M Sc. Basic Science

Agricultural Chemicals

1. Introduction to Agrochemicals
2. Chemical Laboratory Techniques
3. Basic Chemistry
4. Natural Product Chemistry
5. Agrochemical Regulation, Quality Control and Management
6. Agrochemicals for Insect Mite and Termite Management
7. Agrochemicals for Disease Management
8. Agrochemicals for Weed and Crop Management
9. Chromatographic and Spectroscopic Techniques
10. Pesticide Residue Chemistry

Biochemistry

1. Basic Biochemistry
2. Intermediary Metabolism
3. Enzymology
4. Molecular Biology
5. Techniques In Biochemistry
6. Immuno Chemistry
7. Plant Biochemistry
8. Animal Biochemistry
9. Nutritional Biochemistry
10. Nitrogen And Sulphur Metabolism
11. Biochemistry On Xenobiotics

Microbiology

1. Techniques in microbiology
2. Principles of microbiology
3. Microbial physiology and metabolism
4. Microbial genetics
5. Soil microbiology
6. Microbial biotechnology
7. Food microbiology
8. Bacteriophages
9. Environmental microbiology
10. Industrial microbiology
11. Biofertilizer technology
12. Cyanobacterial and algal biotechnology

Plant Physiology

1. Principles of Plant Physiology-I: Plant Water Relations and Mineral Nutrition
2. Principles of Plant Physiology-II: Metabolic Processes and Growth Regulation
3. Plant Developmental Biology: Physiological and Molecular Basis
4. Physiological and Molecular Responses of Plants to Abiotic Stresses
5. Hormonal Regulation of Plant Growth and Development
6. Physiological and Molecular Mechanisms of Mineral Nutrient Acquisition and their Functions
7. Photosynthetic Processes, Crop Growth and Productivity and Concepts of Crop Modeling
8. Physiology of Field Crops
9. Physiology of Horticulture Crops
10. Seed Physiology
11. Phenotyping Physiological Processes
12. Crop Growth Regulation and Management

Agricultural Chemicals

1. Introduction to Agrochemicals

Content: Agrochemicals and Trade Statistics. Agrochemicals and Pest Management Definition of pests and pesticides, Synthetic and natural plant protection chemicals – history and classification, House-hold pesticides, Non-pesticidal agrochemicals like nitrification inhibitors, chemical hybridizing agents, hydrogels, soil conditioners, and plant growth stimulants, Pesticide toxicity (LD50, LD90, LC50, EC50, I50),Pesticide antidotes. Safety precautions in pesticide application, Introduction to integrated pest management (IPM). Pesticide Production, Consumption and Trade Statistics Pesticide production and consumption in India and other countries, Pesticide export and import Pesticide Groups, Botanical and Biopesticides History of botanical and biopesticide use, Structure, properties, and use of conventional botanical insecticides - nicotine, pyrethrins, rotenones and neem limonoids. Plant allelochemicals, Biopesticides and bioagents. Synthetic Pesticides History of synthetic pesticide use, Structure, properties, and uses of insecticidesorganochlorines, organophosphates, carbamates, synthetic pyrethroids, fungicides (inorganic and organic), nematicides, rodenticides, herbicides, and plant growth regulators (PGR). Pesticide Formulation, Solid and Liquid Formulations Formulation of pesticides- objective and classification, Conventional solid and liquid formulations such as EC, WP, Dust, Granule etc. Physico-chemical properties of formulations. Role of Adjuvants in Pesticide Formulations Pesticide adjuvants like synergists, stabilizers and surfactants, Pesticide carriers and diluents General methods of preparation of solid and liquid formulations Pesticide Residues, Their Adverse Effects And Safe Disposal Pesticide Residues in Food and the Environment Pesticide residue - definition and significance, Pesticide residues in food commodities and in water, air and in soil environment. Adverse Effect of Pesticides on Non-target Organisms Adverse effect of pesticides on human health, soil health, and on non-target organisms Safe Disposal of Pesticides Various techniques for disposal of unused, obsolete, and expired pesticides and their solid and liquid formulations, Disposal of pesticide containers.

Question Bank:

1. Chemical Laboratory Techniques

Content: Laboratory Hygiene and Safe Laboratory Practices. Safe Storage and Handling of Chemicals Laboratory hygiene and safety, Handling and storage of hazardous (flammable, volatile, and corrosive) chemicals, Accurate weighing of chemicals, Maintenance of lab-wares, Maintenance of lab notebooks and records of laboratory chemicals/solvents. Safety Practices in Chemical Laboratory Precautions while carrying out lab experiments, Use of safety gadgets, Safe disposal of reaction wastes and used solvents, Laboratory accidents and their management. Distillation, Extraction and Separation Techniques. Theory and Practice of Distillation and Drying of Solvents Solvent distillation, Fractional distillation, Steam distillation, Hydro-distillation, Drying of solvents, Theory and Practice of Extraction and Other Techniques Different extraction techniques, Cold extraction, Soxhlet extraction, liquid-liquid partitioning, Crystallization and sublimation, Determination of melting point, boiling point, and density of organic compounds. Theory and Practice of Chromatographic Techniques Chromatography - principle and practice, Partition and adsorption chromatography (TLC, Preparative TLC, HPTLC, Paper chromatography, Column chromatography), Chromatography solvents and chromogenic reagents.

Practicals: Simple distillation, vacuum distillation, and fractional distillation of solvents/ volatile materials (e.g. essential oils); Determination of melting point, boiling point, density, etc.; Purification and drying of organic solvents; Crystallization and sublimation techniques.; Solvent extraction techniques (cold extraction, Soxhlet extraction, percolation, accelerated solvent extraction), and refluxing a reaction; Chromatographic separation of organic compounds by paper chromatography and thin layer chromatography (TLC); Separation of compounds by preparative TLC, HP-TLC and column chromatography.

Question Bank:

1. Basic Chemistry

Theory: Basics of Inorganic Chemistry. Properties of Atoms, Molecules and Basic Elements Modern periodic law and periodic table, Properties of atoms, molecules and basic elements like C, H, O, S, and N, Atmospheric pollutants (oxides of C, N, and S), Atomic and ionic radii, Oxidation states and chemical reactivity, Acid-base chemistry, Introduction to organometallic and coordinated compounds. Chemical Bonding and Electronic effects Nature of chemical bonding, hydrogen bonding, Van der Waals forces, Inductive effect, electromeric effect, Resonance effect, Hyperconjugation, Electronegativity and Dipole moment. Basics of Physical Chemistry, Chemical Kinetics Kinetic theory of gases, Collision theory, Maxwell - Boltzmann distribution law, Order and molecularity of reactions, First order and second order reactions, Effect of concentration, temperature, pressure and catalyst on rate of reaction, Arrhenius equation, Enzyme kinetics, Catalysis. Chemical Thermodynamics First law of thermodynamics, concept of work, internal energy and enthalpy, Second law of thermodynamics, entropy and free energy, Third law of thermodynamics. Surface Chemistry Introduction to surface chemistry, Adsorption, physi-sorption, and chemisorption, Factors affecting adsorption of gases on solids- Freundlich and Langmuir adsorption isotherm. Solution and Electrochemistry Colligative properties of solutions, law of mass action, Ionic equilibria in solutions, Phase rule and its application to one- and two- component systems, Hydrolysis, Solubility product, pH and buffer solutions, True solutions, colloid and suspensions, Electrochemistry, Redox reactions, Potentiometric analyses, Conductance in electrolytic solutions, Laws of electrolysis, Nernst equation, Metal corrosion. Basics of Organic Chemistry Reactive Intermediates in Chemical Reactions Carbenes, carbanions, carbonium ion, free radicals and their role in organic reactions. Introduction to Stereochemistry Chirality and optical isomerism, Geometric isomerism, Designation of configuration (D-L and R-S system), Conformations of acyclic and cyclic systems. Chemistry of Aliphatic and Aromatic Compounds Preparation, properties and uses of some important aliphatic, alicyclic and aromatic compounds (halogenated, nitro, amino-compounds, diazonium salts, aromatic sulphonic acids, phenols, quinones and aromatic acids, naphthalene and naphthaquinone). Chemistry of Heterocyclic Compounds Preparation, properties and uses of some important heterocyclic compounds (furan, thiophene, pyrrole, pyrazole, imidazole, oxazole, thiazole, pyridine, piperidine, quinnoline, isoquinnoline etc.)

Practicals: Micro-weighing of compounds and preparation of different concentration of solutions Preparation of different pH solutions and buffer solutions; Detection of elements (C, H, O, N, S Halogens) in organic compounds; Detection of functional groups; Experiments to demonstrate adsorption of a chemical on solid substrate; Separation and identification of organic compounds in binary mixtures.; Rate kinetics and Colligative properties.

Question Bank:

1. Natural Product Chemistr

Content: Natural Products: Chemistry and Uses. Chemistry of Fats, Lipids, Terpenoids, and Carotenoid Introduction to natural products, Structure, chemistry, properties and function of fats, lipids, terpenoids, and carotenoid group of natural products. Chemistry of Alkaloids, Flavonoids, Steroids, and Triterpenoids Structure, chemistry, properties and function alkaloids (berberine, morphine, caffeine, atropine), flavonoids (Luteolin, quercetin, catechin, naringin, anthocyanins, theaflavins) and phenolic acids (benzoic acid and cinnamic acid derivatives), steroids (cholesterol, cortisone, testosterone, progesterone), and saponin (steroidal, triterpenic and steroid-alkaloidal) group of natural products. Chemistry of Carbohydrates, Amino Acids, Proteins, and Nucleic Acids Structure, chemistry, properties and function of carbohydrates, amino acids, proteins, and nucleic acids. Introduction to Metabolomics Definition, Plant and microbial metabolomics, Metabolome analysis (profiling of secondary metabolites) by GC-MS, LC-MS and NMR spectrometery, Application of metabolomics in different fields. Natural Antioxidants and Food Colorants From Food and Nonfood Sources. Natural Antioxidants and Food Colorants from Food Crops Natural oxidants and their mode of action, Different types of natural oxidants from vegetable, fruit and cereal crops (Examples: carotene, lycopene, betanaine, capsanthins, capsicinoids, anthocyanins, curcuminoids etc.). Nutraceuticals and Phytoceuticals from Non-Food Sources Nutraceuticals and phytoceuticals from microalgae (e.g. phycocyanins), seabuckthorn (phenolics and flavonoids), medicinal plants (boswellic acid, artemisinin, andrographinolides, withanolides, taxol, forskolinetc.) and marine products. Natural Polymers and Enzymes. Natural Polymers and their Application Different types of natural polymers, Chemistry of natural polymers (Starch, cellulose, Agar, inulin, chitosan, alginate, dextran, guar gum, gum Arabic, gum tragacanthin, xanthan gum, pectin, psyllium etc.). Application of polymers in agrochemical, food and other industries. Enzymes and their Industrial Application Major classes of enzymes, Enzymes in food industry, industrial enzymes and their application in pharma, leather, textile, detergent and other industries.

Practicals: Extraction of essential oil from mint leaves, lemon and orange peel etc.;  Extraction and purification of bioactive natural products like lycopene, from tomato or watermelon; Extraction and purification of curcuminoids from turmeric rhizome; Extraction and purification of anthocyanins from black carrot, purple cabbage, grapes or jamun etc; Extraction and purification of bioactive natural products namely capsanthin and capsaicinoids from chili/paprika. Identification and characterization of the phytochemicals by GC-MS/LC-MS.

1. Agrochemical Regulation, Quality Control and Management

Content: Pesticide Registration in India, The Insecticides Act (1968) and Rules (1971) Provisions of the Insecticides Act 1968 and Insecticides Rules 1971, Schedule of the Insecticide Act. Directorate of Plant Protection, Quarantine & Storage (DPPQ&S), Central Insecticide Board and Registration Committee (CIB&RC),Guidelines for production and use of pesticides. Food Safety and Standard Act (2006) & Rules (2011) Provisions of the Food Safety and Standard Act (2006) & rules (2011), Acts relating to protection of air, water and the general environment. Pesticide Registration in India Requirement of data (Chemistry, Bioefficacy, Residue, Toxicology, Packaging etc) for pesticide registration in the country, Guidelines for pesticide export and import, Current status of registered, restricted, and banned pesticides in India. National/ International Guidelines for Safe Use of Pesticides. Good Agricultural Practices (GAP) and Good Laboratory Practices (GLP) Definition of GAP and GLP, National and international guidelines for GAP, and GLP. International Guidelines for Safe Use of Pesticides WHO/FAO Joint Meeting on Pesticide Residues (JMPR), Codex Alimentarius Commission (CAC) EU and EPA guidelines for food safety, Sanitary and phytosanitary (SPS) measures and food safety. Quality Control, Quality Assurance and Accreditation. Quality Assurance and Quality Control in Pesticide Analysis Spurious/ fake pesticides and pesticide formulations, Quality Assurance (QA) and Quality Control (QC) Quality control procedures for pesticide residue analysis, Problems related to pesticide residue analysis in a regulatory laboratory. Accreditation of Laboratories Accreditation and its importance, General criteria for accreditation of chemical and food laboratories, Introduction to ISO/IEC 17025. NABL and GLP compliance of laboratories, Role of International Laboratory Accreditation Cooperation (ILAC) and Asia Pacific Laboratory Accreditation Cooperation (APLAC) in promoting accreditation recognition arrangements (MRAs) and practices.

