Download Unit-I - University of Mysore

University of Mysore
Department of Studies in Biotechnology
Manasagangotri, Mysore – 570 006
Scheme of Study
Honor’s Degree Program in Biotechnology (40 Credits)
Credits to be earned
40
Core papers
28 credits
Open elective paper*
04 credits
Transborder/ Cross disciplinary/
04 credits
Discipline centric elective papers
Term Work/ Minor Project Work
04 credits
*Open elective shall be entirely from different discipline of study
Details of the Study papers (Honors Program)
Sl.
Code
Type of
Paper title
No
Paper
1
2
3
4
5
6
7
8
9
10
Semester I
BTC-101
BTC-102
BTC-103
BTC-104
Core
Core
Core
Core
Transborder
Elective
Semester II
BTC-201 Core
BTC-202 Core
BTC-203 Core
BTC-205 Core
Open
Elective
Credit
pattern
(L:T:P)
Credit
value
Biophysics and Structural Biology
Bioanalytical Techniques
Bioprocess Technology
Molecular Genetics
Select one from List of Elective Papers
2:1:1
2:1:1
2:1:1
2:1:1
2:1:1
4
4
4
4
4
Food & Environmental Biotechnology
Advanced Molecular Biology
Gene Technology
Term work (Minor project work)
Selected from other discipline
2:1:1
2:1:1
2:1:1
0:1:3
-
4
4
4
4
4
Open elective: 4 credits (Offered for students other than Honors in Biotechnology)
Code
Paper title
Credit pattern
Credits
(L:T:P)
BTO-206 Applied Biotechnology
2: 2: 0
4
1
Master’s Degree Program in Biotechnology (36 Credits)
Credits to be earned
Cumulative total of credits to be earned
Core papers
Transborder/ Cross disciplinary/ Discipline
centric elective papers
Project Work
36
40 (Honors) + 36 (Masters) = 76 credits
24 credits
04 credits
08 credits
Details of the Study papers (Masters Program)
Sl.
No
1
2
3
4
5
6
7
8
Code
Semester I
BTC-301
BTC-302
BTC-303
BTC-304
Type of
Paper
Paper title
Credit
pattern
(L:T:P)
Credit
value
Core
Core
Core
Core
Transborder
Elective*
Biostatistics & Bioinformatics
Molecular Biodiversity
Immunotechnology
Cell Signalling & Communication
Select one from List of Elective Papers
2:1:1
2:1:1
2:1:1
2:1:1
2:1:1
4
4
4
4
4
Plant Biotechnology
Animal Biotechnology
Project work
2:1:1
2:1:1
4
4
8
Semester II
BTC-401 Core
BTC-402 Core
BTC-403 Core
List of Elective Papers for Honor’s/ Masters Programme in Biotechnology
Sl.
No
Code
Type of
Paper
Paper title
1
2
3
4
5
6
7
8
9
10
BTE-101
BTE-102
BTE-103
BTE-104
BTE-105
BTE-106
BTE-107
BTE-108
BTE-109
BTE-110
Elective
Elective
Elective
Elective
Elective
Elective
Elective
Elective
Elective
Elective
Enzyme Biotechnology
Seed Health and Diagnostics
Molecular Phytobacteriology
Proteomics
Cancer Biology
Biological control
Molecular Marker Technology
Medicinal Plant Biotechnology
Molecular Virology
Metabolomics
Credit
pattern
(L:T:P)
2:1:1
2:1:1
2:1:1
2:1:1
2:1:1
2:1:1
2:1:1
2:1:1
2:1:1
2:1:1
Credit
value
4
4
4
4
4
4
4
4
4
4
2
Honor’s degree program/ PG Diploma program (40 Credits)
Semester I
BTC-101
Biophysics and Structural Biology
32 h
Unit-I
Carbohydrates: Structure of starch, glycogen, mucins and bacterial cell wall
polysaccharides. Structure and biological significance of glycoproteins and proteoglycans.
Structural elucidation of glycans.
Lipids: Classification, structure and functions of fatty acids, phospholipids, glycolipids,
isoprenoids and eicosanoids.
Unit-II
Bioenergetics: Electron transport chain and Oxidative phosphorylation: organization of
respiratory chain complexes, structure and function of components, Oxidative
phosphorylation. Mechanism of ATP synthesis, ATP synthase complex, proton motive force,
Mitchell’s hypothesis, integration of metabolism to bioenergetics. Photobiophysics, Radiation
Physics.
Unit-III
Proteins: Structure of peptide bond, conformational determination of peptide, Ramachandran
plot, helix-coil transition, structural organization in proteins. Primary structure determination
and synthesis of peptides, Secondary structure- Alpha helix, beta sheet and amorphous
structures, tertiary structure of myoglobin, Quartenary structure-Structural organization of
haemoglobin and collagen. Structural organization in globular, fibrous and conjugated
proteins. E.g., albumin, keratin, haemoglobin, immunoglobulin and other metallo-proteins.
End group and sulfydral group titration in proteins. Denaturation and renaturation of proteins.
Work of Cristian Anfinsen on ribonuclease. Influence of charge in characterization of
proteins, Scatchard and Hill plots.
Unit-IV
Nucleic acid: Bases, nucleosides, nucleotides and polynucleotides, chemical synthesis of
DNA, Tm, Cot curve, Isolation and characterization, hypo- and hyperchromic effects,
Chargaff’s rule of base pairing in DNA. Interaction of DNA with other molecules (small
molecules-ethidium bromide; large molecules-proteins), structure of RNA and tRNA.
Practicals
 Measurement of pH
 Preparation buffers and solutions
 Determination of pKa of amino acids
 Estimation of reducing sugar by DNS method
 Estimation of proteins by Lowry's method
 Estimation of proteins by Bradford's method
 Estimation of proteins by Bicinchoninic acid method
 Wavelength scan of proteins and nucleic acids
3
BTC-102
Bioanalytical techniques
32 h
Unit-I
General considerations, pH and buffers, cell disruption techniques.
Chromatographic techniques: General principles, Sample preparation, Selection of
chromatographic system, Low pressure column chromatography, HPLC, Adsorption
chromatography, Partition chromatography, Ion exchange chromatography, Exclusion
chromatography, Affinity chromatography, GLC, TLC, Paper chromatography.
Unit-II
Electrophoretic Techniques: General principles, Support media, Native gels, SDS-PAGE,
IEF, 2D gel electrophoresis, Agarose gel electrophoresis, Pulse field gel electrophoresis
(PFGE), Capillary electrophoresis (CE).
Centrifugation Techniques: Introduction, Basic principles of sedimentation, Types of
centrifuges and their uses, Preparative and density gradient separation, Analytical
ultracentrifuges and their applications.
Unit-III
Spectroscopic techniques: Introduction, UV and visible light spectroscopy, IR and Raman
spectroscopy, Electron Spin Resonance (ESR), NMR, Spectrofluorimetry, Luminometry,
