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M.Sc Syllabus>>

Course Details

Bot C 11: Phycology   

Theory

1. Evolution and Biodiversity of algae: Evolution of algae at Morphological and Ultrastructural level. Algal diversity of Different Habitat and their Conservation.                                    

2. Phylogenetic Relationship of Pro- and Eukaryotic Algae: What is  the place of Algae in the system,Phylogenetic theories in systematics; Phylogenetic methods- Molecular markers, Symbiosis theory- Primary, Secondary and Tertiary endosymbiosis ,Fan shaped phylogenetic tree, Concept of Picobiliphytes, Chlorarachinophyta, Apicomplexan and Streptophyta .                                 

3. Horizontal gene Transfer and Evolution of Eukaryotic algal Chloroplast: The prokaryotic Ancestry of Plastids and their subsequent evolution, Origin of peridinin and fucoxanthin containing plastids through tertiary endosymbiosis. Molecular phylogeny of algal chloroplasts and higher plant chloroplast .                                                  

4. Cyanobacteria: Genome and genetic Properties, Soil and rice field reclamation; Heterocyst- ultra structure, biochemistry and nif-gene regulation; Cyanobacterial bloom – ecological significance and its control.           

5. General overview of Algal Divisions: Glaucophyta- Principle Chacteristics and primitive features, Dinophyta : General Features, Redtides and Toxins ,Bioluminiscence, Heterotrophism.                         

6. Cytomorphology and Ultrastructure of Algal Cell: Cell surface with extracellular Mucilage, Flagellar Motor, Photoreceptor Apparatus and Nuclear division .       

7. Phytoplankton Ecology – Types of phytoplanktons; Primary Production; Species Diversity Index; Physical Environment (Light, Heat, Turbulance); Chemical environment (Nitrogen, Phosphorus, Silicon, Carbon);Nutrient Uptake Models (Michaelis- Menten  and Monod  , Droope Model) 

Practical

1. Algal Diversity Study : Identification of members of  Different Groups(maximum 5 genera from each group) - Cyanobacteria , Bacillariophyta,Euglenophyta and Chlorophyta.

2.Seaweed Identification: Enteromprpha, Ulva, Halimeda, Bryopsis, Caulerpa,Macrocystis Sargassam, Padina, Dictyota, Catenella,Kappaphycus, Gracilaria.

3. Phytoplankton sampling and Identification:

4. Estimation of Phosphate, nitrate, DO and BOD from water samples.

5. General principles of Culturing Algae in Laboratory and growth measurement.

6. Algal chromosome study from Chara .

Bot C 12: Microbiology    

Theory

Methods in Microbiology

Culture of microorganisms: Methods for isolating pure cultures, types of culture media, enrichment culture techniques, maintenance and preservation of pure cultures. Control of microorganisms: physical and chemical methods.

Microbial Diversity and Extremophilies

Phototrophic bacteria; Chemolithotrophic bacteria; Spirochetes; Rickettsias; Chlamydias; Mycoplasmas; Myxobacteria and Extremophiles (thermophilic, halophilic, acidophilic and alkalophilic bacteria). Unculturable bacteria.

Growth and Differentiation

Bacterial growth: definition, growth parameters, measurement of growth, synchronous growth, growth kinetics, factors affecting growth. Batch and continuous culture. Differentiation: endospore formation-cytological, physiological and genetic aspects, germination; life cycle of Caulobacter.

Microbial Metabolism

Outlines of biosynthesis of peptidoglycan, major amino acids and proteins. Regulatory mechanisms in bacteria - induction, repression, feed back inhibition, catabolite repression and attenuation; Manipulation of biochemical regulatory mechanisms for overproduction of metabolites. Nitrogen metabolism: ammonification, nitrification, denitrification and nitrogen fixation.

Bacterial Genetics

Organisaition and replication of genetic material in bacteria: chromosome and plasmid, Gene transfer mechanisms: conjugation, transformation and transduction. Recombination in bacteria

Medical Microbiology

Pathogenic properties of bacteria: toxins and extracellular enzymes; brief account of major human disease and their bacterial pathogens. Principles of chemotherapy, general account of chemotheraputic agents, sulfa drugs and antibiotics. 

Fundamentals of Immunology

History of immunology, innate and acquired immunity, humoral and cell mediated immunity, organ and cells involved in immunity, T cell and B cells; antigens: characteristics and types, adjuvants. Immunoglobulis: types, structure and properties.

Viruses and acellular microbes

Nomenclature and classification, distinctive properties of virus, morphology and ultrastrucutre, capsid and their arrangements, types of envelops and their composition, viral genome, their types and structure, virus related agents (viriods and prions). Viral replication: lytic and lysogenic.

Practical

1. Preparation of culture media (synthetic, semisynthetic and complex); methods of sterilization and aseptic methods.

2. Isolation of microorganisms from natural samples by dilution plating method and development of pure cultures by streak-plate and pour-plate methods.

3. Determination of morphological (simple and differential staining), physiological and biochemical characteristics of some selected isolated bacteria.

4. Turbidimetric estimation of bacterial growth, construction of bacterial growth curve; influence of physical and chemical factors on bacterial growth.

5. Enrichment and isolation of free-living nitrogen fixing bacteria from soil and isolation of Rhizobium from root nodule.

6. Determination of antibiotic sensitivity of some bacteria by disc diffusion method.

7. Recombination in bacteria using auxotrophic mutants/ antibiotic-, metal resistant organisms.

8. Isolation of bacteriophage and determination of phage-titer.

Visit to some industries of microbiological interest.

Bot C 13: Plant Anatomy and Developmental Biology    

Theory

General Aspects: Novel features of plant growth and development; concepts of plasticity in plant development; analyzing plant growth.

Seed development and dormancy- Embryo and endosperm development; cell lineages during late embryo development; Seed maturation and dormancy.

Shoot, Leaf and Root development- Organization of Shoot Apical Meristem (SAM); Control of cell division and cell-to-cell communication; Molecular analysis of SAM; Leaf development and differentiation; Organization of Root Apical Meristem (RAM); cytohistological logical zonation of SAM; Root hair and trichome development; cell fate and lineages.

Floral induction and development- Hormonal control; Inflorescence and floral determination; sex determination, development of pollen grains.

Seed germination and Seedling growth- Mobilization of food reserves during seed germination; tropisms; hormonal control of seed germination and seedling growth.

Differentiation of primary and secondary plant bodies- Ontogeny, differentiation of sclerides, fibres and their control of differentiation; vascular cambium; factors influencing cambial activity.

Physiological plant anatomy- Anatomical response to mineral deficiency; response of plants to wounding and invasion by microorganisms.

Plant anatomy in systematics and evolution: Xylem evolution; wood anatomy, nodal anatomy, floral vasculature, mineral inclusion in systematics and evolution.

Ecological anatomy: Leaf and wood anatomy in ecological perspective; anatomical response to pollutants.

Applied plant anatomy: Application of anatomical studies in climatology, genetics and plant breeding, biomedical research and forensic science.

Practical

1. Cell types- trichomes, sclerides, tracheids, vessel members and sieve tube elements.

2. Secretary structures and cell inclusions- necteries, glandular hairs, oil glands, salt glands, resin canals, laticifers, cystolith and crystals.

3. ; Nodal anatomy- unilacunar , trilacunar, multilacunar.

4. Secondary phloem from TS, TLS, RLS of the bark and anatomy of lenticels.

5. Wood anatomy from TS, TLS, RLS of woods.

6. Study of shoot apical organization in pteridophytes, gymnosperms and angiosperms.

7. Anatomy of sun and shade leaves, xeromorphic leaves, succulent leaves, halophyte leaves, hydromorphic leaves.

Study of different types of embryo.

Bot C 14: Cell Biology and BioMolecules 

Theory

Macro-molecules- Carbohydrates- mono, di- and polysaccharides; amino acids and peptides; lipids-classification, structure and function, their roles in biological membranes. Primary, Secondary, Tertiary and Quaternary structure of proteins; α-helix, β-sheet and collagen structure; Nucleic acid classification, physical and chemical properties.

Cell: Ultra-structural organization of cell; origin and evolution.

Biomembranes: Structural models; Composition and dynamics; Biogenesis and assembly, Dynamic aspects of cell wall during growth and differentiation; Transport of ions and macromolecules; Pumps, carriers and channels; Endo- and exocytosis.

Cell-Cell Interaction and signaling: Cellular adhesions; adhesion receptors; intercellular junctions in plants and animals; Intracellular signal transduction, signaling molecules and cell surface receptors.

Mitochondria: Mitochondrial DNA and male sterility; Biogenesis of mitochondria; Origin and evolution.

Chloroplast: Chloroplast DNA and its significance; Chloroplast biogenesis; Origin and evolution.

Nucleus: Macromolecular trafficking; Chromatin organization and packaging; Higher order structure of chromatin, chromosomes; specialised chromosomes, nucleosome positioning.

Ribosomes and Protein Synthesis: Organization and biogenesis of ribosomes; Ribosome structure and its significance in protein synthesis; translation prokaryotes and eukaryotes.

Endo-membrane System: Structure and function of microbodies, Golgi apparatus, lysosomes and endoplasmic reticulum; Membrane maturation and specialization.

Cytoskeleton: Nature of cytoskeleton, intermediate filaments, microtubules, cilia and centrioles, actin filaments, actin binding proteins.

Cell cycle: Introduction, phases, cell cycle control in yeast.

Deoxyribonucleic acid: Structure and properties of DNA, aberrant structures; Melting and reassociation of DNA, Cot curves, repetitive and unique sequences, Rot curves and gene expression.

DNA replication- Mode of replication of circular and linear DNA molecules, machinery of DNA replication in prokaryotes and eukaryotes; replication of nucleosomes.

Ribonucleic acid: Structure and properties of RNA, Types of RNA, RNA processing – Processing of tRNA, rRNA; mRNA processing- G capping, intron splicing, polyadenylation. mRNA localization.

Transcription in prokaryotes and eukaryotes: Promoters, enhancers, transcription factors; initiation, elongation and termination of transcription in prokaryotes and eukaryotes.

 RNA and DNA polymerases: Types, structure and function; polymerase chain reaction: theory, applications and modifications.

Bot C 14: Cell Biology and BioMolecules

Practical

Subcellular fractionation of plant tissues and isolation of cellular organelles.

Isolation of plant genomic DNA and estimation of purity by spectrophotometry and agarose gel electrophoresis. Protein Gel Electrophoresis: Native and SDS-PAGE

Bot C 15: Bryophytes, Pteridophytes and Gymnosperms    

Theory

Bryophyta

1. Broad outline of classification and evolutionary trends among Bryophytes.

2. Bryophyte ecology: substrate colonized by bryophytes, growth forms and ecotypes.

3. Bryophyte as site indicators-responses of bryophyte to environmental pollution, initial colonization and succession.

4.Bryophyte chemistry and taxonomic implications.

Pteridophyta

1. Introduction; Outline of systematic treatment of Pteridophytes; distribution of extant groups in time and space.

2. Early land plants; vegetative and reproductive organography, evolutionary significance of the members of Zosterophyllopsida, Trimerophytopsida, Isoetales and Sphenophyllales.

3. Stomatal types and their development; evolution of stele; ecology, karyology and affinity of Ophioglossaceae, Osmundaceae, Cyatheaceae, Polypodiaceae, Salviniaceae.

4. Types of spore, induction of spore germination, gametophyte types, biochemical aspects of gametophyte differentiation; antheridogens- chemical nature and mode of action; determination of femaleness in free sporing heterosporous plants; phytochemistry of pteridophytes.

5. Diversity of ferns in an ecological perspective; insect, microorganism –pteridophyte interactions, endangered and endemic pteridophytes and their conservation.

6. Cytogenetics and reproductive biology of ferns: polyploidy, apospory, apogamy, apomixis and hybridization; genetic variability in fern population- genetic load.

Gymnosperms

1. Concept of progymnosperms and its evolutionary significance

2. Introduction; Outline of systematic treatment; distribution of extant taxa in time and space.

3. Brief account of extinct Cycadales and Coniferales with emphasis on evolutionary aspects.

4. Vegetative morphology and reproductive biology (Pollination mechanism, embryogeny) of extant Cycadales, Coniferales, Ginkgoales, Taxales and Gnetales.

5.Karyology and phytochemistry of important taxa, biotechnology of important taxa; endangered and endemic taxa and their conservation.

Practical

Pteridophyta

1. Study of general habitat, external and internal morphology of vegetative and reproductive structures (spore types, soral anatomy etc.) of the following taxa: Psilotum, Lycopodium japonicum, L. serratum, L. cernuum, Selaginella monospora, Isoetes coromandelina, Equisetum diffusum, Botrychium, Angiopteris, Osmunda, Lygodium, Dicraopteris, Oleandra, Nephrolepis, Aplenium, Blechnum, Adiantum, Christella, Cyathea/ Alsophila/ Hemitelia, Microsorum, Phymatosorus, Ceratopteris and Salvinia.

2. External morphological features of the following taxa: Tmesipteris, L. squarrosum, L. selago, Ophioglossum, Schizaea, Marattia, Cibotium, Drynaria, Acrostichum, Selaginella bryopteris, Pteris vittata, Pyrrosia, Helminthostachys, Cheilanthes and Onychium.

Gymnosperms

1. Study of general habit, external and internal morphology with special reference to their male and female reproductive structures, pollen grains: Cycas, Ginkgo, Pinus, Cryptomeria, Thuja, Araucaria, Podocarpus, Cephalotaxus, Taxus, Ephedra, Gnetum.

2. Study of leaf and wood anatomy of the following taxa: Abies, Cryptomeria, Cupressus, Araucaria, Taxus and Gnetum.

3. Study of external morphology of the following taxa: Zamia, Encephalartos, Tsuga, Taxodium, Cunninghamia, Juniperus, Callitris, Agathis, Welwitschia, Sequoia and Metasequoia.

Bot C 21: Mycology and Plant Pathology    

Theory

Mycology

  1. Modern systematics, origin and phylogenetic relationship in fungi.
  2. Dormancy, germination and growth.
  3. Carbohydrate metabolism.
  4. Molecular mechanism of asexual and sexual reproduction.
  5. Cell cycle in Yeast.
  6. Fundamentals of fermentation technology: Industrial production of citric acid, alcohol and antibiotics.
  7. Fungal diseases in animal and man and disease management.
  8. Practical utilization of mycorrhiza in agriculture.
  9. Biotechnological approaches in mushroom production.
  10. Bioremediation.

Plant Pathology

  1. Epidemiology of plant disease.
  2. Mechanism of penetration and the process of disease development.
  3. Mechanism of disease resistance.
  4. Genetics of host pathogen interaction.
  5. General overview of plant diseases caused by different biotic and abiotic stress.
  6. Mechanism of disease control by chemical and biological means.
  7. Biotechnological approaches for diseases resistance.
  8. Plant disease diagnosis utilizing molecular tools.
  9. Biopesticides.

