M.Sc. Botany Course Syllabus

An M.Sc. in Botany, or Master of Science in Botany, is a postgraduate degree program that delves deeper into the scientific study of plants. The student should be proficient in research methodologies, data analysis, and scientific writing. Practical experience in fieldwork, laboratory work, and plant tissue culture is crucial. Staying updated with the latest botanical research is essential for success in the field.

CORE PAPERS (SEMESTERS I AND II)

SEMESTER I

Subject 1: CELL AND MOLECULAR BIOLOGY

Introduction to modern tools and techniques of cell biology
advances in light and electron microscopy, techniques supplementing microscopy (cytochemistry, microprobe analysis, x-ray diffraction, etc.), Cell fractionation and visualization/characterization of various cell fractions.

Cell components and their functions: Dynamic structure, functions and biogenesis of cell wall and plasma membrane; new insights in structure and function of cytoplasmic cell organelles and biopolymers; nucleus; its components, chromatin structure in eukaryotes,
condensation and packaging of DNA in prokaryotes, their dynamic state and role in gene regulation; structure and function of plant cytoskeletal genes and gene products; protein sorting and intracellular trafficking.

Cell multiplication and turnover: cell cycle and apoptosis

Gene structure, regulation and expression in eukaryotes: Gene and promoter architecture, cistrons, regulatory sequences, enhancers and their mechanism of action, DNA replication; transcription – RNA polymerases, transcription factors, Introns, RNA splicing, alternative
splicing, RNA stability – cap structure and function, polyadenylation; translation, posttranslational modifications.

Organellar genomes: Organization and function of mitochondrial and chloroplast genomes, diversity and evolution of organelle genomes, chloroplast protein targeting to different compartments, mitochondrial DNA and male sterility, transfer of genes between nucleus and organelles.

SUGGESTED READINGS

1. .Alberts B, Johnson A, Lewis J, Raff Martin, Roberts K and Walter P. (2007) Molecular Biology of the Cell. Garland Publ., New York.
2. Bonifacino JS, Dasso M, Harford JB, Liipincott-Schwartz J and Yamada KM. (2004) Short Protocols in Cell Biology. John Wiley & Sons, New Jersey.
3. Bregman AA (1987) Laboratory Investigations in Cell Biology. John Wiley & Sons, New York.
4. Hawes C and Satiat-Jeunemaitre B (2001) Plant Cell Biology: Practical Approach. Oxford University Press, Oxford.
5. Hirt RP and Horner DS (2004) Organelles, Genomes and Eukaryote Phylogeny: An evolutionary synthesis in the age of genomics. CRC Press.
6. Karp G. (2008) Cell and Molecular Biology: Concepts and Experiments. John Wiley & Sons.
7. Lodisch H, Berk A, Kaiser CA, Krieger M, Scott MP, Bretscher A, Ploegh H and Matsudaire P (2008) Molecular Cell Biology. WH Freeman & Co., New York.
8. Ruzin SE (1999) Plant Microtechnique and Microscopy. Oxford Univ. Press, Oxford.
9. Wischnitzer S. (1989) Introduction to Electron Microscopy. Pergamon Press, New York.

Subject 2: GENETICS AND CYTOGENETICS

Microbial Genetics
Viral and bacterial genomes and derived vectors; Recombination in viruses and bacteria (transformation, conjugation and transduction); Fine structure of gene; Prokaryotic gene regulation; Fungal genetics – mating types and genetic exchange, heterokaryosis, parasexual cycle.

Mendelian and Non-Mendelian Inheritance
Meiosis; Chromosome theory of inheritance; Mendelian laws; Gene interactions; Organelle inheritance.

Eukaryotic Genome
Evolution, structure and organization; Gene regulation.

Recombination in Eukaryotes
Linkage and crossing over: basic concepts, linkage maps, correlation of genetic and physical maps, molecular markers and construction of linkage maps; Molecular mechanism of recombination; QTL mapping.

Mutation
Basic concept, spontaneous and induced mutations, allele theory, physical and chemical mutagens; Molecular basis of mutations; Transposons and their use in mutagenesis and gene tagging in plant systems; Oncogenes and cancer.

Concepts in
Developmental genetics; Behavioral genetics; Population genetics and Quantitative genetics.

Cytogenetics
Chromosome structure and nomenclature, centromere and telomere; Sex determination: mechanisms, sex chromosomes; Chromosomal aberrations: Duplications, deficiencies/deletions, inversions, interchanges/translocations; Role of chromosomal aberrations in crop evolution; Ploidy changes: Haploids, polyploids and aneuploids; Genome analysis in crop plants; Molecular Cytogenetics: FISH, GISH, FIBER-FISH, Flow Cytogenetics, Flow karyotyping, Applications of molecular cytogenetics,

SUGGESTED READINGS

1. Acquaah G (2007). Principles of Plant Genetics and Breeding, Blackwell Publishing Ltd. USA.
2. Allard RW (1999). Principles of Plant Breeding (2nd Edition), John Wiley and Sons.
3. Hartl DL and Jones EW (2007). Genetics – Analysis of Genes and Genomes, 7th edition, Jones and Barlett publishers.
4. Hartwell LH, Hood L, Goldberg ML, Reynolds AE, Silver LM, Veres RC (2006). Genetics – From Genes to Genomes, 3rd edition, McGraw Hill.
5. Lewin B (2008). Genes IX, Jones and Barlett Publishers.
6. Singh RJ (2002). Plant Cytogenetics, 2nd edition, CRC Press.
7. Smartt J and Simmonds NW (1995). Evolution of Crop Plants (2nd Edition) Longman.
8. Strickberger MW (2008). Genetics, 3rd Edition, Pearson (Prentice Hall).
9. Weising K, Nybom H, Wolff K and Kahl G (2005) DNA Fingerprinting in Plants: Principles, Methods and Applications, 2nd ed. Taylor and Francis Group, Boca Raton, FL.

Subject 3: PHYSIOLOGY AND BIOCHEMISTRY

Protein structure
Hierarchical structure of proteins; folding; ticketing; degradation; purification, detection and functional characterization; sequence alignments; molecular motors and pumps.

Enzymes and bioenergetics
Application of principles of thermodynamics in biology; origin and evolution of biocatalytic reactions; significance of ribozymes; abzymes; artificial enzymes; enzyme technology; regulation of enzymatic activity; evolution of electron transport chain and its coupling to ATP synthesis; bioelectricity, photosynthesis and respiration.

Signal Transduction
Overview, second messengers, receptors and G-proteins, phospholipid signaling, role of cyclic nucleotides, calcium-calmodulin cascade, diversity in protein kinases and phosphatases, specific signaling mechanisms and their regulation, e.g. simple and hybrid, type of two-component sensor-regulator system in bacteria and plants (examples of chemotaxis, osmosensing, ethylene and cytokinin signaling), quorum sensing.

Sensory Photobiology
Structure, function and mechanisms of action of phytochromes, cryptochromes and phototropins; stomatal ovement; scotomorphogenesis and photomorphogenesis.

Molecular Basis of intercellular and intracellular uptake and transport of water, ions and macromolecules
Apoplastic and symplastic transport mechanisms, role of aquaporins and transporter proteins, structure-function relationship of inward and outward ion channels, dual action of ATPases/pumps and modulation of their activity, specialized mechanisms for phosphorus and iron uptake, monitoring of ion channel activity.