Atomic spectroscopy, X-ray diffraction, ORD, CD.
Mass spectrometric techniques: Introduction, mass spectrometer, Ionization techniquesElectron impact ionization (EI), Electrospray Ionization, Chemical ionization (CI), Field
ionization (FI), MALDI, Ion disruption methods, Ion desorption and evaporation methods,
Analyzers- Magnetic sector, time-of-flight, quadropole, ion trap, Detectors- electron
multipliers, Tandem mass spectrometry, applications.
Unit-IV
Radioisotope techniques: Nature of radioactivity, detection and measurement, GM counter,
scintillation counting, autoradiography, Safety aspects and applications of radioisotopes in
biology.
Electrochemical techniques: Introduction, Principles, Redox reactions, Types of electrodespH electrode, ion-sensing electrodes, gas sensing electrodes, oxygen electrode, Biosensors.
Practicals
 Ascending, descending and circular paper chromatography for separation of amino
acids
 TLC of amino acids (1D and 2D)
 UV-Visible Spectrophotometry
 Column chromatography- gel filtration, ion-exchange
 HPLC (Demonstration)
 Gel electrophoresis- native and SDS-PAGE and estimation of molecular weight of
proteins
 High speed centrifugation
4
BTC-103
Bioprocess Technology
32 h
Unit-I
General introduction: Primary and secondary metabolites. Batch culture, the growth cycle,
effect of nutrients, energetic of growth, growth rate and cell cycle.
Design of bioreactors, control systems, operation, optimization, control and monitoring of
variables such as temperature, agitation, pressure, pH, online measurements and control, use
of biosensors in bioreactors
Transport phenomena in bioprocess: Scale up of bioreactors, mass transfer resistance,
oxygen transfer coefficients, biological heat transfer, heat transfer coefficients.
Unit-II
Downstream processing of biologicals: Separation of cells, foam separation, flocculation,
filtration, plate filters, rotary vacuum filter, centrifugation, Stokes law, continuous
centrifugation, basket centrifuge, bowl centrifuge, disintegration of microorganisms,
mechanical and non-mechanical methods, membrane filtration, ultra filtration and reverse
osmosis, chromatographic techniques, absorption, spray drier, drum dryers, freeze dryers.
Unit-III
Microbial products: Microbial production of vitamins, enzymes, organic acids, amino acids,
polysaccharides, antibiotics, ethanol, biosurfactants.
Microbes for sustainable agriculture: Biological nitrogen fixation, legume (Rhizobium)
inoculants, Free-living nitrogen fixers, Azotobacter and Azospirillum inoculants, Endophyte
bacteria and fungi, Plant Growth Promoting Rhizobacteria (PGPR), Blue-Green
(Cyanobacterial) inoculants, Azolla biofertilizer, phosphate-solubilizing microorganisms,
Actinorrhizal associations, mycorrhizae, organic matter recycling and composting, organic
farming, Biological control – fungal, bacterial and viral biocontrol agents, biomethanation,
molecular techniques for ecological studies
Unit-IV
Biopesticides: Importance, biocontrol agents, Trichoderma, Beauveria bassiana,
Pseudomonas fluorescens, Bacillus spp., Metarhizium anisopliae, Verticillium lecanii,
Chaetomium spp., nuclear polyhedrosis virus, baculoviruses, Genetically engineered bacteria
as biopesticides, PGPR.
Mechanism of action, Mass cultivation, formulation, shelf- life, quality control.
Drug development and pharmaceutical process: Production of pharmaceuticals by
genetically engineered cells (hormones, interferons), microbial transformation for production
of important pharmaceuticals (steroids and semi-synthetic antibiotics), new generation
antibiotics, protein engineering, drug design, drug targeting.
Practicals
 Study of fermenter (demonstration).
 Immobilization of yeast by calcium alginate gel entrapment and assay for enzymesinvertase and catalase.
 Screening of antibiotic producing microorganisms.
 Study of alcohol fermentation- alcohol from different substrates-estimation of alcohol
content.
 Bioassay methods- Vitamins and amino acids.
 Biofertilizer preparation.
 Isolation and characterization of endophytic actinomycetes.
5
BTC-104
Molecular Genetics
32 h
Unit-I
Laws of inheritance in haploid organisms- Chlamydomonas and Neurospora, uniparental,
maternal and cytoplasmic inheritance in yeast, Neurospora, Paramecium and plants.
Genomic organization: Prokaryotes, eukaryotes, viral genome, extrachromosomal genomeplasmids, mitochondria and chloroplast, repetitive elements-LINES and SINES, simple
sequence repeats.
Mobile genetic elements: discovery, insertion sequence in prokaryotes, complex transposons
(Tn10, Tn5, Tn9 and Tn3 as examples), mechanisms, control, consequences and applications
of transposition by simple and complex elements.
Unit-II
Mutation: Types, causes and detection, mutant types – lethal, conditional, biochemical, loss
of function, gain of function, germinal verses somatic mutants, Molecular basis of mutations,
insertional mutagenesis.
Recombination: Homologous and non-homologous recombination, Holliday model, sitespecific recombination.
DNA Repair: Mechanism of genetic repair- direct repair, photoreactivation, excision repair,
mismatch repair, post-replicative recombination repair, SOS repair.
Unit-III
Gene mapping methods: Linkage maps, tetrad analysis, mapping with molecular markers,
mapping by using somatic cell hybrids, development of mapping population in plants.
Microbial genetics: Methods of genetic transfers – transformation, conjugation, transduction
and sex-duction, mapping genes by interrupted mating, fine structure analysis of genes.
Quantitative genetics: Polygenic inheritance, heritability and its measurements, QTL
mapping,
Unit-IV
Genes and development: Model systems for studying development- Drosophila,
Caenorhabditis, Arabidopsis.
Genetic control of development in Drosophila: anterioposterior axis specification, role of
maternal genes, segmentation of larval body, gap genes, pair rule genes, homeotic genes,
complex gene interaction in development, sequential gene action.
Floral meristems and floral development in Arabidopsis.
Practicals