Practical

1. Sterilization and incubation- principles and uses of instruments.

2. Culture media and their preparation.

3. Preparation of stabs, slants and pouring of plates.

4. Isolation of fungi from water, soil and air by culture plate technique.

5. Isolation of pathogen from diseased tissues (leaf, stem and fruit).

6. Preparation of pure culture and sub culturing.

7. Preparation of monosporous-, polysporous- and tissue- culture.

8. Inoculation of tuber, stem and fruit.

9. Study of hyphal types and hyphal system.

10. Study of production of organic acid / alcohol / enzyme.

11. Study of fungal nuclei.

12. Biological control by dual culture technique.

13. Morphological and reproductive structure of some macro and micro fungi.

14. Symptomology and histopathology of some common diseases with diagnostic characteristics.

15. Preparation of spawn.

Cultivation of Pleurotus.

Bot C 22: Taxonomy of Angiosperms      

Theory

1. Introduction: Definitions  of terms: Systematics, taxonomy, classification, identification, nomenclature, aims and scope of taxonomy, history and phases of taxonomy. 

2. Data sources of Taxonomy: Concepts of character, relevance of embryology, palynology, phytochemistry, ultra structure and molecular taxonomy.

3. Tools of Taxonomy:  Functions of field, herbarium, botanic gardens, floras/literature, GIS (geographic information system).

4. Biosystematics: Definition, methods, categories, relationship with classical taxonomy.

5. Concepts of Taxonomical Hierarchy: Species/genus/family and other categories, specied concept.

6. Nomenclature: History of ICBN, aims and principles, rules (incl fossils and cultivated plants) and recommendations, proposed bio and phylocodes.

7. Concepts and Principles of Assessing Relationship: Phenetic numerical taxonomy- principles, philosophies, methods, merits and demerits.

8. Major systems of angiosperm classification:  Outlines, philosophies and principles, relative merits and demerits, recent trends in classification- molecular and cladistics ones.

9. Angiosperm diversity: Salient features, evolutionary trends and phylogeny in magnollidae, Hamamelidae, Caryophyllidae, Asteridae, Alismatidae and Liliidae (Sensu Cronquist ,1981), concepts of palaeoherbs, eu-dicots etc.

10. Biodiversity: Concepts, levels, hotspots, megadiversity centers, status (with special reference to India); Concerns- extinction and threats (IUCN categories), conservation-needs and methods.

Practical

1. Workout of plant specimens and description of vegetative and reproductive characters from representative locally available families.

2. Training in using  local floras and other literature and herbaria for identification of specimens described in the classes.

3. Study of various taxa of a genus, location of key characters and preparation of keys at specific level.

4. Field excursion for familiarization with and study of vegetation types(s) and flora(s) of areas outside the state and training in collection and preservation methodologies.

Bot C 23: Palaeobotany and Palynology    

Theory

1. Basic geological information related to palaeobotany:

Sedimentary rocks; Taphonomy; dating the pages of earth history; nomenclature and reconstruction of fossil plants; Stratigraphy; Basic concepts of continental drift and plate tectonics.

2. Origin and evolution of plant life forms:

The earliest environments; Brief idea of Origin of life; first prokaryotes; evolution of eukaryotes; geological records of algae (stromatolites, diatoms, dinoflagellates), fungi (endomycorrhiza and epiphyllous fungi), bryophytes and their ecological significance.

3. The colonization of land:

Environmental changes before terrestrialization, land adaptive features, evolution of land plants- different evidences, biogeographical distribution of early land plants (Silurian- early Carboniferous), earliest trees in the fossil record.

4. Emergence of seed plants:

Preovules, hydrasperman reproduction; evolution of closed carpel; evidences from the ovulate fructifications of Glossopteridales, Corystospermales, Caytoniales, Bennettitales, Pentoxylales.

5. Appearance of Angiosperms:

Evidence for the first angiosperms: leaves, flowers and pollen grains; place of origin and radiation; cladistic and molecular biological approaches on phylogeny of angiosperms.

6. Past plant life as source of energy:

Organic deposits of commercial value- coal, petroleum- their origin and depositional environment; coal and petroliferous basins of India.

7. Palynology:

Branches of palynology; Spore, pre-pollen and pollen morphology, wall chemistry, evolution of aperture types;

8. Applied palaeobotany and palynology:

i. Fundamentals of palaeofloristics, palaeogeography, palaeoecology and palaeoclimatology;  Application of neopalynology and palaeopalynology.

ii. Ancient DNA and other fossil biomolecules and their potential in evolutionary research; stable isotopes and tree ring in reconstruction of palaeoclimate.

Practical

1. Types of fossils, and modes of preservation.

2. Techniques of study of plant fossils:

Thin section method (demonstration and study of prepared slides), peel techniques (demonstration and study of prepared peel sections); maceration of peat, lignite, coal: (demonstration).

3. Systematic study of fossil plants through ages- Stromatolites, Precambrian biota, Cooksonia, Rhynia, Zosterophyllum, Lepidodendron, Sigillaria, Lepidophlois, Sphenophyllum, Calamites, Sharmastachys, members of Filicopsida- Coenopteridales members of Lyginopteridales, Medullosales, Glossopteridales: upright Glossopteris plant, Vertebraria root, Peltaspermales, Caytoniales, Bennettitales, Cycadales, Ginkgoales, Pentoxylales, Cordaitales, Coniferales, angiosperm fossils (to be studied in stratigraphic sequence).

4. Acetolysis method (demonstration); study of morphology of modern spores and pollen grains; pollen analysis of honey.

5. Study of macerated sample (to be supplied) of peat, lignite and coal. Quantitative and qualitative study of palynomorphs. Interpretation of data on stratigraphic age and environment of deposition.

Bot C 24: Genetics and Genomics    

Theory

Introduction and importance of Plant Genetics: Basic discoveries in  classical and molecular genetics; Extension of Mendelism:Allelism; gene function to produce polypeptides; interaction with environment; penetrance and expressibility; gene interaction-epistasis, pleiotropy, continuous variations Model organisms for genetic studies : Life cycle of Neurospora, Arabidopsis and Corn.

Linkage, crossing over and chromosome mapping-:Crossing over as the physical basis

of  recombination; chromosome mapping; three point test cross.Construction of genetic and physical map;molecular polymorphism..

Microbial Genetics -- Principles, basic procedures and terminology of microbial genetics; Gene mapping in bacteria and viruses; Genetic analysis in fungi, tetrad analysis to detect linkage in fungi

Genome organization in Eukaryotes – types of genomes, genetic features of eukaryotic nuclear genomes; development of gene concept, gene replication, organization of structural and functional elements of chromosome:-centromere, telomere  heterochromatin and  telomerase, sex chromosomes in plants; special chromosomes in different eukaryotes ;genome duplication and alterations and their role in evolution; Genes and gene number; Law of constancy and C-value paradox.

Gene expression -- Control of gene expression; Control of gene expression in bacteriophage lambda, T-phages; RNA phages; Regulation of prokaryotic gene expression (lac, his, trp operons and catabolite repression); Regulation of gene expression in eukaryotes, heterochromatin in gene silencing.

Genetic Integrity and Diversity – Physical and chemical basis of equational separation of chromosomes; Recombination, Mechanism of recombination; Evolutionary significance of  recombination; genetic control of recombination. Mutagenesis:  Molecular basis of spontaneous and  induced mutations; Transposon mutagenesis,  In vitro mutagenesis, Site-directed mutagenesis,  Environmental mutagenesis; Repair and retrieval systems; Mobile genetic elements: Structure and function of transposable elements and their role in evolution. Extranuclear genetics.

Marker Assisted Breeding: Quantitative and qualitative traits, marker assisted selection for genes of agronomic importance; QTL mapping and cloning.

Population Genetics-- Definition of populations, Gene frequency in a population, genetic equilibrium, Hardy-Weinberg principle, barriers to gene flow and mechanism of speciation, Using highly polymorphic DNA sequences in DNA typing, Inbreeding and genetic consequences of self-pollination in plants.

Genomes and Comparative Genomics – Concept; Genome sequencing; High throughput genome sequencing; Arabidopsis, rice and human genomes; Genome annotation; Synteny; Gene search and comparison tools.

Functional Genomics -- Approaches to analyze differential expression of genes - ESTs, SAGE, microarrays and their applications; Principles in reverse genetics: Gene tagging; Gene trapping; Gene silencing; Knockout mutants; Transcriptome; Ribotype concept.

Introduction to proteomics—The concept of proteome, definitions and conceptualization; Applications of proteomics: protein mining, protein-expression profiling, protein network mapping, protein modification and analysis.

Practical

Mitotic and meiotic chromosome analysis and phases of division

Analysis of polyploids and structural hybrids

Cytogenetic biomarkers of mutagenesis

Analysis of genetic polymorphisms using isozymes and molecular markers

PCR based site-directed mutagenesis to demonstrate gene silencing and knockout mutation

Bot S 21: Instrumentation (Supportive Course)      

Theory

Principles and application of colorimetry in biological systems:

Spectrometry: Basic principle, double beam UV/VIS and IR spectrometers, atomic absorption spectrometer, principle and instrumentation of fluorescence spectrophotometer, applications, MALDI-TOF, LC-MS-MS.

Chromatography, Electrophoresis, Centrifugation: Basic principles, types and application. 

Optical microscopes, optical microscopy; phase, ultraviolet and interference microscope- their basic principles; optical systems and ray diagrams- their applications in cell biology; fluorescence microscope; micro spectrophotometry of cells and tissues,

Electron microscopy: theory of magnetic and electrostatic lenses and their focal length; construction of electron microscope; limiting resolution and useful magnification; contrast formation; shadowing and staining technique; scanning and transmission electron microscopy; specimen preparation techniques; application of electron microscopy in cell and molecular biology.

Fluorescence activated cell sorter (FACS), Micro array, NMR, FRET.

Bot C 31: Plant Physiology and Biochemistry   

Theory

1. The atom and chemical bonds, reaction orders, pH , buffer, indicator , physico chemical properties of water.

2. Plant water relationship.

3. Ion uptake mechanism of individual cells and roots, interaction between ions, ion competition, antagonism and synergism.

4. Phloem translocation: symplastic and apoplastic flow of solvents, phloem loading and unloading.

5. Reactive oxygen species- formation and role in plants.

6. photosynthesis : complexes of electron transport in chloroplast , mechanism of electron transport generation of proton gradient and ATP generation, bioenergetics of light reaction, CO2  concentrating mechanism in plants, regulation of C3- C4 and CAM cycles

7. Respiration, metabolic regulation of glycolysis, acetyl CoA , kreb’s  cycle, gluconeogenesis and glyoxylate cycle.

8. Nitrogen metabolism: structure and function of nitrogenase, nif gene and nod gene organization.

9. Plasticidal pigments- chlorophyll structure and biosynthesis, hormonal regulation of growth and development.

10. Structure, biosynthesis, role and mechanism of action of auxin, gibberellins, cytokines, ethylene and abscisic acid.

11. Phytochrome; chemistry and photo-morphogenetic responses. Chryptochrome and blue light responses.

12. Dormancy and generation of seeds: orthodox and recalcitrant seeds, types of seed dormancy, breaking of dormancy, biochemical changes during dormancy, hormonal regulation of dormancy and germination.

13. Bio-energetics : an overview.

14. Energy conservation: ATP cycle, oxidative phosphorylation and photophosphorylation.

15. Lipid metabolism: oxidation of fatty acids and biosynthesis of fatty acids.

16. Protein: primary, secondary, tertiary and quaternary structure of proteins, biosynthesis purification and characterization, Ramachandran plot.

17. Mechanism of enzyme action, enzyme kinetics, enzyme inhibition.

18. Senescence- hormonal and environmental control of senescence, programme cell death in life cycle of plants.

19. Metabolomics: networking and application.

Practical

  1. Assay of enzymes: Catalase, Peroxidase, Amylase, Phosphatase, Protease, Ascorbic acid Oxidase and Urease.
  2. Complexometric method of analysis of calcium and magnesium
  3. Colorimetric estimation : IAA , reducing sugar, sugar test by copper reduction method, amino acids, DNA , RNA Protein
  4. Isolation of chloroplast and determination of Hill activity.
  5. Demonstration of instruments: Different Centrifuges, including Ultracentrifuge spectrophotometry, and spectroflurometry, Chromatography, colorimetry.
  6. Tetrazolium test of seed viability.
  7. Protein purification by salting and isoelectric precipitation
  8. Qualitative test of organic acids, sucrose, glucose, maltose, and arabinose
Bot C 32: Phytochemistry and Pharmacognosy    

Theory

  1. Introduction, history, scope.
  2. Classification and pharmacological action of plant drugs.
  3. Origin of secondary metabolites – a brief account of acetate malonate, acetate mevalonate and shikimic acid pathway.
  4. Carbohydrates –  starch,  cellulose derivatives, gums.
  5. Glycosides, general account, biosynthesis, glycosidal drugs
  6. Cyanogenic glycosides and glucosinolate compounds.
  7. Alkaloids, definition, properties, classification, alkaloidal drugs – Datura stramonium, Atropa belladona, opium, Cinchona, tea, ergot, Rauvolfia, Holarrhena, Catharanthus – alkaloidal constituents, uses, allied drugs.
  8. Phenolic compounds produced by plants, types, biological activity, drugs – Senna, Aloe, Hypericum, Capsicum.
  9. Betacyanins
  10. Steroidal compounds, different types, biological activity and pharmaceutical importance
  11. Volatile oils, composition, drugs – clove, Mentha, Eucalyptus, Foeniculum, Cinnamomum, citronella
  12. Resins, different types, uses
  13. Lipids
  14. Antibiotics and vitamins
  15. Hallucinogenic, allergenic and other toxic plants
  16. Pesticides (plant and microbial origin)
  17. Methods of extraction, isolation and characterisation of secondary metabolites.
  18. Chemical races.
  19. Production of important secondary metabolites by tissue cell and organ culture.
  20. Quality control of plant drugs.

Practical

1.Choice of solvent for extraction of  alkaloids, phenols.
2. Chemical tests for the detection of alkaloids, phenols, anthraquinones, cardenolides, anthocyanins, betacyanins, carotenoids.
3.Extraction and chromatographic detection of some common plant drugs.
4. Study of unorganized drugs – starches, gums, resins etc.
5.Techniques of studying stomatal index, vein islet number, palisade ratio.
6.Organoleptic  and microscopic evaluation of selected powdered and whole plant  drugs

Bot C 33: Plant Molecular Biology and Biotechnology    

Theory

1. Molecular improvement of crops (Molecular breeding, Mutagenesis, Transgenesis,  Metabolomics and Hybrid technology)

2. System Biology: Structure to Function in plants

3. Plant genes, promoters, intron splicing, vectors, codon optimization, gene mapping and cloning of plant genes

4. Recombinant DNA technology: Principles and methods of recombinant DNA technology- expression of cloned genes in E. coli, cloning in yeast: transformation in yeast, yeast artificial chromosome (YAC), retrovirus like vector (Ty) in yeast/shuttle vector.

