National Institute of Plant Genome Research
 
Course Work for Ph.D. Students
National Institute of Plant Genome Research

Course Co-ordinator: Dr. Niranjan Chakraborty


Course MaterialCredits
Molecular Cell Biology and Genetics3
Genomics3
Plant Biology3
Emerging Trends in Plant Sciences2
Research Methodology2
Term Paper- A review in an emerging area of research1
Seminar 1
Total 15
 
Molecular Cell Biology and Genetics

Total Credit : 3
Total Number of Lectures : 48
Course In-charge: Dr. Manoj Majee & Dr. Naveen Chandra Bisht

Fundamental knowledge of Molecular Cell Biology and Genetics is the basis of unraveling nature's secret hidden in biological system. The students are expected to refresh their knowledge on cellular biology, molecular biology and genetics through this course. Emphasis will be given to explain the topics giving relevant examples that might help Ph.D. students in designing their experiments and interpretation of their observations.
1. Cellular Biology (16 lectures)
  1. Constituents of Plant Cells: Extracellular matrix, Cytoskeleton, and Organelles.
  2. Cell Cycle Regulation: Phases of cell cycle, Restriction and check point, Cell division and cell growth, Cell cycle progression.
  3. Enzyme Function.
  4. Protein Turnover: Biosynthesis and degradation.
2. Molecular Biology (12 lectures)
  1. Genetic Material: Genome organization, DNA replication and recombination, Source of genetic variation (natural and induced).
  2. Gene Expression: Transcription, Cis-acting elements and transcription factors, RNA editing and processing.
  3. Protein Targeting and Trafficking: Protein trafficking (classical and non-classical pathways), ER and Golgi dynamics, Protein sorting and trafficking, Dynamics of membrane-bound protein, Mechanism of protein secretion.
3. Genetics (20 Lectures)
  1. Law of Inheritance: Mendelian principles, Concept of dominance, Segregation and independent assortment, Codominance, Incomplete dominance, Gene interactions, Pleiotropy, Linkage and crossing over.
  2. Allelic and Non-allelic Interaction: Concept of allele, Lethal alleles, Multiple alleles, Test of allelism, Complementation and epistatsis.
  3. Mutation: Types of mutation, Repair mechanism, Role in genetic analysis and evolution.
  4. Cytoplasmic Inheritance: Basis and mechanism, Role of organellar genes.
  5. Recombination: Homologous and non-homologous recombination including transposition.
  6. Structural and Numerical Alterations of Chromosomes: Polyploidy, Aneuploidy, Chromosomal rearrangements – deletion, duplication, inversion and translocation.
Suggested Reading
  1. Nelson DL and Cox MM (2008) Lehninger “Principles of Biochemistry”. Fifth Edition, Freeman & Co Ltd., NY, USA.
  2. Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P (2008) Molecular Biology of the Cell. Fifth Edition, Garland Science, NY, USA.
  3. Voet D and Voet JG (2011) Biochemistry. Fourth Edition, John Wiley & Sons, NY, USA.
  4. Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D and Darnell J (2012) Molecular Cell Biology. Seventh Edition, Taylor & Francis Publishers, NY, USA.
  5. Krebs JE, Goldstein ES and Kilpatrick ST (2011) Lewin’s Genes X. Tenth Edition, Jones & Bartlett Publishers, MA, USA.
  6. Latchman DS (2007) Gene Regulation. Fifth Edition, Taylor & Francis Publishers, NY, USA.
  7. Brown TA (2007) Genomes. Third Edition, Garland Science, NY, USA.
  8. Snustad DP and Simmons MJ (2012) Principles of Genetics. Sixth Edition, John Wiley & Sons, NY, USA.

 
Genomics

Total Credit : 3
Total Number of Lectures : 48
Course In-charge: Dr. Praveen Verma and Dr. Mukesh Jain

