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6••Fourth Semester MSC BOTANY SYLLABUS

 FOURTH SEMESTER MSC BOTANY SYLLABUS & NOTES  

(KERALA UNIVERSITY) 

Click on each text, you will gets Notes 





SEMESTER IV

BO 541: SPECIAL PAPER-I BIOINFORMATICS AND BIOPHYSICS 


 

A. BIOINFORMATICS

1.Introduction to Bioinformatics: Definition and History of Bioinformatics Internet.

 Computational Biology and Bioinformatics.


2. Biological databases - Types of data and databases,

 Nucleotide sequence database 

(EMBL, GENBANK,    DDBJ) 


Protein sequence database (PIR, SWISS - PROT, TREMBEL),

 Secondary Databases (PROSITE, PRINTS, BLOCKS), 


Protein Structure Database (PDB)


3. Information retrieval from databases - search concepts, Tools for searching, homology searching, finding Domain and Functional site homologies.


4. Structural Bioinformatics - Molecular Structure viewing tool - Rasmol, Protein Structure Prediction - Secondary Structure prediction (Chou Fasman method and other Bioinformatics tools for secondary structure prediction) and Tertiary structure prediction (Comparative modeling, Abinitio prediction, Homology modeling)

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5. Genomics Types (Structural and Functional), Genome Annotation, Gene Finding, Comparative genomics, Single nucleotide Polymorphism Gen - SNIP 


6.Proteomics Protein expression analysis, Mass spectrometry in protein identification, Protein Sorting, Metabolomics, KEGG, Systems Biology - an introduction


7. Sequence Analysis - Global Alignment, pairwise analysis, Scoring Matrices (anintroduction), Multiple Sequence Analysis


8. plecular Phylogeny - Gene and Species tree. Molecular evolution and Kimuras (12 hrs) theory, Phylogenetic Trees, Terminology in Phylogenetic tree. Cladogram and Phylogram, Significance of Molecular Phylogeny.

9. Computer Aided Drug Design and Molecular Docking, Breif study about Docking tools, AutoDock, molegro virtual docker, GOLD


10. Tools (Softwares) used in Bioinformatics - BLAST (including ALGORITHM of BLAST), Sequin, ClustalX, Clustal W, RasMol, Treeview, Phylip, GRAIL, GENSCAN, BIO - PERL.


11. Applications of  Bioinformatics

Transcriptomics, Metabolomics,

Pharmocogenomics, combinational synthesis (Brief Accounts).


B. BIOPHYSICS


1. Chemical bonds   :    

Ionic bond,   Covalent bond,   Vander Vaal's forces,    hydrogen bonding and hydrophobic interactions. 


Bonding in organic molecules. Effect of bonding on reactivity. Polarity of bonds. Bond length. Bond angle. Dissociation and association constant.

2. Bioenergetics: Concepts of free energy, Thermodynamic principles in Biology. Energy rich bonds. Coupled reactions and group transfers. Biological energy transducers.

3. Principles and applications of light and electron microscopy, resolving power, (10 hrs) depth of field. bright field and dark field, phase contrast (negative and positive phase contrast), fluorescence, fluorescence resonance energy transfer (FRET), differential interference contrast (DIC) microscopy, scanning and transmission electron microscopy. different fixation and staining techniques for EM, freeze fracture methods for EM, atomic force microscopy (AFM). Flow cytometry, confocal microscopy - different types, FISH, GISH.

4. Chromatography: Planar and column chromatography, Adsorption and partition chromatography, partition coefficient, Principle and applications of Gel filtration, Ion exchange and affinity chromatography, Thin layer chromatography, gas chromatography, 

HPLC,     HPTLC      , LCMS, GCMS.



 5. Electrophoresis. Horizontal and vertical gel electrophoresis, PAGE, SDS - PAGE, DIGE (Differential gel electrophoresis), PFGE (Pulsed field gel electrophoresis), Immuno electrophoresis. Enzyme localization by electrophoresis. Zymogram and isozyme analysis. ELISA. Isoelectric focusing.

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6. Centrifugation. Basic principles of centrifugation, RCF (relative centrifugal force), sedimentation coefficient, Ultra centrifugation Differential centrifugation, density gradient centrifugation (zonal and isopycnic).

7. Principles of biophysical methods used for analysis of biopolymers: X-ray diffraction Bragg equation, fluorescence, UV, visible, IR, NMR, ESR Spectroscopy, ORD/CD, Fourier transform techniques, hydrodynamic methods, plasma emission spectroscopy. Atomic absorption spectroscopy, Mass spectroscopy

8. Principles and applications of tracer techniques in biology. Radiation dosimetry. Radioactive isotopes. Autoradiography. Cerenkov radiation. Liquid scintillation.