5. Plant tissue culture: Organogenesis, Embryogenesis, in vitro fertilization, Apomixix and application of haploidy and DH populations in transgenic breeding and crop improvement; Molecular and Biochemical markers of in vitro regenerability of  plants

6. Genetic transformation: Vector construction, Protoplast system (electroporation and PEG), Agrobacterium system, en-planta transformation and Biolistic system; Screenable and selectable markers and their use; Chloroplast transformation; Marker-free methodologies; Gene stability, Inheritance and Differential expression of transgenes in plants

7. Molecular characterization, management and regulatory system of transgenic crops

9. Weed management: Implications of herbicide resistant crops

10. Pest management in crop plants, Biopesticides, Built-in plant protection (Bt technology) safety and environmental issues

11. Molecular breeding for abiotic stress tolerance (stress regulated genes expression, osmotic stress signalling, application in salt, cold and drought tolerance in plants)

12. Molecular breeding for Biotic stress tolerance: Fungal resistance, Bacterial resistance, Virus resistance, Transgenes pyramiding and Integrated Pest Management (IPM)

13. Biofortified crops (improvement of micronutrients in food crops; e.g. Iron and pro-vitaminA enriched rice, Vitamin E-maize, Protein improvement in rice and potato etc.)

14. Bio-and Food-safety, Intellectual Property Rights and Ethical Issues – Intellectual property rights (IPR); Patents, trade secrets, copyright, trademarks; Plant genetic resources; Plant varietals protection and registration; GATT & TRIPPS; Patenting of biological material; Bio-safety and containment practices and Food-safety of GMO crops

15. Plants as Biofactories – Concept of bio-pharming; Renewable Bio-fuel production in plants

16. Economic and social impact of Biotech-crops (ex-ante analysis and commercial release of GM-crops)

Practical

1. Plant tissue culture techniques (media preparation, culture of explants (embryo, shoot tips, nodal segment)

2. Anther culture of dicot and monocot plants

3. Plant Transformation system (demonstration)

4. Molecular Biology tools: PCR, Gel electrophoresis, Isolation of plasmid and genomic DNAs (demonstration)

Bot C 34: Microbial Biotechnology      

Theory

Fermentation Technology:

Introduction to microbial biotechnology, interaction between microbiology, chemical engineering and biochemistry.

Introduction to bioprocessing, classification of fermentation, isolation of industrially important microbial cultures, screening and strain improvement, media formulation, and process optimization.

Fermentation systems:

Design and operation of fermenters, basic concepts for selection of a reactor. Growth and non growth synthesis. Open and closed system of fermentation.

Downstream processing:

Introduction, removal of microbial cells and solid matter, foam separation, precipitation, filtration, centrifugation, cell disruptions, liquid-liquid extraction, chromatography, membrane processes. Drying and crystallization.

Fermentation products:

Microbial production of enzymes, polysaccharides, polyesters, ethanol, single cell protein, recombinant proteins, antibiotics and vaccines.

Fungal Biotechnology: Gene manipulation of fungi for industrial and agricultural applications, protoplast technology in fungi, enzyme based techniques for identification of microbes, cloning of gene for direct chemical analysis, proteomics of host pathogen interaction, genetic improvement and formulation of mycoherbicides.

Algal Biotechnology:

Scope of algal biotechnology, source of fine chemicals, therapeutics, hydrogen and methane  production, culture and cultivation of auto and heterotrophic algae. 

Practical

Study of the design and components of fermenter and its working principle.

Isolation and screening of microorganisms for production of enzymes and antibiotics.

Fermentative production of  protease/amylase/invertase/antibiotics .

Determination of BOD from sewage/fermentation broth sample

Transformation of E. coli for antibiotic/metal resistance gene, selection of transformed clones and plasmid isolation, restriction digestion, gel electrophoresis.

Isolation of fungal DNA

RAPD/PCR based analysis of typical fungi

Studies of protein profile during host pathogen interaction

Demonstration of precipitation reaction based immunodiffusion test

Bot S 31: Environmental Botany (Supportive Course)  

Theory

1. Concept and Dynamics of Ecosystems, Components,

2. Habitat and plant structure, Response of plants to pollutions ,Frost and Hardiness

3. Importance and Conservation of Biological Diversity,

4. Over exploitation of selected species,

5. Population ecology and Biological control, Sustainable development,

6. Seed Bank, Gene Bank and Germplasm Reserve

7. Environmental Laws : Public Interest Litigation, Public Nuisance, Environmental nuisance.

8.Environmental education.

Bot S 41: Computer Application and Bioinformatics  (Supportive Course)  

Theory

General ideas on computer: Why computer, Information explosion in life sciences< need for processing; human being as information processor, as information generator, Class of problems that can be solved by a digita computer, problems which may not solved by digital computers.

Components of a digital computer: Block diagram of digital computer-detail of input  units, output units, central processing unit pointing devices, fast input devices. Exotic input/output devices. Secondary storage devices. Types of digital computer, generation of digi9tal computer. Organization; low level and high-level language: binary number system Structured computer Organization: Various levels of digital computer, operating system as resource manager.

Windows-basic concepts and commands Unix as a multi user, multi tasking operating system Introduction to Linux Introduction to programming in C/MATLAB word processing, Spreadsheets, computer graphics and presentation software Algorithm and flow chart Sequential, conditional and looping problems

Artificial vis-a-vis Natural language Low and high level languages the basic concepts Binary number system Basic concepts of translation process (syntax, semantics etc) C as a programming language Alphabets and language elements Operators and separators strings Flow control, Relational operators Construction of compound statements Functions and structured programming- Top down approach, character processing Network and Internet Introduction and applications

Bioinformatics: Applications and Prospects, Genome and protein information resources, sequence analysis, multiple sequence alignment, homology and analogy, pattern recognition, analysis package.

Optional Courses : Special Papers

Bot O 41: Advanced Cell Biology     

Theory

1.Origin of life, nucleus and   organelles -: Mitochondria, Chloroplast, Peroxisome Nucleus : Protein trafficking into these organelles

2.Cellular communications; General principles, G proteins, protein kinases and protein phophatases; MAPKs; signal transduction in disease and immunity.

3.Eukaryotic cell cycle: Overview, principles of assembly, cohesion and segregation, Experimental systems: Microtubule: Structure, formation; associated proteins; centriole-origin and function; drug effects on microtubules: Biochemical and genetic approaches, Cell cycle control in yeast vs mammalian cells, Universality in cell cycle control.

4 Architecture of the eukaryotic nucleus: Chromosome model, nucleosome, Chromatin modification   and genome expression;  genome expression  and silencing; DNA  binding proteins and their attachment sites. Chromosome constitution; forces involved in cell division and recombination genome duplication, alteration and importance, mobile genetic elements.

5.Genomes, Transcriptomes and proteomes: Eukaryotic Nuclear Genome:  genetic features of eukaryotic nuclear genome;.genomes of prokaryotes – bacterial and viral genomes functioning  of Genomes- elucidation of transcriptome, proteome; and the metabolome.

6. Mutations: Types and molecular basis; genetic basis of complementation; chromosomal aberration; structural basis of DNA mutagenesis ; oxidative DNA damage and mutagenesis and in vitro mutagenesis.

7. DNA repair and diverse functions in the cellular DNA damage response:

Mechanism of DNA repair in prokaryotes, lower eukaryotes and higher plants. Identification and molecular characterization of repair enzymes.

9. Cancer Characteristics of tumor cells: Transformed cell lines, Oncogene vs tumor suppressor, immunocytochemistry, strategies for combating cancer.

10  Molecular Evolution: Evolution of  gene structure, Protein Domains, Ribozyme and RNA world; Micro RNA, Si RNA and importance of RNAi  in differentiation and evolution; evolution of major phyletic lines; antiquity of introns; transposable elements Evolution and Horizontal Transfer, molecular clock.

Practical

Based on Theory paper

Bot O 41:Advanced Phycology and Algal Biotechnology    

Theory

1.Latest development in algal classification and phylogeny

2.Cyanobacteria in Geothermal Habitat : Geographic distribution, Distribution determination by chemistry (lipid biomarker) and molecular analysis (16S rRNA).

3.Molecular systematics of Cyanobacteria & Prochlorophyta ( The ‘other’ cyanobacteria), Dinophyta and Streptophyta. Molecular approach to Cyanobacterial Evolution.

4  Molecular Biology of Cyanelles : Wall biosynthesis and structure, molecular genetics, Protein transport, Phylogenetic analysis.

5. Targeted genetic modifications of Cyanobacteria; Microalgae as platform for Recombinant proteins, Genetic behavior of Chlamydomonas .

6.Algal Light Harvesting Complex : Phycobiliproteins constituting core and rod elements of PBS, Linker polypepties, Chromatic adaptation, Structure and Regulation of light harvesting genes.

7.Enviornmental Stress Physiology:

    1. Ecotoxicology of Inorganic chemical stress on Algae : Adsorption and uptake, Response of algal communities to inorganic stressors, Mechanism of tolerance, Algal bioassay of Inorganic stressors.
    2. Photoacclimation.
    3. Photo-inhibition and Culture Productivity.
    4. Salinity Stress.

8.Role of algae in Wet Land Ecology: Algal assemblages in wetlands, Factors affecting Algal production, Conceptual Models of wetland Algae(Dry state, Open state, Sheltered state, Lake state).

9.Phytoplankton community structure and function: Spatial distribution of biomass, Seasonal cycle of plankton growth, Community analysis, Process in plankton succession.

10. Biogeochemical Role of Algae :Limiting nutrients, Algae in Biogeochemistry ( phosphorus, nitrogen, silicon and carbon/oxygen cycles)

11.Microalgae in Human Welfare: Production of fine chemicals (Polysaccharides, bio-active molecules, antioxidants, lipids and PUFA), Micro-algae in human nutrition, Algae in aquaculture.

12.Water pollution and Phycoremediation : Eutrophication and water poisoning, Algae in wastewater oxidation pond, Removal of heavy metals, Impacts of micro-algae in quality of drinking water

13.Basic culturing Techniques and mass cultivation: Biological principles, Types of reactors for phototrophic algae, Down stream processing of cell mass production, Heterotrophic production of Marine Algae for Aquaculture.

14.Industrial  production of microalgal cell mass and secondary products : Spirulina, Dunaliella, Haematococcus, Porphyridium.

Practical:

Based on theory paper

Bot O 41:Microbiology       

Theory

Microbial Systematics

Classical approaches to bacterial taxonomy, chemo-taxonomic characteristics (peptidoglycan, lipids, fatty acids and proteins) and genotypic characteristics (DNA-base composition, -fingerprinting, -relatedness; RNA-sequence analysis, DNA-RNA hybridization); bacterial phylogeny.

Medical

Normal microbiota of human body; host-parasite relationship in baterial pathogenecity: non-specific mechanisms of host defense, mechanism of bacterial virulence, genetics of bacterial virulence; chemotherapy: antibiotics (origin, classification, chemistry and mode of action); semisynthetic antibiotics; antibiotic resistance in bacteria, mechanism of antibiotic resistance.

Immunology

Theories of antibody production, antibody diversity; antigen-antibody reactions; immunoassay methods and their applications, major histocompatibility complex (structure and function), complement system and complement activation; monoclonal antibodies (production and applications).

Virology

Cultivation of viruses, methods for detection and assay, phage typing, major human viruses: HIV, Hepatitis B and C, their salient properties, diagnosis, prevention and treatment. Viral vaccines, interferon and antiviral drugs.

Microbial Ecology

Population interactions (microbe-microbe interactions, plant-microbe interactions, animal-microbe interactions), quorum sensing; microbial consortia; bacterial biofilms- formation and applications; biogeochemical cycling of carbon, nitrogen, phosphorous and sulphur.

Environmental Microbiology

Biological treatment of wastes and pollutants: solid wastes disposal, treatment of liquid wastes; Biodegradation of environmental pollulants: petroleum hydrocoarbons and xenobiotics. Bioremediation of heavy metals; Bioleaching and recovery of metals.

Microbes in Agriculture

Biological nitrogen fixation, nitrogenase and alternative nitrogenase system, nif genes; degradation of cellulose, hemicellulose and lignin, production of biofertilizers (mass production of Rhizobium  and Azotobacter); Microbial  control of insects.  Use of viruses in agriculture.

Food Microbiology

Food produced by microbes: Fermented foods (fermented dairy products, alcoholic beverages, vinegar, fermented vegetables), microbial cells as food. Food as substrate for microorganism, food borne disease; contamination and spoilage of food ( meat and meat products, fish, fruits and vegetables,  milk and milk products), methods of food preservation (physical and chemical).

Practical

Based on theory paper

Bot O 41: Molecular Mycology & Plant Pathology       

Theory

Molecular Mycology

  1. Nutrient sensing and uptake in fungi.
  2. Regulation of carbohydrate and nitrogen compound metabolism. 
  3. Genetic control of vegetative growth, asexual and sexual development
  4. Genome organization in fungi.
  5. Extra chromosomal inheritance in fungi.
  6. Principles and general methods of fungal genetic engineering.
  7. Retroposon and retrotransposon in fungi.
  8. Regulation of protein synthesis in fungi.
  9. Heat shock protein and chaperon.
  10. Signal transduction pathway. 
  11. Control of cell cycle in yeast; genetic manipulation of brewing yeast.
  12. Medical mycology: General account of cell mediated and humoral immunity.
  13. Mushroom in modern medicines: Mushroom nutraceutials.

Plant Pathology

  1. Molecular basis of plant-pathogen interaction- physiology and genetics of plant-pathogen interaction; genetics of pathogenicity; gene for gene hypothesis and its molecular explanation; resistance genes and avirulent genes.
  2. Molecular biology of disease resistance- Plant chemicals (phenolics) involved in resistance: Phytoalexins; pathogenesis related (PR) proteins; systemic acquired resistance (SAR).
  3. Host specific and non specific toxin and molecular basis of their roles in pathogenicity.
  4. Crown gall tumerogenesis- nature of tumor; the Ti plasmid and its use as a transformation vector.
  5. Development of disease resistant variety by mutation breeding and recombinant DNA technology.
  6. Molecular diagnoses of plant pathogens- DNA-DNA hybridization; PCR amplification and finger printing; protein profiling by gel electrophoresis (SDS-PAGE); immunological assays.
  7. RNAi in plant pathology.
  8. Biological control by biotechnological methods- use of hyper parasite, hypovirulence plasmids and recombinant DNA technology.
  9. Integrated disease management.     

Practical

Based on theory paper

Bot O 41: Palaeobotany and Palynology     

Theory

1. Brief introduction to physical geology related to Palaeobotany: types of rock; from sediments to sedimentary rock- types, rock units; tectonics and tectonic features, taphonomy.

2. Outline of stratigraphy, code of stratigraphic nomenclature, Biostratigraphy, Lithostratigraphy, Chronostratigraphy; code of nomenclature for fossils.