The primary objective of this course is to familiarize students with fundamental concepts of plant structural, functional and comparative genomics and make them aware of genomics-assisted advanced technologies including various traditional as well as modern genetic and molecular breeding approaches having potential applications in crop improvement. This course further aims at helping students gain a deeper understanding of the latest in-silico genomics and proteomics tools and methodologies. On the whole, the course will enhance overall comprehension of the subject, improve computational skills and eventually assist in proper planning, execution and analysis of research work.
1. Genome Analysis (5 lectures)
  1. Basic concepts of genes, genome and genomics.
  2. Cloning systems used in genomics (Cosmids, P1 bacteriophage, BAC and PAC cloning vectors).
  3. Physical mapping of the genome.
2. Sequencing, Analyzing Genomes and Transcriptomes (15 lectures)
  1. Sequencing strategies for the systematic sequencing of complex genomes.
  2. Analysis of sequenced model plant genomes (Arabidopsis and rice).
  3. Next generation sequencing methods and their assembly and annotation.
  4. Principles of genome annotation and gene prediction: tools and resources.
  5. Introduction to various sequence formats and different methods of database searches.
  6. Connecting sequence to function and plant genome databases.
3. Functional Genomics (6 lectures)
  1. Strategies to find gene function at genome-wide level: Gene tagging, Tilling and gene targeting.
  2. Differential gene expression profiling: Methodology and analysis.
4. Molecular Markers and Their Applications in Molecular Breeding (12 lectures)
  1. Overview, development and application of molecular markers.
  2. Methods of assessing genetic diversity and germplasm characterization, DNA fingerprinting and its application.
  3. Concept of linkage mapping: Principles, mapping populations, recombination fractions, LOD score and establishment of linkage groups, gene mapping tools and resources.
  4. QTL analysis and concept of marker-assisted selection in plant breeding.
  5. Map-based gene isolation.
  6. Allele mining, association mapping and their applications in crop improvement.
  7. Statistical approaches to biological systems.
5. Evolutionary and Comparative Genomics (4 lectures)
  1. Introduction to genome evolution: Molecular phylogenetics and applications.
  2. Multiple sequence alignments and phylogenetic analysis.
  3. Evolution of exon and introns, Gene duplication, Acquisition of new genes in non-coding regions, Multigene families: neo-, pseudo-, and sub-functionalization.
  4. Transposable elements and their role in genome evolution.
  5. Intergenome comparison for synteny analysis.
6. Protein Structure Analysis (6 lectures)
  1. The peptide bond and structural basis of protein function
  2. From sequence to structure and from structure to function
Suggested Reading
  1. Brown, T.A. (2010) Gene cloning and DNA analysis: an introduction. West Sussex: Wiley-Blackwell, NJ, USA.
  2. Xu Y (2010) Molecular Plant Breeding. CABI International, Wallingford, Oxfordshire, UK.
  3. Caetano-Anolles G (2010) Evolutionary Genomics and Systems Biology. Wiley-Blackwell, Hoboken, NJ, USA.
  4. Somers DJ, Langridge P, Gustafson JP (2011) Plant Genomics: Methods and Protocols, Methods in Molecular Biology. Humana Press Inc., NY, USA.
  5. Pevsner J (2009) Bioinformatics and Functional Genomics. Wiley-Blackwell, Hoboken, NJ, USA.
  6. Brown TA (2007) Genomes. Third Edition, Garland Science, NY, USA.
  7. Galperin MY and Koonin EV (2003) Frontiers in Computational Genomics. Caister Academic Press, Norfolk, UK.
  8. Primrose SB and Twyman R (2006) Principles of Gene Manipulation and Genomics. Seventh Edition, Wiley-Blackwell, NJ, USA.
  9. Xu Y (2010) Molecular Plant Breeding. CABI International, Oxfordshire, UK.
  10. Somers DJ, Langridge P and Gustafson JP (2011) Plant Genomics: Methods and Protocols, First Edition, Humana Press Inc., NY, USA.
In addition, recent literature will be suggested by the faculty during the course of teaching.
 
Plant Biology

Total Credit : 3
Total Number of Lectures : 48
Course In-charge:Dr. Subhra Chakraborty and Dr. Senthil Kumar Muthappa