Plant hormones and other growth regulators
Concept of hormones as chemical messengers, techniques for etection and quantitation of plant hormone, classical approaches and use of mutants in understanding hormone actions, hormones in defense against abiotic and biotic stresses, synthetic regulatory compounds and their uses.

Physiology of plant reproduction
Reproductive strategies in higher plants and their significance. Sexual and non-sexual modes. Flowering as a multi-organ function, floral induction, evocation and development. Regulation of flowering by light and temperature. Role of circadian rhythm. Involvement of hormones. Genetic, molecular and biotechnologicalaspects. Manipulation of flowering and floriculture. Vegetative propagation with special reference to epiphyllous budding.

SUGGESTED READINGS

1. Ainsworth C (2006) Flowering and its Manipulation, Annual Plant Reviews, Vol. 20. Blackwell Publishing, Oxford, U.K.
2. Brown TA. (2002) Genomes, BIOS Scientific Publishers Ltd, Oxford, UK.
3. Buchanan B, Gruissem G and Jones R. (2000) Biochemistry and Molecular Biology of Plants, American Society of Plant Physiologists, USA.
4. Davies P J. (2004) Plant Hormones: Biosynthesis, Signal Transduction, Action. 3rd Edition, Kluwer Academic Publisher, Dordrecht, The Netherlands.
5. Jordan BR. (2006) The Molecular Biology and Biotechnology of Flowering, 2nd Edition, CAB International, Oxfordshire, U.K.
6. Lodish H, Berk A, Kaiser CA and Krieger M. (2008) Molecular Cell Biology, 6th Edition, W.H. Freeman and Company, New York, USA.
7. Nelson DL and Cox MM. (2004) Lehninger Principles of Biochemistry, 4th Edition, W.H. Freeman and Company, New York, USA.
8. Taiz L and Zeiger E. (2006) Plant Physiology, 4th Edition, Sinauer Associates Inc. Publishers, Massachusetts, USA.

RECOMBINANT DNA TECHNOLOGY AND PROTEOMICS

Principles and tools of recombinant DNA technology
Restriction and nucleic acid modifying enzymes; restriction mapping; Principles of gel electrophoresis; choice of vectors; plasmids, phages, cosmids, plant viruses, synthetic DNA vectors; cDNA and genomic libraries; Isolation of specific genes from bacteria and higher plants; cloning; PCR and its applications; Principles of DNA sequencing.

Proteomics
Comparative account of translation in prokaryotes and eukaryotes, post translational modifications, Use of vectors for over-expression of proteins, Protein extraction/purification techniques viz., electrophoresis and column chromatography, Introduction to proteome and proteomics and its relevance/significance in the post genomic era, Proteomics as a tool for plant genetics, breeding and diversity studies.

SUGGESTED READINGS

1. Buchanan B, Gruissem G and Jones R (2000). Biochemistry and Molecular Biology of Plants, American Society of Plant Physiologists, USA.
2. Harlow and Lane D (Eds.) (1988). Antibodies – A Laboratory Manual; Cold Spring Harbor Laboratory, USA.
3. Lieber DC (2006). Introduction to Proteomics: Tools for New Biology; Humana Press, NJ.
4. Pennington SR, Dunn MJ (Eds.) (2002). Proteomics: From Protein Sequence to Function, BIOS Scientific Publishers, United Kingdom.
5. Sambrook J and Russell DW (2001). Molecular Cloning – A Laboratory Manual, Vols I – III, Cold Spring Harbor Laboratory, USA.
6. Singer M and Berg P (1991). Genes and Genomes: A Changing Perspective; University Science Books, CA, USA.

SEMESTER II

Subject 1: DEVELOPMENTAL BIOLOGY

Section A: Plant Diversity

Algae
Habitat diversity, thallus organization, cell structure and reproduction.

Archegoniatae
Comparative morphology and developmental anatomy of Hepaticae, Anthocerotae and Musci; comparative anatomy of vegetative organs of Pteridophytes; study of stem apex, leaf initiation and early leaf ontogeny in ferns; development of long and short shoots, origin and pattern of development of cortex, pith and procambium in conifers.

Vascular plants
Meristems; patterns of cell fate, determination and lineage in root and shoot;leaf growth and differentiation; secondary growth; wood development and its diversity; cambial variants; ultrastructure and control of xylem and phloem differentiation; secretory ducts and laticifers; flower, seed and fruit anatomy; patterns of evolution in seed; anatomical adaptations for special habitats, biotic and abiotic stresses; Applications (in brief) of anatomical studies in
systematics, archaeology, climate studies, pharmacology, forensic sciences and biomedical research.

Section B: Reproductive Biology

Development of flower
Transition to flowering – vegetative to reproductive evocation, floral homeotic mutations in Arabidopsis, Antirrhinum and Petunia, axis development in flower, gender expression in monoecious and dioecious plants.

Developmental biology of male and female gametophytes
Regulation of anther and ovule development, microsporogenesis and microgametogenesis, megasporogenesis and megagametogenesis, male sterility- echanisms and applications, pollen embryogenesis.

Pollen-pistil interaction
In vivo and in vitro pollen germination, pollen tube growth and guidance, double fertilization, self-compatibility mechanisms, incongruity.

Embryogenesis and seed development
Polarity during embryogenesis, pattern mutants, in vitro fertilization, endosperm development, apomixis, polyembryony, somatic embryogenesis.

SUGGESTED READINGS

1. Anderson RA (2005) Algal Culturing Techniques. Physiological Society of America. Elsevier Academic Press, USA.
2. Bhatnagar SP and Moitra A (2005) Gymnosperms. New Age Interactive (P) Ltd. Publishers, New Delhi.
3. Carlquist S (2001). Comparative Wood Anatomy, Springer-Verlag, Germany.
4. Cutler DF (1978). Applied Plant Anatomy, Longman, United Kindom
5. Cutter EG (1978) Plant Anatomy, Part I & II, Edward Arnold, United Kingdom.
6. Dickinson WC (2000). Integrative Plant Anatomy, Harcourt Academic Press, USA.
7. Fahn A (1974) Plant Anatomy, Pergmon Press, USA & UK.
8. Fosket DE. (1994) Plant, Growth and Development: A Molecular Approach, Academic Press.
9. Fritsch FE (1935, 1945). The Structure and Reproduction of Algae Vols. I and II. Cambridge University Press, Cambridge, UK.
10. Hopkins WG. (2006). The Green World: Plant Development, Chelsea House Publication
11. Howell SH. (1998) Molecular Genetics of Plant Development, Cambridge University Press.
12. Leyser O and Day S (2003) Mechanism of Plant Development, Blackwell Press
13. Mauseth JD (1988). Plant Anatomy, The Benjamin/ Cummings Publisher, USA
14. Nair MNB (1998). Wood Anatomy and Major Uses of Wood, Faculty of Forestry, University of Putra Malaysia, Malaysia.
15. Parihar NS (1993) An Introduction to Embryophyta: Vol I – Bryophyta, Vol II – Pteridophyta, Central Book Dept. Allahabad.
16. Raghavan V (2000) Developmental Biology of Flowering Plants, Springer, Netherlands
17. Raghavan V (1997). Molecular Embryology of Flowering Plants. Cambridge. University Press.
18. Richards AJ (1986) Plant Breeding System, George Allen and Unwin.
19. Shivanna KR (2003) Pollen Biology and Biotechnology, Science Publishers.