3. Application of palaeobotany in geological investigations, plate tectonics, palaeoenvironment and palaeogeography; Co-existence approach for quantitative reconstruction of palaeoclimate, determination of pCO2 concentration.

4.  Antiquity of life; Major events in the Precambrian- early life forms, Indian records, stromatolites and palaeoecology.

5. Fossil algae, fungi, bryophytes- distribution in time, evolutionary and palaeoenvironmental significance.

6. Evolutionary theories and the plant fossil record; Evolutionary trends of early land plants:  palaeobotanical, biochemical and molecular evidences.

7. Environmental changes during Permian, Permo-Carboniferous floral provinces. Early Paleozoic and Lower Carboniferous flora of India. Origin and relationships of cycads, bennettites, ginkgos and glossopterids.

8.  Distribution of Glossopteris flora in time and space, Glossopteris plants. Seedling of Glossopteris.

9. The modern concepts of Angiosperm phylogeny and evolution in the light of recent palaeobotanical, palynological discoveries in conjunctions with data of other modern science: cladistics, molecular biology, palaeophytochemistry.

10. Origin of mangrove vegetation with special reference to palaeocoastline reconstruction; evolution of plants using the C4 and CAM photosynthetic pathway: the first grasses.

11. Brief concept of Mass extinction: evidence in the geological record: plants versus animals; floral changes across the Cretaceous – Tertiary boundary.

12.  Biotic interactions: Plant animal interaction and their co evolution.

13. Palaeopalynology of peat, lignite and coal. Artificial classification of sporae-dispersae, role of palaeopalynology and microfossils in oil exploration, identification of isobotanical line, source rocks and palaeoshoreline; kerogen.

14. Coal petrology- Depositional facies, Diagenesis, Lithification, Microlithotypes, reflectance, fluorescence study (brief), Application of coal petrology (brief).

15. Microfossils- geological occurrence, structure and palaeoecology of Acritarchs, Dinoflagellates, Hystrichosphaerids, Radiolaria, Microforaminifera, Ostracods, Silicoflagellates, Diatoms, Botryococcus, Coccolithophores.

16. Palaeobotany-Palaeopalynology of Quaternary sediments in understanding global warming, climate changes, eustatic sea level change, coastal evolution with special reference to Bengal Basin.

17. Ancient DNA and biomolecular record: Extraction, characterization and potential in evolution and climate research; fossil evidence of physiological and developmental mechanism-polar auxin flow.

18. Archaeobotany: study of plant economy from Palaeolithic to Historic age; vegetation dynamics and palaeoclimatic reconstruction through phytolith analysis.

19. Mega – Mio floristic divisions of Indian Gondwana- Dicroidium and Ptilophyllum flora, organography of Glossopteris seedling.

20. Deccan- Intertrappean flora and palaeoecological consideration.

21. Siwalik flora.

22. Pleistocene flora- palaeobotany and palynology with special reference to Kashmir.

23. Different aspects of Neopalynology and their applications: Melittopalynology, Aeropalynology, Forensic palynology, Copropalynology, Entomopalynology; Natural traps of pollen grains and their importance.

Practical

Based on theory paper

Bot O 41: Phytochemistry  And  Pharmacognosy   

Theory

1.Origin of  secondary metabolites – detailed account of acetate malonate, acetate
 mevalonate and shikimic acid pathway.

2.Turnover and degradation of secondary metabolites – physiological and developmental aspects - compartmentation  of secondary metabolism.

3.Phytochemistry, biosynthesis and sources of drugs:

(i) Phenols and phenolic glycosides : structural types, biosynthesis, importance (simple phenolic compounds,  tannins, anthraquinones, coumarins and furanocoumarins, flavones and related flavonoid glycosides, anthocyanins, stilbenes, lignins and lignans).

(ii)Steroids, sterols, saponins, withanolides, ecdysones, cucurbitacins: Biosynthesis, commercial importance.

(iii)Miscellaneous isoprenoids – iridoids, sesquiterpenes, diterpenoids, triterpenoids, tetraterpenoids, polyterpenoids.

(iv) Alkaloids –  different groups, biosynthesis, bioactivity.

(v)Volatile oils, aromatherapy

(vi)Resins and balsams

(vii)Lipids

4. Enzymes, proteins and amino acids as drugs

5.Vaccine, toxins and toxoids, antitoxins, immune globulins, antiserums

6.Vitamins

7. Antibiotics – chemical nature, mode of action.

8.Pharmacological action of plant drugs – tumour inhibitors, hypoglycaemic,  antihepatotoxic, antiprotozoal, antiviral, immunomodulators, PAF  antagonists, antioxidants, phytoestrogens and others.

9.General methods of  phytochemical analysis – extraction, isolation (different chromatographic techniques, principles), characterisation, immunoassay, monoclonal antibody.

10. Application of genetics and plant breeding in pharmacognosy

11. Plant metabolomics: a brief idea

12. Tissue culture and biotechnology for production of  secondary metabolites - microbiological conversion – metabolic engineering

13.Ethnopharmacology

Practical

Based on theory paper

Bot O 41: Plant Cell and Tissue Culture   

Theory

1. Basic concept of plant in vitro technology: History of in vitro plant biology Organization of a tissue culture laboratory, Equipment and supplies, Basic techniques, Medium components, Medium preparation, Differentiation/ Regeneration

2. Organogenesis: Organogenesis process, Developmental sequences, Mechanism of action of plant hormones, multiple hormonal control on organogenesis, Cell cycle control of organogenesis, Mechanisms of morphogenesis, Genetic control of morphogenesis, Genetic and physiological regulation of plant organ size and shape.

3. Embyogennesis: Major processes in Embryonic development; Formation of the Apical-Basal Axis, Establishing the Radial Axis, Mechanisms that establish cell fate in the embryo, Role of phytohormone in embryogenesis; Somatic Embryogenesis-Structural and developmental ontogeny, Physiological and Biochemical aspect of somatic embryogenesis, Molecular markers and genes for somatic embryogenesis.Gene expression and signal transduction.Regulation;  Application; synthetic seeds.

4. Haploid and Triploid culture; Androgenesis, Gynogenesis and Endosperm culture; Techniques and its applications in genetics and crop improvement.

5. Protoplast culture and somatic hybridization: : Isolation, Purification and Culture of Protoplasts; Protoplast fusion and Somatic Hybridization, Principle and scope; Nuclear and Cytoplasmic hybrids; Selection of hybrids; Regeneration; Possibilities; Applications; Limitations.

6. Micropropagation: methods and stages of clonal propagation; Production of virus-free plants, virus free assessment methods, genetic assessment -by RAPD and ISSR markers, Field evaluation, certification for quality plants, Packaging technology & Transport methods.

7. Somatic cell genetics; Somaclonal variation; Genotypic and Phenotypic variations in cell cultures and in regenerated plants, Origin; Types; chromosomal and genetic basis of somaclonal variation; Applications in crop improvement.

8. Germplasm preservation: Concept of Biodiversity and role of In situ and ex situ conservations of germplasms; Cryopreservation; Principle, Techniques and Applications.

9. Bioreactors: concept, types and use in plant tissue culture

10. Genetic manipulations in  plants; Strategies and Methods of genetic manipulations in plants ;  Agrobacterium-mediated gene transfer; Genetic elements and engineering of Ti and Ri plasmids;; Direct gene transfer – electroporation, particle bombardment and other alternative methods; Role of markers in plant transformation; Application of plant transformation for productivity and performance; Molecular farming, benefits and risks; Transgene stability and gene silencing; Strategies to avoid gene silencing and improve gene expression in transgenic plants.

11. Production of secondary metabolites by cell and organ cultures: Secondary product formation and storage in plants, Manipulation of biosynthetic capacity of secondary metabolites in cell cultures; factors determining the accumulation of secondary metabolites by plant cells and organ cultures; strategies for improvement of metabolite production; Screening and selection of variant cell lines with increased secondary product level. Biotransformation using plant cell cultures;Transformed cell and root cultures for production of secondary metabolites ; Metabolic engineering for production of secondary metabolites. Commercial applications.

Practical

Based on Theory paper

 

Bot O 41: Plant Genetics And Genomics   

Theory

Genetic analysis and an overview of Genomics:

Overview of genetic analysis; Epistasis analysis, genetic analysis of pathways; suppressor/enhancer screens;.forward and reverse genetics; Evolution of the concept of the Gene, genetic definition of the gene; Complex gene-protein relationships. Genomics an overview; correlated genetic, cytological, physical maps of chromosomes in plants; map position based cloning of genes; RNA and protein assays of genome function; evolution of genome in cereal grasses.

Regulation of gene expression:

Chromatin modification and genome expression. Various protein motifs involved in DNA protein interactions during eukaryotic transcription; chromatin remodeling, different modes of mRNA , tRNA splicing; general discussion on various snRNPs; capping ,polyadenylation and other processing events in eukaryotes, RNA editing; discussion on ribozyme;  RNA interference: mechanism and enzymology regulation of gene expression by miRNP pathway.; plant virus interactions and silencing  of RNA.

Breeding:Development of hybrid cultivars and molecular breeding

Evaluation of combining ability, prediction of double cross hybrid performance; production of hybrids through the use of cytoplasmic genetic male sterility systems, Classes of molecular markers, detecting DNA polymorphisms, genetics of mapping molecular loci, specialized mapping techniques. QTL, mapping QTL with molecular markers, application of markers to selection.

Tansposon tagging of plant genes:

McClintock and the Ac/Ds transposable elements of corn; Cloning maize Ac/Ds elements; molecular features of the maize Ac/Ds system; Transposon tagging; Cloning the Cf-9 gene of tomato by transposon tagging

Genes controlling flower development in plants: Mendelian Genetics to Molecular Sequence The steps of flower development- genes are implicated; Mendelian genes define the committment to flowering; Mendelian genes define floral organ identity; Cloning commitment to flowering and flower organ genes; MADS-box genes; Analyzing gene expression with in situ hybridization; Molecular expression of floral commitment genes; Molecular expression of floral organ genes..

Plant metabolic engineering: technological advances in gene discovery that have helped metabolic engineering, eg, in  lipid metabolism, carotenoid pathway, phenylpropanoid pathway; Manipulating structural genes for pathway enzymes to affect change in metabolism; Identification and study of transcriptional factors controlling pathways of metabolism.

Gene discovery in plant metabolism; Genetic characterization of molecular mechanism driving plant natural product biosynthesis; Combinatorial Biochemistry and Metabolomes;

Genomics and proteomics: Genomic tools; Sequencing technology, sequencing strategies, sequence databases (ESTs, BAC ends, genomic etc.), annotation of sequence data, Using TAIR (BAC contigs in areas of interest, obtaining their sequences), the annotation process, BLAST searches, DNA microarrays for global gene expression studies, Computer tools: BLAST searches, multiple alignments, phylogenetic trees.

Importance of proteomics in post genomics era; studying the proteome; interactive session: virtual proteomeics; analyzing a protein; application of proteomics.

Plant Genome Informatics. Plant Proteomics and Gene Expression Profiling.

Quantitative and evolutionary  genetics

Quantitative inheritance: traits controlled by many loci; location and significance of polygenic inheritance; QTL mapping with molecular markers; population statistics; heritability;partitioning of the variance; measurement of heritability; quantitative inheritance in plants.Quantifying heritability; testing for fit to Hardy- Weinberg equilibrium; extension of H-W equilibrium – multiple alleles;multiple loci;Non random mating-inbreeding and population analysis;

Evolutionary Genetics:

Evolutionary forces: processes that change allelic frequencies; models for population genetics;The ribonucleic acid and  ribonucleic protein worlds. The DNA world; the evolution of major phyletic lines;Evolution by Genome Duplication; Evolution by Gene Duplication: Evolution of Protein Domains; Evolution and introns; Evolution and Horizontal Transfer : Evolution and transposable elements.molecular clock.

Practical

Based on theory paper

Bot O 41: Plant Physiology, Biochemistry and Molecular Biology    

Theory

1. Organization of photosynthetic apparatus and light absorbing antenna system. Genes and polypeptide components of photosynthetic complexes. Rubisco and Rubisco genes.

2. ATP generation mechanisms in chloroplast and mitochondria.

3. Nitrate assimilation in plants. Structure function and regulation of nitrate assimilation enzymes.

4. Nif gene, nod gene – structure, function and regulation.

5. Physiology and molecular biology of stress – abiotic stress, biotic stress, heavy metals, reactive oxygen species and their protection mechanism.

6. Senescence and programmed cell death (PCD) – Senescence and its regulations, hormonal and environmental control of senescence. Molecular Biology of PCD; fruit ripening.

7. Pumps, carriers and Channels – Structure and function, energetics of active transport, isophore and ionophore; vacuoles – structure and function.

8. Uptake and metabolism of sulphur.

9. Floral induction and development – hormonal control; molecular genetics of floral development and floral organ differentiation.

10. Immunology: Antigen structure and function of different classes of immunoglobulins; primary and secondary immune response, humoral and cell mediated immunity, mechanism of the immune response. Effector mechanisms, applications of immunological techniques.

11. Post translational modification of protein, protein targeting, protein transport, chaperon and protein folding.

12. Signal Molecules, signal perception and transduction in plants.

13. Protein purification, characterization, methods for the determination of amino acids sequences in proteins.

14. Biosynthesis of carotenoids, amino acids, biological significance of carotenoids.

15. Chloroplast structure, function and genetic engineering.

16. Proteomics applied to functional genomics.

17. Metabolic engineering: An overview.

18. Plant genes: Structure, tagging, recombinant DNA technology, Vectors, transposon and mobile elements.

19. Phytohormones - biosynthesis, transport, mechanism of action, bioassay.

20.  Molecular characterization of transgenic events; Food and Biosafety, Risk assessment, IPR and transboundary movement of biotech seeds and materials, Economic impact of transgenic crops.

Practical

Based on theory paper

Bot O 41: Taxonomy And Biosystematics   

Theory

1. History of taxonomy in India.

2. Taxonomic Literature.

3. International Code of Botanical Nomenclature.

4. Phenotypic plasticity: definition, causes, methods of study, Role of vegetative morphology, phytochemistry, serology, SEM, TEM, and molecular biology.

5. Centers of origin and diversity of cultivated plants; Indian centers of wild plant genetic resources; Role of IBPGR and NBPGR.

6. Vegetation of India: classifications; description of Himalayan, peninsular and desert vegetation.

7. Flora of India: composition, bio-geographic evolution, endemism, disjunction.

8. Biodiversity: concept, kinds/levels, importance, methods of study, concern, protection from depletion.

9. Conservation: principles, causes of threats and categories of threatened plants
(IUCN), methods of assessment, strategies of conservation-­in situ and ex situ; concept and types of protected areas; role of botanic gardens and gene banks.