Question Bank:

1. Agrochemicals for Insect, Mite and Termite Management

Content: Organochlorine, Carbamate and Organophosphorus Insecticides. Chemistry and Use Of Organochlorine Insecticides Introduction and classification of synthetic insecticides, Chemistry, use and mode of action of some important conventional organochlorine and cyclodiene insecticides, Present status of organochlorine pesticides. Chemistry and Use of Carbamate Insecticides Chemistry, use, and mode of action of carbamate insecticides, Present status of carbamate pesticides. Chemistry and Use of Organophosphorus Insecticides Chemistry, use and mode of action of some important organophosphorus insecticides. Important reactions namely Michaelis- Arbuzov reaction, Perkow reaction, Thionothiolo rearrangement. Present status of OP pesticides. Synthetic Pyrethroid and Neonicotenoid Insecticides. Chemistry and Use of Synthetic Pyrethroid Insecticides History and evolution of synthetic pyrethroid insecticides, Synthesis, properties, structure activity relationships, and mode of action of some important ester and non-ester synthetic pyrethroids. Current status of synthetic pyrethroids insecticides. Chemistry and Use of Neonicotinoid Insecticides Neonicotinoids: Chemistry, classification, mode of action and uses, Preparation, properties anduses of some important neonicotinoids, Current status of neonicotinid insecticides. Block  Acaricides, Termiticides, Insect Growth Regulatorsand Newly Discovered Insecticidal Molecules. Chemistry and Use of Acaricides Chemistry, classification, mode of action of some important acaricidal molecules. Chemistry and Use of Termiticides Termites of different types infesting crops and building materials, Chemistry, mode of action and uses of some important termiticides. Chemistry and Use of Igrs and Newly Discovered Insecticidal Molecules Chemistry of insect growth regulators: Juvenile hormone mimics, anti-JH, Chitin synthesis inhibitors. Chemosterilants, Mode of action of IGRs, Endocrine disruptor compounds, Chemistry of newly discovered insecticidal molecules. Insecticde Resistance, Insecticide Resistance and its Management Definition, types and mechanism of insecticide resistance, Insecticide Resistance Action Committee (IRAC) guidelines for resistance management, Status of resistance to neo-nicotinoid, synthetic pyrethroids, and other group insecticides

Practicals: Preparation and characterization of organochlorine insecticides and their intermediates, metabolites and degradation products; Preparation of representative organochlorine insecticide like dicofol; Preparation of representative organophosphorus insecticide; Preparation and characterization of a pesticide intermediate (oxime/oxime ether/ ester etc.); Phytotoxicity evaluation of insecticides through germination and growth inhibition study; Bioefficacy of insecticides against stored grain insect pests.

1. Agrochemicals for Disease Management

Content: Introduction to Fungicides and Plant Disease Management. Important Fungicides, Plant Pathogenic Fungi and Diseases Historical development of fungicides, Some important plant pathogenic fungi and crop diseases, Fungicide movement (translocation) in plant. Classification of Fungicides Fungicide classification based on chemical nature, Fungicide classification based on mode of action. Chemical Control of Plant Diseases. Inorganic and Dithiocarbamate Fungicides Chemistry, use and mode of action of inorganic fungicides (S, Cu, Hg, Sn, As), Dithiocarbamate fungicides. Heterocyclic and Organophosphorus Fungicides Chemistry, use and mode of action of heterocyclic fungicides (Imidazole, benzimidazole, triazole, oxazole, thiazole, pyridine, pyrimidine, quinoline, quinoxaline, morpholine etc.), Organophosphorus fungicides. Strobilurin (â-methoxy-acrylate) Group Fungicides Chemistry, use and mode of action of strobilurin (-methoxyacrylaye) group synthetic fungicides e.g. azoxystrobin, kresoximmethyl, picoxystrobin, fluoxastrobin, pyraclostrobin and trifloxystrobin. Miscellaneous and New Emerging Fungicidal Molecules Chemistry, use and mode of action of phenol, quinone, polyhalogen, alkane sulfenyl group, formamide, alkane, alkane carboxylic acid carboxamide and dicarboximide group of fungicides, Chemistry of newly discovered fungicide molecules. Chemical Control of Plant Parasuitic Nematodes. Chemical Nematicides Plant parasitic nematodes, Historical development of nematicides. Preparation, properties and uses of aliphatic halogen compounds, methyl isocyanate liberators, organophosphates and carbamates for nematode control. Fungicide Resistance. Fungicide Resistance and its Management Definition and development of fungicide resistance in crop pathogens, Fungicide Resistance Action Committee (FRAC) guidelines for resistance management, Fungicide resistance status in India.

Practicals: Preparation of chemical fungicide intermediate(s) like triazoles/ benzimidazoles; Preparation and characterization of some important fungicides (e.g. Zineb, Bordeaux mixture, Burgundy mixture, dichlorophen, Glyodin, DBCP (nematicide), and an organophosphorus fungicide; Determination of antifungal activity of the representative test agrochemical (bioassay); Characterization of the select fungicides by spectral (IR, UV, NMR or MS) analysis.

1. Agrochemicals for Weed and Crop Management

Theory: Herbicides and Weed Management. Introduction to Herbicides and Weed Management Important crop weeds, Introduction to synthetic herbicides, Classification of herbicides based on time of application, mode of action and selectivity, Herbicide resistance and its management. Aliphatic and Aromatic Group Herbicides. Aliphatic Acid and Aromatic Acid Group Herbicides Chemistry, mode of action, and factors governing structure activity relationship of aliphatic and benzoic acid herbicides, phenoxy acid herbicides, phenoxy-phenoxy acid and phenoxy-phenoxy alkanoic acid herbicides. Carbamate, Substituted phenyl urea, and s-Triazine group Herbicides Chemistry, mode of action, and factors governing structure activity relationship of carbamate, thiocarbamate, biscarbamate, oxime carbamate, sulfonyl carbamate, Substitutred phenyl urea herbicides, s-Triazine group herbicides. Diphenyl Ethers, Dinitroanilines, Amide, and Anilide Group Herbicides Chemistry, mode of action, and factors governing structure activity relationship ofdiphenyl ethers, dinitroanilines, amide, and anilide group herbicides. Heterocyclic and Sulfonyl Urea Herbicides. Chemistry and Use of Heterocyclic and Sulfonyl Urea Group Herbicides Chemistry, use, mode of action and factors governing structure activity relationship of triazine, pyridine, bipyridylium, pyridazine, pyrimidine, oxadiazole, imidazolinoneand sulfonylurea and sulfonylamides herbicides. Plant Growth Regulators, Herbicide Safeners, and Newly Discovered Herbicidal Molecules. Chemistry and Use of Plant Growth Regulators and Herbicide Safeners Chemistry and use of plant growth regulators (auxins, gibberallin, cytokinins, brassionosteroids, triacontanol, protein hydrolysates), Synthesis, structure activity relationships of auxins and gibberellins, Herbicide safeners and pro-safeners. Newly discovered Herbicidal Molecules Structure and herbicidal activity of newly discovered herbicidal molecules. Herbicide Resistance. Herbicide resistance and its management History and types of herbicide resistance, Factors and mechanism of herbicide resistance, Management of herbicide resistance.

Practicals: Synthesis and characterization of 2,4-D by m.p, TLC, and NMR,; Identification and collection of weed samples from Institute research farm; Preparation of propionyl chloride and its use in the synthesis of the propanil herbicide; Synthesis of maleic hydrazide and its characterization by TLC, NMR,; Estimation of 2,4-D, alachlor, propanil, simazine and/or other available herbicides by HPLC and spectrophotometry.

1. Agrochemicals for Weed and Crop Management

Content: Chromatographic Techniques. Introduction to Separation Science Techniques Principles of separation science, GC, GPC, and LC chromatography, Super critical fluid chromatograph (SCFC), and Ion exchange chromatography (IEC). Gas Chromatography and its Application Theory, principle and instrumentation of GC, GC detectors and columns of different types, Application of GC in analysis of organic compounds, Advantages and limitations of GC. High Performance Liquid Chromatography (HPLC) and its Application Theory, principle and instrumentation of HPLC, LC detectors and columns of different types, Mobile phase, Application of HPLC in separation and analysis of organic compounds. Advantages and limitations of HPLC. Spectroscopic Techniques Unit 1: UV, Visible and IR Spectrophotometry and its Application Theory, principle, and instrumentation of absorption (UV, Visible and IR) spectroscopy, Application of UV and IR in structure elucidation of organic compounds. NMR (1H, 13C) Spectroscopy and its Application Theory, principal and instrumentation of NMR (1H, 13C) spectroscopy, Application of NMR spectroscopy in characterization of organic compounds. Mass Spectroscopy (MS) and its Application Theory, principal, instrumentation of mass spectroscopy, Mass fragmentation pattern, Application of MS in structure elucidation and confirmation. Tandem GC-MS and LC-MS Techniques Tandem chromatographic and spectroscopic techniques (GCMS-MS/LCMS-MS), Application of tandem techniques for confirmation of the chemical structure of the analyte constituents.

Practicals: Separation of organic compound mixture by GC and HPLC; Application of UV and IR spectrophotometry for detection of organic compounds; Identification and structure elucidation of organic compounds by NMR (1H, 13C) and MS; Identification and structure elucidation of organic compounds by GC-MS, LC-MS and MS fragmentation patter.

1. Pesticide Residue Chemistry

Content: Introduction to Pesticide Residue Chemistry. Pesticide Residue – Concept and Significance Pesticide residue definition, source, Significance of Certified Reference Materials (CRMs) in pesticide residue analysis, Planning and layout of experiments, Good agricultural practices (GAP) and experimental design, Post-harvest interval (PHI). Laboratory Data Documentation and Proficiency Testing Documentation and audit of laboratory data, Inter laboratory comparison and laboratory proficiency testing, legal implications of pesticide residue data Analysis of Pesticide Residues. Extraction, Clean Up and Recovery Sampling, sample processing and testing, Different extraction and clean up techniques for optimum recovery Method Development and Validation Method development, Validation and performance verification through linearity, sensitivity, matrix effect, limit of quantification (LOQ), limit of dete ection (LOD), accuracy and precision of recovery, Measurement uncertainty (MU). Monitoring of Pesticide Residue Monitoring of pesticide residue in agricultural produce and environment, Multiresidue analysis by quick, easy, cheap, effective, rapid and safe (QuEChERS) method, GC/LC, GC-MS, LC-MS method. ELISA and Radiotracer techniques in residue analysis. Consumer Risk Assessment and MRL Fixation Consumer Risk Assessment Hazard and risk, Ecological and human health risk assessment, Acceptable daily intake (ADI), theoretical maximum daily intake (TMDI),estimated daily intake, Maximum Residue Limit, No Observed Adverse Effect level (NOAEL), Food factor. MRL fixation of Pesticides in Food Commodities Safe waiting period, Lowest, highest and median residue data, OECD MRL Calculator, Significance of Codex, EU and FSSAI MRLs. Practicals: Collection, storage and preparation of samples for pesticide residue analysis; Extraction and clean-up of food, soil and water sample prior to analysis of pesticide residues; Study the percent recovery of pesticide residues from vegetable, soil, and/or water samples fortified with the standard pesticide analyte; Validation of analytical method by studying linearity, matrix effect, LOD, LOQ, accuracy (recovery) and precision as per SANTE guidelines; Identification of organochlorine insecticides in soil and water by TLC/GC/HPLC; Identification of Carbamate insecticides in water by TLC/GC/HPLC; Estimation of carbamate insecticide residues in vegetable by visible spectroscopic method and HPLC; Estimation of OP insecticide residues in soil by spectroscopic method and HPLC.

Biochemistry

1. Basic Biochemistry

Content:  Introduction to Biochemistry. Scope and importance of biochemistry (1 Lecture) Biochemistry as modern science and its various divisions, Scope and importance of biochemistry in agriculture and allied sciences. Foundation of life (2 Lectures) Fundamental principles governing life, supramolecular structures, significance of weak non covalent interactions in biology. Water (3 Lectures) Structure of water, ionization of water, acid base concept, pH and buffers, significance of structure-function relationship. Physical techniques for structure determination (2 Lectures) General introduction to physical techniques for determination of structure of biopolymers. Structure And Function of Biomolecules. Biomolecules (10 Lectures) Structure, classification, properties and function of carbohydrates, amino acids, proteins, lipids and nucleic acids. Immunoglobulins and PR proteins (2 Lectures) Structure, formation and different forms of immunoglobulins, PR proteins and their classification. Plant secondary metabolites (3 Lectures) Structure, classification and function of plant secondary metabolites. Metabolism – The Basics Unit 1: Molecules aiding metabolism (2 Lectures) Structure and biological functions of vitamins and coenzymes, enzymes: classification and mechanism of action; regulation, factors affecting enzyme action. Hormones: animal and plants. Thermodynamics –principles and energetic of life (2 Lectures) Fundamentals of thermodynamic principles applicable to biological processes, Bioenergetics. Block 4: Catabolism and its Regulation. Catabolism of energy molecules (5 Lectures) Important and basic degradative metabolic pathways of carbohydrates, lipids and proteins and their regulation. Unit 2: ATP formation (3 Lectures) Formation of ATP, substrate level phosphorylation, electron transport chain and oxidative phosphorylation, chemiosmotic theory and proton motive force. Fundamentals of Molecular Biology and Genetic Engineering. Molecular biology processes (4 Lectures) Overview of replication, transcription and translation. Recombinant DNA technology (3 Lectures) Restriction enzymes, DNA cloning, applications of cloning, transgenics.

Practicals: Preparation of standard and buffer solutions; Detection of carbohydrates, amino acids and proteins; Extraction and estimation of sugars; Extraction and estimation of amino acids; Extraction and estimation of proteins; Estimation of acid value of fat/oil; Estimation of peroxide value of fat/oil; Estimation of saponification value in fats and oils; Fatty acid composition in fat/oil by GC; Estimation of DNA and RNA by spectroscopic methods; Estimation of Ascorbic acid; Separation of biomolecules by TLC and Paper chromatography; Estimation of alpha amylase activity; Qualitative tests for secondary plant metabolites.