The course will focus on major biochemical processes and regulatory control that operate in plant development. With an increasing awareness of environmental problems, the course will include various aspects of stress biology, especially the biotic and abiotic stresses which illustrate mechanism/s of stress tolerance in plants. Understanding the biology of plants, different aspects of signal transduction, and the impact of genetic engineering for crop improvement are many of prime issues of this course that will continue to fuel the expansion of plant biology research.
1. Biochemical Processes (10 lectures)
  1. Photosynthesis: Light harvesting complexes,Mechanism of electron transport, Chlorophyll fluorescence,Photoprotective mechanism, CO2 fixation- C3, C4 and CAM pathways.
  2. Respiration and Photorespiration: Citric acid cycle,Plant mitochondrial electron transport and ATP synthesis,Alternative oxidase, Photo respiratory pathway.
  3. Water and Solute Transport and Photo-assimilates Translocation: Uptake, transport and translocation of water, ions, solutes and macromolecules from soil, through cells, across membranes, through xylem and phloem,Transpiration,Mechanism of loading and unloading of photo-assimilates.
  4. Plant Nutrients: Essential nutrients (macro-nutrient & micro-nutrient) and their deficiency disorders.
  5. Nitrogen metabolism: Nitrogen fixation,Ammonia uptake and transport,Nitrate uptake and reduction.
  6. Secondary Metabolism: Biosynthesis and uses of alkaloids, glycosides, terpenes and phenolics.
2. Development (8 lectures)
  1. Molecular basis of stem, leafand root development.
  2. Molecular basis of reproduction: Male and female gametophyte, Male sterility, Fertilization, Seed, Apomixis.
3. Signal Transduction (10lectures)
  1. Overview of cell signalling.
  2. Membrane receptors and receptor proteins.
  3. c. Secondary messengers: Ca2+/CaM, NO etc.
  4. d. Kinase signalling and reversible phosphorylation.
  5. e. Plant Hormones: Biosynthesis, perception, signaling and role in plant growth and development.
  6. f. Light Signaling: Perception, signaling and role in plant growth and development.
  7. g. Sugar Signaling: Perception, signaling and role in plant growth and development.
4. Plant Response to Environment (12 lectures)
  1. Abiotic Stress: Drought, Salinity, Light, Temperature and heavy metals. Stress perception,Adverse effect of stresses on plant growth and development,Cellular, physiological and biochemical responses to stresses.
  2. Plant Immunity:Genetics of immune response,Signal perception,Host-pathogen interaction (bacteria, fungus, and virus).
  3. Symbiosis: Mycorrhizal and rhizobial interaction.
5. Genetic engineering & crop improvement (8 lectures)
  1. Recombinant DNA technology, cloning of genes and regulatory elements.
  2. Gene manipulation (over-expression and RNA interference).
  3. Plant genetic transformation, cis-genics and transgenics.
  4. Agronomic, industrial and quality traits.
  5. Bioethics, Biosafety, Intellectual property rights and implications in plant research.
Suggested Reading
  1. Buchanan B Gruissem W and Jones R (2000)Biochemistry & Molecular Biology of Plants. American Society of Plant Physiologists Press, Rockville, MD, USA.
  2. Nelson DL and Cox MM (2008) Lehninger “Principles of Biochemistry”. Fifth Edition,Freeman& Co Ltd., NY, USA.
  3. Alberts B Johnson A Lewis J Raff M Roberts K and Walter P (2008) Molecular Biology of the Cell. Fifth Edition, Garland Science, NY, USA.
  4. Lea P and Leegood RC (1999) Plant Biochemistry & Molecular Biology.John Wiley & Sons, NY, USA.
  5. Tropp BE(2008) Molecular Biology: Genes to Proteins. Third edition,Jones & Bartlett Publishers, MA, USA.
Other updated literature will be suggested by the concerned faculties during the course of teaching.
 
Emerging Trends in Plant Sciences

Total Credit : 2
Total Number of Lectures : 32
Course In-charge: Dr. Gitanjali Yadav and Dr. Jitendra K. Thakur

