University of Kerala Courses

M.Phil. (Botany)

Course Structure

Semester I

• Paper – I: Research Methodology
• Paper – II: Advanced Botany

Semester II

• Paper – III: Methods of crop improvement

Course Syllabus

Semester - I

Paper I: Research Methodology

Unit I: Biological instrumentation and techniques

• Cell Biology: Microscopy- Principles of Light, Phase contrast, Interference, Fluorescent, Electron microscopy – Scanning and Transmission. Principles and practice of staining, molecular cytogenetics- FISH, GISH,SKY
• Molecular Biology: DNA isolation, chromosome walking, chromosome jumping, principles and applications of recombinant DNA technology, DNA fingerprinting, DNA foot printing, DNA sequencing, PCR, RFLP, RAPD, AFLP, ISSR, Southern, Northern and Western blotting techniques. Exon shuffling, exon trapping, protein isolation.
• Extraction of secondary metabolites and Separation techniques- Cell fractionation- Chromatography-principle and classification, Paper chromatography-, TLC, Column chromatography, Adsorption- Gel filtration- Ion exchange- Affinity chromatography- GC, HPTLC. Electrophoresis- Principle, type, paper, starch gel, polyacrylamide, agarose, immuno electrophoresis. Centrifugation.
• Enzyme assay and kinetics, ELISA, RIA, calorimetric studies,
• Spectroscopy-nature of Electromagnetic Radiation. Theory of spectroscopy – UV and visible spectroscopy, IR spectroscopy. Spectroflurometry. Electron spin Resonance- NMR-Mass spectrometry and spectrophotometry.
• Microbiological techniques – culture media, colony isolation, anti microbial assays.
• Site directed mutagenesis – cassette mutagenesis, suppressor mutations. primer extension methods, PCR based methods.
• Karyotype and pachytene analysis, acetolysis, banding techniques, scoring of chromosomal aberrations

Unit II: Techniques in Plant Biotechnology

• Suspension culture and low density culture
• Somatic embryogenesis and artificial seed production
• Embryo rescue technique, anther culture technique
• Tools and Technique for the production of transgenic plants: purification and separation of nucleic acids, vectors, recombinant DNA technology, gene transfer technology, Introducing genes into prokaryotes: transformation, transduction, conjugation transposition, identifying the right clones

Unit III: Bioinformatics

• Detecting open reading frames, gene prediction, programs for finding genes, secondary databases of functional domains
• Molecular phylogenetic programmes, comparing nucleotide and amino acid sequences using BLAST.
• Programmes for determination of protein structure

Unit IV: Manuscript preparation

• Literature survey, Theses writing, scientific publications.
• Data analysis and, statistical software packages (SPSS, MVSP) and dendrogram preparation.

Paper II: Advanced Botany

Unit I: Molecular Genetics

• Molecular Biology of gene expression: Brief overview of the Central Dogma and Teminism. Transcription in prokaryotes and eukaryotes. Types and structure of RNA polymerase, Different types of RNA, Regulatory sequences and transcription factors involved. Mechanism: Initiation, elongation and termination. Split genes and RNA splicing in eukaryotes. Translation in prokaryotes and eukaryotes. Salient features, exceptions, tRNA-suppressor mutations. Mechanism of translation: Chain initiation, elongation and termination, proteins involved, factors affecting translation accuracy. Molecular mechanism of mutation, cancer biology, human cytogentics
• Molecular mechanism of Gene Regulation: Regulation in prokaryotes, Regulation in Eukaryotes, Epigenetic mechanisms: methylation and transcriptional inactivation, cosuppression through transcriptional silencing, genome imprinting. RNA processing->alternative splicing, RNA stability, RNA interference. Translational regulation: Gene amplification, mating type interconversion.
• Genomics: Structural genomics, Genetic and physical mapping ( RFLP), microsatellite maps, cyotogenetic maps, physical maps, positional cloning, chromosome walks and jumps, Genome sequencing, genome databases, human genome sequencing project. Functional genomics. transcriptome, proteome and metabolome, Microarrays and gene-chips. Comparative genomics. Functional and evolutionary relationships prokaryotes, organelles and eukaryotes, orthologues and paralogues. Metabolomics: Identification and quantification of cellular metabolites in biological samples. Pharmacogenomics and drug designing.