1. Intermediary Metabolism

Content:  Introduction To Metabolism. Overview of metabolism (4 Lectures) The living cell - a unique chemical system, biochemical reaction types, bioenergetics, bioavailability of nutrients, transport mechanism, signal transduction. Metabolic pathways (5 Lectures) Catabolism and anabolism, compartments of metabolic pathways, experimental approaches to study metabolism, metabolic profiles of major organs. Metabolism of Energy Nutrients Carbohydrate metabolism (5 Lectures) Major catabolic and anabolic pathways of carbohydrate metabolism, the glyoxylate pathway. Lipid metabolism (5 Lectures) Fatty acid oxidation, ketone bodies, fatty acid biosynthesis, synthesis of triacylglycerols, cholesterol, eicosanoids. Protein metabolism (3 Lectures) General reactions of amino acid metabolism, degradative and biosynthetic pathways of amino acids, urea cycle, amino acids as metabolic precursors. Energy transduction and oxidative phosphorylation (4 Lectures) Mechanisms of energy transduction, electron transport system, oxidative phosphorylation, control of ATP production.sulphur and Nucleotide Metabolism Sulphur metabolism (5 Lectures) Sulphate reduction and incorporation of sulphur in to amino acids. Nucleotide metabolism (3 Lectures) Synthesis and degradation of purine and pyrimidine nucleotides. Metabolic Regulation and Defects in Metabolism Regulation of metabolic pathways (4 Lectures) Regulation of carbohydrate, lipid, protein, nucleotide metabolism and oxidative phosphorylation. Defects in metabolism (4 Lectures) Disorders of carbohydrates, lipids, amino acids and nucleic acid metabolism, and inborn errors of metabolism. Metabolic pathway engineering.

1. Enzymology

Content: Introduction To Enzymes, Structure and function of enzyme (2 Lectures) Historic perspective, general properties of enzymes, enzyme compartmentalization in cell organelles, nomenclature and classification of enzymes, ribozymes, isozymes, abzymes.: Extraction and purification of enzymes (2 Lectures) Extraction of soluble and membrane-bound enzymes, purification of enzymes, measurement of enzyme activity. Enzyme Structure and Function. Chemical nature of enzyme (3 Lectures) Enzyme specificity, monomeric and oligomeric enzymes, catalytic mechanism, mechanism of enzyme action, pseudoenzymes, enzyme promiscuity. Cofactors and coenzymes (2 Lectures) Chemical nature and involvement of cofactors and coenzymes in enzyme catalyzed reactions, metal activated enzymes and metalloenzymes, mechanism of enzyme catalyzed reactions without cofactors. Nature of active site (2 Lectures) Active site, identification of binding sites and catalytic sites. Block 3. Enzyme Kinetics Single substrate kinetics (4 Lectures) Relationship between initial velocity and substrate concentration, Michaelis-Menten equation, Lineweaver-Burk and Eadie-Hofstee plots, analysis of kinetic data, numerical exercises. Enzyme inhibition (2 Lectures) Reversible and irreversible enzyme inhibition, uses of enzyme inhibition. Kinetics of allosteric enzymes (3 Lectures) Nature of allosteric enzymes, sigmoidal kinetics, MWC model and allosteric regulation, KNF model and allosteric regulation. Regulation of enzyme activity (3 Lectures) Feedback regulation, regulatory enzymes, control of enzymatic activity, symmetry and sequential model, reversible covalent modification of enzymes. Application of Enzymology Industrial application of enzymes (3 Lectures) Industrial application of enzyme catalysis in sectors like food processing, detergents, biofuels, paper and pulp, biosensors and clinical applications of enzymes. Biotechnological application of enzymes (2 Lectures) Large scale production and purification of enzymes, immobilization of enzymes.

Practicals: Soluble protein estimation; Enzyme assay by taking any model enzyme; Isolation and purification of any model enzyme; Study of the effect of enzyme and substrate concentrations on enzyme activity; Determination of Km and Vmax; Determination of pH and temperature optima; Effect of inhibitors on enzyme activity; Determination of pH and temperature stability of enzyme; Electrophoretic analysis of is ozymes.

1. Molecular Biology

Content: Introduction to Nucleic Acids. History (1 Lecture) Historical development of molecular biology, nucleic acids as genetic material. Properties of nucleic acid (2 Lectures) Nucleic acid structure, chemical and physical properties of nucleic acids, spectroscopic and thermal properties of nucleic acids, DNA supercoiling. Genes and genome (3 Lectures) Concept of genes and genome,genome complexity, genome organization in prokaryotes and eukaryotes, chromatin structure and function, repetitive and nonrepetitive DNA, satellite DNA central dogma, genome editing. Synthesis of Nucleic Acid DNA replication (3 Lectures) Modes of replication, DNA polymerases, topoisomerases, DNA ligase, model of replisome, semi conservative replication in prokaryotes and eukaryotes, inhibitors of replication, DNA damage and repair. Transcription (3 Lectures) Basic principles of transcription, transcription initiation, elongation and termination, RNA processing, RNA interference, siRNAs, miRNAs and other ncRNAs, DNA/ RNA editing. regulation of transcription, reverse transcription. Protein Synthesis Unit 1: Translation machinery (2 Lectures) Ribosomes structure and function, organization of ribosomal proteins and RNA genes, genetic code, aminoacyl tRNA synthases Unit 2: Mechanism of protein synthesis (2 Lectures) Initiation, chain elongation and termination of translation, energetics, inhibitors of translation. Post-translational events (2 Lectures) Post translational modifications of nascent polypeptide, protein targeting and turnover, regulation of gene expression in prokaryotes and eukaryotes, nucleases and restriction enzymes. Gene Manipulation. DNA sequencing (3 Lectures) Importance, Sanger method,High-Throughput Sequencing (HTS) techniques, applications of DNA sequencing. Recombinant DNA technology (4 Lectures) Vectors, isolation of genes, recombinants vector, selection of recombinants, characterization and expression of cloned DNA, transformation, transgenesis, mutation, molecular mechanism of mutation, site directed mutagenesis, in vitro mutagenesis. Techniques in molecular biology (3 Lectures) Polymerase chain reaction (PCR), expression cloning, gel electrophoresis, molecular markers, macromolecule blotting and probing, arrays (DNA array and protein array) – principles and application.

Practicals: Isolation and purification of DNA and RNA; To check the purity of isolated DNA and RNA; Restriction fragmentation of genomic DNA; Separation of oligos by agarose gel electrophoresis; Southern blotting experiments; Northern blotting experiments; Cloning of DNA fragment in vector; Selection of recombinant; SSR analysis of DNA; cDNA synthesis using RT- PCR; Basic tools in bioinformatics analysis.

1. Techniques in Biochemistry

Content: Separation Techniques Principles and applications of separation techniques. Chromatography techniques (4 Lectures) Principles and applications of paper, thin layer, gel filtration, ion-exchange, affinity, column & HPTLC, GC, HPLC and FPLC. Electrophoretic technique (2 Lectures) General principles,paper and gel electrophoresis, native and SDS-PAGE, 2D-PAGE, capillary electrophoresis. Hydrodynamic methods (2 Lectures) Hydrodyanmic methods of separation of biomolecules such as viscosity and sedimentation velocity, - their principles. Centrifugation (2 Lectures) Basic principles of sedimentation, type, care and safety aspects of centrifuge preparative and analytical centrifugation. Spectroscopic Techniques. Spectrophotometry (3 Lectures) Principles and applications of UV-visible, Fluorescence, IR and FTIR, Raman, NMR and FTNMR, ESR and X-Ray spectroscopy. Mass spectroscopy (3 Lectures) MS/MS, LC-MS, GC-MS, MALDI-TOF, applications of mass spectrometry in biochemistry. Atomic absorption spectrophotometry (2 Lectures) Principle, function and instrumentation ofatomic absorption spectrophotometry. Microscopy Microscopic techniques (2 Lectures) Principles and applications, light, UV, phase contrast, fluorescence and electron microscopy, flow cytometry. Tracer, Imaging, Immunochemical and Other Techniques Tracer technique (2 Lectures) Tracer techniques in biology: concept of radioactivity, radioactivity counting methods with principles of different types of counters, concept of á, â and ã emitters, scintillation counters, J-ray spectrometers, autoradiography, applications of radioactive tracers in biology. Imaging techniques (2 Lectures) Principles and applications of phosphor imager, MRI and CT scan. Immunochemical technique (2 Lectures) Production of antibodies, immunoprecipitation, immunoblotting, immunoassays, RIA and ELISA. Unit 4: Other techniques (2 Lectures) Cryopreservation, polymerase chain reaction (PCR), FACS.

Practicals: Expression of concentration in terms of dilution, molarity, normality, percent expression; pH measurement and buffer preparation; Determination of absorption maxima of biomolecules; Estimation of biomolecules through spectrophotometry and other methods; Separation of carbohydrates and amino acids by paper chromatography; Separation and analysis of fatty acids/lipids by GC; Separation/estimation of biomolecules through HPLC and FPLC; Separation of proteins using ion exchange, gel filtration and affinity chromatography; Electrophoretic separation of proteins and nucleic acids; Centrifugation- differential and density gradient; (NH4)2SO4 precipitation and dialysis; Use of radioisotopes in metabolic studies; PCR; ELISA; Western blotting/ Dot blotting.

1. Immunochemistry

Content: Basics of immunology Introduction to immunology (7 Lectures) History and scope of immunology, antigens, adjuvants, immune system, organs, tissues and cells, immunoglobulins, molecular organization of immunoglobulin. Haptens, ag-ab interaction, plant immunity, proteasome mediated process, plantibodies. Antibodies (5 Lectures) Classes of antibodies, antibody diversity, theories of generation of antibody diversity, vaccine, monoclonal and polyclonal antibodies, hybridoma, recombinant antibodies, complement system - classical and alternate. The immune responses (8 Lectures) Cellular interactions in immune response, major histocompatibility complex, cell mediated immune response, cytokines. Immunoregulation and immunological techniques (8 Lectures) Immunoregulation, immunological tolerance, hypersensitivity, mechanisms of immunity, innate resistance and specific immunity, current immunological techniques – elisa, ria, immunoblotting, facs; basics of pcr and hybridization based methods of detection, microarray based detection, multiplexing.

Practicals:  Handling, inoculation and bleeding of laboratory animals; Preparation of antigens and antisera, natural antibodies; Carbon clearance test; Lymphoid organs of the mouse; Morphology of the blood leucocytes; Separation of lymphocytes from blood, viable lymphocyte count; Antigen-antibody interaction,; Precipitation and agglutination; Direct and indirect haemagglutination; Immunoelectrophoresis; Complement fixation; Quantitation of immunoglobulins by zinc sulphate turbidity and single radial immunodiffusion; ELISA; Western blotting; Fluorescent Ab test; Hybridoma technique.

1. Plant Biochemistry

Content: Photosynthesis. Photosynthetic machinery (3 Lectures) Structure and function of plant cell and its organelles, phytochromes, chloroplast morphology structure, structure and chemistry of photosynthetic pigments, light reaction of photosynthesis. Photosynthesis – the process (4 Lectures) Carbon reduction in C3, C4 and CAM plants, photorespiration, sucrose-starch interconversion. Conversion of Photosynthates Synthesis of major biomolecules (3 Lectures) Biosynthesis of structural carbohydrates, storage proteins and lipids. Nitrogen and sulphur metabolism (5 Lectures) Basic concepts of nitrogen and sulphur metabolism: biological nitrogen fixation, nitrate assimilation in plants, sulphur chemistry and function, reductive sulphate assimilation pathway, sulphated compounds. Growth and Develpoment Germination and fruit ripening (4 Lectures) Biochemistry of seed germination – stages, requirements, metabolism and mobilization of storage material; Biochemistry of fruit ripening – ripening process, cell wall degrading enzymes, role of ethylene and regulation of ethylene production. Phytohormones (3 Lectures) Different classes of phytohormones, their biosynthesis and mode of action. Secondary Metabolites Biochemistry of plant secondary metabolites (6 Lectures) Biochemistry and significance of plant secondary metabolites – phenolics, terpenoids, alkaloids, cyanogenic glycosides and glucosinolates, effect of biotic and abiotic factors on plant metabolism and plant defense system.

Practicals: Fractionation of cell organelles; Estimation of starch,; Assay of ADPG pyrophosphorylase/starch synthase,; Assay of PAL/SOD; Assay of PPO/LOX,; Estimation of individual amino acids,; Qualitative tests of secondary metabolites (alkaloids, sterols etc.); Content and composition of carotenoids, anthocyanin and chlorophylls; Determination of polyphenols/phenolics; Fractionation of storage proteins; Estimation of glucosinolates; Estimation of cyanogenic compounds.

1. Animal Biochemistry

Content: Animal Biochemistry. Biochemistry of assimilation (7 Lectures) Digestion and absorption of food, Detoxification, biochemistry of specialized tissues – connective tissue, skin, muscle, nervous tissue and blood and other body fluids. Nutrients and their biochemistry (7 Lectures) Water, electrolyte and acid-base balance, structure, function and mechanism of major trace elements, vitamins, energy nutrients and biochemistry of respiration, bioactive peptides and functional oligosaccharides. Hormones and their role (7 Lectures) Hormones of thyroid, hypothalamus, pituitary, pancreas, adrenals and sex hormones, Membrane receptors of hormones, signal transduction. Immune system (7 Lectures) Immune systems, immunoglobulins, monoclonal antibodies, formation of antibody, antibody diversity, complement system – classical and alternate, major histocompatibility complexes, cell mediated immune response, mechanisms of immunity.

