CIMAP - JNU Ph.D.

PROGRAMME
SYLLABUS FOR PRE - PhD COURSE WORK STRUCTURE OF COURSE CREDIT DISTRIBUTION OF CIMAP - JNU PRE - Ph.D. PROGRAMME FOR THE AWARD OF Ph.D. DEGREE IN LIFE SCIENCES OF JAWAHARLAL NEHRU UNIVERSITY, NEW DELHI AT CIMAP Pre - Ph.D programme for the award of Ph.D. degree in Life sciences (Plant Sciences, Biotechnology and Bioinformatics and Chemical Sciences) of Jawaharlal Nehru University, New Delhi will be of total 19 credits. The over all structure of the course credit distribution will be as follows: 1. Major Courses (Three) credits 2. Minor courses (Two) credits 3. Seminar credit 4. Cross discipline laboratory credit Orientation & its utilization 5. Project assignment credits Three credits each (2 + 1) Two credits each One credit One credit (1 +1) 9 4 1 1

Two credits

4

A student is required to qualify five courses (three core courses and two optional courses) during the course duration of two semesters. A student has the option of selecting any three core courses (total nine credits) out of four from his / her own discipline and two optional courses (total four credits) from any of three disciplines out of the courses prescribed in syll abus. Each core course carries three credits each with 2 + 1 scheme (two credits for theory and one credit for practical) and each optional course carries two credits each with 1 + 1 scheme (one credit for theory and one for practical ). Each credit comprises of minimum of 12 lectures or 12 practicals. Thus, in each core course in each discipline as stated below there will be a total of twenty four lectures (two credits) and 12 practicals (one credit) and in each optional course there will be twelve le ctures (one credit) and twelve practicals (one credit). A candidate has the option to choose optional courses from any of the three disciplines (Plant Sciences, Biotechnology & Bioinformatics and Chemical Sciences) of his / her choice from the pre scribed courses in consultation with guide, but preferably it should be from cross discipline area. Seminar (1 credit), cross discipline laboratory orientation and its utilization (1 credit) and project assignment (4 credits) are mandatory for all students admitted in various disciplines.

INSTITUTIONAL [CIM] *
CIM 100 CREDIT CIM 200 CREDIT SEMINAR CROSS DISCIPLINARY LABORATORY 1 (1 +0) 1 (0 +1)

ORIENTATION AND ITS UTILIZATION CIM 300 PROJECT ASSIGNMENT CREDITS TO BE OFFERED IN EACH SEMESTER

4 (0 +4)

COURSES OFFERED FOR PRE - Ph.D. WORK IN DIFFERENT DISCIPLINES

CORE COURSES CREDITS
PLANT SCIENCES [PSC]
SEMESTER – I PSC 201 credits PSC 202 credits SEMESTER – II PSC 203 credits PSC 204 credits Fundamentals of plant protection Agriculture economics and extension

TOTAL 9

Principles of plant breeding and its application Principles of crop production

3 (2 + 1) 3 (2 + 1)

3 (2 + 1) 3 (2 + 1)

BIOTECHNOLOGY AND BIOI NFORMATICS [BTB] SEMESTER – I
BTB 201 credits BTB 202 credits Fundamentals of molecular genetics Bio – informatics 3 (2 + 1) 3 (2 + 1)

SEMESTER – II
BTB 203 credits BTB 204 credits Principles and techniques of plant molecular biology Plant biotechnology 3 (2 + 1) 3 (2 + 1)

CHEMICAL SCIENCES [CSC] SEMESTER – I
CSC 201 credits CSC 202 credits Natural products chemistry Analytical chemistry 3 (2 + 1) 3 (2 + 1)

SEMESTER – II
CSC 203 credits CSC 204 credits Advances in synthetic chemist ry Advances in extraction and processing technologies 3 (2 + 1) 3 (2 + 1)

OPTIONAL COURSES CREDITS
SEMESTER – I
PSC 101 credits PSC 102 credits BTB 101 credits BTB 102 credits CSC 101 credits CSC 102 credits SEMESTER – II PSC 103 credits PSC 104 credits BTB 103 credits BTB 104 credits CSC 103 credits CSC 104 credits Post harvest technology Agro physiology

TOTAL 4

(1 + 1) (1 + 1)

Plant tissue culture techniques Biochemistry

(1 + 1) (1 + 1)

Modern instrumentation Structure elucidation of organic molecules

(1 + 1) (1 + 1)

Principles of plant taxonomy and pharmacognosy Basic and applied statistics

(1 + 1) (1 + 1)

Microbiology Basic genetics

(1 + 1) (1 + 1)

Chromatographic techniques Pharmaceutical chemistry

(1 + 1) (1 + 1)

CIMAP - JNU Ph.D. PROGRAMME
SYLLABUS FOR PRE - Ph.D COURSE WORK
CORE COURSES TOTAL 9 CREDITS

PLANT SCIENCES [PSC]
PSC - 201 PRINCIPLES OF PLANT BREEDING AND ITS APPLICATION [2 + 1 CREDITS]
SEMESTER – I THEORY [2 CREDITS] Evolution, domestication, introduction centers of origin and ge ne introgression Reproductive systems, pollination control and breeding plans Genetic concepts in breeding self pollinated crops Selection under self fertilization. (Pure line theory). Consequences of hybridization. Inheritance of quantitative traits. Role of genotype and environment in continuous variation. Genetic basis of breeding open pollinated plants Systems of pollination control. Systems of mating and their consequences Theory of selection Responses to selection and genetic organization Heterosis and inbreeding depression. Designing model cultivar - ideotype concept Breeding methods with self pollinated crops . (pure line breeding and mass selection, pedigree method, bulk population and back cross breeding, multiline, population breeding approach (diallel selective mating), rapid isolation of homozygous lines, Hybrid varieties - male sterilities) Breeding methods with crops pollinated crops Selection in cross pollinated crops. Hybrid varieties. Recurrent selection Synthetic composites varieties. Principles & methods of breeding for resistance to diseases & pests, herbicides pollutants and adverse climatic conditions Assessment of variability, components of variance, genetic diversity, relationship and path coefficient, diallel, line x tester, g eneration mean, biparental cross analysis, North Carolina design I, II, III, Triple test cross, different models for varietal adoptation Polyploidy in plant breeding; Aneuploidy (nullisomics, monosomics, trisomics, monoploids and haploids), autoplyploid y, allopolyploidy, classical examples: evolution of bread wheat. Nicotiana tobacum, Gossipium hirsutum, amphideploids in Brassica species