Morphology of Drosophila melanogaster.

Identification of at least 10 mutants of Drosophila.

Preparation of salivary gland chromosomes from Drosophila.

Transformation in bacteria.

Conjugation in bacteria.

Transduction in bacteria.

Replica plating.
6
Semester II
BTC-201
Food and Environmental Biotechnology
32 h
Unit-I
Fermented foods, milk-based products, fermented vegetables, fermented meats, fish,
beverages, vinegar, mould fermentation - tempeh, soysauce, rice wine.
Enzymes in dairy industry, cheese making and whey processing, impact of enzyme
technology (bioethanol, protein hydrolysates, bioactive peptides), Enzymatic processing of
fruit juices; role of enzymes in baking, meat and meat processing, phytase in animal feeds,
DNA-based methods for food authentication, comparative methods of toxicity testing in
(novel) foods, biological approach to tailor-made foods, catabolic processes and oxygendependence reactions in food, application of generic technologies in food and nutritional
sciences; anti-cancer components in foods. Utilization of food waste for analysis of food,
food additive colors, flavour, vitamins, microbial safety of food products, heavy metal, fungal
and bacterial toxins, pesticide and herbicide contamination.
Unit-II
Functional foods and Biotechnology: Biochemical processing in the improvement of
functional foods with targeted health benefits and increased nutrient value; applying
molecular, biochemical, cellular and bioprocessing concepts, bio-mobilization of major
nutrients such sterols, lipids, vitamins and minerals, use of specific phenolic metabolites from
botanical species, disease prevention, role of ingredients in oxidation-linked disease, nonnutrition constituents, immune factors from eggs, phytochemicals as antimicrobials, passive
immune improvement
Pre- and Pro-biotics, single cell protein, single cell lipids.
Manipulation of fruit ripening process.
Food processing, principles and practices, food ingredients and processing aids from
biotechnological processes, corn sweeteners, bacterial starter cultures, cold-adapted enzymes.
Food spoilage, preservation, mycotoxins in food commodities.
Genetically modified foods, designer foods, Nutraceuticals, detection of GM foods.
Unit-III
Renewable and non-renewable resources, current status of biotechnology in environment
protection
Waste water management: Bioreactors for waste-water treatment, Aerobic biological
treatments, anaerobic biological treatments, treatment of industrial effluents-dairy, distillery,
paper and sugar industries. Membrane-based waste water treatment.
Oil pollution – treatment with microorganisms.
7
Unit -IV
Bioremediation: Concepts and principles, bioremediation using microbes, in situ and ex situ
bioremediation, biosorption and bioaccumulation of heavy metals.
Xenobiotics: Degradation capabilities of microorganisms with reference to toxicology,
pesticides, herbicides, polyaromatic hydrocarbons.
Renewable energy: Relevance of GMO to the environment.
Solid waste management: Waste as a source of energy, biotechnology in paper and pulp
industry, production of oil and fuels from wood waste, anaerobic and aerobic composting,
vermiculture, biofuels.
Practicals

Analysis of microbial quality of foods.

Assay for polygalacturonase enzyme.

Estimation of dietary fibre.

Assay methods for antimicrobial activity.

Mycotoxin analysis from food samples.

Determination of total dissolved solids of water.

Study of microflora of industrial wastes and effluents.

Isolation of bacteriophages from sewage.
8
BTC-202
Advanced Molecular Biology
32 h
Unit-I
DNA helix topology: closed and super-coiled DNA, DNA topoisomerases, DNases- exo and
endo nucleases, restriction endonucleases-types.
DNA replication: Enzymes in DNA replication, DNA Pol I, II, III, replication in single
stranded DNA viruses, replication in prokaryotes, Eukaryotic DNA replication, eukaryotic
DNA polymerases, role of other proteins and enzymes in replication, fidelity of replication,
replication of mitochondrial DNA, inhibitors of replication.
Unit-II
Transcription: Transcription unit, RNA polymerase in prokaryotes, mechanism of
transcription, eukaryotic transcription, eukaryotic RNA polymerases, transcription factors,
initiation, elongation and termination of transcription, inhibitors of transcription, post
transcriptional modifications- capping, polyadenylation, splicing, introns and exons,
structural organization of mRNA, tRNA and rRNA, nuclear export of mRNA and mRNA
stability.
Genetic code: Elucidation, triplet binding assay, Wobble hypothesis.
Unit-III
Translation: Molecular anatomy and biogenesis of ribosomes, partial reconstitution
experiments, amino acid activation, amino acylation of tRNA, prokaryotic and eukaryotic
translation- mechanism of initiation, elongation and termination, inhibitors of translation,
post translational modifications.
Protein localization: synthesis of secretory proteins and membrane proteins, import into
nucleus, mitochondria, chloroplasts and peroxisomes.
Regulation of gene expression in Prokaryotes: Basic control circuits, positive and negative
regulation, operon concept-lac, ara and trp operons, catabolite repression, regulatory
elements in prokaryotes, attenuation, antitermination, regulation of gene expression in
bacteriophage - lytic and lysogenic cycle.
Unit-IV
Regulation of gene expression in Eukaryotes: Cis control elements- promoters, enhancers,
Trans acting factors, DNA binding motifs of transcription factors, mechanism of regulation
by transcription factors, role of chromatin in regulating gene expression and gene silencing,
histone acetyl transferase and deacetylase, hormonal regulation of gene expression, posttranscriptional control.
Antisense RNA and ribozymes: Molecular mechanism of antisense molecules, inhibition of
splicing, polyadenylation and translation, disruption of RNA structure and capping.
Ribozyme biochemistry, hammerhead, hairpin and other ribozymes, strategies for designing
ribozymes, application of antisense and ribozyme technologies.
RNA interference, RNA induced gene silencing.
9
Practicals
 Estimation of DNA by Diphenylamine (DPA) method
 Estimation of RNA by orcinol method
 Isolation of DNA different samples: plant leaves, coconut endosperm, yeast, animal
tissues
 Determination of purity and concentration of isolated DNA using spectrophotometer
 Isolation of plasmid DNA from E. coli
 Agarose gel electrophoresis of DNA
 Determination of RNAse activity
10
BTC-203
Gene Technology
32 h
Unit-I
Cloning and Expression vectors: Plasmids, lambda vectors, M13 Phage, Cosmids,
Phagemids, BACs, PACs, plant and animal viruses as vectors, Transposons, YAC and MAC
vectors, Expression vectors: Promoters, expression cassettes, Baculovirus, Virus expression
vectors for mammalian cells, binary and shuttle vectors.
Recombinant DNA and Molecular probes: Restriction enzymes for cloning, Technique of
restriction mapping, construction of chimeric DNA: cloning in plasmid, Phage and cosmid
vectors, hosts for cloning vectors.
Molecular probes: preparation, labelling, amplification, techniques of molecular probing,
applications, and Molecular markers.
Unit-II
Gene analysis techniques: Nucleic acid hybridization, Southern and Northern blotting,
mapping genes to chromosomes, in situ hybridization, Polymerase chain reaction- Types,
RAPD, AFLP, RT-PCR, realtime PCR, microsatellites, applications.
Gene libraries: Construction and screening of genomic and cDNA libraries, chromosome
walking, Chromosome Jumping, BAC libraries and assembly of BACs into contigs.
Unit-III
Isolation, Sequencing and synthesis of genes: Isolation of genes for: specific proteins,
proteins having tissue-specific expressions, isolation of genes using DNA or RNA probes.
Sequencing by Maxam and Gilberts methods, Sangers dideoxy method, automatic DNA
sequencers by PCR, DNA sequencing through transcription, sequencing using DNA chips,
sequencing by DE-MALDI-TOFMS. Gene synthesis machines, gene synthesis using PCR,
mRNA.
Gene Therapy: Human diseases targeted for gene therapy, Vectors and other delivery
systems for gene therapy, Ex vivo and In vivo gene therapy, tissue of choice for gene therapy,
In vitro gene therapy, gene therapy of genetic diseases: eg. Neurological, metabolic disorders
and cystic fibrosis, gene therapy for acquired diseases infections, cardiovascular, cancer.
Nanotechnology for drug targeting and gene therapy, Future of gene therapy.
Unit-IV
Genomics and Proteomics: Concept of a genome – information content in genome
sequences, Whole genome analysis – construction of cosmid libraries, BAC libraries, shotgun
cloning and sequencing, automated sequencing, sequence assembly.
Understanding genome sequence – sequence annotation – searching for ORF’s and expressed
sequences, homology analysis, sequence similarity and structural similarity, comparative
genomics.
Functional genomics – DNA microarray, microarray fabrication, gene expression using
microarrays, transcriptome.
Proteome analysis – two dimensional separation of total cellular proteins, isolation and
sequence analysis of individual protein spots by mass spectroscopy; protein microarrays
Human genome project.
11
Practicals