1. Nutritional Biochemistry

Content: Nutritional Biochemistry. Fundamentals of human nutrition (7 Lectures) Fundamentals of human nutrition, concept of balanced diet, biochemical composition, energy and food value of various food grains (including cereals, pulses, oilseeds), fruits and vegetables. Physico-chemical, functional and nutritional characteristics of carbohydrates, proteins and fats and their interactions (emulsions, gelation, browning etc.). Digestion and absorption, digestive secretions, their characteristic features and control, protection of microflora of the GI tract. Biochemical functions of nutrients (7 Lectures) Biochemical functions of nutrients, macro- and micronutrients- carbohydrates, fats and proteins, vitamins, water soluble and fat soluble vitamins, mineral and phytonutrients, prebiotics and probiotics, enzymes and metabolic protein factors, cofactor role, electrolytic function, constituents of skeletal tissues, interrelationship in nutrient functions, mineral deficiency diseases; nutraceuticals, antinutritional factors, biochemistry of postharvest storage. Bioavailability of nutrients (7 Lectures) Factors affecting bioavailability of nutrients, biological value of proteins; effect of cooking, processing and preservation of different food products on nutrients, energyand micronutrient malnutrition, deficiency diseases of macro and micronutrients. Food sensitivity (7 Lectures) Food sensitivity: immunologically mediated food sensitivity, nature and properties of antigens in foods, mechanism of induction of all allergic reactions, diagnostic tests for food, hypersensitivity, non-immunologically mediated food sensitivity, food sensitivity due to metabolic diseases, gastrointestinal diseases, food additives, pharmacologic agents, food toxins and poisonous and psychological factors.

Practicals: Estimation of amylose and amylopectin; Estimation of resistant starch; Estimation of ù3, ù6 and trans fatty acid; Estimation of phenols in plant tissue/sample; Estimation of carotenoids; Estimation of amylase, trypsin and chymotrypsin inhibitor activities; Estimation of Vitamin C in fruits; Estimation of reducing & non reducing sugar in fruits; Estimation of protein contents; Estimation of dietary fibre; Determination of limiting amino acids; Estimation of phytate/ oxalate; Estimation of total antioxidant activity by different methods; Estimation of curcumin.

1. Nitrogen and Sulfur Metabolism

Content: Nitrogen and Sulfur Metabolism. Nitrogen metabolism (18 Lectures) Nitrogen cycle, assimilation of inorganic nitrogen, nitrate uptake and transporters, enzymology of nitrate reduction - Nitrate reductase (NR) and Nitrite reductase (NiR), NR regulation, nitrate signaling. Assimilation of inorganic nitrogen and N-transport amino acids - glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate dehydrogenase (GDH), aspartate amino transferase (AspT) and asparagine synthetase (AS), interaction between carbon metabolism and amino acid synthesis, biosynthesis of amino acids. Nitrogen fixation - an overview, enzymology of nitrogen fixation - nitrogenase, nif genes and their regulation, symbiotic nitrogen fixation - biochemical basis of rhizobial infection, nodule development. Mechanism of creation of microaerobic environment for nitrogen fixation. metabolic exchange between host plant and bacteroids. Sulphur metabolism (10 Lectures) Overview of sulfate assimilation, sulfur chemistry and function, sulfate uptake and transport, reductive sulfate assimilation pathway, synthesis and function of sulfur containing amino acids, glutathione and its derivatives, role of sulfated compounds in metabolism.

Practicals: Estimation of nitrite content,; Estimation of nitrate content,; In vivo assay of nitrate reductase activity,; In vitro assay of nitrate reductase activity;,  In vitro assay of nitrite reductase activity,;  In vitro assay of glutamine synthetase activity,;  In vitro assay of glutamate synthase and glutamate dehydrogenase activity,; Estimation of ureides and amides,; Assay of nitrogenase activity by acetylene reduction method,; Estimation of hydrogen evolution by legume nodules;, Estimation of cysteine, methionine, pyruvate and glutathione,; Assay of APS activity.

1. Biochemistry on Xenobiotics

Content: Biochemistry on Xenobiotics. Xenobiotics (7 Lectures) Xenobiotics: classification and their effects on biological systems, Problems related to xenobiotics degradation, potential effects of toxic agents on immune system function, biotic metabolism of xenobiotics - biodegradation/biotransformation. Mode of degradation (7 Lectures) Mode of degradation - Enzymatic and Non-enzymatic, Metabolism of toxic compounds with reference to role of detoxifying enzymes, Mechanism of xenobiotics detoxification - in animal using the enzymes of Phase I and Phase II, Role of microbes in xenobiotics degradation and co-metabolism, Biodegradation and its genetics, manipulation of xenobiotic degradative genes. Plant metabolism of xenobiotics (7 Lectures) Plant metabolism of xenobiotics - transformation, conjugation and compartmentation, Metabolic responses of pesticides in plants, Impact, metabolism, and toxicity of heavy metals in plants, Regulation of xenobiotics in higher plants: signalling and detoxification. Phytoremediation (7 Lectures) Phytoremediation, Advances in development of transgenic plants for remediation of xenobiotic pollutants, safety assessment of xenobiotics.

Microbiology

1. Techniques in Microbiology

Practicals: Awareness about lab safety measures; Study of general microbiological equipment, cleaning of glassware and apparatus for laboratory use; Methods of sterilization used in microbiology laboratory; Use of simple techniques in laboratory (Colorimetry, Centrifugation, electrophoresis and chromatography); Types of culture media; Isolation techniques and direct microscopic count; Environmental factors affecting bacterial growth: physical chemical, temperature, pH, osmotic pressure, light (UV) and bacteriostatic agents. Bacteriology of air, water, and soil.; Characteristics of important types of micro-organisms: major functional groups of bacteria, lactic acid, spore forming and coliforms bacteria, fungi, yeast and mold; Assessment of microbial quality of portable water.; Working in microscope.

1. Principles of Microbiology

Content: Scope and History of Microbiology and Microscopy. Scope of microbiology Scope of microbiology, microbes and microbiologist. Emergence of Special Fields of Microbiology. History Routes The Germ Theory of Disease, Early Studies: Pasteur’s Further Contributions, Koch’s Contributions, Work Toward Controlling Infections, spontaneous generation theory. Staining and microscopy Microscopy; Bright field, Dark field, Phase contrast, Confocal, Fluorescence, TEM, SEM – Working Principles and applications; Properties of light; Simple staining, differential and special staining. Evolutionary Link of Prokaryotes. Phylogenetic classification Evolutionary relationship among prokaryotes. Prokaryotes and Eukaryotes, Phylogenetic and numerical taxonomy. Species concept. Methods of sequencing Use of DNA and r-RNA sequencing in classifications. Microbial Growth, Characterization And Regulation Unit1: Microbial growth and reproduction Microbial growth and reproduction-communication, bacteria, yeast and virus growth, Replication, Cultivation methods, Normal micro flora of Human body; Immune response- specific and non-specific host resistance. Sterilization techniques Physical and chemical methods of sterilisation. Nutritional requirements for microbial growth Classification of microbes: electron, energy and carbon sources.

Practicals: Working principles and handling of different types of microscopes – Bright and Dark field microscopy; Working principles and handling of different types of microscope- SEM and TEM; Methods of isolation from different environments – soil, water, milk and food; Use of selective media for isolation; Purification techniques of bacteria and fungi; Enumeration and Quantification techniques; Maintenance and preservation of cultures; Assessment of microbial quality of portable water.; Morphological characterization of Bacteria; Morphological characterization of fungi;  Biochemical characterization of bacteria; Biochemical characterization of fungus.

1. Microbial Physiology and Metabolism

Content: Scope of Microbial Growth and Physiology. Structure, function and biosynthesis of cellular components Microbial nutrition – Chemical composition of microbial cell – Structure, function and assembly of cell membrane in prokaryotes, archaea and fungi – Macro and Micro- nutrients and their physiological functions – Transport of solutes across the membrane. Pathways and their Significance; Growth Kinetics and Nutritional Classifications. Growth Kinetics, cell cycle, cell division, pathways and fermentation metabolism Microbial growth. Cell cycle and cell division. Bioenergetics -carbohydrate utilization via EMP, HMP, ED, TCA pathways, Aerobic and anaerobic respiration. Fermentative metabolism. Assimilation of nitrogen and sulphur - Oxygenic and anoxygenic photosynthesis - Mechanisms of carbon-dioxide fixation in prokaryotes. Ethanol, lactic acid, butanol, acetone and mixed acid fermentation. Fermentation of nitrogenous organic compounds Regulation of microbial metabolism. Growth and factors affecting growth and culture systems Effects of physical, chemical and other environmental factors on growth Continuous culture, Diauxic growth and Synchronous culture. Method of growth measurement. Morphogenesis and cellular differentiation. Nutritional classification and spore formation and germination Metabolic diversity in photoautotrophs, photoheterotrophs, chemoautotrophs and chemoheterotrophs. Nutritional grouping/classification of microorganisms. Bacterial endospore-types, morphology, biochemistry and regulation of formation and germination. Enzymes and Microbial Metabolisms. Kinetics and Mechanism of Enzymes Enzyme kinetics: Michaelis Menten kinetics - mechanisms of inhibition of enzyme activity - coenzymes and prosthetic groups. Microbial metabolism Methods to determine free energy of biochemical reactions - high energy compounds. Microbial metabolism: generation of ATP, reducing power, development of proton gradient and biosynthesis of ATP. Synthesis of Macromolecules. Biosynthesis of macromolecules Biosynthesis of macromolecules – Synthesis and assembly of cell wall components – Methods of studying biosynthesis - regulation of microbial metabolism.

Practicals: Use of simple techniques in laboratory (Colorimetry, Centrifugation, electrophoresis and GLC, etc.).;  Determination of viable and total number of cells.; Measurement of cell size.; Gross cellular composition of microbial cell. Growth – Factors affecting growth.; Study of bacterial spores and factors affecting germination.; Enzyme activity and kinetics – calculating Km and Vmax of enzyme.; Demonstration of thermos-, meso-, and psychrophilic micro-organisms.; Production and testing of inducible enzymes in bacteria.; Sporulation and spore germination in bacteria.; Protoplasts formation and regeneration.; Estimation of generation time and specific growth rate for bacteria and yeast.; Diauxic growth curve.; Production of synchronous cells.; Effect of chemicals and environmental factors on bacterial growth.; Isolation and Identification of reserve food material (Glycogen/ polyphosphates, PHB) from bacteria (Azotobacter, Bacillus megaterium).; Growth of microorganisms on various carbon and nitrogen sources.

1. Microbial Genetics

Content: Introduction to Microbial Genetics. Historical perspectives of microbial genetics Introduction to Microbial genetics; Historically important events and major contributions of scientists in the field of Microbial genetics; Terminologies employed in microbial genetics and definitions; Nucleic acid – overview DNA, RNA. Genome of prokaryote, eukaryote (fungi) and virus Bacterial genome Eukaryotic genome; Viral genome; Difference between prokaryotic and eukaryotic genome; Mechanisms and role of prokaryotic genome- an overview. Geneticelements - chemical structure and property, enzymes associated and replication Structure of DNA – A form, B form, Z form; RNA- tRNA, mRNA, rRNA; Role and Replication of DNA and RNA; Enzymes involved in Replication and its role. Unit 4: Extra-chromosomal DNA in bacteria and eukaryotic cells Plasmids, Mitochondrial DNA, Chloroplast DNA – structure and function. Gene Expression and Regulation. Introduction to gene structure and expression Gene structure and expression, principles of operon, gene expression in prokaryote and eukaryotes, intron and exons, post transcriptional modifications. Regulation of gene expression Regulation of gene expression, negative expression (lac operon and trp operon), positive regulation (cAMP). Mutation, Genetic Recombination and Sequencing. Principles of mutation and types Principles of mutation, spontaneous and induced mutation, different types of mutations, selection principles of mutants. Mutagens and their mode of action Mutagens and their mode of action, transposable elements and insertion sequences. DNA damage - DNA repair mechanisms DNA damage, DNA repair mechanisms in bacteria. Genetic recombination in bacteria Genetic recombination in bacteria, mechanisms of recombination, transformation, conjugation, transduction. Gene sequencing Gene cloning and gene sequencing. Impact of gene cloning, polymerase chain reaction, DNA sequencing, recombinant DNA technology.

Practicals: Isolation of genomic DNA from pure cultures of bacteria and fungi.; Visualization of mega plasmids of bacteria. Isolation of bacterial plasmids and Plasmid curring. Qualitative and quantitative assay of DNA by spectrometry and gel-electrophoresis. Inducing mutation by chemicals, physical and biological agents.  Transformation and selection of transformants. Amplification of gene of interest by PCR – cloning and expression.  Isolation of metagenomic DNA from environmental samples.

1. Soil Microbiology

Content: Developments in Soil Microbiology and Soil Parameters. Historical prospective of soil microbiology. Factors affecting soil microflora. Landmarks in the history of soil microbiology. Abiotic factors (physical and chemical) affecting soil microflora as pH, chemicals, moisture, air, temperature etc. Ecology of soil microbiology Soil biota, Soil microbial ecology, types of organisms in different soils; Soil microbial biomass; Microbial interactions: unculturable soil biota. Block 2: Microbiology and Biochemistry of Plant Parts. Plant parts and soil interface interaction Microbiology and biochemistry of root-soil interface; phyllosphere, plant growth promoting rhizobacteria, soil enzyme activities and their importance. Role of Microorganisms in Nutrient Biocycle. Microbial transformation of various nutrients Microbial transformations of nitrogen, phosphorus, sulphur, iron and manganese in soil. Siderophores and antimicrobials. Microbial degradation of organic matter Biochemical composition and biodegradation of soil organic matter and crop residues. Microbial diversity Endophytic microorganisms Mycorrhizae, types and role in phosphate mobilization. Potassium releasing bacterium. Microbes in biotic and abiotic stress management. Role of microorganisms in biodegradation of xenobiotics and pesticides Biodegradation of pesticides, Organic wastes and their use for production of biogas and manures: Biotic factors in soil development.