Subject 2: SYSTEMATICS, EVOLUTION AND ENVIRONMENTAL SCIENCE

Systematics and Evolutionary Biology
History of developments in taxonomy: Linnaean to post-Linnaean era; Systematics – concepts and components; Botanical Nomenclature; Evolutionary ecology-concepts and principles; Microevolution – theory and concepts; Species and speciation; Phylogenetic systematics; Macroevolution – inferring phylogenies; Diversity and classification of flowering plants; Taxonomic evidence – structural and biochemical; Molecular systematics; Diversity and classification of flowering plants; Biological diversity-concepts and applications; Diversity- patterns, indices and applications.

Environmental Science
Introduction to Environmental Science and Sustainability, Environmental laws, Ecosystems and living organisms, Major ecosystems of the world and India, Human health and environmental change, Population issues, the search for fuels, natural resources and their management, applications of GIS and RS technology in environmental studies, the future of planet earth.

SUGGESTED READINGS

1. Angiosperm Phylogeny Group (2003) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnaean Society 141: 399-436.
2. Cracknell AP, Hayes L (2009) Introduction to Remote Sensing. CRC Press, Boca Raton, USA (Special Indian Edition)
3. Crawford DJ (2003) Plant Molecular Systematics. Cambridge University Press, Cambridge, UK.
4. Cronquist A (1981). An integrated system of classification of flowering plants. Columbia University Press, New York.
5. Hollingsworth PM, Bateman RM and Gornall RJ (1999). Molecular systematics and Plant Evolution. Taylor and Francis, London.
6. Judd WS, Campbell CS, Kellogg EA, Stevens PA and Donoghue MJ (2002) Plant Systematics: A Phylogenetic Approach. Sinauer Associaes, Inc., Massachusetts.
7. Nei M and Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York.
8. Raven PH, Begr LR, Hassenzahl DM (2008) Environment. 6th edition. John Wiley & Sons, Inc., New York.
9. Semple C and Steel MA (2003) Phylogenetics. Oxford University Press, Oxford.
10. Simpson MG (2006) Plant Systematics. Elsevier, Amsterdam.
11. Stuessy TF (2008) Plant Taxonomy: The systematic Evaluation of Comparative Data. Columbia University Press, New York.
12. Swafford DL (2001) PAUP. Phylogenetic analysis using parsimony ( and other methods), version 4. Sinauer Associates, Sunderland.

Subject 3: PLANT BIOTECHNOLOGY AND RESOURCE UTILIZATION

Plant tissue culture
History, concepts of cell differentiation and totipotency; pathways for in vitro regeneration: organogenesis, somatic and gametic embryogenesis; protoplast isolation, culture and regeneration; somatic hybridization; Applications: micropropagation, meristem culture, embryo rescue, synseed production, somaclonal and androclonal variations,
cryopreservation and germplasm storage.

Principles, methods and applications of genetic transformation
Agrobacterium biology and biotechnology; Plant – Agrobacterium interactions; Direct gene transfer methods: particle
bombardment, electroporation, PEG-mediated and floral-dip; marker and reporter genes; case studies of transgenic traits in plants; marker-free transgenics; transgene silencing; environmental, social and legal issues.

Plant resource utilization
World centres of primary diversity and secondary centres of cultivated plants; crop domestication genes; Uses and introduction to current research paradigms in major cereals, oilseeds, legumes, medicinal plants, forest trees and non-alcoholic beverages.

SUGGESTED READINGS

1. Adrian S, Nigel WS, Mark RF (2008). Plant Biotechnology: The genetic manipulation of Plants, Oxford University Press.
2. Buchanan B, Gruissem G and Jones R (2000) Biochemistry and Molecular Biology of Plants, American Society of Plant Physiologists, USA.
3. Butenko RG (2000) Plant Cell Culture, University Press of Pacific.
4. Davies PJ (2004) Plant Hormones, Kluwer Academic Publishers, Netherlands.
5. Halford N (2006) Plant Biotechnology – Current and future applications of genetically modified crops, John Wiley and Sons, England.
6. Wickens GE (2004) Economic Botany: Principles and Practices, Springer, ISBN 978-0-7923-6781-9.

Subject 4: PATHOGENS AND PESTS OF CROP PLANTS

General characteristics of plant pathogenic organisms and pests including viruses, bacteria, fungi, insects and nematodes with reference to the following:

• Life cycles
• Nature of disease(s) and damage caused
• Host range
• Control mechanisms based on genetics, chemical treatments, biological control and genetic engineering.

Case studies of economically important causative agents with specific references to crop plants:

• Plant-virus interactions with emphasis on potyviruses and horticultural crops.
• Plant-bacterial interactions with emphasis on Erwinia sp. and potatoes.
• Plant-fungus interactions with emphasis on Magnaporthe sp. and rice.
• Plant-nematode interactions with emphasis on Meloidogyne sp. and tomato.
• Plant-Insect interactions with emphasis on Pieris sp. and crucifers.

SUGGESTED READINGS

1. Agrios GN (2005) Plant Pathology, 5th Edition.
2. Buchanan B, Gruissem G and Jones R (2000) Biochemistry and Molecular Biology of Plants”, American Society of Plant Physiologists, USA

OPTIONAL PAPERS (SEMESTERS III AND IV)

SEMESTER III

Subject 1: ALGAE, ENVIRONEMT AND WELFARE

Diversity and distribution of the algae
Thallus organization, cell structure and reproduction in various groups. Chlamydomonas and Porphyra as modern experimental systems.

Classification
Molecular taxonomy – recent developments in algal classification, special emphasis on emerging trends in molecular phylogeny and inter relationship of principal groups of algae. The following groups will be covered: Cyanophyta, Chlorophyta, Phaeophyta and Rhodophyta.

Algal Biotechnology
Historical perspectives, algal culturing techniques in the laboratory, tissue and cell culture studies in seaweeds, cryopreservation, aquaculture (micro and macro algae cultivation), bioremediation, recent developments and future of algal biotechnology; Algal biofuels – algal biodiesel, bio-ethanol and biological hydrogen production; Algae in global warming – carbon capture by algae.

Industrial Phycology
Products, processes and applications, seaweeds polysaccharides like Agar, Carrageenan and Alginates. Bioactive compounds from algae: Bio-fertilizers; Algae in bioengineering, photo-bioreactors and raceway ponds.

SUGGESTED READINGS

1. Andersen RA (2005). Algal Culturing Techniques. Physiological Society of America. Elsevier Academic Press, USA.
2. Cole KM and Sheath RG (1990). Biology of the Red Algae. Cambridge Univ. Press, Cambridge.
3. Fritsch FE (1945). The Structure and Reproduction of Algae. Vol. II. Cambridge Univ. Press. Cambridge, London.
4. Isabella A. Abbott, George J and Hollenberg (1993). Marine Algae of California. Stanford University Press. USA.
5. Lee RE (1989). Phycology. Vol. II. Cambridge Univ. Press. Cambridge, USA.
6. Sahoo D & Qasim SZ (Eds), (2002). “Sustainable Aquaculture”. APH Publishing Corporation, New Delhi, India.
7. South GR and Whittick A. (1987). Introduction to Phycology. Blackwell Scientific Publications. London.
8. Journals: Journal of Applied Phycology, Journal of Phycology, European Journal of Phycology, Phycologia, Botanica Marina.