Isolation of plasmid DNA from E. coli

Agarose gel electrophoresis of DNA

Cloning of DNA into a vector

Restriction digestion of DNA

Polymerase chain reaction, RAPD

Isolation of RNA

Northern blot analysis

Purification of DNA from gel

Phage titration

DNA ligation

Gel retardation assay

Cloning DNA fragments in BL-21 cells

Induction of gene expression by IPTG
12
BTO-206
Open elective
Applied Biotechnology
Unit I
32 Hours
Enzyme Biotechnology
Introduction to application of enzymes in industry: Food & beverage, detergent, textile
pharmaceutical and leather.
Commercial production of enzymes: General considerations, regulation of enzyme
production by microbes, genetic engineering for microbial enzyme production, enzyme
engineering, large-scale purification.
Immobilized enzymes and cells: Methods, properties and stabilization of immobilized
enzymes and cells, enzyme reactors, application – manufacture of commercial products, and
analytical applications.
Biosensors: Types- Electrochemical, Thermometric, Optical, Piezoelectric, Whole cell,
immunobiosensors, applications
Seed Health Technology
Introduction: Importance of Seed health, important seed-borne diseases;
Seed Health diagnostics; Management of seed-borne diseases
Unit II
Plant Cell Culture Technology
Landmarks in Plant Cell culture and different areas of Applications in Plant tissue culture.
Micropropagation: Methods and stages, applications .
Somatic embryogenesis: Induction and development, synthetic seeds. Application of somatic
embryogenesis
Haploid Production: Techniques, factors, androgenesis, applications and limitations
Protoplast culture and somatic hybridization: Isolation and culture of protoplasts, protoplast
fusion and somatic hybridization.
Production of secondary metabolites: Induction, Processes, Biotransformation, Bioreactor
system and model for mass cultivation of plant cells.
Germplasm storage: Long term storage and short term storage
Unit III
Animal Cell Culture Techniques
Tissue culture laboratory: Advantages and limitations of tissue culture, types of tissue culture,
equipment, aseptic and sterile handling, general safety, choice of culture vessel, media,
preparation and sterilization of media, serum free media.
Animal Cell Culture: Primary culture, cell lines, cloning and selection, contamination
management, cryopreservation, quantitation of cells, cytotoxicity assays.
Specialized Cells: different cell types used, development of cell lines,selective culture,
specific tumor types.
13
Unit IV
Plant Transgenic Technology
Introduction, Plant transformation techniques
Transgenic traits: herbicide resistance, abiotic stress tolerance, biotic stress tolerance, disease
resistance for fungal, bacterial and viral pathogens, Pest resistance, nutritional quality, fruit
ripening.
Molecular farming: Edible vaccines, biodegradable plastics, therapeutic proteins.
Environmental, ethical and health issues
Microbial Pesticides and Biofertilizers
Biopesticides: Introduction, Isolation, Identification, Mode of action, Characterization, Strain
variability, Mass production Technology, formulations, and Methods of applications.
Biofertilizers: Importance of biofertilizers, Microorganisms used as biofertilizers, Methods of
Application, Mass production, and Commercial importance.
Reference Books
1. Enzymes. T. Palmer. Harwood Publishing. 1999.
2. Biotechnology. U Satyanarayana. Books & Allied (P) Ltd., Kolkata. 2005.
3. A Textbook of Biotechnology. H. D. Kumar.
4. Microbial Biotechnology. Glazer AN and Nikaido H. W H Freeman. 1995.
5. Agricultural Biotechnology. Purohit. Agrobios India 1999
6. Plant Tissue culture Concepts and Laboratory exercises. Trigiano RN and gray DJ.
CRC Press. 2000.
7. Plant Cell Culture. Bojawani and Razdan
8. Seed Pathology, Volume I and II. P. Neergaard. The Macmillan Press Ltd., London.
1977.
9. Plant Pathology. G. N. Agrois, Academic Press, USA., 2000
10. Common Laboratory Seed health Testing Methods for Detecting Fungi. S. B. Mathur
and O. Kongsdal. ISTA, Zurich. 2003
11. Culture of Animal Cells. A Manual of Basic Techniques. R. I. Freshney
12. Plant Biotechnology. Hammonds.
BTC-205
Term work (Minor project work)
14
Master’s degree program (36 Credits)
Semester I
BTC-301
Biostatistics and Bioinformatics
32 h
Biostatistics
Unit-I
Statistical concepts: Data structure, sampling methods, collection, classification and
tabulation of data, graphical and diagrammatic representation, histogram, frequency polygon,
frequency curve, bar graph, pie chart etc.
Measure of Central Frequency: Mean, median, mode.
Measure of dispersion of data: Range, semi-interquartile range, mean deviation, standard
deviation, standard error, coefficient of variation, confidence limits.
Types of distribution of data: Normal, Binomial, Poisson.
Unit-II
Z-test, t-test, ANOVA, multiple comparisons, LSD and DMRT, Chi-square test.
Regression estimate, correlation coefficient.
Experimental designs, data transformation.
Bioinformatics
Unit-III
Introduction, History, Internet and Bioinformatics, Knowledge Discovery & Data mining,
Problems faced in Bioinformatics area, Opportunities in Bioinformatics, Human Genome
Project.
Biological Databases & their Management: Database Concepts, Introduction, History of
Databases, Database Management System, Types of Databases, Codd Rules, Data
Normalization.
Biological Databases, Introduction, Biological Database and its Importance, Biological
Database and their Functioning, Types of Biological Database, Microbiological Databases,
Primary Sequence Databases, Carbohydrate Databases, RNA Databases, Genome Databases,
Organism Databases, Biodiversity.
Unit-IV
Sequence Database: Introduction, Nucleotide Sequence Database, Protein Sequence
Databases, The EMBL Nucleotide Sequence Databases, Structure Databases
Bioinformatics Softwares: ClustalV Multiple Sequence Alignments, ClustalW Version 1.7,
RasMol, Oligo, MolScript, TREEVIEW, ALSCRIPT, Genetic Analysis Software, Phylip.
Computational Biology: Introduction, Datamining and Sequence Analysis, Database
Similarities Searches , Practical aspects of Multiple Sequence Alignment, Phylogenetic
Analysis, Predictive methods using Nucleic acid and Protein Sequences, Submitting DNA
Sequences to the Databases.
15
Practicals