Practicals: Determination of soil microbial population; Determination of Soil microbial biomass; Decomposition studies in soil, Soil enzymes; Measurement of important soil microbial processes such as ammonification, nitrification; N2 fixation, S oxidation, P solubilization and mineralization of other micro nutrients; Study of rhizosphere effect; Microbial diversity Endophytic microorganisms; Mycorrhizae, types and role in phosphate mobilization Potassium releasing bacterium; Microbes in biotic and abiotic stress management.

1. Microbial Biotechnology

Content: Scope of Microbial Technology and Fermentation Metabolism. Microbial Biotechnology: Introduction, Scopes, historical development, application and challenges. Fermentation Metabolism Fermentative metabolism, isolation, preservation screening and genetic improvement of industrially important microbes; Microbial growth kinetics. Fermenter/bioreactor design and operation Fermenters – types of fermenter, stirred tank reactor, bubble column reactor, airlift reactor, packed bed reactor, fluidized bed reactor and trickle bed reactor, agitation and aeration in a reactor, mass transfer. Foam formation and control. Fermentation system Types, Batch, Fed batch and continuous fermentation- multistage system. Solid state fermentation, Overproduction of primary and secondary metabolites e.g. amino acids, organic acids, alcohols, enzymes, organic solvents, antibiotics, etc. Immobilization of enzymes; and cells; Scale-up principles; Down-stream processing, etc. Recombinant Products, Production of recombinant Current advances in production of antibiotics, vaccines, and biocides; Steroidtransformation; Bioprocess engineering; Production of recombinant DNA products, Immobilization techniques. Microbial Conversion and their Product Formation. Industrial production of beverages, acid and solvent Production of alcohol (ethanol, wine and beer) and improvement by genetic engineering. Microbial production of acids (citric, acetic and gluconic acid) solvents (glycerol acetone and butanol) aminoacids (lysine and glutamic acid). New tools and recent advances in microbial biotechnology Concept of probiotics and applications of new tools of biotechnology for quality feed/food production; Microorganisms and proteins used in probiotics; Lactic acid bacteria as live vaccines; Bioconversion of substrates, anti-nutritional factors present in feeds; Microbial detoxification of aflatoxins; Microbial polysaccharides: fermentative production of xanthan gums. Bacterial bioplastics, genetic engineering of microorganisms for the production of poly-3 hydroxyalkanoates. Single cell protein, Bio-insecticides; Bio-fertilizers; Waste as source of energy/food Microbiologicallyproduced food, colours, and flavours. Retting offlax. Recent advances in microbial biotechnology.

Practicals: Isolation and maintenance of industrially important microbes; Production of alcohol; Production of beer; Production of citric acid; Production of lactic acid; Standardization of physical factors for the higher production of citric acid;  Production and assay of antibiotics;  Production of pullulan; SCP production; Study of bioreactors and their operation.

1. Food Microbiology

Content: Historical Perspective and Scope of Microbiology in Relation to Food. Importance and significance of microorganisms in food Introduction and scope; Food Microbiology Important microorganisms in food and their sources. Importance and significance of microorganisms in food. Factors of special significance in Food Microbiology Intrinsic and extrinsic factors influencing microbial growth in foods; Spores and their significance; Indicator organisms and Microbiological criteria. Microbial spoilage of different types of foods Microbial spoilage of meat, milk, fruits, vegetables and their products. Food-bornepathogens (bacteria, fungi and viruses) and intoxication. Fermentation and Food Preservation Methods. Food fermentation Fermented dairy, vegetable, meat products. Preservatives and preservation methods Physical methods, chemical preservatives and natural antimicrobial compounds. Biologically based preservation systems. Foods for Specified Health Probiotic bacteria; Bifidus factor. Bacteriocins and their applications; Pre-, probiotics and symbiotics. Microbes as food single cell protein. Food Safety and Quality Management Systems. Advanced techniques in detecting food-borne pathogens and toxins Food safety and Quality Management Systems- General principles of food safety risk management, Recent concerns on food safety- Safe food alternatives (Organic foods), Good agricultural Practices (GAP), Food Indicators of water and food safety and quality Advanced techniques in detecting food-borne pathogens and toxins. HACCP (Hurdle technology and Hazard analysis. Critical control point) CODEX, FSSAI (Food Safety and Standard Authority of India) systems in controlling microbiological hazards infoods. Food safety regulations

Practicals: Statutory, recommended and supplementary tests for microbiological analysis of various foods; Infant foods, canned foods, milk and dairy products, eggs, meat, vegetables, fruits, cereals, surfaces, containers, normal, spoiled, processed, fermented food and water; Testing of antimicrobial agents; Analysis of water; HACCP Plan; Visit to Food processing Industries.

1. Bacteriophages

Content: Bacteriophages, Historical prospective of bacteriophages. Historical developments and classification of bacteriophages. Biological processes of phage bacterial interaction Physiology, biochemistry, enzymology and molecular biology of phage- bacterial interactions. Life cycle of bacteriophages. Structure, functions and life cycles of P2 phage, Lambda phage, M13 phage, ÕX174 phage. Biotechnological Genetic manipulation Phages in the development of molecular biology and genetic engineering.

Practicals: Titration of phages and bacteria.  Absorption of phages. Preparation of phage stocks. Isolation of new phages and phage resistant bacteria. One step growth curve, phage bursts. Induction of lambda. Complementation of T4rII mutantsetc.

1. Environmental Microbiology

Content: Microbial Ecology, Scope of Environmental microbiology and Ecological Niche Scope of environmental microbiology, Microbial ecology: Microbial evolution and biodiversity – Ecological niches – Definitions, biotic and abiotic environment. Environmental segments. Composition and structure of environment. Concept of biosphere, communities and ecosystems. Ecosystem characteristics, structure and function. Food chains, food webs and trophic structures. Ecological pyramids. Microorganisms and their natural habitats Microorganisms and their natural habitats: Aeromicrobiology, Astrobiology, Methaneand chlorates on Mars, terrestrial analogues. Biofilms and microbial mats, Aquatic ecosystems- Public Health Microbiology. Extremophiles Extremophiles: Definition and ecological aspects. Thermophiles, Xerophiles, Psychrophiles, Piezophiles, Alkaliphiles, Acidophiles- Halophiles and Barophiles. Environmental Distribution and Taxonomic Diversity, Physiology, Adaptive mechanisms, Enzymes, Applications. Microbial Interaction, Biogeochemical cycles Biogeochemical cycling and its consequences. Global environmental problems. Waste water and solid waste treatment Microbiology of wastewater and solid waste treatment: - Waste-types-solid and liquid waste characterization, physical, chemical, biological, aerobic, anaerobic, primary, secondary and tertiary treatments. Anaerobic processes-Bioremediation of nuclear wastes. Bioconversion of Solid Waste and utilization as fertilizer. Bioaccumulation of heavy metal ions from industrial effluents. Biomining. Microbiology of degradation of xenobiotics in the environment, ecological considerations, decay behavior. Microbial upgradation in fossil fuels and interaction in rumen and gastrointestinal tract. Microbial upgradation of fossil fuels and coal gas. Microbial interaction in rumen and gastrointestinal tract.

Practicals: Determination of indices of pollution by measuring BOD/COD of different effluents. Analysis of natural waters. Quality control tests, waste treatment and anaerobic digestion; Demonstration of waste water treatment processes such as activated sludge processes, biofilter and fluidized bed process. Bacterial reduction of nitrate from ground waters. Isolation and purification of degradative plasmid of microbes growing in polluted environments.  Recovery of toxic metal ions of an industrial effluent by immobilized cells. Utilization of microbial consortium for the treatment of solid waste [Municipal Solid Waste]; Biotransformation of toxic metal ions into non-toxic metals ions. Microbial dye decolourization/adsorption. Biotrap based isolation of selective functional microbes. Thermophlic enzyme in biomass deconstructions. Halophilic microbes from salt lake-Pesticide degradation by microbes.

1. Industrial Microbiology

Content: Basics of Industrial Microbiology, Historical account of microbes in industrial microbiology Introduction to Industrial Microbiology. Sources and characters of industrially important microbes; their isolation, purification and maintenance. types of fermentation and fermenters. Microbial growth kinetics in batch, continuous and fed-batch fermentation process. Fermented Microbial products Bioreactors: Types and configuration. Microbiology and production of alcoholic beverages; Malt beverages, distilled beverages, wine and champagne; Commercial production of organic acids like acetic, lactic, citric, and gluconic acids Commercial production of important amino acids (glutamic acid, lysine and tryptophan), vitamins (riboflavin and vitamin A), enzymes, antibiotics and single cell proteins. Bioplastics, Biopolymers and Biofuels, Biocontrol agents and Biopesticides Biocontrol agents and Biopesticides: Biocontrol agents and their scope in control of plant diseases, nematodes and insect pests. Role of bioagents in sustainable agriculture. Industrial production of Bioplastics and biopolymers Introduction & industrial production of Bioplastics: Microorganisms involved in synthesis of biodegradable plastics and microbial pigments and biopolymers.Biosensors: Development of biosensors to detect food contamination and environment pollution. Biofuels: Production of ethanol, biogas and hydrogen from organic residues, fuels from algae; Mushroom cultivation. Production of valuable products Genetic engineering of microbes, Role of recombinant microbes in industrial sectors for enhanced production of valuable products. Mechanisms of pesticide degradation by microbes. Biomining: Coal, mineral and gas formation, prospecting for deposits of crude, oil and gas, recovery of minerals from low-grade ores.

Practicals: Isolation and purification of industrially important microbes (Bacteria, fungus and yeasts); Production of industrial compounds such as alcohol, beer, citric acid, lactic acidacetic acids gluconic acid and their recovery; Demonstration of biogas production; Production and assay of enzymes, organic acids and pigments; Mass production of biocontrol agent; Visit to industries.

1. Biofertilizer Technology

Content: Agriculture Important Beneficial Microorganisms. Agriculturally important beneficial nitrogen fixing microorganisms. Different agriculturally important beneficial microorganisms: Chemical Vs Biofertilizers: Current Scenario in biofertilizer technology in world-In India-List of biofertilizers-their applications in agriculture. Brief introduction about Agriculturally beneficial microorganisms (free living, symbiotic (rhizobial, actinorhizal), associative and endophytic nitrogen fixers including phosphobacteria, cyanobacteria, their types and importance taxonomic classification, Nitrogen fixing biofertilizers: nodule formation, competitiveness and quantification of N2 fixed and their use. Mechanism of phosphorous solubilization by photobacteria. BIS standards of biofertilizers. Agriculturally important beneficial microorganisms related to phosphorous, potassium, Sulphur and Zinc nutrition Different agriculturally important beneficial microorganisms: phosphate solubilizing bacteria and fungi, including mycorrhiza; Mechanism of phosphorous solubilization by phosphobacteria. Bacteria for potassium, Sulphur and Zinc nutrition. Agriculturally important beneficial microorganisms having plant growth promoting rhizobacteria. Different agriculturally important beneficial microorganisms: plant growth promoting rhizobacteria. FCO norms and biofertilizer production and usage at national and international levels. Agriculturally important biocontrol microbial inoculants Different agriculturally important beneficial microorganisms: Biocontrol microbial inoculants. Requirements for establishing bioinoculants production unit Economics of biofertilizers production Constraints in biofertilizers production and usage. Economics of biofertilizer production Different agriculturally important beneficial microorganisms for recycling of organic waste and compositing, bioremediators and other related microbes. Production of Biofertilizer. Production and quality control of biofertilizer Different agriculturally important beneficial microorganisms - selection, establishment, competitiveness, crop productivity, soil & plant health, mass scale production and quality control of bio inoculants. Biofertilizer inoculation and microbial communities in the soil. Different formulations of biofertilizers. Advantages and limitations of Liquid formulations.

Practicals: Isolation of phosphate solubilizing microorganisms. Development and production of efficient microorganisms, Determination of beneficial properties in important bacteria to be used as biofertilizer, Nitrogen fixing activity, indole acetic acid (IAA), siderophore production etc, Bioinoculant production and quality control.  Population dynamics in broth and carrier materials during storage. Development of cultures from starter. Preparation of broth for large scale cultivation in fermenter/ large containers. Inoculation and development of culture. Mass production of carrier based and liquid biofertilizers. Mass production of important two or three biocontrolagents (Trichoderma viride, Pseudomonas fluorescens and Metarhiziumanisopliae). Form, dose and method of application. Mass production of AM fungi in pot and root organ culture. Quality control and BIS standards. Mass production of Azolla and BGA. Visit to a biofertilizer production plant.