Subject 2: MICROBES AND MICROBIAL TECHNOLOGY

General Microbiology
Diversity of the microbial world – Microbial taxonomy and phylogeny; Microbial nutrition, growth and metabolism; Genetics of bacteria and their viruses.

Agricultural Microbiology
Agriculturally important microorganisms; Biological nitrogen fixation; Mycorrhizae, microbial mineralization, Biocontrol of plant diseases, Plant growth promoting rhizobacteria (PGPR).

Environmental Microbiology
Microbes and quality of environment; Distribution and implications of microbes in air – bio-aerosols, microbial flora of water, water pollution, drinking water and domestic waste treatment systems; Microbial pesticides, Biotransformations: microbial degradation of pesticides and toxic chemicals, biodegradation of the agricultural residues, bioremediation of contaminated soils and water. Microbes in nanotechnology, biosensors; Microbes in extreme environments.

Food and Industrial Microbiology
Recent developments in food and industrial microbiology– Fermentation, fermented foods, fermenter design and growth processes, food spoilage, methods of food preservation; Microbes in recovery of metal (bioleaching) and oil, Recombinant-DNA technology; Cell and enzyme immobilization, microbial enzymes of industrial interest; Novel medicines from microbes.

SUGGESTED READINGS

1. Prescott L, Harley J, Klein D (2005) Microbiology, 6th edition, Mc Graw-Hill.
2. Singh VP and Stapleton RD (Eds.) (2002) Biotransformations: Bioremediation Technology for Health and Environmental Protection. “Progress in Industrial Microbiology Vol. 36”, Elsevier Science.
3. Subba Rao NS (1982) Advances in Agriculture Microbiology, Butterworth-Heinemann.
4. Subba Rao NS and Dommergues YR (Eds.) (2001) Microbial Interactions in Agriculture and Forestry Vol. 2, Science Pub. Inc.
5. Waites MJ, Morgan NL, Rockey JS, Higton G (2001) Industrial Microbiology: An Introduction, Wiley-Blackwell.

Subject 3: ADVANCES IN ARCHEGONIATAE

Bryophytes
Vegetative and reproductive innovations of early land plants, Role of bryophytes in ecosystem dynamics and in the global carbon budget, bryophyte association with microorganism and animals, Symbiotic fungal associations in early land plants, Poikelohydry, Desiccation tolerance. Bryogeography and conservation. Hormonal regulation of gametophyte development in bryophytes. Breeding system, population ecology and population genetics, Anisospory and sexual dimorphism.Biologically active compounds in Bryophytes. Cytogenetics of bryophytes, Molecular genetic studies of moss species with special reference to Physcomitrella patens, Expression of genes under stress conditions.

Pteridophytes
Morphological diversity and evolution of vegetative organs in Pteridophytes, Diversity of Ferns – an ecological perspective, Genetics and reproductive biology of ferns, Culture of fern gametophyte for experimental investigation, photomorphogenesis, Model system in Ceratopteris, Trichomanes, Osmunda, Marsilea.

Gymnosperms
Evolution of pollination mechanisms and embryogeny of gymnosperms: propagation of conifers using plant tissue culture approaches, advances in synthetic seeds technology of conifers, somatic embryogenesis and plantlet regeneration; Acclimatization and adaptive responses of conifers to environmental stresses. Drought tolerance and cold hardiness, stimulation of reproductive growth seed and seedling ecology, litter decomposition rate, Conifer plantation as seed trap, impact of coniferous forest on human life.

SUGGESTED READINGS

1. Shaw AJ and B Goffinet (2000) Bryophyte Biology. Cambridge University Press.
2. Geissler and Greene SW (1982) Bryophyte Taxonomy, methods, practices and floristic exploration. J Cramer, Germany.
3. Dyer AF (Ed) (1979) The experimental Biology of Ferns. Academic London.
4. Richardson DHS (1981) The Biology of mosses. John Wiley & Sons, Inc New York.
5. Bhatnagar SP and Moitra A (1996) Gymnosperms. New Age International (P) Limited, Publishers, New Delhi
6. Singh Hardev (1978) Embryology of Gymnosperms. Encyclopedia of Plant Anatomy. Vol X Gebruder Borntraegrl, Berlin, Stuttgart.

Subject 4: PRINCIPLES OF ECOLOGY

UNIT I
Introduction to ecology, evolutionary ecology, environmental concepts – laws and limiting factors, ecological models. Characteristics of population, population size and exponential growth, limits of population growth, population dynamics, life history pattern, fertility rate and age structure, population growth. Competition and coexistence, intra-specific interactions, inter-specific interactions, scramble and contest competition model, mutualism and commensalism, prey-predator interactions.

UNIT II
Nature of ecosystem, production, food webs, energy flow through ecosystem, biogeochemical cycles, resilience of ecosystem, ecosystem management. The biosphere, biomes and impact of climate on biomes

UNIT III
Environmental Stresses and their management, global climatic pattern and variations over time, global climatic changes and global warming, atmospheric ozone, acid and nitrogen deposition, coping with environmental variations. Environmental pollutants- air, water and soil pollution, chemical fate and transport in air, water and soil. Use of fertilizer, pesticides and other chemicals in agriculture and hygiene and their disposal. Chemical usage and disposal from industry and pollution. Impact of chemicals on biodiversity of microbes, animals and plants. Bioindicator and biomarkers of environmental health. Biodegradation and bioremediation of chemicals, environmental issues, policies and regulations

UNIT IV
Biodiversity – assessment, conservation and management, biodiversity act of India and related international conventions. Sustainable development, natural resource management in changing environment. Molecular ecology, genetic analysis of single and multiple population, phylogeography, molecular approach to behavioural ecology, conservation genetics.

SUGGESTED READING

(Books meeting the needs of Botany, Zoology and Environmental Biology programs)

1. Conklin, A.R. Jr. 2004. Field Sampling: Principles and Practices in Environmental Analysis. CRC Press.
2. Fahey, T.J. and Knapp, A.K. 2007. Principles and Standards for Measuring Primary Production. Oxford.
3. Grant, W.E. and Swannack, T.M. 2008. Ecological Modeling. Blackwell.
4. Wilkinson, D.M. 2007. Fundamental Processes in Ecology: An Earth system Approach. Oxford.

Subject 5: EVOLUTIONART BIOLOGY

Introduction
Evolutionary Biology before Darwin, Darwin, after Darwin. Evolutionary synthesis. Fact and theory.

Biological diversity
Species and classification. Phylogenetic trees, reading and using trees. Tree of Life. The fossil record. Geological fundamentals. Phylogeny and the fossil record. Evolutionary trends. Rates of evolution. The geography of life. Major patterns of distribution. Historical biogeography, phylogeography. Genetic diversity: Genes, genomes, mutations, karyotypes. Sources of phenotypic variation. Genetic variation in populations. Variation among populations. karyotypes. Sources of phenotypic variation. Genetic variation in populations. Variation among populations.

Microevolution
Genetic drift, sampling, coalescence. Founder effects. Neutral theory of molecular evolution. Natural selection. Adaptation in action. Experimental studies. Levels of selection. Genetical theory of natural selection. Fitness, modes and models of selection. Evolution of phenotypic traits, Conflict and co-operation. Species and speciation. Reproductive success. Co-evolution.

Macroevolution
Inferring phylogenies. Gene trees, species trees. Patterns of evolutionary change. Adaptive radiation. Evolution and development.