Execution of some statistical packages

Testing of statistical hypotheses

Database search for nucleotide and amino acid sequences using BLAST

Six-frame translation of the nucleotide sequences

Study of sequence alignment

Construction of trees/ dendrograms using sequence analysis

Structure prediction using homology searches
16
BTC-302
Molecular Biodiversity
32 h
Unit -I
Biodiversity and its conservation: Current levels of biodiversity, extinction and endangered
species, steps to preserve biodiversity, convention on biological diversity, species
conservation.
Plant Biodiversity: Concept, status in India, utilization and concerns. Basic concepts of
Sustainable development.
World centres of primary diversity of domesticated plants: The Indo-Barmese centre,
plant introductions and secondary centres.
Strategies for conservation - in situ conservation: International efforts and Indian
initiatives, protected areas in India -sanctuaries, national parks, biosphere reserves, wetlands,
mangroves and coral reefs conservation of wild biodiversity.
Strategies for conservation - ex situ conservation: Principles and practices, botanical
gardens. field gene banks, Seed banks, in vitro repositories, cryobanks, general account of the
activities of Botanical Survey of India (BSI), National Bureau of plant Genetic Resources
(NBPGR), Indian Council of Agricultural Research (ICAR), Council of Scientific and
Industrial Research (CSIR), and the Department of Biotechnology (DBT) for conservation,
non-formal conservation efforts.
Unit -II
Comparison of methods for detection- genetic variation – morphological characters and
allozymes vs. DNA markers, different types of molecular markers.
Future prospects: Improvement of existing methods, Polymorphic single locus hybridization
probes, PCR-Amplified microsatellite Sequence Characterized amplified Regions (SCARs),
Miscellaneous targets, Metagenomics.
Genetic variation at the DNA level – molecular markers, protein markers, DNA sequencing,
RFLP, DNA fingerprinting based on hybridization, DNA amplification, miscellaneous
markers.
Minisatellites and simple sequences, DNA polymorphism by PCR-based finger printing.
Unit -III
Application of DNA fingerprinting in plants and fungi: Minisatellite DNA probes to
detect genetic variation, oligonucleotide probes, PCR-based methods, wild plant species –
DNA finger print to detect genetic diversity and relatedness in plant populations. DNA
fingerprinting insights into plant taxonomy – Apomictic, sexual species.
Cultivated plant species – cultivar identification and estimation of genetic relatedness,
paternity testing identification of hybrids.
Inheritance of DNA fingerprints, linkage analysis and genome mapping in plants, molecular
diagnostics.
Molecular taxonomy and DNA fingerprinting in plants, fungi, bacteria, viruses, and
humans.
17
Unit -IV
Bioprospecting
Genetic and Biochemical Resources: Biochemical resources from plants and fungi, natural
products, pharmaceuticals,
Natural Products as Drugs: history of natural products in medicine, natural products as
modern drugs, production of drugs based on natural products, role of natural products in drug
discovery.
Prospecting for New Compounds from Plants and fungi: Discovery of novel compounds,
Ethnobotanical approach and screening, Fungi a source of low molecular weight
pharmaceuticals, Actinomycetes as a Source of Bioactive Compounds, production from wild
or cultivated plants, collecting and harvesting medicinal plants and storage, preparation of
crude compounds, Isolation of pure compounds, bio-assay guided isolation, high throughput
screening of extracts.
Biosynthesis of Natural Products: Natural products derived biosynthetically from Shikimic
acid, natural products synthesized from acetate, natural products synthesized from amino
acids, alkaloids, purines.
Conventions on Biodiversity and Bioprospecting: How bioprospecting relates to
biodiversity conservation, Bioprospecting agreements, bilateral and multilateral contracts,
bio-piracy, legal implications, current status and application in India.
Practicals
 Identification of some medicinal plants.
 Calculation of Shannon index.
 Identification of genetic variation of medicinal plants.
 Amplification of ITS regions of medicinal plants.
 Isolation and identification of bioactive compounds by thin layer chromatography.
 Bioassay guided isolation.
 Antioxidant assay for bioactive compounds.
 Cytotoxicity assay.
 DNA damage studies.
 Metabolite profiling by HPLC.
18
BTC-303
Immunotechnology
32 H
Unit-I
Immunity and nonspecific immune system: Immunity, mechanical, chemical and
physiological factors, phagocytosis, humoral factors, lymphocytic cells.
Antigens and immunogenicity: The immune response, immunogenicity, molecular
differences in epitope structure.
Imunoglobulins: General structure, structure and functions of specific immunoglobulins,
antibody diversity, plasma cell dyscrasias.
Unit-II
The complement system: Complement, pathways of complement activation, membrane
attack pathway, biological consequences of complement activation, regulatory mechanisms.
The immune response system: Exposure to an antigenic substance, the lymphoid system,
cells involved in the immune response, events in the induction of the immune response,
intracellular events occurring during cell maturation, phases of the humoral immune
response.
Unit-III
Immune regulation: Introduction, immunosuppression, tolerance, immunopotentiation.
Immunization: Introduction active immunization, passive immunization, experimental
immunization procedures, adverse reactions of vaccines.
Immunological techniques: In vitro antigen- antibody reactions, procedures for direct
observation and demonstration of reactions, complex serological procedures, assays of
immune competence, identification of specific allergens in type I hypersensitive reactions,
detection of immune complexes, production and use of monoclonal antibodies.
Immunologic mechanisms of tissue damage: Introduction, immediate hypersensitivity
(typeI) reactions, cytotoxic (typeII) reactions, immune complex- mediated (typeIII) reactions,
cell-mediated (type-IV) reactions: delayed hypersensitivity and cell –mediated cytotoxicity.
Unit-IV
Auto immune diseases: General considerations, representative auto immunodisorders.
Immunodeficiency disorder: Phagocytic cell defects, B-cell deficiency disorders, T-cell
deficiency disorders, secondary immunodeficiency disorders combined B-cell and T-cell
deficiency disorders, secondary immunodeficiency conditions, complement deficiencies.
Transplantation immunology: Introduction, histocompatibility gene complex, clinical
transplantation immunology.
Tumor immunology: Neoplasms, tumor-associated antigens, immune response to tumor
antigens, immunologic factors favouring tumor growth, immunotherapy.
19
Practicals