Biotechnology in plant breeding , tissue and cell culture, genetic engineering, embryo culture, anther and pollen cul ture somatic hybridization, molecular markers Consequences of inter -specific and distant hybridization Mutation breeding Evaluation, maintenance of varieties, quality seed, seed industry, seed act, seed production, processing, seed testing IPR, PBR, UPOV conventions and recent developments PRACTICAL [1 CREDIT] Floral biology in self and cross pollinating plant species, selfing, crossing and maintenance of cross pollinating populations with special reference to breeding work in medicinal and aromatic plants ANOVA, means, variances, partitioning of variances in various models, analysis in NC designs, diallel and line x tester Estimation of genetic diversity through D 2 statistic, correlation, hertability, and genetic advance, stability analysis using different models Seed testing for germination, creation and screening plants for biotic and abiotic stress, estimation of oil content, and secondary metabolites in major medicinal and aromatic plants

PSC - 202

PRINCIPLES OF CROP PRODUCTION [2+1 CREDITS]
THEORY [ 2 CREDITS ] SEMESTER - I PART- I

Principles of crop production; Crop plants in relation to environment; G x E interaction Factors determining crop distribution; Agroclimatic zones of India; Agronomic practices and crop productivity Principles of weed control, crop -weed competition; herbicides - formulation, classification, selectivity and mode of action; Zero/minimum tillage. Allelopathy in agriculture Soil-water-plant relationship; Soil water constants; Measurement of soil moisture; methods of scheduling irrigation. Methods of irrigation, Strategies for minimizing water losses under field conditions; Micro irrigation system Dryland agriculture; Soil moisture stress and plant growth; drought resistance in crops; Soil moisture conservat ion techniques; Cropping system approach for maximizing crop productivity Concept of crop rotation; Intercropping and multistorey cropping Agroforestry - concepts and methodology; Production management of field and commercial crops under agroforesty; cro p diversification Crop modelling in agronomic systems; Biodiversity and environmental conservation

PART – II Soils - their origin, morphology, composition and nature Physical, chemical and biological properties of soil Factors and process for soil fo rmation; Classifications of soils; major soils of India Criteria of essentiality of nutrients, Mineral nutrition of crops, functions of nutrients in plants; Macro - and micro-nutrients in soils Fixation, biological and chemical transformation and release of nutrients in soils Soil fertility evaluation, Manures and fertilizers, Organic farming Problem soils, salt affected, waterlogged and acid soils; Soil amendments, Quality of irrigation water Soil organic matter and its dynamics Instrumental methods of analysis of soils, plant and water Biological N fixation, Natural P solubilization & fixation PRACTICAL [1 CREDIT] Soil sampling and processing Soil test procedures (Mechanical and Physico -chemical) Soil Analysis (organic C, P H, Ec, CEC, major, micro and heavy metals) Determination of nutrients (P, K) fixing capacity of soil Plant sampling, Plant Analysis (for N, P, K, Fe, Cu, Mn, Zn and h eavy metals) Water Quality Assessment for Irrigation ( P H, Ec, SAR, RSC, hardness, B, NO3) Instruments Used in Soil, Plant and Water Analysis (UV -VIS spectrophotometer, AAS, ICP, Flame photometer) Microbiological analysis of soil (Bacteria, Fungi, Actinomycetes, Total microbial biomass)

PSC - 203

FUNDAMENTALS OF PLANT PROTECTION [2 + 1 CREDITS]
THEORY [2 CREDITS] SEMESTER - II PART- I

I. Principles of Plant Pathology An overview of plant pathology, plant disease definition, mode of infection of plant pathogens, disease symptoms and disease cycles and plant disease diagnosis including principles (Koch ’s postulates) Disease epidemiology: definition, scope and models, historical development, quantitative measurement of disease, host, pathogens and environment Fungal & Bacterial pathogens: characteristics, classification, identification and diseases they cause Viruses and Phytoplasma: characteristics, classification, identification and diseases they cause

Factors leading to disease build-up:Inoculum potential, humidity, temperature Ii. Host –Pathogen Interaction Enzymes (cellulolytic & pectolytic) , and phytotoxins (host specific & non host specific) as weapons of the plant pathogens Plant defense mechanisms in plant against plant pathogens such as anatomical modification (lignifications, suberization & callose formation), phytoalexin and PR prot ein accumulation III. Principles of Plant Disease and Insect Pest Management Preventive measures Cultural practices: Sanitation, soil solarization, crop rotation, organic amendment Plant Quarantine: Plant resistance: Types, breeding approaches a nd uses of resistant variety Curative measures Disease control chemicals: History; major groups of chemicals (pesticides, fungicides, nematicides, bactericides, viricides & biocides), chemistry, mode of action and method of application Biological control: principles and overview , biocontrol agents (fungal antagonists, arbuscular mycorrhizae, actinomycetes and PGPRs) and their application Biotechnological approaches: A case study of BT -cotton PART- II Types of insect-pests Insect-pests of agricultural importance Insect-pests of medical importance Insect-pests of veterinary importance Beneficial insects – honey bee, lac insects, silkworm etc. Insects as vectors – whitefly, aphids, thrips etc. Classification of insects based on feeding habits and as diseas e vectors Biting and chewing type Sucking insects Piercing and rasping type Nature of damage Economic threshold In plants – viral diseases In humans – viral and parasitic diseases Chemical control: Insecticides Classification of insecticides based on che mical nature Classification of insecticides based on mode of action Structure-activity relationships Ecological approaches in insect -pest management Insect chemical communication

