Guha, R. 1995.Ecology and equity.The use and abuse of nature in contemporary India. New Delhi: Penguin Books.
	4.	Jain, L.C., Krishnamurthy, B.V. and Tripathi, P.M. 1986. Grass without roots under Government Auspices.Sage Publications, New Delhi.
	5.	Minakshi Bhardwaj, Fumi Maekawa, Yuki Niimura, Darryl RJ Macer. 1999. Ethics in Food and Agriculture: Views from FAO.
	6.	Rivera, Roberto and David Borasky 2009. Research Ethics Training Curriculum, Family Health International. P.O. Box 13950 Research Triangle Park, NC 27709. USA.
	7.	Singh, Kartar 2001.Rural Development – Principles, Policies and Management.Sage Publications, New Delhi.
	8.	Thompson, P. 1997. The spirit of the soil: Agriculture and environmental ethics. New York: Routledge Press.

PGS 506 Disaster Management (1+0)

OBJECTIVE
To introduce learners to the key concepts and practices of natural disaster management; to equip them to conduct thorough assessment of hazards, and risks vulnerability; and capacity building.
THEORY
Unit I :
Natural Disasters- Meaning and nature of natural disasters, their types and effects. Floods, Drought, Cyclone, Earthquakes, Landslides, Avalanches, Volcanic eruptions, Heat and cold Waves, Climatic Change: Global warming, Sea Level rise, Ozone Depletion
Unit II :
Man Made Disasters- Nuclear disasters, chemical disasters, biological disasters, building fire, coal fire, forest fire. Oil fire, air pollution, water pollution, deforestation, Industrial waste water pollution, road accidents, rail accidents, air accidents, sea accidents.
	Unit III :
	Disaster Management- Efforts to mitigate natural disasters at national and global levels. International Strategy for Disaster reduction. Concept of disaster management, national disaster management framework; financial arrangements; role of NGOs, Community-based organizations, and media. Central, State, District and local Administration; Armed forces in Disaster response; Disaster response: Police and other organizations.
	SUGGESTED READINGS
	1.	Gupta, H.K. 2003.Disaster Management.Indian National Science Academy.Orient Blackswan.
	2.	Hodgkinson, P.E. and M. Stewart. 1991. Coping with Catastrophe: A Handbook of Disaster Management. Routledge.
	3.	Sharma, V.K. 2001.Disaster Management.National Centre for Disaster Management, India.