10. Palynology: scope; branches, structure, types and evolution of pollen grains; applications/importance.

11. GIS and applications in Botany

Practical

Based on theory paper

   

 

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M.Sc Syllabus>>

Course Details

Bot C 11: Phycology   

Theory

1. Evolution and Biodiversity of algae: Evolution of algae at Morphological and Ultrastructural level. Algal diversity of Different Habitat and their Conservation.                                    

2. Phylogenetic Relationship of Pro- and Eukaryotic Algae: What is  the place of Algae in the system,Phylogenetic theories in systematics; Phylogenetic methods- Molecular markers, Symbiosis theory- Primary, Secondary and Tertiary endosymbiosis ,Fan shaped phylogenetic tree, Concept of Picobiliphytes, Chlorarachinophyta, Apicomplexan and Streptophyta .                                 

3. Horizontal gene Transfer and Evolution of Eukaryotic algal Chloroplast: The prokaryotic Ancestry of Plastids and their subsequent evolution, Origin of peridinin and fucoxanthin containing plastids through tertiary endosymbiosis. Molecular phylogeny of algal chloroplasts and higher plant chloroplast .                                                  

4. Cyanobacteria: Genome and genetic Properties, Soil and rice field reclamation; Heterocyst- ultra structure, biochemistry and nif-gene regulation; Cyanobacterial bloom – ecological significance and its control.           

5. General overview of Algal Divisions: Glaucophyta- Principle Chacteristics and primitive features, Dinophyta : General Features, Redtides and Toxins ,Bioluminiscence, Heterotrophism.                         

6. Cytomorphology and Ultrastructure of Algal Cell: Cell surface with extracellular Mucilage, Flagellar Motor, Photoreceptor Apparatus and Nuclear division .       

7. Phytoplankton Ecology – Types of phytoplanktons; Primary Production; Species Diversity Index; Physical Environment (Light, Heat, Turbulance); Chemical environment (Nitrogen, Phosphorus, Silicon, Carbon);Nutrient Uptake Models (Michaelis- Menten  and Monod  , Droope Model) 

Practical

1. Algal Diversity Study : Identification of members of  Different Groups(maximum 5 genera from each group) - Cyanobacteria , Bacillariophyta,Euglenophyta and Chlorophyta.

2.Seaweed Identification: Enteromprpha, Ulva, Halimeda, Bryopsis, Caulerpa,Macrocystis Sargassam, Padina, Dictyota, Catenella,Kappaphycus, Gracilaria.

3. Phytoplankton sampling and Identification:

4. Estimation of Phosphate, nitrate, DO and BOD from water samples.

5. General principles of Culturing Algae in Laboratory and growth measurement.

6. Algal chromosome study from Chara .

Bot C 12: Microbiology    

Theory

Methods in Microbiology

Culture of microorganisms: Methods for isolating pure cultures, types of culture media, enrichment culture techniques, maintenance and preservation of pure cultures. Control of microorganisms: physical and chemical methods.

Microbial Diversity and Extremophilies

Phototrophic bacteria; Chemolithotrophic bacteria; Spirochetes; Rickettsias; Chlamydias; Mycoplasmas; Myxobacteria and Extremophiles (thermophilic, halophilic, acidophilic and alkalophilic bacteria). Unculturable bacteria.

Growth and Differentiation

Bacterial growth: definition, growth parameters, measurement of growth, synchronous growth, growth kinetics, factors affecting growth. Batch and continuous culture. Differentiation: endospore formation-cytological, physiological and genetic aspects, germination; life cycle of Caulobacter.

Microbial Metabolism

Outlines of biosynthesis of peptidoglycan, major amino acids and proteins. Regulatory mechanisms in bacteria - induction, repression, feed back inhibition, catabolite repression and attenuation; Manipulation of biochemical regulatory mechanisms for overproduction of metabolites. Nitrogen metabolism: ammonification, nitrification, denitrification and nitrogen fixation.

Bacterial Genetics

Organisaition and replication of genetic material in bacteria: chromosome and plasmid, Gene transfer mechanisms: conjugation, transformation and transduction. Recombination in bacteria

Medical Microbiology

Pathogenic properties of bacteria: toxins and extracellular enzymes; brief account of major human disease and their bacterial pathogens. Principles of chemotherapy, general account of chemotheraputic agents, sulfa drugs and antibiotics. 

Fundamentals of Immunology

History of immunology, innate and acquired immunity, humoral and cell mediated immunity, organ and cells involved in immunity, T cell and B cells; antigens: characteristics and types, adjuvants. Immunoglobulis: types, structure and properties.

Viruses and acellular microbes

Nomenclature and classification, distinctive properties of virus, morphology and ultrastrucutre, capsid and their arrangements, types of envelops and their composition, viral genome, their types and structure, virus related agents (viriods and prions). Viral replication: lytic and lysogenic.

Practical

1. Preparation of culture media (synthetic, semisynthetic and complex); methods of sterilization and aseptic methods.

2. Isolation of microorganisms from natural samples by dilution plating method and development of pure cultures by streak-plate and pour-plate methods.

3. Determination of morphological (simple and differential staining), physiological and biochemical characteristics of some selected isolated bacteria.

4. Turbidimetric estimation of bacterial growth, construction of bacterial growth curve; influence of physical and chemical factors on bacterial growth.

5. Enrichment and isolation of free-living nitrogen fixing bacteria from soil and isolation of Rhizobium from root nodule.

6. Determination of antibiotic sensitivity of some bacteria by disc diffusion method.

7. Recombination in bacteria using auxotrophic mutants/ antibiotic-, metal resistant organisms.

8. Isolation of bacteriophage and determination of phage-titer.

Visit to some industries of microbiological interest.

Bot C 13: Plant Anatomy and Developmental Biology    

Theory

General Aspects: Novel features of plant growth and development; concepts of plasticity in plant development; analyzing plant growth.

Seed development and dormancy- Embryo and endosperm development; cell lineages during late embryo development; Seed maturation and dormancy.

Shoot, Leaf and Root development- Organization of Shoot Apical Meristem (SAM); Control of cell division and cell-to-cell communication; Molecular analysis of SAM; Leaf development and differentiation; Organization of Root Apical Meristem (RAM); cytohistological logical zonation of SAM; Root hair and trichome development; cell fate and lineages.

Floral induction and development- Hormonal control; Inflorescence and floral determination; sex determination, development of pollen grains.

Seed germination and Seedling growth- Mobilization of food reserves during seed germination; tropisms; hormonal control of seed germination and seedling growth.

Differentiation of primary and secondary plant bodies- Ontogeny, differentiation of sclerides, fibres and their control of differentiation; vascular cambium; factors influencing cambial activity.

Physiological plant anatomy- Anatomical response to mineral deficiency; response of plants to wounding and invasion by microorganisms.

Plant anatomy in systematics and evolution: Xylem evolution; wood anatomy, nodal anatomy, floral vasculature, mineral inclusion in systematics and evolution.

Ecological anatomy: Leaf and wood anatomy in ecological perspective; anatomical response to pollutants.

Applied plant anatomy: Application of anatomical studies in climatology, genetics and plant breeding, biomedical research and forensic science.

Practical

1. Cell types- trichomes, sclerides, tracheids, vessel members and sieve tube elements.

2. Secretary structures and cell inclusions- necteries, glandular hairs, oil glands, salt glands, resin canals, laticifers, cystolith and crystals.

3. ; Nodal anatomy- unilacunar , trilacunar, multilacunar.

4. Secondary phloem from TS, TLS, RLS of the bark and anatomy of lenticels.

5. Wood anatomy from TS, TLS, RLS of woods.

6. Study of shoot apical organization in pteridophytes, gymnosperms and angiosperms.

7. Anatomy of sun and shade leaves, xeromorphic leaves, succulent leaves, halophyte leaves, hydromorphic leaves.

Study of different types of embryo.

Bot C 14: Cell Biology and BioMolecules 

Theory

Macro-molecules- Carbohydrates- mono, di- and polysaccharides; amino acids and peptides; lipids-classification, structure and function, their roles in biological membranes. Primary, Secondary, Tertiary and Quaternary structure of proteins; α-helix, β-sheet and collagen structure; Nucleic acid classification, physical and chemical properties.

Cell: Ultra-structural organization of cell; origin and evolution.

Biomembranes: Structural models; Composition and dynamics; Biogenesis and assembly, Dynamic aspects of cell wall during growth and differentiation; Transport of ions and macromolecules; Pumps, carriers and channels; Endo- and exocytosis.

Cell-Cell Interaction and signaling: Cellular adhesions; adhesion receptors; intercellular junctions in plants and animals; Intracellular signal transduction, signaling molecules and cell surface receptors.

Mitochondria: Mitochondrial DNA and male sterility; Biogenesis of mitochondria; Origin and evolution.

Chloroplast: Chloroplast DNA and its significance; Chloroplast biogenesis; Origin and evolution.

Nucleus: Macromolecular trafficking; Chromatin organization and packaging; Higher order structure of chromatin, chromosomes; specialised chromosomes, nucleosome positioning.

Ribosomes and Protein Synthesis: Organization and biogenesis of ribosomes; Ribosome structure and its significance in protein synthesis; translation prokaryotes and eukaryotes.

Endo-membrane System: Structure and function of microbodies, Golgi apparatus, lysosomes and endoplasmic reticulum; Membrane maturation and specialization.

Cytoskeleton: Nature of cytoskeleton, intermediate filaments, microtubules, cilia and centrioles, actin filaments, actin binding proteins.

Cell cycle: Introduction, phases, cell cycle control in yeast.

Deoxyribonucleic acid: Structure and properties of DNA, aberrant structures; Melting and reassociation of DNA, Cot curves, repetitive and unique sequences, Rot curves and gene expression.

DNA replication- Mode of replication of circular and linear DNA molecules, machinery of DNA replication in prokaryotes and eukaryotes; replication of nucleosomes.

Ribonucleic acid: Structure and properties of RNA, Types of RNA, RNA processing – Processing of tRNA, rRNA; mRNA processing- G capping, intron splicing, polyadenylation. mRNA localization.

Transcription in prokaryotes and eukaryotes: Promoters, enhancers, transcription factors; initiation, elongation and termination of transcription in prokaryotes and eukaryotes.

 RNA and DNA polymerases: Types, structure and function; polymerase chain reaction: theory, applications and modifications.

Bot C 14: Cell Biology and BioMolecules

Practical

Subcellular fractionation of plant tissues and isolation of cellular organelles.

Isolation of plant genomic DNA and estimation of purity by spectrophotometry and agarose gel electrophoresis. Protein Gel Electrophoresis: Native and SDS-PAGE

Bot C 15: Bryophytes, Pteridophytes and Gymnosperms    

Theory

Bryophyta

1. Broad outline of classification and evolutionary trends among Bryophytes.

2. Bryophyte ecology: substrate colonized by bryophytes, growth forms and ecotypes.

3. Bryophyte as site indicators-responses of bryophyte to environmental pollution, initial colonization and succession.

4.Bryophyte chemistry and taxonomic implications.

Pteridophyta

1. Introduction; Outline of systematic treatment of Pteridophytes; distribution of extant groups in time and space.

2. Early land plants; vegetative and reproductive organography, evolutionary significance of the members of Zosterophyllopsida, Trimerophytopsida, Isoetales and Sphenophyllales.

3. Stomatal types and their development; evolution of stele; ecology, karyology and affinity of Ophioglossaceae, Osmundaceae, Cyatheaceae, Polypodiaceae, Salviniaceae.

4. Types of spore, induction of spore germination, gametophyte types, biochemical aspects of gametophyte differentiation; antheridogens- chemical nature and mode of action; determination of femaleness in free sporing heterosporous plants; phytochemistry of pteridophytes.

5. Diversity of ferns in an ecological perspective; insect, microorganism –pteridophyte interactions, endangered and endemic pteridophytes and their conservation.

6. Cytogenetics and reproductive biology of ferns: polyploidy, apospory, apogamy, apomixis and hybridization; genetic variability in fern population- genetic load.

Gymnosperms

1. Concept of progymnosperms and its evolutionary significance

2. Introduction; Outline of systematic treatment; distribution of extant taxa in time and space.

3. Brief account of extinct Cycadales and Coniferales with emphasis on evolutionary aspects.

4. Vegetative morphology and reproductive biology (Pollination mechanism, embryogeny) of extant Cycadales, Coniferales, Ginkgoales, Taxales and Gnetales.

5.Karyology and phytochemistry of important taxa, biotechnology of important taxa; endangered and endemic taxa and their conservation.

Practical

Pteridophyta

1. Study of general habitat, external and internal morphology of vegetative and reproductive structures (spore types, soral anatomy etc.) of the following taxa: Psilotum, Lycopodium japonicum, L. serratum, L. cernuum, Selaginella monospora, Isoetes coromandelina, Equisetum diffusum, Botrychium, Angiopteris, Osmunda, Lygodium, Dicraopteris, Oleandra, Nephrolepis, Aplenium, Blechnum, Adiantum, Christella, Cyathea/ Alsophila/ Hemitelia, Microsorum, Phymatosorus, Ceratopteris and Salvinia.

2. External morphological features of the following taxa: Tmesipteris, L. squarrosum, L. selago, Ophioglossum, Schizaea, Marattia, Cibotium, Drynaria, Acrostichum, Selaginella bryopteris, Pteris vittata, Pyrrosia, Helminthostachys, Cheilanthes and Onychium.

Gymnosperms

1. Study of general habit, external and internal morphology with special reference to their male and female reproductive structures, pollen grains: Cycas, Ginkgo, Pinus, Cryptomeria, Thuja, Araucaria, Podocarpus, Cephalotaxus, Taxus, Ephedra, Gnetum.

2. Study of leaf and wood anatomy of the following taxa: Abies, Cryptomeria, Cupressus, Araucaria, Taxus and Gnetum.

3. Study of external morphology of the following taxa: Zamia, Encephalartos, Tsuga, Taxodium, Cunninghamia, Juniperus, Callitris, Agathis, Welwitschia, Sequoia and Metasequoia.

Bot C 21: Mycology and Plant Pathology    

Theory

Mycology

  1. Modern systematics, origin and phylogenetic relationship in fungi.
  2. Dormancy, germination and growth.
  3. Carbohydrate metabolism.
  4. Molecular mechanism of asexual and sexual reproduction.
  5. Cell cycle in Yeast.
  6. Fundamentals of fermentation technology: Industrial production of citric acid, alcohol and antibiotics.
  7. Fungal diseases in animal and man and disease management.
  8. Practical utilization of mycorrhiza in agriculture.
  9. Biotechnological approaches in mushroom production.
  10. Bioremediation.

Plant Pathology

  1. Epidemiology of plant disease.
  2. Mechanism of penetration and the process of disease development.
  3. Mechanism of disease resistance.
  4. Genetics of host pathogen interaction.
  5. General overview of plant diseases caused by different biotic and abiotic stress.
  6. Mechanism of disease control by chemical and biological means.
  7. Biotechnological approaches for diseases resistance.
  8. Plant disease diagnosis utilizing molecular tools.
  9. Biopesticides.