Biodiversity
Estimating changes in biodiversity. Taxonomic diversity through the Phanerozoic. The future of biodiversity.

SUGGESTED READINGS

1. David Briggs, Stuart Max Walters (1997). Plant Variation and Evolution, Cambridge University Press.
2. Douglas J. Futuyma (1998). Evolutionary Biology (3rd Edition), Sinauer Associates. 23
3. Mark Ridley (2003) Evolution (3rd edition), Blackwell.
4. Roderic D. M. Page, Edward C. Holmes (1998). Molecular Evolution: A Phylogenetic Approach, Blackwell.
5. Scott R, Freeman and Jon C. Herron (2003). Evolutionary Analysis, Prentice Hall.

Subject 6: BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOSTATISTICS

Bioinformatics and Computational Biology

1. Databases – NCBI, EMBL, DDBJ, Genbank, Pubmed, Patent databases, TAIR, PDB, ATIDB).
2. Online tools – BLAST, ORF finder, Primer3, protein motif and structure prediction tools; Vector NTI, DNASTAR.
3. Bioinformatics in genome sequencing and annotation.
4. Fundamentals of computer programming.
5. Programming in PERL.
6. Introduction to in silico drug design and molecular modeling

Biostatistics

Introduction
The scope of biostatistics; Classification of study design, Observational studies and Experimental studies (uncontrolled studies, trials with external controls, crossover studies, trials with self controls, trials with independent concurrent controls).

Exploration and presentation of data
Scales of measurement, Tables, Graphs, Histograms, Box and Whisker plots, Frequency polygon, Scatter Plots.

Descriptive statistics
measures of central tendency, measures of dispersion, rates and proportions.

Probability
Definition, mutually exclusive events and addition rule, independent events and multiplication rule. Sampling: Reasons for sampling, methods of sampling, SRS, Systematic, Stratified, Cluster, NPS. Probability distribution: Binomial, Poisson, Gaussian, Standard normal distribution. Drawing inferences from data: Confidence intervals,
Confidence limits, Hypothesis tests, Types of errors, P-values.

Estimating and comparing means
Decision about single mean (normal population and non-normal population), decision about single group, decision about paired groups, decisionabout two independent groups, equality of population variances, computer-aided illustration for comparison of means.

Comparing three or more means
ANOVA – one way, two way, A priori comparison, Posterior or Post Hoc comparison, randomized block design, LSD, Kruskal-wallis one way ANOVA.

Estimating and comparing proportions
Proportion in single group, Comparing two independent proportions, Risk ratios v/s
2, comparing proportions in more than two groups, comparing proportions in paired groups,
2 as goodness of fit.

Correlation and Regression
Pearson’s correlation coefficient, Spearman’s rho, Linear regression, Least Square method, Predicting with regression equation, Comparing two regression lines, Dealing with nonlinear observation, Common errors in regression, Comparing correlation and regression.

Statistical methods for multiple variables
Multiple regression, Predicting with more than 1 variable, Statistical test for regression coefficient, Role of R and R2 in multiple regression, Confounding variable (ANACOVA), Predicting categorical outcomes – logistic regression, discriminant analysis.

SUGGESTED READINGS

1. Attwood TK and Parry-Smith DJ (2004) Introduction to Bioinformatics, Pearson Education (Singapore) Pvt. Ltd.
2. David Edwards (Ed.) (2007) Plant Bioinformatics: Methods and Protocols, Humana Press, New Jersey, USA.
3. Kulas JT (2008) SPSS Essential: Managing and Analyzing Social Science Data. John Wiley & Sons, New York.
4. Pagano M, Gauvreau K (2007) Principles of Biostatistics. Thomson India Edition, New Delhi.
5. Randal Schwartz, Tom Phoenix and Brian d Foy (2005) Learning Perl (4th edition), O’Reilly & Associates, ISBN: 0-596-10105-8.
6. Rex A. Dwyer (2004) Genomic Perl: From Bioinformatics Basics to Working Code, Cambridge University Press, 1st South Asian Edition.
7. Rosenkrantz WA (2009) Introduction to Probability and Statistics for Science, Engineering and Finance. CRC Press, Boca Raton.

Subject 7: GENOMICS AND PROTEOMICS

Genomics
Genome sequencing strategies and programs, new technologies for highthroughput sequencing, methods for sequence alignment and gene annotation; Approaches toanalyze differential expression of genes – ESTs, SAGE, microarrays and their applications; gene tagging; gene and promoter trapping; knockout and knock-down mutants; dynamic modulation of protein structure and function; Comparative genomics of model plants and
related crop species; Recombination-based cloning techniques; RNAi and gene silencing, genome imprinting, small RNAs and their biogenesis, role of small RNAs in heterochromatin formation and gene silencing, genomic tools to study methylome and histone modifications.

Proteomics
Analysis of proteins by different biochemical and biophysical procedures like CD (Circular Dichroism), NMR, UV/Visible and fluorescent spectroscopy, protein identification and analysis on ExPASy server, other protein related databases, 1-D and 2-D gel electrophoresis for proteome analysis, Sample preparation, gel resolution and staining; Mass spectrometry based method for protein identification like PMF (protein mass fingerprinting) and LCMS; Image analysis of 2D gels: Data acquisition, spot detection & quantitation, gel matching, data
analysis, presentation, databases, conclusions; DIGE (Differential In Gel Electrophoresis), alternatives to 2-DE for protein expression analysis; Analysis of post-translational modifications and protein-protein interactions; protein chips and arrays, future directions in proteomics, scope of functional proteomics.

SUGGESTED READINGS

1. Buchanan B, Gruissem G, and Jones R (2000) Biochemistry and Molecular Biology of Plants, American Society of Plant Physiologists, USA.
2. Hammes GD (2005) Spectroscopy for the Biological Sciences; Wiley Interscience, USA.
3. Harlow and Lane D (Eds.) (1988) Antibodies – A Laboratory Manual; Cold Spring Harbor Laboratory, USA.
4. Lieber DC (2006) Introduction to Proteomics: Tools for New Biology; Humana Press, NJ.
5. Pennington SR, Dunn MJ (Eds.) (2002) Proteomics: From Protein Sequence to Function, BIOS Scientific Publishers, United Kingdom.
6. Sambrook J and Russell DW (2001). Molecular Cloning – A Laboratory Manual, Vols I – III, Cold Spring Harbor Laboratory, USA.
7. Singer M and Berg P (1991). Genes and Genomes: A Changing Perspective; University Science Books, CA, USA.

Subject 8: IMMUNOLOGY

Fundamentals of Immunology
Basic principles and overview of immunity, antigens and antibody production, cellular interactions in the immune system, Innate immunity, Complement, antibody structure and antigen recognition, Immunoglobulin genes, Ig/TCR gene rearrangement and generation of diversity, Introduction to Immunogenetics & the MHC,
Antigen recognition by T cells, TCR, Co-receptors & MHC structure, antigen processing and presentation.

Immunity in Health & Disease
Immune response to infectious diseases, Immunodeficiency and AIDS, Hypersensitivity, transplant rejections, autoimmunity, vaccines, evolution of the immune system.

SUGGESTED READING

1. Kuby Immunology; by Richard A. Goldsby, Thomas J. Kindt, Barbara A. Osborne, Janis Kuby, W. H. Freeman Publishing (4e-6e).