Preparation of antigen and antibody production.

Purification of IgG.

Slide agglutination test/ Blood grouping.

Immunoprecipitation test- Ouchterlony double diffusion.

Immunoaffinity purification of IgG.

Immunofluorescence for localization of an antigen.

ELISA for quantification of an antigen.

Rossette assay.

Assay for activation of phagocytic cells.

Western blotting and detection.
20
BTC-304
Cell Signalling and Communication
32 h
Unit- I
The importance of the matrix in signal transduction: Cell surface receptors as reception of
extra-cellular signals, Amplification of signal during transmission - a quantitative study,
Tyrosine kinase and tyrosine phosphatase, Cell membrane components and adapter proteins
required for signal transmission, Upstream and downstream signal transduction without cell
surface receptor activation, G-protein coupled signaling; the secondary messengers in signal
transduction pathways cAMP, Ca2+, Reactive Oxygen Species and Hypoxia Signalling,
Apoptosis Signaling Transduction Pathway, PI3K/AKT Cell Survival Pathway.
Unit-II
Various signal transduction pathways from cell surface to nucleus: MAP kinase pathway,
SAP/JNK pathway, p38 pathway, NFkB pathway, Cell survival pathway, Wnt signaling
pathway, Jak/Stat pathway, Smad pathway, TGF  Signaling, EGFR, VEGF And their
Signalling, Cytoskeleton And Cell Signalling, Carbohydrate Recognition Signaling, MMPs
And Cell Signalling, Cross talk among cell surface receptors, Cross talks among cytoplasmic
components, Translocation of signal components during signal transmission, From cytoplasm
to cell membrane, NF-B Signaling from cytoplasm to nucleus, Cell cycle and its Signalling.
The end point of signal transduction--- gene transcription: Nuclear receptors and
transcription factors in signalling, signalling from single gene expression to multiple gene
expression: Super array as a tool for the study of multiple gene transcription, Practical
application of the signal transduction research, RNA Interference and Cell Signalling,
Senescence and its signalling Pathways.
Unit-III
Signal transduction in plants: Cross-talk with the environment- wound and mechanical
signalling - fatty acid signalling, peptide signalling, oligosaccharide signalling; protein
kinases and signal transduction. Abiotic stresses - Dehydration-stress, salt-stress, cold
acclimation, heat-stress;.
Role of active oxygen species (AOS) in plant signal transduction: AOS in plants, AOS as
signal molecules, AOS-part of a signalling network.
Action of phytohormones: Multiple signals regulating growth and development of plant
organs and their adaption to environmental stresses.
Unit-IV
Symbiotic plant-microbe interaction: Rhizospheric signals (PGPR) and early molecular
events in the ectomycorrhizal symbiosis; Lipo-chito-oligosaccharides (LCO) signalling in the
interaction between rhizobia and legumes; endophytes.
Recognition and defence signalling in plant-microbe interaction: Resistance genes - genefor-gene resistance; co-evolution and specificity of R genes; the TIR domain, the NBS
domain; genetic organization of resistance genes; quorum sensing.
Plant-insect interaction: Induction of direct and indirect defence.
21
Defence signal transduction pathways: Genetic analyses; Ethylene and jasmonate defence
pathways; the oxidative burst, nitric oxide, co-ordination of cell death responses, systemic
acquired resistance, interplay of downstream signalling pathways; signalling in plant-virus
interactions; plant-bacterial interactions; applications of defence signal transduction in plant
disease management.
Practicals
 Assay of Protein Kinase
 Assay of phosphoprotein Phosphatase
 Assay for MMP activity
 Assay for apoptosis
 Demonstration of translocation of NFkBeta
 FACS analysis for cell cycle
 Estrogen and progesterone receptor detection
 Study of defence-related enzymes and pathogenesis-related proteins –
phenylalanine ammonia lyase, peroxidase, polyphenol oxidase; β-1, 3 glucanase,
chitinase.
 Oxidative burst in host-pathogen interaction- hypersensitive cell death, cell necrosis,
Histochemical detection of hydrogen peroxide accumulation and lignin deposition.
 Isolation and identification of endophytic microorganisms from medicinal plants.
 Isolation and characterization of plant growth promoting rhizobacteria- Isolation of rhizobacteria
- Root colonization bioassay
- IAA production by PGPR
- Phosphate solubilization
- Siderophore production
- HCN production
- Antagonism
- Plant growth promotion
22
Semester II
BTC-401
Plant Biotechnology
32 h
Cell and Tissue Culture Technology
Unit-I
Role of hormones in growth and development of plants, tissue-specific hormones. Callus
Induction, Organogenesis, Somatic embryogenesis, cell suspension culture and synthetic
seeds.
Micropropagation: Propagation from pre-existing meristem, shoot apical meristem, shoot
and node culture, micropropagation stages and applications.
Commercial laboratory production: The facility, process- stock plant preparation,
production scheduling.
Germplasm preservation: Preservation of seed-propagated species, preservation of pollen,
preservation of vegetatively propagated species, pre-treatment of plant and propagule,
cryopreservation, cryoprotectant, warming rate and recovery, gene banks, applications.
Unit-II
Haploid Technology: Methods of haploid culture, Factors affecting anther and microspore
cultures, applications.
Protoplast Technology: Isolation, purification and culture of protoplasts, protoplast fusion
and somatic hybridization, applications of somatic hybrids/ cybrids.
Secondary metabolite production: Induction of secondary metabolites by plant cell culture,
technology of plant cell culture for production of chemicals, biotransformation using plant
cell culture. Bioreactor systems and models for mass cultivation of plant cells.
Unit-III
Seed Biotechnology
Seed development and structure: Flower formation, production and development of the
male and female gametophytes, pollination, fertilization, and formation of the zygote;
Molecular basis of embryogenesis, post-embryonic vegetative development, seed structure
and composition, genetic determinants of seed structure.
Hybrid seed production technology: Variability and its conservation in crop plants, Mode
of reproduction in relation to plant breeding, breeding systems, controlling pollination,
genetic principles, qualitative and quantitative traits, gene action, genotype environment
interaction, different methods of breeding for self and cross pollinated crops, plant
introduction and acclimatization, wide crosses, male sterility, apomixes, polyploidy.
23
Unit-IV
Transgenics
Plant transformation techniques: Methods of gene transfer in plants, Agrobacterium
mediated transfer- mechanism of DNA transfer, general features of Ti and Ri plasmids, role
of vir genes, design of expression vectors, use of promoters and reporter genes; viral vectors,
direct gene transfer methods- electroporation, microinjection, particle bombardment,
selection of transformants, screening and field trials.
Transgenic plants: Herbicide resistance, resistance against biotic stress- bacterial, viral,
fungal and insect resistance, abiotic stress, improved crop productivity, improved nutritional
quality, transgenic plants for floriculture, Qualitative trait loci and marker studies.
Molecular farming: Transgenic plants as production systems-production of alkaloids,
steroids, colouring agents, flavoring agents, biodegradable plastics, industrial enzymes,
therapeutic proteins, biopharmaceuticals, edible vaccines, plantibodies.
Intellectual Property Rights (IPR): IPRs and agricultural technology- implications for
India, WTO, WIPO, GATT, TRIPS. Plant Breeder's Rights, legal implications, commercial
exploitation of traditional knowledge, protection. Ethical issues associated with consumption
of GM food, labelling of GM crops and foods.
Practicals
 Preparation of plant tissue culture media.
 Organ culture: Shoot tip, nodal, anther and leaf culture.
 Protoplast isolation and fusion.
 Synthetic seeds.
 TLC of plant secondary metabolites.
 Alkaloid estimation.
 Seed structure.
 Agrobacterium culture, transformation and selection of transformants.
 GUS expression in transformed tissues.
24
BTC-402
Animal Biotechnology
32 H
Unit-I
Culture of animal cells: Advantages and limitations of tissue culture, aseptic handling,