In the past decade, our understanding about plant biology has immensely increased largely because of the availability of enriched genomic information and emerging techniques in plant biology. The course will broaden our understanding about the emerging concepts of plant gene regulation at in-depth level involving micro-RNA regulation and epigenetics. Various ‘Omic’-based studies, which broadened our knowledge about various plant processes and plant functioning as a whole, will be discussed. A brief account of emerging application of nanotechnology in plant sciences are also included.
1. Regulation Biology (12 lectures)
  1. RNA interference, RNA editing, Plant Mediator Complex- discovery, phylogeny, structure and diverse roles.
  2. Post-transcriptional and post-translational regulation.
  3. Chromatin remodeling, DNA methylation, Histone modifications.
  4. Epigenetic regulation in plants, Epigenomics and its scopes, Paramutation, Genomic imprinting, RNA-mediated epigenetic phenomenon.
2. Stem Cells (8 lectures)
  1. Stem cell concept, plant and animal stem cell niches including totipotency.
  2. Molecular regulation of shoot stem cell niche and its importance.
  3. Molecular regulation of root stem cell niche and its importance. Comparison between stem cell niches of different organs.
  4. Cambium stem cells and their role in vascular development.
3. Nanotechnology in Plant Science (4 lectures)
  1. Introduction to nanotechnology.
  2. Application and limitation of novel nanotechnology strategies in plant biotransformation.
4. Systems Biology (8 lectures)
  1. Introduction to systems biology.
  2. Tools of systems biology.
  3. Modeling the biological pathway.
  4. Gene regulatory / co-expression network analysis.
  5. Primary / secondary metabolite networks of plants: a case study.
Suggested Reading
  1. Hartl DL and Jones EW (2005) Genetics: Analysis of Genes and Genomes. Sixth Edition, Sudbury, MA, USA.
  2. Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P (2008) Molecular Biology of the Cell. Fifth Edition, Garland Science, NY, USA.
  3. Nelson DL and Cox MM (2008) Lehninger “Principles of Biochemistry”. Fifth Edition Freeman, NY, USA.
  4. Taiz L and Zeiger E (2010) Plant Physiology, Fifth Edition. Sinauer Associates, Sunderland, MA, USA.
  5. Howell SH (1998) Molecular Genetics of Plant Development. Cambridge University Press, NY, USA.
  6. Srivastava LM (2002) Plant Growth and Development: Hormone and Environment. Academic Press, Amsterdam, The Netherlands.
  7. Overview and Implications of Nanotechnology (2008). http://www.ifpri.org/sites/default/files/20080618Roco.pdf.
  8. Nanotechnology in Agriculture and Food (2006). European Nanotechnology Gateway.
    http://www.nanoforum.org/dateien/temp/nanotechnology%20in%20agriculture%20and%20food.pdf.
In addition, recent literature will be suggested by the concerned faculties during the course work.
 
Research Methodology

Total Credit : 2
Total Number of Lectures : 24
Course In-charge: Dr. Ashverya Laxmi and Dr. Swarup K. Parida

Our understanding about the plant biology has increased largely because of the availability of latest techniques and instruments. The ‘Research Methodology’ course will broaden the understanding of students about general instrumentation and its requirement in various day-to-day lab activities. Various techniques involved in gene expression analysis such as Real-Time PCR and Microarray will be introduced. A brief account of proteomics studies will also be given. An elaborate account of various microscopic, sequencing and mapping techniques will be given. Further, a detailed account of radioisotope and imaging tools will be discussed with special emphasis to various aspects of radiation safety. The functioning of various other instruments such as photometry, chromatography, pulse-field gel electrophoresis will also be discussed. Finally, the functioning and uses of computational network and computational facility will also be introduced. The introduction and visualization of these techniques/instrumentations will help students to know about their usage/applications and help in designing experiments for their research work accordingly.
  1. General instrumentation.
  2. Computer networks and computational facility.
  3. Basic bioinformatic tools.
  4. Radioisotope and imaging.
  5. Photometry.
  6. Chromatography.
  7. Proteomics.
  8. Sequencing, Real-Time PCR and pulse-field gel electrophoresis.
  9. Advanced microscopy.
  10. Microarray.
Suggested Reading
  1. Bisen PS and Sharma A (2012) Introduction to Instrumentation in Life Sciences. Taylor & Francis, California, USA.
  2. Cazes J (2009) Encyclopedia of Chromatography. Taylor & Francis, Florida, USA.
  3. Wilson K and Walker J (2000) Principles and Techniques of Practical Biochemistry. Fifth edition, Cambridge University Press, UK.
  4. Tuimala J and Laine MM (2005) DNA Microarray Data Analysis. Second Edition, CSC Scientific Computing Ltd., Helsinki.
  5. Berrar DP, Dubitzky W and Granzow M (2003) A Practical Approach to Microarray Data Analysis. Kluwer Academic Publishers, NY, USA.
  6. Reinders J and Scickmann A (2009) Proteomics- Methods and Protocols. Humana Press, NY, USA.
  7. Spector DL and Goldman RD (2006) Basic Methods in Microscopy. Protocols and Concepts from Cells: A Laboratory Manual. Cold Spring Harbor University Press, NY, USA.
  8. Confocal Microscopy: Methods and Protocols (1999) In: Methods in Molecular Biology, Vol 122, Ed., Stephen W. Paddock, Humana Press Inc., Totoya, NJ.
  9. Manual: Training course on safety aspect in the research applications of ionizing radiations (2005): Radiological Physics and Advisory Divisions, Atomic Energy Regulatory Board, BARC.
  10. Oliphant A, Barker DL, Stuelpnagel JR and Chee MS (2002) BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques, 32, S56.
  11. Fan JB, Chee MS and Gunderson KL (2006) Highly parallel genomic assays. Nat. Rev. Genet., 7, 632–44.