Insect-insect and insect-plant interactions Ecological niche Tritrophic relationships Organic pest control & Quarantine Use of parasites and predators Use of botanicals Use of cultural practices Quarantine control Biotechnological approaches in insect -pest management Applications of bacteria, viruses, fungi and nematodes in inse ct control Genetic control – sterile techniques Transgenic PRACTICAL [1 CREDIT] PART - I Diagnostic symptoms and signs of fungal, bacterial, viral, phytoplasma and nematode diseases Pathogen isolation, culture maintenance, methods of culture preservati on media preparation, sterile techniques, etc Study on cultural as well as morphological characters of different plant pathogens, their identification through classical and molecular methods Establishment of Koch's postulates for the diseases they cau se In vitro production of enzymes and phytotoxins by fungal and bacterial pathogens and their role in pathogenesis Bioinoculant isolation, culture maintenance, screening for antagonistic and plant growth promotion activity, in vitro and in vivo efficacy t est and their formulations Fungicides, protectant and systemic: efficacy test in vitro & in vivo and mode of application PART - II Identification of major insect -pests of agricultural, Identification of major insects pest of storage and medical importa nce Insects as models for drug research: Drosophila Morphology Life stages Mutants utility in research

PSC - 204

AGRICULTURE ECONOMICS AND EXTENSION [2 + 1 CREDITS]

THEORY [2 CREDITS] SEMESTER – II PART-1 Agriculture Economics: Scope and method of ag riculture economics Demand, supply, factor affecting demand and supply Price fluctuations & price determination Introduction to farm management Principles of farm management Cost concepts & principals, Risk and uncertainty Farm planning and Budgeting Introduction to marketing and agriculture marketing, Marketing and markets Marketing function, Market structure and conduct Surpluses in marketing and price spread Marketing efficiency & Integration, Marketed and Marketable surplus Role of government in promot ing agricultural marketing Introduction to agricultural finance and banking Agriculture prices, International trade Diversification and sustainability PART - II Extension Education: Extension Education- Scope, importance, process, principles, philosophy and objectives. Rural development- meaning, objectives, Major agricultural extension system and Transfer of Technology projects in India. Public Private Partnership model (PPP) including forward and backward linkages eg. Bio-village approach, Broad Based extension system- its feature. Roles and functions of voluntary and non-governmental organization, Co -operatives, Youth clubs, Mahila mandals, SHGs and Schools. Participatory Technology Development meaning, principles and approaches. Role of co-operatives and banks in rural development. Methods of communication and technology dissemination. (2L) Programme planning- nature, scope, principles, objectives, importance, steps. Evaluation- Degrees, steps, keys, - Monitoring and evaluation techniques and tools in the evaluation of different agriculture development programmes. PRACTICAL [1 CREDIT] PART – I
Farm Management, Farm financial management

Agriculture Marketing and commodity price, Marketed and Marketable surplus PART – II

Organisational pattern, Role and responsibilities of Panchayat Raj system, State Department of Agriculture- District Rural Development Agency, Co -operative societies, developing village level agricultural production plan , Study of Biovillages.

BIOTECHNOLOGY AND BIOINFORMATI CS [BTB]
BTB - 201 FUNDAMENTALS OF MOLECULAR GENETICS [2 + 1 CREDITS]
SEMESTER - I THEORY [2 CREDITS] Basic concept: life forms from prokaryotes to eukaryotes; molecules, building blocks, macromolecules and cells, genomes and genes; the similarities and distinguishing characters. Bacteria, viruses, plasmids, trasposons and vectors for molecular genetics studies. The genetic material: definition, pre -requisites, nature, structure and functions – experimental evidences and land mark discoveries. Perpetuation and utilization of genetic material: replication, transcription and translation process. Gene transfer in prokaryotes: transformatics, conjugation and transduction. Genetic variation: mechanisms and use of mutation, recombination and segregation. Genetic code: nature, deciphering and application. Forward and reverse genetics approaches for genetic analysis and gene manipulation. Principles of genetic and physical mapping Microbial Genetics: Application in agriculture, medicine and industry. Eukaryotic genome organization: nucleosome concept, chromosome organization, Genome size, C -value paradox and repetitive DNA Gene structure and organization; split genes, concept of introns and mobile genetic elements. Distinctive features of eukaryotic DNA and chromosome replication, processes of transcription and translation Basic models of gene expression and regulation: prokaryotes to eukaryotes. Application of molecular genetics and genomics tools in genotype designing and drug discovery.

PRACTICAL [1 CREDIT] Strain purification and genotype - phenotype understanding in bacterial system

Growth kinetics and measurement methods for bacteria and understanding of antibiotics action and drug resistance basis. Bacteriophage multiplication as a model for viral repl ication and genetics Gene transfer experiments in bacteria: transformation, conjugation and transduction. Use of vectors: plasmids, cosmids, phages and transposons, etc. Transformation in plants, Agrobacterium mediated electroporation and biolistic methods. Induced mutagenesis in bacteria: chemical and transposon mediated; mutant selection, isolation and characterization. Genetic complementation experiments using mobilized genes in bacterial merodiploids. Genomic and cDNA library construction and screenin g for targeted genes and functions through reverse genetics approaches including PCR and hybridization methods. Gene cloning, restriction analysis and DNA sequencing methods for physical and genetic maps.

BTB - 202

BIO - INFORMATICS
SEMESTER - I

[2 + 1 CREDITS]

A.

THEORY [2 CREDITS] Biological databanks & sequence analysis Introduction to Bioinformatics; Genomics; Proteomics; Structural Genomics; Pharmainformatics; Pharmacogenomics; Biodiversity; System Biology. Biological databases including Nuclei c acid sequence data banks:Genbank, EMBL nucleotide sequence data bank, Protein sequence data banks: NBRF -PIR, SWISSPROT, NCBI’s Entrez, OMIM. Dynamic Programming methods for global and local alignments (NEEDLEMAN and Wunsch, Smith Waterman algorithms), PS I-BLAST algorithms. Database searching - BLAST, FASTA, Statistical and Biological Significance, Scoring Matrices. Nucleic Acid Sequence Analysis —Reading Frames; codon usage; Translational & Transcriptional signals, gene prediction methods. Multiple sequence alignments – CLUSTALW, T-Coffee Computing evolution: Phylogenetic analysis. Sequence-Function Relationship Sequence Homology and conserved regions, conserved DNA sequences: Promoters, Restriction sites, RNA folding patterns, Protein Motifs, Domains, and GCG pattern recognition tools: FINDPATTERNS, MOTIFS, PROFILESCAN, MEME, Other pattern recognition software. Derived Databases of patterns, motifs and profiles: Prosite, Blocks, Prints-S, Pfam, etc.; Primer Design] Concepts in computing & computer prog ramming

B.