Practical

1. Sterilization and incubation- principles and uses of instruments.

2. Culture media and their preparation.

3. Preparation of stabs, slants and pouring of plates.

4. Isolation of fungi from water, soil and air by culture plate technique.

5. Isolation of pathogen from diseased tissues (leaf, stem and fruit).

6. Preparation of pure culture and sub culturing.

7. Preparation of monosporous-, polysporous- and tissue- culture.

8. Inoculation of tuber, stem and fruit.

9. Study of hyphal types and hyphal system.

10. Study of production of organic acid / alcohol / enzyme.

11. Study of fungal nuclei.

12. Biological control by dual culture technique.

13. Morphological and reproductive structure of some macro and micro fungi.

14. Symptomology and histopathology of some common diseases with diagnostic characteristics.

15. Preparation of spawn.

Cultivation of Pleurotus.

Bot C 22: Taxonomy of Angiosperms      

Theory

1. Introduction: Definitions  of terms: Systematics, taxonomy, classification, identification, nomenclature, aims and scope of taxonomy, history and phases of taxonomy. 

2. Data sources of Taxonomy: Concepts of character, relevance of embryology, palynology, phytochemistry, ultra structure and molecular taxonomy.

3. Tools of Taxonomy:  Functions of field, herbarium, botanic gardens, floras/literature, GIS (geographic information system).

4. Biosystematics: Definition, methods, categories, relationship with classical taxonomy.

5. Concepts of Taxonomical Hierarchy: Species/genus/family and other categories, specied concept.

6. Nomenclature: History of ICBN, aims and principles, rules (incl fossils and cultivated plants) and recommendations, proposed bio and phylocodes.

7. Concepts and Principles of Assessing Relationship: Phenetic numerical taxonomy- principles, philosophies, methods, merits and demerits.

8. Major systems of angiosperm classification:  Outlines, philosophies and principles, relative merits and demerits, recent trends in classification- molecular and cladistics ones.

9. Angiosperm diversity: Salient features, evolutionary trends and phylogeny in magnollidae, Hamamelidae, Caryophyllidae, Asteridae, Alismatidae and Liliidae (Sensu Cronquist ,1981), concepts of palaeoherbs, eu-dicots etc.

10. Biodiversity: Concepts, levels, hotspots, megadiversity centers, status (with special reference to India); Concerns- extinction and threats (IUCN categories), conservation-needs and methods.

Practical

1. Workout of plant specimens and description of vegetative and reproductive characters from representative locally available families.

2. Training in using  local floras and other literature and herbaria for identification of specimens described in the classes.

3. Study of various taxa of a genus, location of key characters and preparation of keys at specific level.

4. Field excursion for familiarization with and study of vegetation types(s) and flora(s) of areas outside the state and training in collection and preservation methodologies.

Bot C 23: Palaeobotany and Palynology    

Theory

1. Basic geological information related to palaeobotany:

Sedimentary rocks; Taphonomy; dating the pages of earth history; nomenclature and reconstruction of fossil plants; Stratigraphy; Basic concepts of continental drift and plate tectonics.

2. Origin and evolution of plant life forms:

The earliest environments; Brief idea of Origin of life; first prokaryotes; evolution of eukaryotes; geological records of algae (stromatolites, diatoms, dinoflagellates), fungi (endomycorrhiza and epiphyllous fungi), bryophytes and their ecological significance.

3. The colonization of land:

Environmental changes before terrestrialization, land adaptive features, evolution of land plants- different evidences, biogeographical distribution of early land plants (Silurian- early Carboniferous), earliest trees in the fossil record.

4. Emergence of seed plants:

Preovules, hydrasperman reproduction; evolution of closed carpel; evidences from the ovulate fructifications of Glossopteridales, Corystospermales, Caytoniales, Bennettitales, Pentoxylales.

5. Appearance of Angiosperms:

Evidence for the first angiosperms: leaves, flowers and pollen grains; place of origin and radiation; cladistic and molecular biological approaches on phylogeny of angiosperms.

6. Past plant life as source of energy:

Organic deposits of commercial value- coal, petroleum- their origin and depositional environment; coal and petroliferous basins of India.

7. Palynology:

Branches of palynology; Spore, pre-pollen and pollen morphology, wall chemistry, evolution of aperture types;

8. Applied palaeobotany and palynology:

i. Fundamentals of palaeofloristics, palaeogeography, palaeoecology and palaeoclimatology;  Application of neopalynology and palaeopalynology.

ii. Ancient DNA and other fossil biomolecules and their potential in evolutionary research; stable isotopes and tree ring in reconstruction of palaeoclimate.

Practical

1. Types of fossils, and modes of preservation.

2. Techniques of study of plant fossils:

Thin section method (demonstration and study of prepared slides), peel techniques (demonstration and study of prepared peel sections); maceration of peat, lignite, coal: (demonstration).

3. Systematic study of fossil plants through ages- Stromatolites, Precambrian biota, Cooksonia, Rhynia, Zosterophyllum, Lepidodendron, Sigillaria, Lepidophlois, Sphenophyllum, Calamites, Sharmastachys, members of Filicopsida- Coenopteridales members of Lyginopteridales, Medullosales, Glossopteridales: upright Glossopteris plant, Vertebraria root, Peltaspermales, Caytoniales, Bennettitales, Cycadales, Ginkgoales, Pentoxylales, Cordaitales, Coniferales, angiosperm fossils (to be studied in stratigraphic sequence).

4. Acetolysis method (demonstration); study of morphology of modern spores and pollen grains; pollen analysis of honey.

5. Study of macerated sample (to be supplied) of peat, lignite and coal. Quantitative and qualitative study of palynomorphs. Interpretation of data on stratigraphic age and environment of deposition.

Bot C 24: Genetics and Genomics    

Theory

Introduction and importance of Plant Genetics: Basic discoveries in  classical and molecular genetics; Extension of Mendelism:Allelism; gene function to produce polypeptides; interaction with environment; penetrance and expressibility; gene interaction-epistasis, pleiotropy, continuous variations Model organisms for genetic studies : Life cycle of Neurospora, Arabidopsis and Corn.

Linkage, crossing over and chromosome mapping-:Crossing over as the physical basis

of  recombination; chromosome mapping; three point test cross.Construction of genetic and physical map;molecular polymorphism..

Microbial Genetics -- Principles, basic procedures and terminology of microbial genetics; Gene mapping in bacteria and viruses; Genetic analysis in fungi, tetrad analysis to detect linkage in fungi

Genome organization in Eukaryotes – types of genomes, genetic features of eukaryotic nuclear genomes; development of gene concept, gene replication, organization of structural and functional elements of chromosome:-centromere, telomere  heterochromatin and  telomerase, sex chromosomes in plants; special chromosomes in different eukaryotes ;genome duplication and alterations and their role in evolution; Genes and gene number; Law of constancy and C-value paradox.

Gene expression -- Control of gene expression; Control of gene expression in bacteriophage lambda, T-phages; RNA phages; Regulation of prokaryotic gene expression (lac, his, trp operons and catabolite repression); Regulation of gene expression in eukaryotes, heterochromatin in gene silencing.

Genetic Integrity and Diversity – Physical and chemical basis of equational separation of chromosomes; Recombination, Mechanism of recombination; Evolutionary significance of  recombination; genetic control of recombination. Mutagenesis:  Molecular basis of spontaneous and  induced mutations; Transposon mutagenesis,  In vitro mutagenesis, Site-directed mutagenesis,  Environmental mutagenesis; Repair and retrieval systems; Mobile genetic elements: Structure and function of transposable elements and their role in evolution. Extranuclear genetics.

Marker Assisted Breeding: Quantitative and qualitative traits, marker assisted selection for genes of agronomic importance; QTL mapping and cloning.

Population Genetics-- Definition of populations, Gene frequency in a population, genetic equilibrium, Hardy-Weinberg principle, barriers to gene flow and mechanism of speciation, Using highly polymorphic DNA sequences in DNA typing, Inbreeding and genetic consequences of self-pollination in plants.

Genomes and Comparative Genomics – Concept; Genome sequencing; High throughput genome sequencing; Arabidopsis, rice and human genomes; Genome annotation; Synteny; Gene search and comparison tools.

Functional Genomics -- Approaches to analyze differential expression of genes - ESTs, SAGE, microarrays and their applications; Principles in reverse genetics: Gene tagging; Gene trapping; Gene silencing; Knockout mutants; Transcriptome; Ribotype concept.

Introduction to proteomics—The concept of proteome, definitions and conceptualization; Applications of proteomics: protein mining, protein-expression profiling, protein network mapping, protein modification and analysis.

Practical

Mitotic and meiotic chromosome analysis and phases of division

Analysis of polyploids and structural hybrids

Cytogenetic biomarkers of mutagenesis

Analysis of genetic polymorphisms using isozymes and molecular markers

PCR based site-directed mutagenesis to demonstrate gene silencing and knockout mutation

Bot S 21: Instrumentation (Supportive Course)      

Theory

Principles and application of colorimetry in biological systems:

Spectrometry: Basic principle, double beam UV/VIS and IR spectrometers, atomic absorption spectrometer, principle and instrumentation of fluorescence spectrophotometer, applications, MALDI-TOF, LC-MS-MS.

Chromatography, Electrophoresis, Centrifugation: Basic principles, types and application. 

Optical microscopes, optical microscopy; phase, ultraviolet and interference microscope- their basic principles; optical systems and ray diagrams- their applications in cell biology; fluorescence microscope; micro spectrophotometry of cells and tissues,

Electron microscopy: theory of magnetic and electrostatic lenses and their focal length; construction of electron microscope; limiting resolution and useful magnification; contrast formation; shadowing and staining technique; scanning and transmission electron microscopy; specimen preparation techniques; application of electron microscopy in cell and molecular biology.

Fluorescence activated cell sorter (FACS), Micro array, NMR, FRET.

Bot C 31: Plant Physiology and Biochemistry   

Theory

1. The atom and chemical bonds, reaction orders, pH , buffer, indicator , physico chemical properties of water.

2. Plant water relationship.

3. Ion uptake mechanism of individual cells and roots, interaction between ions, ion competition, antagonism and synergism.

4. Phloem translocation: symplastic and apoplastic flow of solvents, phloem loading and unloading.

5. Reactive oxygen species- formation and role in plants.

6. photosynthesis : complexes of electron transport in chloroplast , mechanism of electron transport generation of proton gradient and ATP generation, bioenergetics of light reaction, CO2  concentrating mechanism in plants, regulation of C3- C4 and CAM cycles

7. Respiration, metabolic regulation of glycolysis, acetyl CoA , kreb’s  cycle, gluconeogenesis and glyoxylate cycle.

8. Nitrogen metabolism: structure and function of nitrogenase, nif gene and nod gene organization.

9. Plasticidal pigments- chlorophyll structure and biosynthesis, hormonal regulation of growth and development.

10. Structure, biosynthesis, role and mechanism of action of auxin, gibberellins, cytokines, ethylene and abscisic acid.

11. Phytochrome; chemistry and photo-morphogenetic responses. Chryptochrome and blue light responses.

12. Dormancy and generation of seeds: orthodox and recalcitrant seeds, types of seed dormancy, breaking of dormancy, biochemical changes during dormancy, hormonal regulation of dormancy and germination.

13. Bio-energetics : an overview.

14. Energy conservation: ATP cycle, oxidative phosphorylation and photophosphorylation.

15. Lipid metabolism: oxidation of fatty acids and biosynthesis of fatty acids.

16. Protein: primary, secondary, tertiary and quaternary structure of proteins, biosynthesis purification and characterization, Ramachandran plot.

17. Mechanism of enzyme action, enzyme kinetics, enzyme inhibition.

18. Senescence- hormonal and environmental control of senescence, programme cell death in life cycle of plants.

19. Metabolomics: networking and application.

Practical

  1. Assay of enzymes: Catalase, Peroxidase, Amylase, Phosphatase, Protease, Ascorbic acid Oxidase and Urease.
  2. Complexometric method of analysis of calcium and magnesium
  3. Colorimetric estimation : IAA , reducing sugar, sugar test by copper reduction method, amino acids, DNA , RNA Protein
  4. Isolation of chloroplast and determination of Hill activity.
  5. Demonstration of instruments: Different Centrifuges, including Ultracentrifuge spectrophotometry, and spectroflurometry, Chromatography, colorimetry.
  6. Tetrazolium test of seed viability.
  7. Protein purification by salting and isoelectric precipitation
  8. Qualitative test of organic acids, sucrose, glucose, maltose, and arabinose
Bot C 32: Phytochemistry and Pharmacognosy    

Theory

  1. Introduction, history, scope.
  2. Classification and pharmacological action of plant drugs.
  3. Origin of secondary metabolites – a brief account of acetate malonate, acetate mevalonate and shikimic acid pathway.
  4. Carbohydrates –  starch,  cellulose derivatives, gums.
  5. Glycosides, general account, biosynthesis, glycosidal drugs
  6. Cyanogenic glycosides and glucosinolate compounds.
  7. Alkaloids, definition, properties, classification, alkaloidal drugs – Datura stramonium, Atropa belladona, opium, Cinchona, tea, ergot, Rauvolfia, Holarrhena, Catharanthus – alkaloidal constituents, uses, allied drugs.
  8. Phenolic compounds produced by plants, types, biological activity, drugs – Senna, Aloe, Hypericum, Capsicum.
  9. Betacyanins
  10. Steroidal compounds, different types, biological activity and pharmaceutical importance
  11. Volatile oils, composition, drugs – clove, Mentha, Eucalyptus, Foeniculum, Cinnamomum, citronella
  12. Resins, different types, uses
  13. Lipids
  14. Antibiotics and vitamins
  15. Hallucinogenic, allergenic and other toxic plants
  16. Pesticides (plant and microbial origin)
  17. Methods of extraction, isolation and characterisation of secondary metabolites.
  18. Chemical races.
  19. Production of important secondary metabolites by tissue cell and organ culture.
  20. Quality control of plant drugs.

Practical

1.Choice of solvent for extraction of  alkaloids, phenols.
2. Chemical tests for the detection of alkaloids, phenols, anthraquinones, cardenolides, anthocyanins, betacyanins, carotenoids.
3.Extraction and chromatographic detection of some common plant drugs.
4. Study of unorganized drugs – starches, gums, resins etc.
5.Techniques of studying stomatal index, vein islet number, palisade ratio.
6.Organoleptic  and microscopic evaluation of selected powdered and whole plant  drugs

Bot C 33: Plant Molecular Biology and Biotechnology    

Theory

1. Molecular improvement of crops (Molecular breeding, Mutagenesis, Transgenesis,  Metabolomics and Hybrid technology)

2. System Biology: Structure to Function in plants

3. Plant genes, promoters, intron splicing, vectors, codon optimization, gene mapping and cloning of plant genes

4. Recombinant DNA technology: Principles and methods of recombinant DNA technology- expression of cloned genes in E. coli, cloning in yeast: transformation in yeast, yeast artificial chromosome (YAC), retrovirus like vector (Ty) in yeast/shuttle vector.