Unit II: Advanced trends in systematics

• Basic concepts of:
  
  • Morphology - History, general morphology, types of data, methods of gathering data,
  • Anatomy - History, general anatomy, types of data, methods of gathering data,
  • Embryology - History, , types of data, methods of gathering data;
  • Palynology: History, general palynological characters, types of data, methods of gathering data;
  • Cytology and Cytogenetics: History, general cytological and cytogenetic characters, types of data, methods of gathering data;
  • Ecology, History, general ecology, types of data, methods of gathering data (At least two examples from each section should be studied to substantiate the taxonomic significance)
• Chemotaxonomy:
  • History, general chemical and chemotaxonomic characters, types of data, methods of gathering data.
  • Identification of the major classes of the pharmaceutically important secondary metabolites from natural sources  (phenolics, steroids, terpenoids glycosides and alkaloids).
  • Applications: Phytochemicals in cosmetics, aromatherapy, disease prevention, biotechnology in the production of phytochemicals. Phytochemical databases
• Molecular trends in Biosystematics
  • Molecules and genomes in plant systematics, techniques used in molecular taxonomy, molecular systematics in crop evolution
  • Serology in relation to plant taxonomy- Methods, role of serology in taxonomy.
  • Cladistics and Phenetics
• Molecular trends in Reproductive Biology:
  • Apomixis – Types, cytogenetic basis and induction of apomixes, applications
  • Biochemistry and genetics of incompatibility, methods to overcome incompatibility, pollen viability tests, molecular basis of incompatibility
  • Sterility – Male sterility, CMS, GMS, CGMS, temperature sensitive and photosensitive male sterility, transgenic male sterility, female sterility and zygotic sterility.

Unit III: Plant Physiology

• Modern concepts Photosynthesis – Environmental and agricultural relevance; Respiration – Biochemical control of respiration
• Photomorphogenesis Phytochrome genes and their expression, control of photo-morphogenic responses. Dose-response relations in photomorphogenesis, light induced chloroplast differentiation, effect of photoreceptors.
• Biological clock: Circadian rhythms, rhythm responses to environment, clock mechanism
• Photoperiodism General principles , florigen concept
• Plant growth and development Patterns of growth and differentiation; Gene expression and mutations regulating meristem function, embryogenesis, seedling, root, leaf and flower development. Homeotic genes, ABCD model in Arabidopsis flower, hormonal control of plant tissue development, effect of auxins on root and root formation, gibberellin promoted growth of plants, ethylene and triple response mutants, brassinosteroids and photomorphogenesis.
• Enzymes: General account: Importance and properties of enzymes in biological sciences, the classification and nomenclature of enzymes with examples, Mechanism of enzyme action role of enzyme in chemical action, various factors affecting the enzyme activity
• Molecular genetics in plant physiology, Environmental plant physiology, Stress physiology

Unit IV: Economic Botany

• Economic importance of Cereals, Tuber Crops, Fibre yielding plants, Plantation  Crops, Sugar yielding plants, Narcotics, Vegetables, Oil yielding plants, Pulses and Beverages

Semester - II

Paper III: Methods Of Crop Improvement

Unit I: Plant Breeding

• Modem concept and basis of heterosis - Methodology of producing hybrid varieties in cross and self- pollinated plants. Use of male sterility and self-incompatibility in heterosis breeding.
• Inter-specific and intergeneric sexual hybridization - Incongruity, hybrid inviability and sterility barriers - methods of overcoming - use in Plant Breeding.
• Induction of autopolyploidy in seed and vegetative propagated plants problems and possibilities of auto polyploidy breeding.
• Production of alien genome addition lines. Alien chromosome addition and substitution lines and alien chromosome segmental transfer through induced translocation breeding.
• Biotic and abiotic stress resistance breeding - vertical and horizontal disease resistance, pest resistance, and drought. salinity and pollution resistance. breeding - peculiarities and problems.
• Plant architecture and crop ideotype breeding; Concept of crop ideotypes - redesigning of crop plant types - Integration of special breeding techniques with conventional breeding - Optimization of yield, quality and resistance and development of improved plant types with wider adaptability.

Unit II: Advanced plant tissue culture technology

• Microproagation: culture establishments, new generation sterilizing agents, controlling explants browning- growth regulators- growth retardants-anti auxins, anti cytokinins. In vitro handling of perennials crops- in vitro rejuvenation. Clonal fidelity test, clonal uniformity tests, clonal plantations-significance, rooting- plant hardening techniques. Micropropagation: Global scenario- current propagation status of food crops-plantation crops-ornamentals- medicinal herbs. Somatic Embryogenesis, Artificial- Synthetic Seeds, Somaclonal variation In vitro mutagenesis Low density culture & Cell Suspension Cultures, Secondary metabolites: Secondary products found in plants, method of in vitro production. Bioreactors. In vitro Production of Haploids Protoplast Isolation and Culture
• Germplasm Storage and Cryopreservation: Conservation of germplasm, In vitro strategies, Short, medium and long term (cryopreservation) preservation application, Techniques of cryopreservation, Determination of survival and viability, Plant growth and regeneration, Application of cryopreservation.

Unit III: Transgenic plants

• Procedure and protocols of producing transgenic plants., first commercial transgenic plants- transgenic tomatoes, control of ripening by antisense technology, insect resistance (Bt. protein), golden rice, herbicide resistance, commercializing insect resistant cotton, designer oils and biodiesel, plant secondary products, designer flowers, plants as bioreactors, vaccines, plantibodies, and bioplastics.
• Biodegradation, bioremediation, bioleaching. Biotechnological Applications: Biosensors, Microarrays, Biopesticides.
• Hazards and Impact of GMOs. Biosafety Considerations: Biological risks, ethical issues, economic issues, legal issues.