1. Cyanobacterial and Algal Biotechnology

Content: Importance of Cyanobacteria and Algae. Ecology and evolution of algae and cyanobacteria Introduction to cyanobacteria and algae. Definition, occurrence and distribution, thallus structure, reproduction, life cycles, origin and evolution of cyanobacteria, molecular evolution; role of algae in evolution of land plants and horizontal transfer of genes. Brief classification of algae: different classes, occurrence and distribution. Physiology and Culturing of Cyanobacteria and Algae. Algal pigments, storage products. Algal pigments, storage products, physiology and metabolism including photosynthesis. Metabolism of carbon and nitrogen Ecology of algae –primary colonizers and cycling in soil and water. Cellulardifferentiation and nitrogen fixation, nitrogen metabolism carbon metabolism. Culturing methods Algal culturing and cultivation. Culture types, culture conditions, culture vessels, culture media, sterilization, culture methods, synchronous cultures, photobioreactors, algal density and growth, seaweed cultivation. Role of Cyanobacteria and Algae in Agriculture and their Products of Industrial Importance. Importance as fuels, neutraceuticals and industrial importance. Cyanobacterial and algal fuels, Fine chemicals (restriction enzymes etc.) and nutraceuticals from algae; UV absorbing pigments Industrial products from macro algae - seaweed biotechnology, sustainable aquaculture. Ecology of algae- distribution in soil and water; primary colonizers, carbon sequestration and cycling in soil and water. Cellular differentiation and nitrogen fixation, nitrogen metabolism. Role of algae related to environment. Algae in pollution control - as pollution indicators, eutrophication agents and role in Bioremediation and reclamation of problem soils. Cyanobacterial and algal toxins, allelopathic interactions, Algae in global warming and environmental sustainability. Cyanobacteria and selected microalgae in agriculture – biofertilizers &algalization; soil conditioners; reclamation of problem soils.

Plant Physiology

1. Principles of Plant Physiology I - Plant Water Relations and Mineral Nutrition

Content:  Plant Water Relations. Soil and Plant Water Relations Water and its importance; Molecular structure of water; Properties and functions of water. Concept of water potential; Plant cell and soil water potential and their components; Methods to determine cell and soil water potential; Concept of osmosis and diffusion. Soil physical properties and water availability in different soils; Water holding capacity and approaches to improve WHC; Concept of FC and PWP; Water holding polymers and their relevance. Water Absorption and Translocation Root structure and functions; Root architecture and relevance in water mining; Mechanism of water absorption and translocation; Theories explaining water absorption and translocation; Aquaporins. Mycorrhizal association and its relevance in water mining. Transpiration and Evaporative Cooling Evaporation and transpiration; relevance of transpiration; factors regulating transpiration; Measurement of transpiration; approaches to minimize evaporation and transpiration; Concept of CCATD and its relevance. Energy balance: Solar energy input and output at crop canopy level. Stomata- its structure, functions and distribution; Molecular mechanisms of stomatal opening and closing; Concept of guard cell turgidity; role of K and other osmolytes; role of ABA in stomatal closure; Guard cells response to environmental signals; Signaling cascade associated with stomatal opening and closure. Antitranspirants and their relevance in agriculture. Water Productivity and Water Use Efficiency WUE and its relevance in water productivity; Transpiration efficiency, a measure of intrinsic WUE; Approaches to measure WUE; Stomatal and mesophyll regulation on WUE; Passioura’s yield model emphasizing WUE. Moisture Stress and Plant Growth Physiology of water stress in plants; Effect of moisture stress at molecular, cellular, organ and plant level. Drought indices and drought tolerance strategies. Drought tolerance traits. Mineral Nutrition, Nutrient Elements and Their Importance Role of mineral nutrients in plant’s metabolism; Essential elements and their classification; Beneficial elements; factors influencing the nutrients availability; critical levels of nutrients. Functions of mineral elements in plants. Deficiency and toxicity symptoms in plants. Nutrient Acquisition Mechanism of mineral uptake and translocation; Ion transporters; genes encoding for ion transporters; localization of transporters; xylem and phloem mobility; Nutrient transport to grains at maturity; Strategies to acquire and transport minerals under deficient levels. Role of mycorrhiza, root exudates and PGPRs in plant nutrient acquisition. Concept of Foliar Nutrition Foliar nutrition; significance and factors affecting total uptake of minerals; Foliar nutrient droplet size for effective entry; role of wetting agents in entry of nutrients.

Practicals: Standard solutions and preparation of different forms of solutions; Studies on the basic properties of water; Demonstration of surface tension of water and other solvents; Measurement of plant water status: Relative water content and rate of water loss; Determination of water potential through tissue volume and Chardakov’s test; Determination of water potential using pressure bomb, osmometer, psychrometer; Determination of soil moisture content and soil water potential; Use of soil moisture probes and soil moisture sensors; Measurement of transpiration rate in plants; use of porometry; Measurement of CCATD and its relevance; Demonstration and use of anti-transpirants to reduce transpiration’ Influence of potassium and ABA on stomatal opening and closing respectively; Deficiency and toxicity symptoms of nutrients; Effect of water stress on plant growth and development.

1. Principles of Plant Physiology-II: Metabolic Processes and Growth Regulation

Content: Metabolic Processes and Growth Regulation, Carbon Metabolism – Photochemical Processes; Chloroplast ultra structure with special mention of lamellar system; Excitation, electron and proton transfers and their relevance in energy conservation; Concepts of pigment systems and generation of powerful reductant and oxidant; Water oxidation, Water-water cycle and other aspects of electron transfer; Carbon Metabolism: Biochemical Processes; CO2 diffusion mechanisms and diffusive conductances, concept of Ci determining Photosynthesis; RuBisCO enzyme kinetics and Calvin cycle mechanisms, Regulation of Calvin cycle and metabolite fluxes; Photorespiration: the advantages and inefficiencies of photosynthesis because of photorespiration; Concepts of CO2 concentrating mechanisms (CCM) and spatial and temporal differences in carboxylation; Ecological aspects of C4and CAM photosynthesis; Product synthesis, Starch and Sucrose biosynthesis; Carbon Metabolism: Respiration; Mitochondrial organization and functions; Aspects of Glycolysis, TCA cycle and mitETC; Relevance of growth and maintenance respiration; Concepts of CN resistance respiration – Alternate and SHAM sensitive ETC. Product Synthesis and Translocation Leading to Crop Growth; Phloem loading and sugar transporting, concepts of bi-directional transport of sugars and other metabolites; Source-Sink relationship and modulation of photosynthesis; Concepts and definitions of Growth and Differentiation; Growth and yield parameters, NAR, CGR, HI and concepts of LAI, LAD. Nitrogen Assimilation and Protein Synthesis; Developments in d-nitrgen fixation; Nitrate reduction and assimilation GS-GOGAT process for amino acid synthesis; Inter-Dependence of carbon assimilation and nitrogen metabolisms.  Lipid Metabolism and Secondary Metabolites; Storage, protective and structural lipids.  Biosynthesis of fatty-acids, diacyl and triacyl glycerol, fatty acids of storage lipids.  Secondary metabolites and their significance in plant defense mechanisms. Hormonal Regulation of Plant Growth and Development;  Growth promoting and retarding hormones: biosynthesis, transport, conjugation; Mode of action of these hormones and their application in plant physiology Unit 8: Synthetic Growth Promoters; Different synthetic hormones: Salicylic acid, strigolactones etc. Roles and biological activities of various synthetic hormones;  Commercial application of hormones to maximize growth and productivity. Morphogenesis and Reproductive Phase; Photoperiodism: Phytochromes, their structure and function; Circadian rhythms,  Blue light receptors: Cryptochrome and morphogenesis. Vernalization and its relevance in germination.

Practicals: Radiant energy measurements; Separation and quantification of chlorophylls; Separation and quantification of carotenoids; O2 evolution during photosynthesis; Anatomical identification of C3 and C4 plants; Measurement of gas exchange parameters, conductance, photosynthetic rate, photorespiration; Measurement of respiration rates; Estimation of reducing sugars, starch; Estimation of NO3, free amino acids in the xylem exudates, quantification of soluble proteins; Bioassays for different growth hormones- Auxins, Gibberellins, Cytokinins, ABA and ethylene; Demonstration of photoperiodic response of plants in terms of flowering.

1. Plant Developmental Biology: Physiological and Molecular Basis

Content:  Plant Developmental Biology. Evolutionary Development of Plants and Role of Environment Plant development and plasticity, evolution, Biodiversity. Novel features of plant growth and development, Concept of plasticity-evolution and biodiversity, Model plants for study; Environment and development. Developmental stages and program; Cell-cycle, totipotency and regeneration. Physiological and Molecular Determinants of Seed Biology Seed development- Physiology of seed development, role of hormones in embryo development; seed development and maturation. Seed dormancy- Physiological and molecular mechanism of seed dormancy regulation. Seed germination- seed structure and Hormonal regulation of germination, Mobilization of food reserves during seed germination. Vegetative Growth and Organ Development Regeneration and totipotency- organ differentiation and development – role of hormones- developmental control genes in crop plants. Meristems in plant development. Shoot, Leaf, Trichome and stomate development and differentiation. Axillary shoot branching; Bud dormancy and growth. Root development; Nodule development; Tuber development- hormonal control, signaling and molecular regulation- genes involved. Vascular bundle development- xylem and phloem differentiation. Physiological and Molecular Aspects of Reproductive Growth and Development Floral Induction and Development: Molecular and physiological mechanism of transition -vegetative to reproductive phase- floral organ initiation and development their controls. Development of male and female gametophyte; gametophytic mutants: pollen-stigma interaction- Pollen germination and tube growth; role of imprinting; Male sterility: and fertility restoration; Self incompatibility; Sterility and fertility restoration, Maternal gene effects, Zygotic gene effects. Sex determination in plants, mate choice in plants. Embryo and endosperm development- fertilization, role of imprinting; Parthenocarpy and apomixes Unit 5: Ripening and Senescence Fruit development, enlargement, maturation and ripening; climacteric and nonclimacteric fruit ripening mechanism. Hormonal, biochemical & Molecular aspects of fruit ripening. Senescence and its regulation; Hormonal and environmental control of senescence; PCD in the life cycle of plants. Physiological and Molecular Regulation of Plant Development Influenced by Light and Temperature Light control of plant development: Phytochromes and cryptochromes, phototropins, their structure, biochemical properties and cellular distribution. Molecular mechanisms of light perception, signal transduction and gene regulation. Photoperiodism and its significance, vernalization and hormonal control. Circadian rhythms-biological clocks and their genetic and molecular determinants. Thermomorphogenesis- Thermoperiodism. Application of Morphogenesis and its Practical Application. Tissue culture and micro-propagation Applications of tissue culture for plant production, callus induction, somatic embryogenesis, regeneration from different explants. Micro-propogation, tip and axillary node culture of commercially important crops, hardening and ex-vitro establishment, concept of somatic hybridization and protoplast culture. Application of in-vitro techniques for crop improvement Development of somoclones, identification and exploitation of somoclonal variants. Haploid production, pollen/anther, ovule/ovary culture. Production of secondary metabolites by tissue culture, concept of bio-fermenters. Plant transformation, development of transgenic plants and their characterization. Germplasm storage, cryopreservation and regulation

Practicals: Studying shoot apical meristem, floral meristem development and pollen tube development; Phenotyping photomorphogenesis: (a) Studying effect of day length (short day and long day) in regulating floral induction/ flowering time in short day/long day/day neutral plants and (b) effect of light on seed germination in light-sensitive and - insensitive seeds.Studying effect of temperature on– (a) thermomorphogenesis- measuring hypocotyl elongation under different temperature conditions and (b) sex determination using cucurbits/sesame plants.  Measure physiological paramters of fruit ripening and study the expression of key genes regulating ripening. Study the effect of ethylene, its inhbibitor and scruber on ripening (tomato).  Study different sterilization techniques, prepare media stocks and plant hormones. Inoculate explant (seed and leaf tissue) of model plant for callus induction. Subculture the callus and standerdize regeneration protocol for shoot and root induction using callus and leaf explant.  Micro-propagation using meristem tip and axillary node culture. Standerdize anther/ pollen culture for haploid production in model/crop/horticultural plant. Isolation of protoplast from Arabidopsis/tobacco and its culturing;  Study about selectable marker, reporter gene, PCR, southern and northern blotting techniques. Transformation of tobacco callus or leaf explant by Agrobacterium tumefacines and Agrobacterium rhizogenes for production of transgenic; Molecular characterization of transgenic- PCR, southern blotting, gene expression.

1. Physiological and Molecular Responses of Plants to Abiotic Stresses

Content:  Abiotic Stresses, Introduction to Abiotic Stresses Abiotic stresses major constraints to realize potential yields of crop plants, yield losses. Drought prone areas in India- Frequency of occurrence of drought, Rainfedkharif, Rabi, Areas affected by salinity, heavy metals, water logging, high temperature scenario due to global warming. Drought Stress, Moisture Stress Responses in Plants Drought-characteristic features; water potential in the soil-plant-air continuum. Physiological and biochemical processes affected by drought. Oxidative stressgeneration of ROS and other cytotoxic compounds, their effect on cellular process. Effect on total carbon gain- decrease in photosynthetic area and function, protein turn over and lipid characters, phenology-reproductive aspects, critical stages. Stress Perception and Molecular Responses of Plants to Drought Stress Stress perception andsignal transduction leading to expression of regulatory genes, stress specific kinases, stress specific transcription factors, functional genes associated with adaptive mechanisms. Plant Adaptive Mechanisms to Drought (a) Escape and desiccation avoidance mechanism Concept of stress escape- exploiting genetic variability in phenology, Drought avoidance mechanisms- Maintenance of cell turgor, water mining by root characters. Moisture conservation- Regulation of transpiration- traits reducing heat load, Stomatalfactors guard cell metabolism, moisture conservation by waxes. Water use efficiency (WUE) and concept of water productivity- regulation of transpiration efficiency-stomatal conductance, mesophyll efficiency, relevance of WUE and Passioura’s model. (b) Desiccation tolerance- Concept of acquired tolerance Decreased turgor mediated upregulation of cellular tolerance mechanisms, Osmolytes, managing cytotoxic compounds, ROS, RCC, scavenging - enzymatic and non-enzymatic, protein turnover, stability, chaperones, membrane stability, photoprotection of chlorophylls. Approaches to Improve Drought Tolerance Development of genetic resources- donor genotypes for specific traits, Genomic resources- genes, QTL’s regulating adaptive mechanisms, Conventional, transgenic and molecular breeding approaches to improve relevant adaptive traits, concept of trait introgression. Salt, Heavy Metal, Water Logging, Temperature and Light Stress. Salt Stress Soil salinity-Effect of salt stress, ionic and osmotic effects; species variation in salt tolerance; glycophytes and halophytes, Salt tolerance mechanisms - exclusion, extrusion and compartmentalization, Signaling during salt stress – SOS pathway, Approaches to improve salt tolerance. Heavy Metal Stress and Water Logging Heavy metal toxicity in plants (eg., Al, Cd), tolerance mechanisms and approaches to improve. Plant response to water logging, role of hormones- ethylene, mechanism of tolerance and approaches to improve. Temperature and Light Stress High and low temperatures; effect on plants; adaptive mechanisms, evaporation cooling, concept of cellular tolerance, protein stability, chaperones, HSPs, HSFs, membranes. High light and high ionizing radiation- photo oxidation and photoinhibition; mechanisms of tolerance, plant adaptation to low light, concept of shade avoidance response (SAR).