Fundamentals of computer, Concepts of Hardware & Software, Boolean Algebra, Operating system, Internet Programming Languages for Bioinformatics:’C’,’Perl’, Matlab Programming, Introduction to Relational database management system, SQL]. C. D. An introduction to statistics for bioinformatics Computational biology Anatomy of Proteins - Ramachandran plot, Secondary structures, Motifs, Domains, Tertiary and quaternary structures, Principles of Protein Folding Structural data banks - Protein Data Bank. Secondary structure prediction algorithms, Methods for Prediction of Secondary and Tertiary structures of Proteins – Homology modeling, Fold recognition, Ab initio methods for structure prediction. Methods for comparison of 3D structures of proteins; M ethods to predict three dimensional structures of nucleic acids. Molecular modeling Concepts of Molecular Modeling, Molecular structure and internal energy,Application of molecular graphics, Energy minimization of small molecules, Empirical representa tion of molecular energies, Use of Force Fields and MM methods, Local and global energy minima. Techniques in MD and Monte Carlo. Simulation for conformational analysis. Ab initio, DFT and semi-empirical methods Docking and Drug Design of ligands. Classica l SAR/QSAR, 2D and 3D data searching. Genomics & proteomics Genomics- Genome sequencing technology, Whole genome analysis, Comparative genomics -Paralogs and orthologs, Phylogenetic profiling, Pathway analysis, Repeat analysis, Human genetic disorders, Candidate gene identification, Linkage analysis, Genotyping analysis, SNPs and their applications Proteomics- Introduction to basic Proteomics technology, Bio informatics in Proteomics, Gene to Protein Function: a Roundtrip, Analysis of Proteomes, Analysi s of 2-D gels, Protein to Disease and Vice Versa, Human Genome and science after Genome era. Protein structural genomics Microarray Analysis: Basics of designing a microarray, Microarray in Bioinformatics, target selection, image analysis, normalization, Variability and replication, clustering, Microarray databases. Commercial bioinformatics Definition of Bioinformatics companies. Genome Technology: high throughput sequencing and assembly. Genomics in agriculture, medicine, disease monitoring, profile f or therapeutic molecular targeting. Diagnostic drug discovery and genomics. Pharmacogenomics and its application.. Proteomics in medicine and its applications. Patenting and data generation from patent literature for commercial benefits. IPR and bioinforma tics. Bioinformatics patents.

E.

F.

G.

PRACTICAL [1 CREDIT] Explore Biological databases BLAST & Advance BLAST options Use of similarity, homology and alignment softwares Usage of software for computational biology Practical exercises for Programming in ‘C’’Perl’ Database Design. RASMOL, MOLMOL, Chimera, Hyperchem and other MM/MD software. Software of Microarray analysis – design, processing and analysis

BTB - 203

PRINCIPLES AND TECHNIQUES OF PLANT MOLECULAR BIOLOGY [2 + 1 CREDITS]

SEMESTER - II THEORY [2 CREDITS] Basic concept of metabolism in life processes a. Macro molecules and their interaction for cellular functioning b. Primary and secondary metabolism: need and pathways in plants Genetic make up of plant genome a. Nuclear and organelle genomes b. Chromosomes: Structure and function Genes structure and regulation a. Gene structure and elements b. Regulatory elements (cis and Trans) General models of gene expression and regulation Methods of genetic engineering in plants a. Isolation and utilization of genes. b. Transgenic developments: Methods and problems c. Recent approaches for directed gene modifications Development and differentiation in plants a. Physiological and biochemical basis b. Genetic regulation of spatial and temporal deve lopment Secondary metabolism in plants a. The house keeping functions of genes b. Defense related functions of genes c. Metabolic pathways and genes Functional genomics and beyond Defining the genome: from size to functions DNA fingerprinting to mark ers for gene tagging Expression analysis at transcriptome and proteome level Pathway engineering in medicinal and aromatic plants a. Alkaloids b. Terpenoids c. Others

PRACTICAL [1 CREDIT] DNA RNA isolation and handling Reverse transcription PCR (RT -PCR) cDNA libraries & EST analysis Southern Hybridization Automated DNA sequencing & Synthesis RAPD and AFLP Real time expression analysis Microarray analysis for function ID and 2D electrophoresis Protein structure and function through MALDI -TOF-TOF.

BTB - 204

PLANT BIOTECHNOLOGIES [2 + 1
CREDITS]
SEMESTER - II

THEORY [2 CREDITS] Plants, genes and crop biotechnology – Basic perspectives Strategies for plant improvement – passage from conventional to modern genomic tools Molecular plant breeding – molecular markers and marker assisted selections Manipulation of gene expression Plasmids, vectors and designer gene constructs Techniques for plant transformation – principal and theory Characterization of transgenics Molecular pharming through metabolic en gineering a. Terpenoids b. Alkaloids c. Flavonoids d. Nutraceuticals Recombinant specialty crops for therapeutic proteins and vaccines Transgenic research - ecological impacts, public perception and economics Bio-safety, Regulatory and, IPR considerations for plant biotechnology PRACTICAL [1 CREDIT] Handling and processing of Agrobacterium strains for plant transformation Methods of gene transfer Purification and restriction analysis of plasmids Developing plasmid and gene constructs and their mobilization . Confirmation of transformation (GUS assay, Southern hybridization, RT-PCR) Multiplication and maintenance of transgenics

CHEMICAL SCIENCES [CSC]
CSC - 201 NATURAL PRODUCTS CHEMISTRY [2 + 1 CREDITS]
SEMESTER- I THEORY [2 CREDITS] Natural Product Chemi stry and its importance in our life Classification and chemotaxonomy of Natural Products. Activity guided fractionation, isolation and characterization of leads from natural products Principles and applications of Flash, Low pressure, Medium pressure and Over pressure liquid chromatography Recent advances in drugs from tradition plants
13