BO 542a: SPECIAL PAPER - II (ELECTIVE)

BIOTECHNOLOGY

234 hrs (Theory 144 hrs; Practical 90 hrs)


Module I - Basics of Biotechnology

1. Genesis, projection of biotechnology as an interdisciplinary pursuit, prospects and bottlenecks.

2. Vectors, plasmids, bacteriophage and other viral vectors, cosmids, Ti plasmid, yeast artificial chromosome, BAC, Agrobacterium Ti and Ri plasmid, plant and animal viruses.

3. Enzymes used in genetic engineering, restriction enzymes - their types and target sites; Ligation - Enzymes and optimization

4. Impacts of biotechnology on agri - biodiversity, medicine, industry and environment Module II - Microbial Genetics and technology

1. Replication, regulation of bacterial gene expression.

2. Mutations, genetic transfer, manipulation of gene expression in prokaryotes.

(20 hrs)

3. Microbial production of amino acids, antibiotics, microbial enzymes, organic acids.

4. Methods for laboratory fermentations, isolation of fermentation products, Elementary principles of microbial reaction engineering.

5. Microbial culture selection, fermented foods, probiotics.

6. Applications in microbiology: biopolymers, biosurfactants and biopesticides. Probiotics, Prebiotics, Synbiotis & Problems of Antimicrobial resistance. Bioconversion processes Biosafety considerations

Module III - Genetic Engineering

(40 hrs)

1. Generation of Foreign DNA molecules, cutting and joining of DNA molecules - linkers, adapters, homopolymers.

2. Gene isolation, gene cloning, cDNA and genomic DNA library, expression of cloned genes.

3. Transposons and gene targeting

4. DNA labeling, DNA sequencing - Polymerase Chain Reactions (PCR), Various kinds of PCR, Real Time PCR, Ligation Chain Reaction, Applications of PCR, DNA finger printing.



5. Southern Blotting , Western Blotting 

 and   Northern blotting,   colony Blotting

 plaque Blotting   and Dot blots,  

 in situ hybridization.

 

6. Mapping of DNA: Restriction mapping, 

DNA foot - printing,  Gel retardation analysis,

 chromosome walking and jumping



7. Molecular marker techniques -  RFLP, 

 RAPD,     AFLP,   SCAR,    STR,     SSR,    SNPs. 


8. Site directed mutagenesis. 


9. Gene transfer technologies  : 

Agrobacterium and CaMV mediated gene transfer, 

Recombinant viral technique, 

DNA mediated gene transfer method,   

protoplast fusion, 

 microcell fusion technique, 

metaphase chromosome transfer, 

direct gene transfer using PEG, 

Micro injection,

 Electroporation,   biolistic method,      

      liposome mediated DNA delivery,    

gene therapy.


 

10. Transgenic organisms,   Social and ethical issues, 


        IPR,        Patents   and   Biopiracy. 


Module IV - Plant Tissue Culture Techniques.


1. Techniques and applications


callus culture and regeneration of plants,


 micropropagation for large scale production of

 crop plants,  

micropropagation for large scale production of 

medicinal plants, tree species and ornamentals



2. Suspension culture and development - methodology, kinetics of growth and production formation, elicitation methods, hairy root culture

3. Protoplast culture - isolation, fusion, generation of hybrids, cybrids, preferential elimination of chromosomes, role in cytoplasmic male sterility and genetic transformation.

4. Exploitation of somaclonal and gametoclonal variations for plant improvement. 


Technique for detection and isolation of somaclonal variants, Factors affecting somoclonal variation


5. Production of virus free plants: different methods (brief account only)


6. Germplasm Storage and Cryopreservation - In vitro strategies, short, medium and long term (cryopreservation) 


preservation for germplasm conservation. Cryopreservation of vegetative propagated and recalcitrant seed species. 


Module V - Transgenic organisms

(20 hrs)

1. Microbes production of pharmaceuticals (somatostatin, humulin, interferons)  


Genetically modified microbes - biodegradation, biopesticides, bioremediation, mineral leaching and biofertilizers.

2. Plants insect resistance (Bt), virus resistance - coat protein, satellites, herbicide resistance. Increasing shelf life of foods flavr savr tomatoes, control of seed germination, genetically modified foods.


3. Animals production of vaccine and pharmaceuticals, hybridomas, monoclonal antibodies.

Module VI - Process Biotechnology


1. Bioprocess technology for the production of cell biomass and primary/secondary metabolites. 

  

2. Microbial production, purification and bioprocess applications of industrial enzymes and organic compounds.

3.Bioreactor designs for exploitation of microbial products, scaling up and downstream processing.

4. Chromatic and membrane based bioseparation methods, immobilization of enzymes and cells and their application for bioconversion processes.



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