facilities required, media and cell lines. Primary culture: Isolation of mouse and chick
embryos, human biopsies, methods for primary culture, nomenclature of cell lines, sub
culture and propagation, immortalization of cell lines, cell line designation, selection of cell
line and routine maintenance.
Cloning and Selection: Cloning protocol, stimulation of plating efficiency, suspension
cloning, isolation of clones, isolation of genetic variants, interaction with substrate, selective
inhibitors.
Unit-II
Cell separation and characterization: Density based, antibody based, magnetic and
fluorescence based cell sorting. Characterization of cells based in morphology, chromosome
analysis, DNA content, RNA and protein, enzyme activity, antigenic markers, cytotoxicity
assays, cell quantitation, cell culture contamination: monitoring and eradication,
cryopreservation.
Culturing of specialized cells: Epithelial, mesenchymal, neuro ectodermal, hematopoietic
gonad and tumor cells, Lympocyte preparation, culture of amniocytes, fish cells, confocal
microscopy. Stem cell culture and its applications
Organic and embryo culture: Choice of models, organ culture, histotypic culture, filter-well
inserts, neuronal aggregates whole embryo culture eggs, chick and mammalian embryos.
Unit-III
Cell and Tissue engineering: Growth factors for in situ tissue regeneration, biomaterials in
tissue engineering, approaches for tissue engineering of skin, bone grafts, nerve grafts.
Haemoglobin-based blood substitutes, bio artificial or biohybrid organs. Limitations and
possibilities of tissue engineering.
In vitro fertilization and Embryo transfer: In vitro fertilization in Humans, Embryo
transfer in Humans, Super ovulation and embryo transfer in farm animals e.g: Cow.
Cloning of Animals: Methods and uses. Introduction, nuclear transfer for cloning, cloning
from- embryonic cells, adult and fetal cells. Cloning from short-term cultured cells: cloning
of sheep, monkeys, mice, pets, goats and pigs. Cloning from long-term cultured cells:
Cloning of cows from aged animals. Cloning efficiency, cloning for production of transgenic
animals, gene targeting for cloned transgenic animals, cloning for conservation, human
cloning: ethical issues and risks.
Unit-IV
Transfection methods and transgenic animals: Gene transfer, transfection of fertilized
eggs or embryos, unfertilized eggs, cultured mammalian cells, targeted gene transfer.
Transgenic animals and applications: mice and other animals, sheep, pigs, goats, cows and
fish.
The legal and socio-economic impact of biotechnology at national and international levels,
public awareness.
Biosafety regulations- guidelines for research in transgenic animals, public awareness of the
processes of producing transgenic organisms.
25
Practicals
 Animal cell culture: preparation of media, culture and maintenance of cell lines,
trypsinization
 Culture of transformed cells
 MTT assay for cytotoxicity
 3H- Thymidine uptake assay for cell proliferation
 Cryopreservation and revival of cells
 Transient transfection
 In vitro growth of blood vessels
 Lymphocyte preparation
BTC-403
Project Work
26
Trans-border Electives
BTE-101
Enzyme Biotechnology
32 hours
Unit-I
Introduction, Classification and nomenclature, factors effecting enzyme activity.
Enzyme Kinetics: Rate of a reaction, order, Michaelis-Menten equation, initial velocity and
steady state approach, Vmax and KM, linear transformations of MM equation- LB plot, EH
plot, Hanes plot.
Enzyme inhibition- Competitive, Uncompetitive, non-competitive, mixed, partial, substrate
inhibition, suicide inhibition, determination of Ki.
Unit-II
Active site: Methods for determining active site structure, ES complex, affinity labeling,
chemical modification studies, structure investigation.
Chemical nature of enzyme catalysis: General acid base-, covalent-, metal ion- catalysis,
nucleophilic and electrophilic catalysis, transition state stabilization, orbital steering.
Molecular mechanism of enzyme action: Mechanism of chymotrypsin, ribonuclease,
lysozyme, carboxypeptidase.
Unit-III
Allosterism: Cooperativity-positive and negative cooperativity, binding of ligands to
macromolecules, Sigmoidal kinetics, MWC and KNF models, ATCase.
Coenzyme action of NAD+, FAD, TPP, PLP, Biotin, CoA, Folic acid, lipoic acid.
Isoenzymes and multienzyme
dehydrogenase complex.
complexes:
Lactate
dehydrogenase
and
pyruvate
Unit-IV
Application of enzymes: In medicine- as analytical agents, enzymes as markers for
diagnosis.
In industry - Food and beverage, detergent, textile pharmaceutical and leather.
Commercial production of enzymes: General considerations, regulation of enzyme
production by microbes, genetic engineering for microbial enzyme production, enzyme
engineering, large-scale purification.
Immobilized enzymes and cells: Methods, properties and stabilization of immobilized
enzymes and cells, enzyme reactors, application – manufacture of commercial products, and
analytical applications.
Biosensors: Types- Electrochemical, Thermometric, Optical, Piezoelectric, Whole cell,
immunobiosensors, applications.
27
Practicals
 Assay of acid and alkaline phosphatase and determination of specific activity
 Estimation of KM and VMax (Effect of substrate concentration)
 Time kinetics of Acid and alkaline phosphatase
 Effect of inhibitors and activators on enzyme activity
 Assay of peroxidase, urease, protease
 Isozyme analysis of peroxidase
 Immobilization of enzymes
28
BTE-102
Seed Health and Diagnostics
32 hours
Unit-I: Introduction
Seed Biology: Floral biology, mode of reproduction; Embryogenesis and seed development;
Seed structure of monocots and dicots; Chemical composition of seeds; Orthodox and
recalcitrant seeds, seed dormancy; Apomixis, parthenocarpy, polyembryony; Somatic
embryogenesis and synthetic seeds.
Development of Seed Industry: Agricultural situation in India; impact of green revolution;
cropping systems; International cooperation – ISTA, OECD, UPOV, AOSA, APSA, CGIAR
and other organizations.
Seed Production: Introduction to crop breeding methods; Variety testing, release and
certification; Different classes of seeds and their maintenance; Seed production requirements
and planning; Male sterility; Clonal propagation; Transgenic seeds. Disease tolerance
screening.
Seed drying, processing, storage and marketing: Seed drying principles and methods;
Seed treatment, safe storage seeds and marketing strategies.
Unit-II: Seed Quality Control
Importance of seed quality: Seed legislation - Seed act 1965, seed rules 1969 and new seed
act 2004.
Seed certification - History, concept, organization, phases and seed certification standards;
Field inspection principles and methods; Determination of seed quality - seed sampling,
physical purity, moisture, germination, genetic purity; Seed certification agencies; Testing of
transgenic seeds.
Unit-III: Seed Health
Importance: Designated plant diseases, tolerance, seed health and trade, Pest-free areas
(PFA), Pest Risk Analysis (PRA).
Significance of seed health - important seed borne diseases of cereals, pulses, oil seeds, fiber
and vegetable crops; Mechanism of seed transmission and disease cycle.
Management of seed-borne diseases: Quarantine and phytosanitary certificates, Physical
and chemical control, biological control, cross protection.
Storage fungi and insects: Causes and indices of seed deterioration during storage,
fumigation.
Mycotoxins – Important mycotoxins, factors influencing mycotoxin production, harmful
effects, detection.
29
Unit-IV: Diagnostics - Seed health testing procedures for Fungi – symptoms, dry seed
examination, incubation tests, embryo extraction technique, seedling symptom test; Bacteria
– symptoms, colony appearance, liquid assay, selective and semi-selective media, staining
techniques, biochemical & physiological tests, pathogenicity tests, immune-fluorescent
technique, Biolog; Viruses – symptoms, seed examination, growing-on test, indicator plant
test, electron microscopy, ISEM, ELISA, DIBA, IC-RT-PCR; Nematodes – Extraction and
identification.
Application of serological methods – monoclonal and polyclonal antibodies, conventional
serological techniques – precipitin tests, agglutination tests, ELISA, DIBA, and nucleic acid
based techniques; Multiplex ELISA and PCR, Application of Real Time (RT)-PCR; FTA
technology.
Sequence databases of seed-borne pathogens. Gene targets and primer designing.
Practicals