CNMR Spectroscopy: An extremely dependable probe in the structure elucidation of natural products Structure elucidation of natural products by EI/CI -MS, FAB-MS Hybrid Instruments for Structure elucidation of natural products by LC MS and LC-MS/MS Resolution of enantiomeric mixtures Separation methods in carbohydrates Biogenesis of Steroids, Terpenoids and Carbohydrates Chemistry of Steroids and Triterpenoids Introduction of essential oil: Chemistry of essential oils (structure of mono and sesquiterpenes), occurrence and their isolation processes like cold-press, distillation, enflurage, preparation of concrete and absolute. Quality control in essential oils: Physico -chemical properties, specific gravity, refractive index, solubility, acid value, ester value, ester value after Acetylation and their determination. Analysis of essential oils by GC and GC -MS. Chemistry of essential oils of commercially important aromatic plants Mints and Cymbopogon species as case example. Extraction and isolation of Plants Secondary Metabolites (PSM) Column chromatographic techniques and various adsorbents used in the purification of PSM Advancement in NMR methodology for characterizing PSM Alkaloids used as “Abuse Drugs” Natural Products used in Forensic Science Methods of Natural Products up scaling from Lab to Industrial scale.

PRACTICAL [1 CREDIT] Selection of suitable solvent for extraction of Alkaloids and Saponins Acid-base extraction and fractionation of alkaloids at different pH TLC profiles of alkaloids extracted at different pH. Selection of suitable solvent for extraction of saponins Fractionation of saponin crude extract with different polarity solvents TLC profile of various sapon in fractions Selection of a suitable column and adsorbent for Vacuum Liquid Chromatography (VLC) Packing of VLC column, elution, monitoring and pooling of fractions on the basis of their TLC profile. Selection of adsorbent and preparation of rotor for Chromatotron. Loading of natural product on the rotor, elution of column, monitoring and pooling of fractions on the basis of their Chromatotron TLC profile. Determination of Physical Constants of Essential Oils Determination of Chemical Properties of Essen tial Oils

CSC - 202

ANALYTICAL CHEMISTRY [2 + 1 CREDITS]
THEORY [2 CREDITS] SEMESTER - I

Chemical Separation in Analytical Chemistry: Principles, Techniques and Experiments Modern Thin-Layer Chromatography: practical aspects. Planner chromatography in p lant sciences Statistical assessment of Analytical Data High performance liquid chromatography: principles. Column theory Detection techniques. HPLC methods in natural products Pharmaceutical chemistry Biotechnology Development and Validation of HPLC met hods for drug substances and drug product. HPLC Operational troubleshooting: Instrumental and Chemical considerations Introduction to NMR and NMR Parameters. One Dimensional Experiments: 1H NMR, Carbon -13 NMR and Carbon13 Editing Two Dimensional Experimen ts: Homonuclear Correlations, Heteronuclear Correlations Principle and Methodology: Gas Chromatography GC-MS LC-MS / MS: Principles and application in Natural Products Counter Current Chromatography: Principle and its application in Natural Product Separation Centrifugal Partition Chromatography: Principle and its application in Natural Product Separation

PRACTICAL [1 CREDIT] Development of a suitable solvent system for the better separation of constituents; Preparation of samples and loading on HPTLC pl ate. Multi-wavelength scanning of HPTLC plates Data acquisition and estimation of bioactive c onstituent in the various plant samples using HPTLC. Selection of suitable HPLC column HPLC Method development Sample preparation for HPLC Quantification of bioactive constituent in the extract.

CSC - 203

ADVANCES IN SYNTHETIC CHEMISTRY [2 + 1 CREDITS]
SEMESTER - II THEORY [2 CREDITS]

Total synthesis of natural products Chemical transformation of bioactive natural products into compounds having potential biological activities. Combinatorial Chemistry: Basic principle, solid phase synthesis, resin and linkers for solid phase synthesis, solution phase synthesis, parallel synthesis, analytical techniques. Name Reactions in organic synthesis: Aldol condensation, Arndt-Eistert synthesis, Baeyer-Villiger rear., Barton-Mccombie reaction, Beckman rearrangement, Benzidine rear., Benzilic acid rear., Cannizaro reaction, Chichibabin reaction, Claisen -Schmidt reaction, Dakin reaction, Darzen’s condensation, Dickmann condensation, Ene reaction, Favorskii Rearr., Pinacol -pinacolon rear., Fischer Indole synthesis, Friedel-craft reaction, Fries rear., Mannich reaction, McMurry reaction, Peterson reaction, Heck reaction, Sharpless epoxidation, Jacobson epoxidation, Sharpless dihydroxylation, Swern oxidation, Wittig reaction, Witiig rear., etc. Reagents for Oxidation: Jones reagent, Pyridine chlorochromate, Collins reagent, Serette’s reagent, Corey’s reagent, Selenium dioxide, Potassium permanganate, m-Chloroperbenzoic acid, Swern oxidation, Osmium tetraoxide etc. Reagents for Reduction: Catalytic hydrogenation, Pd -C, Raney Nickel, Lindlar’s catalyst, Wilkinson’ catalyst, Sodium borohydride, Lithium aluminium hydride, DiBAL, Sodium cyanoborohydride, Na -NH3, Clemmensen reduction, Wolff-Kishner reduction, Aluminium alkoxides. Miscellaneous reagents: Diazomethane, poly phosphoric acid, Gilman reagents, Lithium diisopropylamide (LDA), DABCO, Butyl lithium, DCC, EDC, HOBt, Potassium t -butoxide, Phase transfer catalysis, Crown ethers, Baker’s yeast, p-TSA, Diazomethane, N-bromo succinimide, PPA, DBU, DDQ, Trifluoroacetic acid etc.

Protection and deprotection of functional groups in organic synthesis: Reagents for protection and deprotection of alcohols, phenols, carbonyls, carboxylic acid groups, amino groups in organic synthesis. PRACTICAL [1 CREDIT] Oxidation of secondary alcohols. Oxidation at allylic and benzylic positions. Reduction of aldehydes and ketones. Reduction of carboxylic esters. Protection of phenolic groups by etheri fication. Protection of phenolic groups as esterification. Protection of alcohols. Protection of carboxylic acids.