5. Plant tissue culture: Organogenesis, Embryogenesis, in vitro fertilization, Apomixix and application of haploidy and DH populations in transgenic breeding and crop improvement; Molecular and Biochemical markers of in vitro regenerability of  plants

6. Genetic transformation: Vector construction, Protoplast system (electroporation and PEG), Agrobacterium system, en-planta transformation and Biolistic system; Screenable and selectable markers and their use; Chloroplast transformation; Marker-free methodologies; Gene stability, Inheritance and Differential expression of transgenes in plants

7. Molecular characterization, management and regulatory system of transgenic crops

9. Weed management: Implications of herbicide resistant crops

10. Pest management in crop plants, Biopesticides, Built-in plant protection (Bt technology) safety and environmental issues

11. Molecular breeding for abiotic stress tolerance (stress regulated genes expression, osmotic stress signalling, application in salt, cold and drought tolerance in plants)

12. Molecular breeding for Biotic stress tolerance: Fungal resistance, Bacterial resistance, Virus resistance, Transgenes pyramiding and Integrated Pest Management (IPM)

13. Biofortified crops (improvement of micronutrients in food crops; e.g. Iron and pro-vitaminA enriched rice, Vitamin E-maize, Protein improvement in rice and potato etc.)

14. Bio-and Food-safety, Intellectual Property Rights and Ethical Issues – Intellectual property rights (IPR); Patents, trade secrets, copyright, trademarks; Plant genetic resources; Plant varietals protection and registration; GATT & TRIPPS; Patenting of biological material; Bio-safety and containment practices and Food-safety of GMO crops

15. Plants as Biofactories – Concept of bio-pharming; Renewable Bio-fuel production in plants

16. Economic and social impact of Biotech-crops (ex-ante analysis and commercial release of GM-crops)

Practical

1. Plant tissue culture techniques (media preparation, culture of explants (embryo, shoot tips, nodal segment)

2. Anther culture of dicot and monocot plants

3. Plant Transformation system (demonstration)

4. Molecular Biology tools: PCR, Gel electrophoresis, Isolation of plasmid and genomic DNAs (demonstration)

Bot C 34: Microbial Biotechnology      

Theory

Fermentation Technology:

Introduction to microbial biotechnology, interaction between microbiology, chemical engineering and biochemistry.

Introduction to bioprocessing, classification of fermentation, isolation of industrially important microbial cultures, screening and strain improvement, media formulation, and process optimization.

Fermentation systems:

Design and operation of fermenters, basic concepts for selection of a reactor. Growth and non growth synthesis. Open and closed system of fermentation.

Downstream processing:

Introduction, removal of microbial cells and solid matter, foam separation, precipitation, filtration, centrifugation, cell disruptions, liquid-liquid extraction, chromatography, membrane processes. Drying and crystallization.

Fermentation products:

Microbial production of enzymes, polysaccharides, polyesters, ethanol, single cell protein, recombinant proteins, antibiotics and vaccines.

Fungal Biotechnology: Gene manipulation of fungi for industrial and agricultural applications, protoplast technology in fungi, enzyme based techniques for identification of microbes, cloning of gene for direct chemical analysis, proteomics of host pathogen interaction, genetic improvement and formulation of mycoherbicides.

Algal Biotechnology:

Scope of algal biotechnology, source of fine chemicals, therapeutics, hydrogen and methane  production, culture and cultivation of auto and heterotrophic algae. 

Practical

Study of the design and components of fermenter and its working principle.

Isolation and screening of microorganisms for production of enzymes and antibiotics.

Fermentative production of  protease/amylase/invertase/antibiotics .

Determination of BOD from sewage/fermentation broth sample

Transformation of E. coli for antibiotic/metal resistance gene, selection of transformed clones and plasmid isolation, restriction digestion, gel electrophoresis.

Isolation of fungal DNA

RAPD/PCR based analysis of typical fungi

Studies of protein profile during host pathogen interaction

Demonstration of precipitation reaction based immunodiffusion test

Bot S 31: Environmental Botany (Supportive Course)  

Theory

1. Concept and Dynamics of Ecosystems, Components,

2. Habitat and plant structure, Response of plants to pollutions ,Frost and Hardiness

3. Importance and Conservation of Biological Diversity,

4. Over exploitation of selected species,

5. Population ecology and Biological control, Sustainable development,

6. Seed Bank, Gene Bank and Germplasm Reserve

7. Environmental Laws : Public Interest Litigation, Public Nuisance, Environmental nuisance.

8.Environmental education.

Bot S 41: Computer Application and Bioinformatics  (Supportive Course)  

Theory

General ideas on computer: Why computer, Information explosion in life sciences< need for processing; human being as information processor, as information generator, Class of problems that can be solved by a digita computer, problems which may not solved by digital computers.

Components of a digital computer: Block diagram of digital computer-detail of input  units, output units, central processing unit pointing devices, fast input devices. Exotic input/output devices. Secondary storage devices. Types of digital computer, generation of digi9tal computer. Organization; low level and high-level language: binary number system Structured computer Organization: Various levels of digital computer, operating system as resource manager.

Windows-basic concepts and commands Unix as a multi user, multi tasking operating system Introduction to Linux Introduction to programming in C/MATLAB word processing, Spreadsheets, computer graphics and presentation software Algorithm and flow chart Sequential, conditional and looping problems

Artificial vis-a-vis Natural language Low and high level languages the basic concepts Binary number system Basic concepts of translation process (syntax, semantics etc) C as a programming language Alphabets and language elements Operators and separators strings Flow control, Relational operators Construction of compound statements Functions and structured programming- Top down approach, character processing Network and Internet Introduction and applications

Bioinformatics: Applications and Prospects, Genome and protein information resources, sequence analysis, multiple sequence alignment, homology and analogy, pattern recognition, analysis package.

Optional Courses : Special Papers

Bot O 41: Advanced Cell Biology     

Theory

1.Origin of life, nucleus and   organelles -: Mitochondria, Chloroplast, Peroxisome Nucleus : Protein trafficking into these organelles

2.Cellular communications; General principles, G proteins, protein kinases and protein phophatases; MAPKs; signal transduction in disease and immunity.

3.Eukaryotic cell cycle: Overview, principles of assembly, cohesion and segregation, Experimental systems: Microtubule: Structure, formation; associated proteins; centriole-origin and function; drug effects on microtubules: Biochemical and genetic approaches, Cell cycle control in yeast vs mammalian cells, Universality in cell cycle control.

4 Architecture of the eukaryotic nucleus: Chromosome model, nucleosome, Chromatin modification   and genome expression;  genome expression  and silencing; DNA  binding proteins and their attachment sites. Chromosome constitution; forces involved in cell division and recombination genome duplication, alteration and importance, mobile genetic elements.

5.Genomes, Transcriptomes and proteomes: Eukaryotic Nuclear Genome:  genetic features of eukaryotic nuclear genome;.genomes of prokaryotes – bacterial and viral genomes functioning  of Genomes- elucidation of transcriptome, proteome; and the metabolome.

6. Mutations: Types and molecular basis; genetic basis of complementation; chromosomal aberration; structural basis of DNA mutagenesis ; oxidative DNA damage and mutagenesis and in vitro mutagenesis.

7. DNA repair and diverse functions in the cellular DNA damage response:

Mechanism of DNA repair in prokaryotes, lower eukaryotes and higher plants. Identification and molecular characterization of repair enzymes.

9. Cancer Characteristics of tumor cells: Transformed cell lines, Oncogene vs tumor suppressor, immunocytochemistry, strategies for combating cancer.

10  Molecular Evolution: Evolution of  gene structure, Protein Domains, Ribozyme and RNA world; Micro RNA, Si RNA and importance of RNAi  in differentiation and evolution; evolution of major phyletic lines; antiquity of introns; transposable elements Evolution and Horizontal Transfer, molecular clock.

Practical

Based on Theory paper

Bot O 41:Advanced Phycology and Algal Biotechnology    

Theory

1.Latest development in algal classification and phylogeny

2.Cyanobacteria in Geothermal Habitat : Geographic distribution, Distribution determination by chemistry (lipid biomarker) and molecular analysis (16S rRNA).

3.Molecular systematics of Cyanobacteria & Prochlorophyta ( The ‘other’ cyanobacteria), Dinophyta and Streptophyta. Molecular approach to Cyanobacterial Evolution.

4  Molecular Biology of Cyanelles : Wall biosynthesis and structure, molecular genetics, Protein transport, Phylogenetic analysis.

5. Targeted genetic modifications of Cyanobacteria; Microalgae as platform for Recombinant proteins, Genetic behavior of Chlamydomonas .

6.Algal Light Harvesting Complex : Phycobiliproteins constituting core and rod elements of PBS, Linker polypepties, Chromatic adaptation, Structure and Regulation of light harvesting genes.

7.Enviornmental Stress Physiology:

    1. Ecotoxicology of Inorganic chemical stress on Algae : Adsorption and uptake, Response of algal communities to inorganic stressors, Mechanism of tolerance, Algal bioassay of Inorganic stressors.
    2. Photoacclimation.
    3. Photo-inhibition and Culture Productivity.
    4. Salinity Stress.

8.Role of algae in Wet Land Ecology: Algal assemblages in wetlands, Factors affecting Algal production, Conceptual Models of wetland Algae(Dry state, Open state, Sheltered state, Lake state).

9.Phytoplankton community structure and function: Spatial distribution of biomass, Seasonal cycle of plankton growth, Community analysis, Process in plankton succession.

10. Biogeochemical Role of Algae :Limiting nutrients, Algae in Biogeochemistry ( phosphorus, nitrogen, silicon and carbon/oxygen cycles)

11.Microalgae in Human Welfare: Production of fine chemicals (Polysaccharides, bio-active molecules, antioxidants, lipids and PUFA), Micro-algae in human nutrition, Algae in aquaculture.

12.Water pollution and Phycoremediation : Eutrophication and water poisoning, Algae in wastewater oxidation pond, Removal of heavy metals, Impacts of micro-algae in quality of drinking water

13.Basic culturing Techniques and mass cultivation: Biological principles, Types of reactors for phototrophic algae, Down stream processing of cell mass production, Heterotrophic production of Marine Algae for Aquaculture.

14.Industrial  production of microalgal cell mass and secondary products : Spirulina, Dunaliella, Haematococcus, Porphyridium.

Practical:

Based on theory paper

Bot O 41:Microbiology       

Theory

Microbial Systematics

Classical approaches to bacterial taxonomy, chemo-taxonomic characteristics (peptidoglycan, lipids, fatty acids and proteins) and genotypic characteristics (DNA-base composition, -fingerprinting, -relatedness; RNA-sequence analysis, DNA-RNA hybridization); bacterial phylogeny.

Medical

Normal microbiota of human body; host-parasite relationship in baterial pathogenecity: non-specific mechanisms of host defense, mechanism of bacterial virulence, genetics of bacterial virulence; chemotherapy: antibiotics (origin, classification, chemistry and mode of action); semisynthetic antibiotics; antibiotic resistance in bacteria, mechanism of antibiotic resistance.

Immunology

Theories of antibody production, antibody diversity; antigen-antibody reactions; immunoassay methods and their applications, major histocompatibility complex (structure and function), complement system and complement activation; monoclonal antibodies (production and applications).

Virology

Cultivation of viruses, methods for detection and assay, phage typing, major human viruses: HIV, Hepatitis B and C, their salient properties, diagnosis, prevention and treatment. Viral vaccines, interferon and antiviral drugs.

Microbial Ecology

Population interactions (microbe-microbe interactions, plant-microbe interactions, animal-microbe interactions), quorum sensing; microbial consortia; bacterial biofilms- formation and applications; biogeochemical cycling of carbon, nitrogen, phosphorous and sulphur.

Environmental Microbiology

Biological treatment of wastes and pollutants: solid wastes disposal, treatment of liquid wastes; Biodegradation of environmental pollulants: petroleum hydrocoarbons and xenobiotics. Bioremediation of heavy metals; Bioleaching and recovery of metals.

Microbes in Agriculture

Biological nitrogen fixation, nitrogenase and alternative nitrogenase system, nif genes; degradation of cellulose, hemicellulose and lignin, production of biofertilizers (mass production of Rhizobium  and Azotobacter); Microbial  control of insects.  Use of viruses in agriculture.

Food Microbiology

Food produced by microbes: Fermented foods (fermented dairy products, alcoholic beverages, vinegar, fermented vegetables), microbial cells as food. Food as substrate for microorganism, food borne disease; contamination and spoilage of food ( meat and meat products, fish, fruits and vegetables,  milk and milk products), methods of food preservation (physical and chemical).

Practical

Based on theory paper

Bot O 41: Molecular Mycology & Plant Pathology       

Theory

Molecular Mycology

  1. Nutrient sensing and uptake in fungi.
  2. Regulation of carbohydrate and nitrogen compound metabolism. 
  3. Genetic control of vegetative growth, asexual and sexual development
  4. Genome organization in fungi.
  5. Extra chromosomal inheritance in fungi.
  6. Principles and general methods of fungal genetic engineering.
  7. Retroposon and retrotransposon in fungi.
  8. Regulation of protein synthesis in fungi.
  9. Heat shock protein and chaperon.
  10. Signal transduction pathway. 
  11. Control of cell cycle in yeast; genetic manipulation of brewing yeast.
  12. Medical mycology: General account of cell mediated and humoral immunity.
  13. Mushroom in modern medicines: Mushroom nutraceutials.

Plant Pathology

  1. Molecular basis of plant-pathogen interaction- physiology and genetics of plant-pathogen interaction; genetics of pathogenicity; gene for gene hypothesis and its molecular explanation; resistance genes and avirulent genes.
  2. Molecular biology of disease resistance- Plant chemicals (phenolics) involved in resistance: Phytoalexins; pathogenesis related (PR) proteins; systemic acquired resistance (SAR).
  3. Host specific and non specific toxin and molecular basis of their roles in pathogenicity.
  4. Crown gall tumerogenesis- nature of tumor; the Ti plasmid and its use as a transformation vector.
  5. Development of disease resistant variety by mutation breeding and recombinant DNA technology.
  6. Molecular diagnoses of plant pathogens- DNA-DNA hybridization; PCR amplification and finger printing; protein profiling by gel electrophoresis (SDS-PAGE); immunological assays.
  7. RNAi in plant pathology.
  8. Biological control by biotechnological methods- use of hyper parasite, hypovirulence plasmids and recombinant DNA technology.
  9. Integrated disease management.     

Practical

Based on theory paper

Bot O 41: Palaeobotany and Palynology     

Theory

1. Brief introduction to physical geology related to Palaeobotany: types of rock; from sediments to sedimentary rock- types, rock units; tectonics and tectonic features, taphonomy.

2. Outline of stratigraphy, code of stratigraphic nomenclature, Biostratigraphy, Lithostratigraphy, Chronostratigraphy; code of nomenclature for fossils.