SEMESTER IV

Subject 1: IN VITRO TECHNOLOGIES AND INDUSTRIAL APPLICATIONS

(To provide students with an overview of plant tissue culture techniques, their potential in the production of propagative material and interaction with industries)

• Micropropagation (via organogenesis and embryogenesis) of floricultural, agricultural and pharmaceutical crops: Orchids, Chrysanthemum, Gerbera, Carnation, Anthurium, Bamboos, Spilanthes, Stevia, Psoralea, Chickpea and elite tree species of national importance.
• Production of virus free plants through meristem culture in orchids and fruit trees.
• Germplasm conservation in vitro.
• Variations: Somaclonal and gametoclonal variations, spontaneous, genetic and epigenetic variations.
• Culture systems: Differentiated, undifferentiated, physiological, biochemical and molecular role of minerals and growth regulators in understanding differentiation of organs under in vitro conditions.
• Problems in Plant Tissue Culture: contamination, phenolics, recalcitrance.
• Problems in establishment of regenerated plants in nature: hardening, association of mycorrhiza and rhizobia.
• Factors responsible for in vitro and ex vitro hardening.
• Use of bioreactors in secondary metabolite production and scale up automation of plant tissue culture.
• Recent applications of tissue culture techniques and biotechnology in the introduction of economically important traits in horticultural, agricultural and medicinal plants.
• Interactions, training and workshops in Biotech industries and placements.

SUGGESTED READINGS

1. Herman EB (2008) Media and Techniques for Growth, Regeneration and Storage 2005-
2. Agritech Publications, New York, USA.
3. Pierik RLM (1999) In Vitro Culture of Higher Plants. Kluwer Academic Publishers.
4. Prakash J & Pierik RLM (1991) Horticulture – New Technologies and Applications (Current Plant Science and Biotechnology in Agriculture). Kluwer Academic Publishers.
5. George EF, Hall MA and Geert-Jan De Klerk (2008). Plant Propagation by Tissue Culture (3rd Edition), Springer, Netherlands.
6. Journals: Plant Cell, Tissue and Organ Culture, Plant Cell Reports.

Subject 2: REPRODUCTIVE BIOLOGY OF FLOWERING PLANTS

Modes of Reproduction
An overview

Flower development
Regulation of floral architecture and diversification; Floral organogenesis; Pollination regulation of flower development.

Male gametophyte
Sporophyte-gametophyte interaction during micro- and megasporogenesis; interaction of mitochondrial and nuclear genes; male specific cytokinesis; tapetal development and pollen-coat formation; asymmetric division, cell fate and polarity; sperm dimorphism; male germ unit: cytology and 3-d structural organization; pollen biotechnology; manipulation of sperm cells; male-sterility; induction; mechanism of action and breeding; transformation of pollen; embryogenic development of pollen grains.

Female gametophyte
Regulation of pistil and ovule development; megasporogenesis and megagametogenesis: developmental pathways, gene function and organization. Pollen-pistil interaction and double fertilization: Pollen tube guidance; recognition and rejection reaction, barriers to gene flow; signal transduction at the level o f stigma style and ovules, double fertilization: origin, mechanism and in vitro fertilization; preferential fertilization; pistil activation and ovule penetration.

Plant-pollinator interactions and breeding systems
Plant-pollinator interaction: floral display, attractants and rewards, pollen load, temporal details and foraging behaviour, pollinator and pollination efficiency, physicochemical aspects of pollination; pollination energetics, gene flow, applied pollination ecology; phenology; mating systems: diversity and quantitative estimation; differential reproductive success; resource allocation; pollen:ovule ratio; sibling rivalry, ovule abortion.

Fruit biology
Development biology and diversity of fruit types, fruit abortion in relation to resource allocation, dispersal and gene flow. Seed biology: Embryogenesis and embryonic pattern formation; endosperm development and differentiation; ultrastructure and cytology; seed development: pattern, regulation of gene expression and imprinting; agamospermy and parthenocarpy, pseudogamy and autonomous development of endosperm; Embryo and endosperm culture

SUGGESTED READINGS

1. Barrett SCH (2008) Major Evolutionary Transitions in Flowering Plant Reproduction. Univ. of Chicago Press.
2. Faegri K & van der Pijl L (1979) The Principles of Pollination Ecology. Pergamon Press, Oxford. 291 pp.
3. Harder LD & Barrett SCH (2006) Ecology and Evolution of Flowers, Oxford Univ. Press.
4. O’Neill SD & Roberts JA (2002) Plant Reproduction, Sheffield Academic Press.
5. Raghavan V (1997) Molecular Embryology of Flowering Plants, Cambridge Univ. Press.
6. Raghavan V (2000) Developmental Biology of Flowering Plants, Springer Verlag, New York.
7. Richards AJ (1986) Plant Breeding System, George Allen and Unwin, UK.
8. Scott RJ and Stead AD (2008) Molecular and Cellular Aspects of Plant Reproduction. Society for Experimental Biology, Seminar Series 55.
9. Shivanna KR and Johri BM (1985) The Angiosperm Pollen: Structure and Function. New Delhi, India: Wiley-Eastern.
10. Shivanna KR and Rangaswamy NS (1992) Pollen Biology: A Laboratory Manual, SpringerVerlag, Berlin.
11. Shivanna KR (2003) Pollen Biology and Biotechnology. Enfield, New Hampshire, U.S.A.: Science Publishers.

Subject 3: MOLECULAR INTERACTIONS OF PLANTS WITH SYMBIONTS, PATHOGENS AND PESTS

This paper aims is to introduce various aspects of molecular and biochemical interactions of plants with symbionts, pathogens and pests at an advanced level.

1. Introduction to biotic interactions with plants.
2. Recent advances in plant-fungi, plant-insect and plant-nematode interactions: Stages of pathogenesis, Structural and biochemical host defense mechanisms against pathogens and pests, Basal resistance, Systemic acquired resistance, Induced systemic resistance, Gene-for-gene concept, Cloning of resistance genes (R genes) and avirulence genes (Avrgenes) from plants and pathogens, Induced responses to herbivory, Genetic engineering for the production of resistance plants to pathogens and pests.
3. Recent advances in symbiotic interaction with plant with special references to mycorrhiza and plant interaction.
4. Recent advances in parasitic interaction between plants and parasitic plants.

SUGGESTED READINGS

Plant-nematode interactions

1. Williamson VM, Kumar A (2006) Nematode resistance in plants: the battle underground. Trends in Genetics 22: 396–403.
2. Davis EL, Hussey RS, Baum TJ (2004) Getting to the roots of parasitism by nematodes. Trends in Parasitology 20: 134–141.
3. Plant Nematology (2006) Edited by Perry and Moens, CABI.

Plant virology and insect-plant interactions

1. Induced responses to herbivory by R Karban and IT Baldwin (1997) Chicago University Press, Chapter 3, pg47-100.
2. Mathew’s Plant Virology by Roger Hull (2001) Academic Press, NY.

Plant virology and insect-plant interactions

1. Induced responses to herbivory by R Karban and IT Baldwin (1997) Chicago University Press, Chapter 3, pg47-100.
2. Mathew’s Plant Virology by Roger Hull (2001) Academic Press, NY.