CSC - 204

ADVANCES IN EXTRACTION AND PROCESSING TECHONOLOGIES [2 + 1 CREDITS]
SEMESTER - II THEORY [2 CREDITS]

Methods of distillation, Enfleurage, maceration and extraction with volatile solvents, Supercritical extraction, Hydroflurocarbon extraction, Microwave extraction Fractional distillation of essential oils, etc. Processing technologies of MAPs. PRACTICAL [1 CREDIT] Pilot scale processing of medicinal plants o Drying and grinding o Extraction of plant material using different solvents under various conditions. o Fractionation o Distillation of solvent under reduced pressure under optimum conditions. Processing of essential oils from a romatic plants by hydro distillation o Steam distillation, o Maceration o Extraction by solvent. o Fractionation

OPTIONAL COURSES CREDIT TOTAL 4
PSC - 101
POST HARVEST TECHNOLOGY [1 + 1 CREDITS] SEMESTER - I THEORY [1 CREDIT]

Overview of post-harvest handling a. Extent of post harvest losses b. Importance and advantages of appropriate technologies Harvesting of produce a. Concept of maturity b. Maturity indices c. Pre-harvest quality modifiers d. Trimming, cleaning and drying technologies Post-harvest physiology a. Physiological disorders i. Development ii Identification iii. Control Post-harvest diseases and losses by insects a. Types of diseases b. Source of infection c. Factors affecting disease development d. Losses by insects Prevention techniques for post-harvest losses a. Storage techniques b. Biorational approaches Value addition a. Standardization, improvement of quality b. The production process and marketability e.g. marketable products of Aloe c. Herbal tea, soups, biodiesel (Jatropha) etc. Post harvest technology of safed musli, ashwagandha and artemisia etc. Post harvest technology for Ocimum, Geranium etc. Packaging and transport of produce a. Functions of packaging b. Damage caused by packaging c. Types of packaging Processing and utilization of herbs a. Extraction and processing b. Downstream processing c. Post harvest processing equipments PRACTICAL [1 CREDIT] Harvesting methods Drying and processing Extraction methods Identification of diseas es Identification of insect-pests Packaging technologies

PSC – 102

AGRO PHYSIOLOGY [1 + 1 CREDITS]
SEMESTER- I THEORY [1 CREDIT]

Plant cell-structure and functions of organelles Basic understanding of mechanism of Photosynthesis, environment effe cts on photosynthesis Mechanism of respiration, photorespiration Mineral nutrition, Essential Elements, solute transport, phytoremediation Nitrogen assimilation and fixation Water transport ,Water Potential , Relative water content, , Plant water status Stress physiology, biotic and abiotic stresses Pysiology of Plant Growth and Development, effect of environmental factors, growth analysis Auxins and gibberellins, role in flowering, root initiation, leaf and stem growth, seed germination Cytokinins and cell division, ethylene and senescence, fruit ripening Abscisic acid. Role in abiotic stress ,dormancy, stomatal physiology ,Signalling of plant defense responses -jasmonic acid Phytochrome and photomorphogenesis, Daylength and low temperature(chilling) effect on plant growth PRACTICAL [1CREDIT] Mineral nutrition- stock solution preparation, start growing plants in water culture and sand culture Mesurement of gas exchange parameters, light measurement Determination of chlorophyll Measurement of water potential and relative water content of plants Determination of proline content of plant sample Isolation, extraction and estimation of ABA and IAA from plant sample. Bioassay studies on inhibitors Effect of chilling, ethrel on seed germination on amyl ase and acid phosphatase enzymes

PSC – 103

PRINCIPLES OF PLANT TAXONOMY AND PHARMACOGNOSY [1 + 1 CREDITS]
SEMESTER - II THEORY [1 CREDIT]

PART - I PLANT TAXONOMY Fundamentals of plant Classification: History and development of plant taxonomy, ranks and systems of classification Principles of botanical nomenclature : Binomial system, International Code of Botanical Nomenclature-important rules, specific epithets Methodologies for Taxonomic identification of plants : Plant description and terminology, floral formula and diagram, key to the identification of plants of important families Recent trends in plant taxonomy: Numerical taxonomy, Chemotaxonomy, molecular taxonomy Bio diversity and its significance in relation to MAPs PART – II PHARMACOGNOSY Introduction to Pharmacognosy : Natural sources of drug, classification of drug, phyto-constituents of therapeutic value Drug evaluation: Botanical, physical, chemical and biological evaluation of drugs Principles related to commercial production of drugs : Effect of climate, growth period on active constituents, methodologies for harvest and storage Plants in complementary and Traditional systems of medicine - an overview PRACTICAL [1 CREDIT] PART – I Techniques for plant collection and herbarium preparatio n Practical hand on plant identification with particular reference to MAPs PART – II Techniques for macroscopy and microscopy for studying drug samples Determination of identity, purity and strength of drug samples Techniques for Electron microscopy PSC – 104 BASIC AND APPLIED STATISTICS [1 + 1 CREDITS] SEMESTER - II THEORY [1 CREDIT] Introduction, Data Tabulation, Diagrammatic and Graphical Repr esentation: Definition, Aims, Limitation, Classification, Tabulation, Types of Tabulation, Types of Diagrams, Graphical Representations, Utility and Limitations. Measures of Central Tendency and Dispersion: Characteristics of Satisfactory Average, Arithmetic, Geometric, Harmonic, Weighted Mean, Median,