Practicals: Measurement of soil and plant water status. Drought stress imposition and measurement of physiological and biochemical changes in plants under stress –gas exchange and fluorescence measurements. Determination of water use efficiency as a drought resistant trait. Drought Susceptibility Index (DSI) -precise field technique to identify productive genotypes under stress. Approaches to quantify root characters; Determination of stomatal parameters and canopy temperature as a reflection of transpiration and root activity.  Determination of Salinity Tolerance Index. Studying acclimation response - Temperature induction response. Heat tolerance and membrane integrity- Sullivans heat tolerance test. Quantification of osmolytes – proline under stress. Oxidative stress imposition- Quantification of oxidative stress; Quantification of ROS under stress. Estimation of ABA content in leaf and root tissues under stress. Determination of Sodium and Potassium in plant tissue grown under salt stress. Estimation of antioxidant enzymes.

1. Hormonal Regulation of Plant Growth and Development

Content:  Plant Growth and Development: Hormonal Regulation. Introduction to Plant Hormones Growth, differentiation and development regulated by plant growth substances, Definition and classification of growth regulating substances: Classical hormones, Definition and classification of growth regulating substances: Endogenous growth substances other than hormones, Synthetic chemicals. Plant Hormones – Discovery and Metabolism Discovery, biosynthetic pathways and metabolism of Auxin, Discovery, biosynthetic pathways and metabolism of Gibberellins, Discovery, biosynthetic pathways and metabolism of Cytokinins, Discovery, biosynthetic pathways and metabolism of Abscisic acid, Discovery, biosynthetic pathways and metabolism of Ethylene, Discovery, biosynthetic pathways and metabolism of Brassinosteroids, Discovery, biosynthetic pathways and metabolism of Strigolactones. Physiological Role of Hormones in Plant Growth and Development Physiological functions of Auxin and use of mutants and transgenic plants in elucidating the physiological functions, Physiological functions of Gibberellins and use of mutants and transgenic plants in elucidating the physiological functions, Physiological functions of Cytokinins and use of mutants and transgenic plants in elucidating the physiological functions, Physiological functions of Abscisic acid and use of mutants and transgenic plants in elucidating the physiological functions, Physiological functions of Ethylene and use of mutants and transgenic plants in elucidating the physiological functions, Physiological functions of Brassinosteroidsand Strigolactones and use of mutants and transgenic plants in elucidating the physiological functions, Discovery, biosynthetic pathways metabolism and physiological roles of Salicylic acid and Peptide hormones. Endogenous Growth Substances other than Hormones Discovery, biosynthetic pathways metabolism and physiological role of Polyamines and Karrikins, Discovery, biosynthetic pathways metabolism and physiological roles of Jasmonates and Tricontanol, Discovery, biosynthetic pathways metabolism and physiological roles of systemins Concept of death hormone, Recent developments in elucidating responses of Salicylic acid, Peptide hormones and Polyamines at physiological and molecular level, Recent developments in elucidating responses of Jasmonates, Systemins, Karrikins and Tricontanol at physiological and molecular level. Hormone Signaling Hormone signal perception, transduction - Receptors, components and mechanism (Auxin, Gibberellin, Cytokinin, ABA and Salicylic acid), Hormone signal perception, transduction - Receptors, components and mechanism (Ethylene, Jasmonate, Brassinosteroids and strigolactones), Advances in elucidating the structure and function of receptors and signaling components of important hormones. Key Genes Regulating Hormone Levels and Functions Genomics approaches to regulate hormone metabolism and its effect on plant growth and development – case studies. Crosstalk of Hormones in Regulation of Plant Growth and Development Processes Crosstalk of Hormones in Regulation of Plant Growth and Development Processes: Floral transition, reproductive development, Shoot and root apical meristem development. Practical Utility of Growth Regulators in Agriculture and Horticulture Practical Utility of Growth Regulators in Agriculture and Horticulture: Rooting of cuttings, Vine and brewing industry, Promotion of gynoecious flowers, hybrid rice production, induction of flowering in pine apple, cucurbits, Practical Utility of Growth Regulators in Agriculture and Horticulture: Delaying of senescence and ripening, Production of dwarf plants for ornamental purpose, As herbicides, Reduction in flower and fruit drop.

Practicals: Extraction of Auxins from plant tissue; Separation and detection of Auxins by GC / GC-MS / HPLC / Immunological technique; Bioassay of auxin- effect on rooting of cuttings; Extraction of abscisic acid (ABA) from plant tissue; Separation and detection of ABA by HPLC/Immunological technique; ABA bioassays- effect on stomatal movement;  Preparation of samples for ethylene estimation in plant tissue; Estimation of ethylene in plant tissues using gas chromatography; Ethylene bioassays, estimation using physico-chemical techniques- effect on breaking dormancy in sunflower and groundnut; Extraction of Gibberellins from plant tissue- GC / GC-MS / HPLC; Separation and detection of GA by GC / GC-MS / HPLC/Immunological technique; GA bioassays- effect on germination of dormant seeds; Cytokinin- extraction from plant tissue; Separation and detection of cytokinin by GC / GC-MS / HPLC; Cytokinin bioassays- effect on apical dominance and senescence / stay green.

1. Physiological and Molecular Mechanisms of Mineral Nutrient Acquisition and their Functions

Content:  Mineral Nutrient: Classification, Function, Availability, Deficiency and Toxicity, Mineral Elements: Classification, Function, Deficiency and Toxicity Classification based on mobility and characteristic features; physiological role in regulating plant growth, metabolism, development and human health- Regulatory Dietary Allowance (RDA), Deficiency and toxicity of macro, micro and beneficial elements, Tolerance of plants to nutrient toxicity, hyper-accumulators of nutrients: Concept of phytoremediation. Nutrient Availability at Rhizosphere Biological and chemical reactions influencing nutrient availability near the root system, interaction between ions in the rhizosphere, Rhizosphere chemistry in relation to plant nutrition- chemical reactions, root exudates to mobilize nutrients. Nutrient Uptake, Translocation and Acquisition. Ion Uptake Mechanisms Mineral salt absorption- chemical potential of solute- Nernst equation- passive uptake- diffusion, ion exchange-Donnan Equilibrium, mass flow of ions, Mediated transport- Facilitated diffusion-ionophores; membrane transport proteins- active transport-ion channels, Primary and secondary transport- carriers and pumps. Ion Transport to Shoot and Grains Long distance transport in plants - Mechanism of xylem and phloem transport, Radial movement of ions across the root, Mechanism of phloem transport, remobilization of mineral nutrients - phloem loading, phloem unloading. Physiological and Molecular Mechanism of Nutrient Acquisition and Transport: Macronutrients Molecular structures of LAT and HAT, their localization and regulation by various external factors, Nitrate transporters and their functional regulation - Nitrate transporters (NRT1, NRT2, dual-affinity nitrate transporter NRT1.1/CHL1), Phosphate transporters and their functional regulation - PT1/PHT1, PHT2, PHT3, PHT4, Potassium transporters and their functional regulation - KT/HAK/KUP family Ion transporters involved in transport of multiple elements, for example, sulphate transporter for Selenate transport, phosphate transporter for Arsenate transport, etc. Physiological and Molecular Mechanism of Nutrient Acquisition and Transport: Micro and Beneficial Nutrients Plant Strategies: Different Strategies I & II adopted by plants for uptake of Fe under Fe deficient condition, Transporters and genes regulating uptake and transport of micronutrients, genes encoding transport/channel proteins, Examples of genes encoding mineral ion transporters for Zn, Fe, Mn, Cu, B, Mo, Ni, Cl, Na, Si, Se, Beneficial nutrients and their role in plant growth and development – Sodium, Silicon, and Cobalt. Unit 5: Microbes, Fungal Association for Nutrient Acquisition Microbes to improve nutrient availability – Bio-inoculation technology- P solubilizers and Zinc solubilizers in nutrient absorption, Microbial systems for biological nitrogen fixation – process of nodulation, biochemistry of N2-fixation, Endophytes to improve nutrient availability, Mycorrhiza- Mycorrhizal symbiosis on nutrient uptake by root. Role of AMF on nitrogen, phosphorus and zinc uptake. Nutrient Delivery Foliar application of nutrients, absorption and their compartmentation, Concept of slow release fertilizers and chelates (organic and inorganic), Soil less culturesaeroponics, hydroponics, fertigation. Nutrient Efficiency of Crop. Improving Nutrient Acquisition and Efficiency of Crops Concept of nutrient uptake and use efficiency- Genotypic differences- physiology and molecular mechanisms, Nutrient use efficiency in selected crops, Root system architecture (RSA), root characters associated with nutrient acquisition, Genes and QTLs to improve nutrient acquisition and efficiency for important nutrients in few crop species, Transgenic and molecular breeding approaches to improve traits associated with acquisition and efficiency – Case studies, Biofortification strategies – for micronutrients, agronomic approaches, Influence of nutrition status on plant response to biotic and abiotic stresses.

Practicals: Techniques to develop the deficiency symptoms of nutrients –Hydroponics/ Aeroponics- diagnosis of deficiency symptoms in agriculturally important crop plants; Physiological and biochemical markers to identify nutrient deficiency levels; Biochemical markers for essential elements: Assay of nitrate reductase activity for N; Estimation of chlorophyll concentration in leaves of N deficient and N sufficient plants; Collection of acid phosphatase from root exudates and enzyme assay for P; Measuring anthocyanin and chlorophyll pigments concentration in leaves for P; Collection of organic acid in root exudates, characterization and quantification for P; Assay of carbonic anhydrase activity for Zn; Assay of SOD Activity for Cu, Zn and Mn; Estimation of nitrogen concentration in plant tissue - Kjeldhal and Dumas method; Estimation of phosphorus concentration in plant tissue – colorimetric method; Estimation of potassium, magnesium and sodium concentration in plant tissue – flame photometer; Estimation of micronutrients (Zn, Cu, Fe, Mn, Co etc) concentration in plant tissue – atomic absorption spectrometer/ ICP-OES; Measurement of simple root traits such as root length, angle, volume, surface area, etc. (using conventional methods or root scanner and WinRhizo); ‘Shovelomics’ in the field grown crops (for measuring root architecture) and using ‘ImageJ’ for analysis; Non-invasive techniques to quantify nutrients – XRF (X-Ray Fluorescence) and hyper spectral reflectance.

1. Photosynthetic Processes, Crop Growth and Productivity and Concepts of Crop Modelling

Content:  Photosynthetic Processes; Canopy Architecture and Energy Utilization Parameters associated with canopy architecture that determine radiation interception and absorption, Energy absorption by primary and accessory pigments and energy utilization efficiency, Light distribution inside the canopy and concepts of light extinction coefficient. Photochemical Processes Ultrastructure of chloroplast: structure and composition of lamellar system, Components of electron transport, Water oxidation system and energy conservation processes, Pigment systems and the generation of a powerful oxidant and a powerful reductant, Chlorophyll fluorescence and fluorescence quenching: qN, qP, NPQ. Biochemical Processes CO2 diffusion and resistances (gs and gm). Concept of Ci determining CO2 diffusion. RuBisCO activation state, kinetics and catalytic properties, Carboxylation processes in C3, C4 and CAM plants and their relevance, CO2 concentrating mechanisms and their importance in improving carbon assimilation, Ecological significance of C4 and CAM photosynthesis, Photorespiration and Mitochondrial respiration and net carbon gain, Carbon isotope discrimination and its importance as a surrogate of Ci. Product Synthesis and Translocation Triose phosphate utilization and regulation of Calvin cycle mechanisms, Product synthesis and partitioning between starch and sucrose, Concepts of end-product inhibition or Pi-regeneration limitation, Phloem transport and factors that regulate phloem loading and un-loading. Growth and Yield forming Mechanisms Carbon gain and the concepts of Canopy photosynthesis. Relevance of LAI and LAD in determining total carbon gain and crop growth rates, Source: Sink relationship and its relevance in governing differences in crop growth rates and productivity. Concepts of HI and partitioning coefficient and remobilization of carbon from vegetative organs to reproductive structures, Growth analysis and parameters that explain growth rates: NAR, CGR, HI and their inter-dependence. Yield Improvement and Modelling; Molecular Options to Improve Photosynthesis, Growth and Productivity Characteristic features of the Chloroplast genome: its structure and genes associated with various photosynthetic mechanisms, coordinated expression of chloroplast and nuclear genome for maintaining photosynthetic activities. Genomic and genetic resources such as specific genes and QTL associated with photosynthetic processes Transgenic options to enhance photosynthetic performance such as transferring genes to mitigate oxidative stress damage (SOD, APX, AKR etc), Theoretical concepts of crop improvement through inducing CCM in C3 plants and reducing photorespiration. Fundamentals of Dynamic Simulation Models Collection of crop specific genetic coefficient, Crop, soil and historic weather data. Description of Well-established Yield Models Application and limitations of modeling, Yield prediction models such as APSYM, PeanutGrowetc, Machine learning approaches and IoT for making informed onfarm decisions. Examples of Robust Models Extensively Used Duncan’syield prediction model, Passioura’smodelfor growth maximising.