Plant-fungi interactions

1. Plant resistance mechanisms (SAR, ISR) – Strange RN, (2003) Introduction to Plant Pathology, John Wiley & Sons, USA.
2. Signal transduction; Molecular diagnostics; Transgenic approaches for crop protection – Dickinson M, (2003) Molecular Plant Pathology, Bios Scientific Publishers, London.

Subject 4: ADVANCED GENETICS AND PLANT BREEDING

Origin and history of crop plants
Plant domestication – morphological, agronomic and genetic features accompanying domestication of plants, agro-biodiversity, genetic erosion.

Biological diversity and genetic variation
Kinds and patterns of variation, variation and variability; genetics, utilization and analysis of genetic variation; qualitative and quantitative traits and their genetics, polygenic inheritance, partitioning of genotypic variance, inbreeding heterosis, recent development in quantitative genetics. Variation in population, genetic structure of population.

Genetic system and breeding methods
Reproduction and breeding systems in plants. Recombination, genetic control and manipulation of breeding systems including male sterility and apomixis. Selection and breeding strategies for self-pollinated, cross-pollinated and clonally propagated crop plants, breeding for crop quality, biotic and abiotic stresses, gene
pyramiding for multi-trait incorporation.

Sources of variation
Plant genetic resources-genetic consideration on PGR management and conservation, utilization of gene pools in breeding programs; Access and ownership of PGR-changing paradigms and their implications. Chromosome manipulation, induced mutations, polyploidy, somatic hybridization, somaclonal variation, novel sources of variation; molecular markers and construction of linkage maps; QTL mapping; map-based cloning, synteny, MAS (marker assisted selection), tagging of agronomically important traits.

Plant genome and crop improvement
Cytogenetics and its role in evolution and improvement of crops such as wheat, maize, sugarcane, Brassica etc.; location and mapping of genes on chromosomes, molecular cytogenetics. Genome analysis – modern approaches, biochemical and molecular tools for the analysis of plant genome including protein and DNA based techniques; structural and functional genomics in relation to crop improvement.

World food demand vis-à-vis availability
Food availability – International and Indian scenario, national and international agencies for agricultural R&D, green revolution, IPR and post-CBD changing paradigms.

SUGGESTED READINGS

1. Acquaah G (2007). Principles of Plant Genetics and Breeding, Blackwell Publishing Ltd. USA.
2. Allard RW (1999). Principles of Plant Breeding (2nd Edition), John Wiley and Sons, ISBN 0471023094, 9780471023098.
3. Hartl and Jones (2007). Genetics – Analysis of Genes and Genomes, 7th edition, Jones and Barlett publishers.
4. Hartwell, Hood, Goldberg, Reynolds, Silver, Veris (2006). Genetics – From Genes to Genomes, 3rd edition, McGraw Hill.
5. Lewin B (2008). Genes IX, Jones and Barlett Publishers, ISBN-10: 0763740632.
6. Ram J. Singh (2002). Plant Cytogenetics, 2nd edition, CRC Press.
7. Simmonds (1995). Evolution of Crop Plants (2nd Edition) Longman.
8. Strickberger (2008). Genetics, 3rd Edition, Pearson (Prentice Hall).

Subject 5: AGRICULTURAL ECOLOGY – PRINCIPLES AND APPLICATIONS

Ecological experimentation in agriculture; basic chemical process-carbon cycle; Climate and adaptation of agricultural crops; Physical factors affecting crop-water; Energy flow in agroecosystems; Soil type and classification; soil properties and environmental factors; Nitrogen in agroecosystems; fertilizer elements in the environment; Macro and micronutrients and their availability to crops; Decomposition: beneficial soil organisms; Plant succession and competition.

Weed ecology and management; Distribution and sampling of agricultural pests; introduction to insects; Population dynamics; pesticides and the environment; Traditional knowledge systems and agrodiversity management; Plant disease and environment; integrated pest management; plant-parasitic nematodes; Host plant resistance and conservation of genetic resources; Cropping systems and agro-ecosystems in the landscape; crop rotation and cover crops; Intercropping; conservation tillage; Mulches and organic amendments; Dry-land agriculture, irrigation and salinity; Tropical agro-ecosystems; intensive agriculture; Impact of GMOs on crop biodiversity and agroecology; Impact of agricultural policies on crop biodiversity and
agroecology; Human population growth; sustainable agriculture; Agroecology: the future perspective.

SUGGESTED READINGS

1. Gliesmann, S.R. (2006). Agroecology: The Ecology of Sustainable Food Systems. Technology & Engineering.
2. Gliesmann, S.R. (2006). Field and Laboratory Investigations in Agroecology. Technology & Engineering.
3. Paul A. Wojtkowski, P.A. (2004). Landscape agroecology, Haworth Press, Inc., New York. 330 pp.36
4. Warner, K.D. (2007). Agroecology in Action: Extending Alternative Agriculture Through Social Networks. The MIT Press, Cambridge, Massachusetts, USA, 291 pp.

Subject 6: ADVANCED PLANT SYSTEMATICS

Plant systematics
The Components of systematics, Major objectives of systematics; Relevance to society and science.

Taxonomic History
Natural systems to cladistics: Natural systems; Phyletic systems; Phenetics; Cladistics.

Botanical Nomenclature
Kinds of names; International Code of Botanical Nomenclature, Names according to rank; Citation of authors; Priority; Type method; Naming a new species; Legitimacy; Synonyms.

Classification
The components of classification; Characters and their states; Sources of characters; Evaluation of characters.
Systematic evidence: Morphology, Anatomy and ultrastructure; Embryology; Palynology; Cytology; Phytochemistry.

Molecular Systematics
Plant genomes: nuclear, mitochondrial, chloroplast; Molecular markers; Generating molecular data: restriction site mapping, gene sequencing; Analysis of molecular data: alignment of sequences, methods of phylogeny reconstruction.

Phylogenetics
The nature of phylogeny; How we depict phylogeny?; The importance of homology, Polarizing characters of homology; Rooting Trees; The problem of homoplasy.

The plant systematics community
Professional organizations; Work environment; Activities; The role of field studies; The role of the herbarium.

Introduction to the angiosperms
General characteristics; Evolutionary history; Basal angiosperms and Magnoliids; Basal monocots; Petaloid monocots; Commelinids; Basal eudicots and Caryophyllids; Rosids; Asterids.

SUGGESTED READINGS

1. Angiosperm Phylogeny Group 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnaean Society 141: 399-436.
2. Crawford, D.J. 2003. Plant Molecular Systematics. Cambridge University Press, Cambridge, UK.
3. Cronquist, A. 1981. An integrated system of classification of flowering plants. Columbia University Press, New York.
4. Judd, W.S., C.S. Campbell, E.A. Kellogg, P.F.Stevens and M.J. Donoghue 2002. Plant Systematics: A phylogenetic Approach. Sinauer Associates, Inc., Massachusetts.
5. Maheshwari, J.K. 1963. The Flora of Delhi, CSIR, New Delhi.
6. Nei, M. and S. Kumar 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
7. Radford, A. E., W.C. Dickison, J.R. Massey and C.R. Bell 1974. Vascular Plant Systematics. Harper and Row, New York.
8. Semple, C. and M.A. Steel 2003. Phylogenetics. Oxford University Press, Oxford.
9. Simpson, M.G. 2006. Plant Systematics. Elsevier, Amsterdam.
10. Stuessy, T.F. 2009. Plant Taxonomy: The systematic Evaluation of Comparative Data. Columbia University Press, New York.