Mode, Range, Mean Deviation, Standard Deviation, Variance, Coefficient of variation, Standard Error. Test of Significance and Goodness of Fit: Statistical Hypotheses, Parametric and Non-Parametric Hypothesis, Null Hypothesis, Statistical Significance, Levels of Significance, Degrees of Freedom, Student’s t test, Goodness of Fit, χ2-Test, Conditions for the Application of χ 2- Test. Regression and Correlation : Bivaiate universe or population, Arrays and Correlation, Measurement of Corre lation, Intra-class, Rank, Partial and Multiple Correlations, Lines of Regression, Regression Coefficients, Limits and Range of γ- Correlation Coefficient expressed in terms of Regression Coefficients. Probability : Introduction, Definitions, Mathematical and Experimental Approach, Simple and Compound Events, Independent and Dependent Events, Laws of Composition of Events, Certainity and Impossibilty, Limiting values and Range of Probability, Permutation and Combinations. Principles of Experimental Design a nd Analysis of Variance and Covariance: Validity, Soil Heterogeneity and Uniformity Trial, Precision and Accuracy, Basic Principles of Field Experimentation, Experimental Technique. Sampling: Aims of Sampling, Types of Population, Choice of Sampling Methods, Multi-stage and Multi-phase Sampling. Completely Randomized, Randomized Block and Latin Square Design: Description, Treatments, Randomization, Statistical Analysis, Merits and Demerits. Factorial Experiments:Factorial Concept, Simple Effect, Main Effect s and Interactions, Interactions of Higher Order, Comparision or Contrast, Calculation of Sum of Squares due to Comparisions, Statistical Analysis of a 23 experiment. Confounding: Orthogonality, Confounding, Priciples of Confounding in a 2 3 Factorial Experiment, Statistical Analysis of Completely Confounded 2 3 Factorial Experiments. Split-plot Design: Description, Relation to the Confounded Factorial Designs, Structure of Analysis of Variance, Standard Error in Split -plot Experiments, Testing the Significance of the Differences among the treatment means, Statistical Analysis, Advantage and Disadvantage. Statistics and Computer : Calculation in Statistics, Softwares in Aid to Statistcs, Working with Useful Software to Agricultural Researches. PRACTICAL [1 CREDIT] Sampling and Collection of Data Tabulation and Graphical Representation of Data Testing of Hypotheses (Numerical Problems) Numerical Problems on Correlation and Regressioin Analysing the experimental data of completely randomized, randomized bloc k and latin square design Analysing the experimental data from Factorial and Confounding 2 3 factors ) Analysing the experimental data from Split -plot Design Acquainting with menue based Software useful to Agricultural Researches(SPAR-1) Developing the Computing Skills using Excel Analysing the Data generated through various breeding experiments I , II, III

BTB – 101

PLANT TISSUE CULTURE TECHNIQUES [1 + 1 CREDITS]

SEMESTER – I THEORY [1 CREDIT] Journey from a cell to plant – The in vitro morphogeneti c patterns Somatic embryogenesis – Theory, experimental control and molecular basis Protoplast isolation, culture and fusions Tissue banking Secondary metabolism in vitro Bioreactor up-scaling of the in vitro operations Cell culture approaches for crop m odifications Genetic transformations PRACTICAL [1 CREDIT] Formulation and preparation of culture media The sterilization techniques and methods to overcome microbial contamination in plant tissue cultures Initiation and modification of morphogenic pathway s through external factors Protoplast isolation and fusions Preparation of artificial seeds Induction of transformed hairy roots for gene expression and secondary metabolite production In vitro mutagenesis, cell line selections and bio -transformation Hardening and acclimatization of in vitro raised plants

BTB - 102

BIOCHEMISTRY

[1 + 1 CREDITS]

SEMESTER - I THEORY [1 CREDIT] An Overview of Structures and Functions of Major Bio -organic Constituents: Carbohydrates, Proteins, Lipids, DNA, RNAs, Terpenoids, Flavanoids, Alkaloids Enzymes: An Overview of Kinetics and Regulation, Promiscous Biocatalysis and Moonlight Functions Metabolic Pathways and their Regulatory Mechanisms: Some Case Examples Secondary Metabolic Pathways: The Processes, their Biochemica l Craft after Primary Pathways, Metagenomics, Evolutionary Genomics, Biochemicstry and Functional Biology Plant Secondary Metabolism: Metabolic and Molecular Modes of their induction and regulation Biochemical Fate of Secondary Metabolites Too Many Phytochemicals Made and Managed with Few Enzymes Metabolic and Functional Diversity: Anaplerotic routes, divergence of protein sequences vis -à-vis evolution of biochemical functions Biochemistry in Biotechno logy and Metabolic Engineering

Physiology and Biochemistry of Genetically Engineered Plants: Mosaic of Successes and Lessons Genomics of Biotransformation and its Industrial Applications PRACTICAL [1 CREDIT] Analytical Biochemistry: Spectrophotometry, Flouresence Spectrometry, Radiometry etc. Isolation and estimation of protein and nucleic acids Isolation of functional enzymes from plants Enzyme assays Enzyme kinetics Electrophoretic techniques for enzymes, proteins and nucleic acids Comparative Biochemistry: Bioinformatic Analyses.

BTB - 103

MICROBIOLOGY [1 + 1 CREDITS]

SEMESTER - II THEORY [1 CREDIT] Introduction to microbiology : History, Classification Introduction to Microorganisms : Bacteria, Fungi, Algae, Viruses Differentiation in Microorganisms and Prokaryotes Single Cellular and Multi-cellular Life Forms Microbial Physiology : Metabolism, Enzymes & their Regulations Bacterial genetics : Genotypic changes (mutations) Bacterial Genetics : Conjugation, Transduction, Transformation Host-Microbe Interactions Control of Microorganisms : Physical, Chemical, other Therapeutic Agents Agricultural and environmental microorganism Industrial Microorganisms Microorganisms and Diseases : Humans and Plants

PRACTICAL [1 CERDIT] Microscopic examination Cultivation of microorganisms Single colony purificati on and titre estimation Determining growth curve Biochemical characterization including Gram staining Intrinsic antibiotic and drug resistance markers Antimicrobial activity evaluation assays Mutagenesis (Chemical) Isolation of Bacterial Genomic DNA Isolation of Plasmid DNA

BTB - 104

BASIC GENETICS

[1 + 1 CREDITS]