3. Application of palaeobotany in geological investigations, plate tectonics, palaeoenvironment and palaeogeography; Co-existence approach for quantitative reconstruction of palaeoclimate, determination of pCO2 concentration.

4.  Antiquity of life; Major events in the Precambrian- early life forms, Indian records, stromatolites and palaeoecology.

5. Fossil algae, fungi, bryophytes- distribution in time, evolutionary and palaeoenvironmental significance.

6. Evolutionary theories and the plant fossil record; Evolutionary trends of early land plants:  palaeobotanical, biochemical and molecular evidences.

7. Environmental changes during Permian, Permo-Carboniferous floral provinces. Early Paleozoic and Lower Carboniferous flora of India. Origin and relationships of cycads, bennettites, ginkgos and glossopterids.

8.  Distribution of Glossopteris flora in time and space, Glossopteris plants. Seedling of Glossopteris.

9. The modern concepts of Angiosperm phylogeny and evolution in the light of recent palaeobotanical, palynological discoveries in conjunctions with data of other modern science: cladistics, molecular biology, palaeophytochemistry.

10. Origin of mangrove vegetation with special reference to palaeocoastline reconstruction; evolution of plants using the C4 and CAM photosynthetic pathway: the first grasses.

11. Brief concept of Mass extinction: evidence in the geological record: plants versus animals; floral changes across the Cretaceous – Tertiary boundary.

12.  Biotic interactions: Plant animal interaction and their co evolution.

13. Palaeopalynology of peat, lignite and coal. Artificial classification of sporae-dispersae, role of palaeopalynology and microfossils in oil exploration, identification of isobotanical line, source rocks and palaeoshoreline; kerogen.

14. Coal petrology- Depositional facies, Diagenesis, Lithification, Microlithotypes, reflectance, fluorescence study (brief), Application of coal petrology (brief).

15. Microfossils- geological occurrence, structure and palaeoecology of Acritarchs, Dinoflagellates, Hystrichosphaerids, Radiolaria, Microforaminifera, Ostracods, Silicoflagellates, Diatoms, Botryococcus, Coccolithophores.

16. Palaeobotany-Palaeopalynology of Quaternary sediments in understanding global warming, climate changes, eustatic sea level change, coastal evolution with special reference to Bengal Basin.

17. Ancient DNA and biomolecular record: Extraction, characterization and potential in evolution and climate research; fossil evidence of physiological and developmental mechanism-polar auxin flow.

18. Archaeobotany: study of plant economy from Palaeolithic to Historic age; vegetation dynamics and palaeoclimatic reconstruction through phytolith analysis.

19. Mega – Mio floristic divisions of Indian Gondwana- Dicroidium and Ptilophyllum flora, organography of Glossopteris seedling.

20. Deccan- Intertrappean flora and palaeoecological consideration.

21. Siwalik flora.

22. Pleistocene flora- palaeobotany and palynology with special reference to Kashmir.

23. Different aspects of Neopalynology and their applications: Melittopalynology, Aeropalynology, Forensic palynology, Copropalynology, Entomopalynology; Natural traps of pollen grains and their importance.

Practical

Based on theory paper

Bot O 41: Phytochemistry  And  Pharmacognosy   

Theory

1.Origin of  secondary metabolites – detailed account of acetate malonate, acetate
 mevalonate and shikimic acid pathway.

2.Turnover and degradation of secondary metabolites – physiological and developmental aspects - compartmentation  of secondary metabolism.

3.Phytochemistry, biosynthesis and sources of drugs:

(i) Phenols and phenolic glycosides : structural types, biosynthesis, importance (simple phenolic compounds,  tannins, anthraquinones, coumarins and furanocoumarins, flavones and related flavonoid glycosides, anthocyanins, stilbenes, lignins and lignans).

(ii)Steroids, sterols, saponins, withanolides, ecdysones, cucurbitacins: Biosynthesis, commercial importance.

(iii)Miscellaneous isoprenoids – iridoids, sesquiterpenes, diterpenoids, triterpenoids, tetraterpenoids, polyterpenoids.

(iv) Alkaloids –  different groups, biosynthesis, bioactivity.

(v)Volatile oils, aromatherapy

(vi)Resins and balsams

(vii)Lipids

4. Enzymes, proteins and amino acids as drugs

5.Vaccine, toxins and toxoids, antitoxins, immune globulins, antiserums

6.Vitamins

7. Antibiotics – chemical nature, mode of action.

8.Pharmacological action of plant drugs – tumour inhibitors, hypoglycaemic,  antihepatotoxic, antiprotozoal, antiviral, immunomodulators, PAF  antagonists, antioxidants, phytoestrogens and others.

9.General methods of  phytochemical analysis – extraction, isolation (different chromatographic techniques, principles), characterisation, immunoassay, monoclonal antibody.

10. Application of genetics and plant breeding in pharmacognosy

11. Plant metabolomics: a brief idea

12. Tissue culture and biotechnology for production of  secondary metabolites - microbiological conversion – metabolic engineering

13.Ethnopharmacology

Practical

Based on theory paper

Bot O 41: Plant Cell and Tissue Culture   

Theory

1. Basic concept of plant in vitro technology: History of in vitro plant biology Organization of a tissue culture laboratory, Equipment and supplies, Basic techniques, Medium components, Medium preparation, Differentiation/ Regeneration

2. Organogenesis: Organogenesis process, Developmental sequences, Mechanism of action of plant hormones, multiple hormonal control on organogenesis, Cell cycle control of organogenesis, Mechanisms of morphogenesis, Genetic control of morphogenesis, Genetic and physiological regulation of plant organ size and shape.

3. Embyogennesis: Major processes in Embryonic development; Formation of the Apical-Basal Axis, Establishing the Radial Axis, Mechanisms that establish cell fate in the embryo, Role of phytohormone in embryogenesis; Somatic Embryogenesis-Structural and developmental ontogeny, Physiological and Biochemical aspect of somatic embryogenesis, Molecular markers and genes for somatic embryogenesis.Gene expression and signal transduction.Regulation;  Application; synthetic seeds.

4. Haploid and Triploid culture; Androgenesis, Gynogenesis and Endosperm culture; Techniques and its applications in genetics and crop improvement.

5. Protoplast culture and somatic hybridization: : Isolation, Purification and Culture of Protoplasts; Protoplast fusion and Somatic Hybridization, Principle and scope; Nuclear and Cytoplasmic hybrids; Selection of hybrids; Regeneration; Possibilities; Applications; Limitations.

6. Micropropagation: methods and stages of clonal propagation; Production of virus-free plants, virus free assessment methods, genetic assessment -by RAPD and ISSR markers, Field evaluation, certification for quality plants, Packaging technology & Transport methods.

7. Somatic cell genetics; Somaclonal variation; Genotypic and Phenotypic variations in cell cultures and in regenerated plants, Origin; Types; chromosomal and genetic basis of somaclonal variation; Applications in crop improvement.

8. Germplasm preservation: Concept of Biodiversity and role of In situ and ex situ conservations of germplasms; Cryopreservation; Principle, Techniques and Applications.

9. Bioreactors: concept, types and use in plant tissue culture

10. Genetic manipulations in  plants; Strategies and Methods of genetic manipulations in plants ;  Agrobacterium-mediated gene transfer; Genetic elements and engineering of Ti and Ri plasmids;; Direct gene transfer – electroporation, particle bombardment and other alternative methods; Role of markers in plant transformation; Application of plant transformation for productivity and performance; Molecular farming, benefits and risks; Transgene stability and gene silencing; Strategies to avoid gene silencing and improve gene expression in transgenic plants.

11. Production of secondary metabolites by cell and organ cultures: Secondary product formation and storage in plants, Manipulation of biosynthetic capacity of secondary metabolites in cell cultures; factors determining the accumulation of secondary metabolites by plant cells and organ cultures; strategies for improvement of metabolite production; Screening and selection of variant cell lines with increased secondary product level. Biotransformation using plant cell cultures;Transformed cell and root cultures for production of secondary metabolites ; Metabolic engineering for production of secondary metabolites. Commercial applications.

Practical

Based on Theory paper

 

Bot O 41: Plant Genetics And Genomics   

Theory

Genetic analysis and an overview of Genomics:

Overview of genetic analysis; Epistasis analysis, genetic analysis of pathways; suppressor/enhancer screens;.forward and reverse genetics; Evolution of the concept of the Gene, genetic definition of the gene; Complex gene-protein relationships. Genomics an overview; correlated genetic, cytological, physical maps of chromosomes in plants; map position based cloning of genes; RNA and protein assays of genome function; evolution of genome in cereal grasses.

Regulation of gene expression:

Chromatin modification and genome expression. Various protein motifs involved in DNA protein interactions during eukaryotic transcription; chromatin remodeling, different modes of mRNA , tRNA splicing; general discussion on various snRNPs; capping ,polyadenylation and other processing events in eukaryotes, RNA editing; discussion on ribozyme;  RNA interference: mechanism and enzymology regulation of gene expression by miRNP pathway.; plant virus interactions and silencing  of RNA.

Breeding:Development of hybrid cultivars and molecular breeding

Evaluation of combining ability, prediction of double cross hybrid performance; production of hybrids through the use of cytoplasmic genetic male sterility systems, Classes of molecular markers, detecting DNA polymorphisms, genetics of mapping molecular loci, specialized mapping techniques. QTL, mapping QTL with molecular markers, application of markers to selection.

Tansposon tagging of plant genes:

McClintock and the Ac/Ds transposable elements of corn; Cloning maize Ac/Ds elements; molecular features of the maize Ac/Ds system; Transposon tagging; Cloning the Cf-9 gene of tomato by transposon tagging

Genes controlling flower development in plants: Mendelian Genetics to Molecular Sequence The steps of flower development- genes are implicated; Mendelian genes define the committment to flowering; Mendelian genes define floral organ identity; Cloning commitment to flowering and flower organ genes; MADS-box genes; Analyzing gene expression with in situ hybridization; Molecular expression of floral commitment genes; Molecular expression of floral organ genes..

Plant metabolic engineering: technological advances in gene discovery that have helped metabolic engineering, eg, in  lipid metabolism, carotenoid pathway, phenylpropanoid pathway; Manipulating structural genes for pathway enzymes to affect change in metabolism; Identification and study of transcriptional factors controlling pathways of metabolism.

Gene discovery in plant metabolism; Genetic characterization of molecular mechanism driving plant natural product biosynthesis; Combinatorial Biochemistry and Metabolomes;

Genomics and proteomics: Genomic tools; Sequencing technology, sequencing strategies, sequence databases (ESTs, BAC ends, genomic etc.), annotation of sequence data, Using TAIR (BAC contigs in areas of interest, obtaining their sequences), the annotation process, BLAST searches, DNA microarrays for global gene expression studies, Computer tools: BLAST searches, multiple alignments, phylogenetic trees.

Importance of proteomics in post genomics era; studying the proteome; interactive session: virtual proteomeics; analyzing a protein; application of proteomics.

Plant Genome Informatics. Plant Proteomics and Gene Expression Profiling.

Quantitative and evolutionary  genetics

Quantitative inheritance: traits controlled by many loci; location and significance of polygenic inheritance; QTL mapping with molecular markers; population statistics; heritability;partitioning of the variance; measurement of heritability; quantitative inheritance in plants.Quantifying heritability; testing for fit to Hardy- Weinberg equilibrium; extension of H-W equilibrium – multiple alleles;multiple loci;Non random mating-inbreeding and population analysis;

Evolutionary Genetics:

Evolutionary forces: processes that change allelic frequencies; models for population genetics;The ribonucleic acid and  ribonucleic protein worlds. The DNA world; the evolution of major phyletic lines;Evolution by Genome Duplication; Evolution by Gene Duplication: Evolution of Protein Domains; Evolution and introns; Evolution and Horizontal Transfer : Evolution and transposable elements.molecular clock.

Practical

Based on theory paper

Bot O 41: Plant Physiology, Biochemistry and Molecular Biology    

Theory

1. Organization of photosynthetic apparatus and light absorbing antenna system. Genes and polypeptide components of photosynthetic complexes. Rubisco and Rubisco genes.

2. ATP generation mechanisms in chloroplast and mitochondria.

3. Nitrate assimilation in plants. Structure function and regulation of nitrate assimilation enzymes.

4. Nif gene, nod gene – structure, function and regulation.

5. Physiology and molecular biology of stress – abiotic stress, biotic stress, heavy metals, reactive oxygen species and their protection mechanism.

6. Senescence and programmed cell death (PCD) – Senescence and its regulations, hormonal and environmental control of senescence. Molecular Biology of PCD; fruit ripening.

7. Pumps, carriers and Channels – Structure and function, energetics of active transport, isophore and ionophore; vacuoles – structure and function.

8. Uptake and metabolism of sulphur.

9. Floral induction and development – hormonal control; molecular genetics of floral development and floral organ differentiation.

10. Immunology: Antigen structure and function of different classes of immunoglobulins; primary and secondary immune response, humoral and cell mediated immunity, mechanism of the immune response. Effector mechanisms, applications of immunological techniques.

11. Post translational modification of protein, protein targeting, protein transport, chaperon and protein folding.

12. Signal Molecules, signal perception and transduction in plants.

13. Protein purification, characterization, methods for the determination of amino acids sequences in proteins.

14. Biosynthesis of carotenoids, amino acids, biological significance of carotenoids.

15. Chloroplast structure, function and genetic engineering.

16. Proteomics applied to functional genomics.

17. Metabolic engineering: An overview.

18. Plant genes: Structure, tagging, recombinant DNA technology, Vectors, transposon and mobile elements.

19. Phytohormones - biosynthesis, transport, mechanism of action, bioassay.

20.  Molecular characterization of transgenic events; Food and Biosafety, Risk assessment, IPR and transboundary movement of biotech seeds and materials, Economic impact of transgenic crops.

Practical

Based on theory paper

Bot O 41: Taxonomy And Biosystematics   

Theory

1. History of taxonomy in India.

2. Taxonomic Literature.

3. International Code of Botanical Nomenclature.

4. Phenotypic plasticity: definition, causes, methods of study, Role of vegetative morphology, phytochemistry, serology, SEM, TEM, and molecular biology.

5. Centers of origin and diversity of cultivated plants; Indian centers of wild plant genetic resources; Role of IBPGR and NBPGR.

6. Vegetation of India: classifications; description of Himalayan, peninsular and desert vegetation.

7. Flora of India: composition, bio-geographic evolution, endemism, disjunction.

8. Biodiversity: concept, kinds/levels, importance, methods of study, concern, protection from depletion.

9. Conservation: principles, causes of threats and categories of threatened plants
(IUCN), methods of assessment, strategies of conservation-­in situ and ex situ; concept and types of protected areas; role of botanic gardens and gene banks.

10. Palynology: scope; branches, structure, types and evolution of pollen grains; applications/importance.

11. GIS and applications in Botany

Practical

Based on theory paper