Practicals: Plant sampling for leaf area and biomass estimation; analysis of growth and yield parameters – LAD, NAR. CGR, LAI, LAR, SLA portioning efficiency, HI.; Measurement of light interception, light extinction coefficient, energy utilization efficiency based energy intercepted, and realized.; Gas exchange: principles and uses to assess variations in CO2 and water vapour transfer, determination of A/gs and intrinsic WUE; Quantification of chlorophyll content by various methods: colorimetric and SPAD meter. The concept of SLN; Chlorophyll fluorescence and quenching coefficients; Theoretical aspects of carbon isotope fractional and its use in determining WUE; Quantification of RuBisCO content by ELISA (if possible); Determination of RuBisCO activity and activation state using radioactive CO-2; CO2 and light response curves and computation of carboxylation efficiency, quantum efficiency, relative limitations of photosynthesis at single leaf level.; Adoption of crop models: Growth and yield prediction by Duncan’s and Passioura’s models.

1. Physiology of Field Crops

Content: Physiology of Field Crops; Introduction Origin- Variability in physiology of crop plants between wild species and cultivated. Adaptability to growing environments (ecosystems), Importance in food grain contribution. Crop Establishment, Crop Growth and Development Seed characteristic features, dormancy, viability, concept of seed priming seedling establishment and crop stand. Different crop growth stages, concept of source establishment and optimum LAI, Canopy architecture, light interception/radiation use efficiency, thermal time, heat units, GDD, determining growth duration. Reproductive Growth Photo and thermo-periodic response for flowering, sink development, sink source relationship, partitioning efficiency, improvement in HI, yield determining factors, genetic gain in yield over years, structuring of ideal plant type, limitations to improve source to sink size, options to improve yield potential. Seed Nutrient Quality Seed quality, seed as a source of nutrients, seed constituents and their improvement, concept of pathway engineering to improve seed quality. Plant Nutrition Nutrient requirement, genetic variability in nutrient acquisition under constraint conditions, specific nutrient disorders. Abiotic Stress Response Response to different abiotic stresses, plant traits/mechanics to improve adaptation to realize potential yields. Global warming responses, thermomorphogenesis, approaches to overcome the constraints. Crop Specific Physiological Processes and Importance Choosing location specific crop species exposure will be given on physiological process as described above. Besides, emphasis is on providing information on crop specific features/productivity constraints.

1. Physiology of Horticulture Crops

Content:  Physiology of Horticultural Crops; Introduction Origin, distribution and adaptability of crops to different agro-climatic conditions; Crop growth and Development Internal factors (hormone, etc.) influencing various physiological processes linked to vegetative growth or growth of specific organ, correlative and algometric growth External factors (water, nutrition, temperature, etc.) influencing various physiological processes linked to vegetative growth or growth of specific organ, correlative and algometric growth, Propagation methods, grafting, cutting, budding, air layering. Physiology of pruning, dwarfing, branch bending, canopy management etc., Physiological and biochemical aspects of scion and root stock interaction and compatibility. Reproductive Growth Physiology of flowering, photo- and thermo-periodism and response to vernalization, Factors influencing reproductive growth, fruit and seed set/retention, physiology of flower sex ratio, Physiological processes governing source-sink relationship and productivity. Pre and Post Harvest Physiology Preharvest factors influencing postharvest physiology, Physiological and molecular mechanisms of ripening, Physiological and molecular mechanisms of senescence, Hormonal and chemical control of postharvest deterioration of fruits/vegetable/ flowers. Regulation of ripening at physiological and molecular levels, Regulation of senescence at physiological and molecular levels, Approaches to improve shelf life and storability. Approaches to improve postharvest management, Approaches to improve processing and value addition. Plant Nutrition and Abiotic Stress Responses Nutrient acquisition and requirement, plant phenology and nutrient requirement; Role of rootstocks in nutrient acquisition and in abiotic stress tolerance, Adaptive mechanisms and approaches to improve performances under drought and high temperature, Adaptive mechanisms and approaches to improve performances under frost, chilling and nutrient deficient conditions, Root physiology in abiotic stress tolerance. Specific Aspects and Unique Crop Features Specific aspects Polyhouse cultivation, Hormones/PGRs for improving crop performance, Major and micronutrients for improving crop performance, Light interception, shade regulation, dwarfing root stocks, Chilling requirement for flowering, photoperiodic response, pollen viability, stigma receptivity, Flower (blossom) and fruit drop. Unique crop features Maturity and maturity indices, Source-sink relations, Vegetative propagation, Physiology of tuberization and rhizome initiation and formation, Virus free planting material, Bulbs/tubers dormancy, bud break, Physiological disorders, Storage, Packaging, Quality.

1. Seed Physiology

Content:  Physiology of Seed Development; Introduction to Seed Physiology Importance of seed as a propagule, seed structure and functions; chemical composition of seeds. Embryogenesis: pollination and fertilization, pollen and pistil interaction, signal for interaction; pollen load hypothesis; genetical and environmental influence on seed development. Source-Sink relationship affecting seed yield and quality. Concept of seed viability and seedling vigour and their relevance; approaches to improve the storability of seeds. Physiological and molecular mechanisms of seed germination; approaches to improve seed germination; seed size and its influence on seed germination. Seed Development Physiology and molecular mechanisms of embryo, endosperm and seed coat development; cellularization during endosperm development; morphological and cellular changes during seed coat development, anatomy and function of seed coat, programmed cell death (PCD) in seed coat, Deposition of seed storage reserves during development. Seed Maturation Seed maturation and maturation indices; physiological and anatomical changes during seed maturation; Seed drying and acquisition of desiccation tolerance in seeds; mechanisms of desiccation tolerance; role of ABA LEA’s, HSP’s, dehydrins and other stress proteins during seed maturation and drying, Seed abortion and approaches to reduce it. Metabolism in Developing Seed Chemical composition of seeds (carbohydrates, proteins, fats etc.), source of assimilates for seed development, pathways of movement of assimilates to developing seed, approaches to increase the chemical composition of seeds. Seed respiration and mitochondrial activity; seed respiration rate and storability of seeds. Seed ageing, Mobilization of stored resource in seeds; Chemistry of oxidation of starch, proteins and fats; Utilization of breakdown products by embryonic axis. Physiology of Seed Germination and Dormancy; Seed germination Seed germination, types of germination, imbibition kinetics of germinating seed; Physiological events during germination: seed respiration, mitochondrial activity, mobilization of food reserve; energy utilization by the germinating seed. Environmental regulation of germination: hydro-time, thermal time and hydrothermal time models; Influence of environmental factors on germination; Role of plant hormones/PGR’s during seed germination. Seed Dormancy and Viability Physiological and molecular basis of seed dormancy, hormonal regulation of dormancy, After ripening, dormancy breaking treatments; Ecological perspective of seed dormancy. Seed viability: concept and physiology of seed viability, theories of seed ageing, seed storage and regulation of storage life of seeds; methods to prolong seed viability; Conservation of orthodox and recalcitrant seeds. Seed vigour: concept, importance, measurement; Physiological, biochemical and molecular basis of seed vigour.

Practicals: Determination of seed reserves: carbohydrates, proteins and lipids; Study of different seed structures; Kinetics of seed imbibition; Seed germination test, enzymatic activities and respiration during germination and vigour testing methods etc. Accelerated ageing test to know the seed vigour and storability; Measurement of seed moisture content; Determination of amylase activity in germinating seeds; Measurement of electrical conductivity in seed leachate; Measurement of seed viability using tetrazolium chloride; Determination of dehydrogenase activity; Seed germination study- Determination of Germination Index and seedling growth; Measurement ofseed vigour index; Dormancy breaking treatments; Seed priming techniques; Effect of environmental stresses on seed germination and seedling growth; Effect of hormones on seed germination.

1. Phenotyping Physiological Processes

Content:  Phenotyping Physiological Processes; Concept of Phenotyping Phenotyping technologies are essential component for assessing plant responses, identify superior trait donors, mitigation responses, trait introgression and trait based breeding. Phenotyping for Traits for Crop Establishment Seed viability, seed dormancy, seed hydration rates, seed density and weight, Seedling vigour in normal and adverse conditions. Concept and Approaches to Identify Genotypes with Superior Growth Rate Phenotyping for leaf expansion, leaf area index, light interception and crop extinction coefficient. Pigment quantification for nitrogen and chlorophyll status - SPAD, anthocyanin and flavonoids – Duolex. Growth rates by non-invasive techniques like NDVI, Concept of Net assimilation rate and DM/LAD; surrogates for photosynthetic traits; stomatal characteristic. Identifying Photo-insensitive Genotypes-options and Approaches Exposing to longer and shorter photoperiod by staggered sowing; extending the day length- light interception by red light; days to heading/ anthesis, approaches for synchronization of flowering. Identifying Thermo-insensitive Genotypes-options and Approaches Altering total degree days- staggered sowing at lower latitudes or by growth chambers; quantifying heading, anthesis, maturity and grain filling days, grain number and weight, grain filling rate. Yield Structure Analysis- Relevant Yield Attributes Pollen biology, stigma receptivity, spikelet sterility (cereals), floral abscission (other crops), fruiting points / productive tillers, number of grains/ fruits per panicle/ inflorescence and grain characteristic. Phenotyping for lodging- culm traits, intermodal length, lignification, Phenylalanine ammonia lyase (PAL) and Tyrosine ammonia lyase(TAL). Approaches to identify genetic resources with traits to improve yield potential. Source-sink Relationship- Assessment of Limitation Phenotyping for source-sink size, Concept of sink-source limitation- defloration and defoliation. Remobilization of stored metabolites and concept of stay green; estimation of water soluble carbohydrates; partitioning coefficient and harvest index. Identify Genetic Resources for Abiotic Stress Constraints Approaches for precise stress imposition to diverse stresses, Identify trait donor lines for different stresses: approaches by Stress Susceptibility Index (SSI), Stress Induction Response (SIR), Capturing variability for adaptive traits: root traits, stomatal factors/wax, osmolyte, surrogate approach for acquired tolerant traits, Flowering response, Spikelet fertility, Abscission and Senescence, Screening high density response-based on SSI – root adaptation and Shade Avoidance Response (SAR).

1. Crop Growth Regulation and Management

Content:  Propagation - Crop Establishment; Seed as a Propogule Concept of improving seed characteristics for crop establishment. Mechanisms of regulating seed dormancy, precocious germination, ways to control pre-harvest sprouting in crop plants. Seed viability and its regulation, factors to minimize loss of viability and improve seedling vigour. Concept of seed priming, techniques of priming, seed priming to induce tolerance to stresses. Role of media, nutrition and PGPR’s on seedling vigour and subsequent crop establishment. Vegetative Propogule Chemical and hormonal regulation of vegetative propagation. Regulation of rooting, bud sprouting, Bulb/tuber dormancy. Chemical regulation of graft union. Concept of in vitro micropropogation. Regulation of Plant Growth Processes; Regulation of Plant Growth and Flowering Chemical and hormonal regulation of plant architecture, tillering, branching, bud breaking, Regulation of flowering by photo and thermoperiod, nutrients, chemicals and hormones, concept of speed breeding, Flowering synchrony in hybrid seed production, Sex ratio alteration, flower and fruit thinning, Pollen viability in relation to environment, harvesting, storage and transportation, Prevention of abscission, flower and fruit drop, seed and fruit growth regulation- role of hormones. Fruit Ripening and its Regulation Approaches to improve shelf life – storage environment, water loss, respiration, Modified atmosphere, gaseous environment for storage, storage disorders, chilling injury. Concept of Senescence and its Retardation Physiology of senescence and options to regulate, Chemical regulation of senescence, maintenance of chlorophyll during storage, role of hormones/micronutrients in reducing senescence, Concept of stay green, advantages and limitations. Relevance of stay green traits in plant breeding for crop improvement. Protective Cultivation–Stress Mitigation; Protective Cultivation Interventions to Alter Physiological Processes and Growth Spectral characteristics of light in polyhouse, light regulation to optimize plant photosynthetic and photomorphogenic processes and plant growth, LED sources of monochromatic light to regulate growth, etiolating and flowering, High temperature induced thermomorphogenic processes, Artificial growing media, soilless cultures, aeroponics, fogoponics, Concept of CO2 fertilization. Effect of humidity on leaf expansion and growth. Drought Mitigation Options and Approaches Moisture conservation options at soil and plant level, Concept of increasing water holding capacity, role of Hydrogels – water and mineral nutrients release pattern. Approaches to improve transpiration over evapo-transpiration, stomatal and nonstomatal regulation of water loss, antitranspirants, Osmoprotectants, ROS scavengers, plant nutrients, Root stocks in improving tolerance, Chemical regulation of flower drop due to temperature, Chemicals to improve pollen viability during abiotic stress. Specific Plant Processes Regulated by Chemicals and Growth Hormones Rooting of cuttings, Wine brewing industry, Promotion of gynoecious flower, Hybrid rice production, Induction of flowering in pine apple, cucurbits, Delaying of senescence and ripening, Production of dwarf plant for ornamental purpose, Reduction in flower and fruit drop, Increase in berry size in grapes.