Subject 7: CONTEMPORARY CONCEPTS AND METHODS IN CELL BIOLOGY

Infective particles and life forms
prions, viroids, origin and evolution of various life forms, cell theory vs. cell body concept, multicellularity vs. supracellularity.

Cell Wall
temporal and spatial dynamism in structure, structural and functional roles, in planta and ex planta uses, cell wall biotechnology

Biological membranes
from PLP model to Dynamically Structured Mosaic Model, transport through membranes, membranes as sites and routes of intra- and inter-organism and environment interactions

Cytoplasmic components
Endomembranes, organellar architecture, protein sorting and vesicular traffic

Biopolymers
Structural and functional aspects of cytoskeleton and associated motor molecules, their role in cell organization and movement, interaction among cytoskeletal elements, genomics, proteomics and bioinformatics of plant cytoskeleton; cytoskeleton in agrobiotechnology

Nucleus
detailed structure of nuclear pore complex and nuclear lamina, nuclear transport; chromatin subunit structure: from DNA to metaphase chromosome, histone code, states of chromatin during replication and transcription, heterochromatization as a method of gene regulation

Cell turnover
cell division, cell cycle controls, breakdown of cell cycle control: cancer vs. plant tumors, programmed cell death.
Cells to tissues: Cell polarity, cell fate determination, integration of plant cells in tissues.

Introduction to methods in plant cell biology
optical and electron microscopy, fluorescent probes, flow cytometry, transient expression, microinjection and micromanipulation, electrophysiological methods, plant histology, immunocytochemistry, in situ hybridization, cell fractionation and organelle isolation

SUGGESTED READINGS

Books

1. Alberts B, Johnson A, Lewis J, Raff Martin, Roberts K and Walter P. (2007). Molecular Biology of the Cell. Garland Publ., New York.
2. Bonifacino JS, Dasso M, Harford JB, Liipincott-Schwartz J and Yamada KM. (2004). Short Protocols in Cell Biology. John Wiley & Sons, New Jersey.
3. Bregman AA. (1987). Laboratory Investigations in Cell Biology. John Wiley & Sons, New York.
4. Buchanan et al. 2002. Biochemistry & Molecular Biology of Plants 1st edition, American Society of Plant Physiologists: Chapter 4, pp. 160-201 & Chapter 5, pp. 202-256.
5. Hawes C and Satiat-Jeunemaitre B. (2001). Plant Cell Biology: Practical Approach. Oxford University Press, Oxford.
6. Karp G. (2008). Cell and Molecular Biology: Concepts and Experiments. John Wiley & Sons.
7. Lodish H, Berk A, Kaiser CA, Krieger M, Scott MP, Bretscher A, Ploegh H and Matsudaire P (2008). Molecular Cell Biology. WH Freeman & Co., New York.
8. Ruzin SE (1999). Plant Microtechnique and Microscopy. Oxford Univ. Press, Oxford.
9. Wischnitzer S. (1989). Introduction to Electron Microscopy. Pergamon Press, New York.

Research papers / Reviews

• Aguzzi, A. et al. (2007) Molecular mechanisms of prion pathogenesis. Ann. Rev. Path.: Mech. Dis. 3: 11-40.
• Baluska F. et al. (2004) Eukaryotic cells and cell bodies: cell theory revised. Ann. Bot. 94: 9-32.
• Boxma, B. et al. (2005) An anerobic mitochondtion that produces hydrogen. Nature 434: 74-79.
• Delwiche CF (1999). Tracing the thread of plastid diversity through tapestry of life. Amer. Nat. 154:S164-177.
• Dobson CM (2005). Structural biology: prying the prions. Nature 435: 747-749.
• Gruenbaum Y. et al. (2003). The nuclear lamina and its functions in the nucleus. Int. Rev. Cytol. 226: 1-62.
• Meagher, B. et al. (1999) “The evolution of new structures: clues from plant cytoskeletal genes. TIG, 15:7, 278-284.
• Moerschbacher B. (2002). The plant cell wall – structural aspects and biotechnologoical developments. Pp. 445-477. In: Oksman-Caldentey, K-M. and Barz, W.H. Plant Biotechnology and Transgenic Plants. Marcel Dekker, Inc. New York.
• Raven JA and Allen JF (2003). Genomics and chloroplast evolution: what did cyanobacteria do for plants? Genome Biol. 4(3): Art No. 209.
• Rose A. et al. (2003). The plant nuclear envelope. Planta. 218: 327-336.
• Smith and Raikhel (1999). Protein targeting to the nuclear pore: what can we learn from plants?” Plant Physiol. 119:1157-1163.
• van der Giezen et al. (2005) “Mitochondrion-derived organelles in protists and fungi”. Int. Rev. Cytol. 244:175-225.
• Vereb, G. et al. (2003) Dynamic, yet structured: the cell membrane three decades after the Singer-Nicolson model. Proc. Nat. Acad. Sci. USA 100: 8053-8058.
• Wasteneys GO and Yang Z (2004) New views on plant cytoskeleton. Plant Physiol. 136: 3884-3891.

Subject 8: TOPICS IN PLANT PHYSIOLOGY AND BIOCHEMISTRY

Stress physiology
Plant responses to abiotic stresses, mechanisms of abiotic stress tolerance, water deficit and drought tolerance, salinity stress, metal toxicity, freezing and heat stress.

Oxidative and nitrosative stress and antioxidative strategies
Nitrosative and oxidative stress – causes and effects, nitric oxide biosynthesis and metabolism, NO mediated signaling, markers of nitrosative stress, NO crosstalk with other hormones, antioxidant mechanisms.

Secondary metabolites and their biotechnological aspects
Natural products (secondary metabolites), their range and ecophysiological functions. Overview of terpenoidal, alkaloidal, and phenolic metabolites and their biosynthesis. Molecular approaches and biotechnological applications. Metabolic engineering in the production of pharmaceuticals.

Physiology of seed development, maturation, dormancy and germination
Hormonal regulation of seed development, events associated with seed maturation, factors regulating seed dormancy, mechanisms of mobilization of food reserves during seed germination. Fruit development and ripening: Stages of fruit development and their regulation, biochemical and related events during fruit ripening in chimacteric and non-climacteric fruits, physiology and biochemistry of fruit abscission, post-harvest changes, production of transgenic fruits.

Programmed cell death (PCD)
Concept of PCD and its types in plants during vegetative and reproductive stages. Developmental and stress-induced PCD. Plant senescence and its characteristics. Leaf and flower senescence. Altered metabolism during senescence and its regulation. The oxidative stress and the anti-oxidative strategies. Hormonal modulations.
Environmental, genetic and molecular regulations.

Sensory physiology
Biochemical and biophysical mechanisms of sense of touch, electric self-defence, taste, light, explosion, sleeping and rhythms. Stimuli that trigger rapid movements; movements based on mechanical forces; mobility triggered by sense of touch, taste and electricity; motors driving movements in the living world; actin-myosin motors; photosensing; chemistry of excitability; neurotransmitters in plants.

Chemical defence
Biochemical mechanisms of plants’ chemical war against other plants and animals. Plant responses to herbivory; constitutive defence mechanisms; induced phytochemical responses; biochemical mechanisms of allelopathty.

SUGGESTED READINGS

Journals: Annual Review of Plant Biology, Critical Reviews in Plant Science, Current Opinion in Plant Biology, Trends in Plant Science.

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