SEMESTER – II THEORY [1 CREDIT] Concept of inheritance in different life forms

Mendel’s work and laws of inheritance Chromosome theory of inheritance and linkage Evolution of gene concept a. One gene one character b. Cis-trans complementation test and gene as unit of function, mutation and recombination c. Gene interaction d. Polygenes and polygenic inheritance e. Gene environment interaction f. Linkage and crossing over g. Sex linkage and sex determination h. Chromosomal aberrations i. Mutation j. One gene-one enzyme, one gene-one polypeptide hypothesis and beyond Gene structure and function a. Chemical basis of gene/genetic material b. Structure and function of DNA c. Gene structure: Cis and trans elements, overlapping and split genes, transposable elements d. Genetic code, gene expression in prokaryotes Forward and reverse genetics a. Genetic mapping b. Physical mapping c. Gene cloning and modification d. DNA sequencing e. Concept of genomics Molecular genetics and genetic engineering a. Basis b. Applications PRACTICAL [1 CREDIT] Basic genetics experiment in E.coli Inheritance and crossing experiments in Drosophila Scoring for F 1 and F2 populations for contrast traits in plants Mutation experiments in Bacteria DNA isolation from bacteria (Plasmid and Genomic) DNA isolation from plant (Organelle and Genomic) Learning basis of DNA fingerprinting through RAPD and restriction analysis Mendellian segregation and gene interaction: Numericals

CSC - 101

MODERN INSTRUMENTATI ON [1+1 CREDITS]
SEMESTER- I THEORY [1 CREDIT]

Analytical Instrumentation overview: Introduction, Signal and noise

Spectroscopic Methods: Properties of electromagnet ic radiation, Instruments for optical spectroscopy, Atomic spectroscopy and ICP, Molecular spectroscopy, Nuclear Magnetic spectroscopy Mass spectrometry: Introduction, Gas chromatography, High performance liquid chromatography, Capillary electrophoresis an d other separation techniques Electronics: Electrical/electronic components and circuits, Digital electronic Electron Microscopy: Fixation embedding, knife making, microtomy, specimen mounting, Specimen staining TEM use, TEM use SEM specimen preparation, S EM use, dark room data documentation, Scanning tunnelling microscope and atomic force microscope

PRACTICAL [1 CREDIT] Recording of proton and 13C -NMR spectra: Sample preparation, putting the sample inside the magnet, locking on the solvent, shimming the sample, fixing the parameters, acquisition of data, recording of spectra, integration of proton spectra, recording of proton noise decoupled carbon NMR, recording of DEPT 90 and DEPT 135 spectra. Hands on GC and GC-MS analysis: GC analysis of essential oils: selection of suitable column, optimization of GC conditions for best resolution of the oil sample. GC-MS analysis of essential oils: analysis of oil sample on the basis of previously developed GC conditions, recording of GC -MS spectra, identification of individual peaks on the basis of its MS fragmentation pattern with the help of library. Applications of Electron Microscope for Biological Samples.

CSC - 102

STRUCTURE ELUCIDATION OF ORGANIC MOLECULES [1 + 1 CREDITS]
SEMESTER - I THEORY [1 CREDIT]

Unsaturation and functional group identification by UV/IR. Structure elucidation by NMR. Molecular weight determination by Mass spectrometry Structural confirmation of Diterpenoids, Alkaloids, Monoterpenoids, Flavonoids, Carbohydrates, Triterpenoids, Steroids, Sesquiterpenoids, Steroidal alkaloids. PRACTICAL [1 CREDIT] Characterization of unsaturation in organic molecules by UV

Functional group identification by IR Essential oil characterization by GC -MS Structure determination by vari ous NMR experiments Characteristic differentiation of flavonoids on the basis of UV, IR, NMR and Mass spectrometery.

CSC - 103

CHROMATOGRAPHIC TECH NIQUES [1 + 1 CREDITS]
THEORY [1 CREDIT]

High Performance Liquid Chromatography: Principles HPLC: Methods in Natural Products Modern Thin-Layer Chromatography: Practical Aspects TLC Chromatography in Plant Sciences Measuring Diffusion with PFG’s Diffusion Order Spectroscopy (DOSY) Enantioselective GC in flavor and fragrance Analysis: Strategies for Identification of Plant Volatiles GC-MS: Applications in Plant Volatile Identification. Analysis of Natural Products by LC -MS Analysis of Natural Products by LC -MS/MS Centrifugal Accelerated Radial TLC (Cromotron): Principles and its Applications in Natural Product Separation. Vaccum Liquid Chromatography: Principles and its Applications in Natural Product Separation. PRACTICAL [1 CREDIT] Separation of natural products by column chromatography: Selection of suitable adsorbent, preparation of slurry and its loading on the column, elution of the column with gradient solvent system, monitoring and pooling of fractions on the basis of TLC profile. Separation of natural products by Centrifugal Partition chromatography (CPC) Separation and Centrifugal Partition chromatogr aphy (CPC): selection of solvent system, determination of partition coefficient, selection of mobile and stationary phase, injection of compound, separation of compound. Instrumental methods of analysis with HPLC,HPTLC, GC and GC -MS

CSC - 104

PHARMACEUTICAL CHEMISTRY [1+1CREDITS] SEMESTER – II THEORY [1 CREDIT]

Fundamentals of Medicinal chemistry: Drugs history, mechanism of drug action, drug discovery process, modern drug designing, Lead identification, lead optimization, receptor theories, agonists an d antagonists, ADME, Lipinski’s Rule, Drug efficacy, half life of drug, soft drug design, Drug testing and clinical phases. Chemistry and biology of some anticancer leads from plants: Camptothecin, Podophyllotoxin, Taxol, Combretastatin A4. Synthesis of oligosaccharides. Synthesis of drug analogues. Novel anticancer agents from natural products. Nitric oxide synthase (NOS) inhibitors from plants. Medicinal uses and biosynthesis of Nitric oxide.

Recent advances in Immunomodulators from plants. PRACTICAL [1 CREDIT] Chemical transformation of Tritepenoids Preparation of semisynthetic analogs of bioactive natural products Chemical transformation of Taxoids. Preparation of various synthetic analogs of bioactive taxoids Semisynthetic approaches for phenolic compounds. Asymmetric synthesis using Sharpless dihydroxylation. Preparation of / - isomers of sesquiterpenoid Chromatographic purification of / - isomers of sesquiterpene.

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