Floral biology – Cereals, vegetable crops, oil seed crops, legumes
Seed structure – Dicot and monocot
Seed proteins
Estimation of mycotoxins
Seed sampling
Seed quality determination – Physical purity, germination, moisture determination,
TTC test
Seed health testing : Fungi, bacteria, viruses
Electron microscopy
Serological diagnosis
Nucleic acid based techniques – IC-RT-PCR, Real Time-PCR
Designing of primers.
30
BTE-103
Molecular Phytobacteriology
32h
Unit-I
Introduction to Molecular Phytobacteriology, Compatible and incompatible interactions
involved in phytopathogenic bacteria, Identification and characterization of phytopathogenic
bacteria.
Unit-II
Molecular recognition process between plant and bacterial pathogens: Molecules responsible
for physical contact, bacterial genes involved in recognition of hosts and non-hosts, the role
of hrp and avr genes in the early recognition process in plant and phytopathogenic bacterial
interactions.
Unit-III
Molecular communication in Bacteria; Cell-cell communication in bacteria – Quorum
sensing. Biochemical defence mechanism: Bacterial pathogens induce PR proteins, the role
of PR proteins in bacterial disease resistance, defence-related enzymes – PAL, POX, LOX,
Role of AOS and HRGPs in bacterial disease resistance.
Unit-IV
Host defence mechanisms: the cell wall-the first barrier and a source of defence signal
molecules: Plant cell wall components involved in plant defence mechanisms against
bacterial pathogens; bacterial extra cellular enzymes induce host defence mechanisms, cell
wall modifications and bacterial disease resistance. Molecular
diagnostics
for
phytopathogenic bacteria– PCR, RAPD-PCR, SSCP-PCR.
Practicals




Demonstration of Hypersensitive response from Phytopathogenic bacteria.
Biochemical characterization tests for phytopathogenic bacteria.
Estimation of defence-related enzymes – PAL, POX, LOX.
Molecular characterization of phytopathogenic bacteria – PCR, RAPD-PCR, SSCPPCR.
31
BTE-104
Proteomics
32 hours
Unit-I
Introduction to proteomics: Proteome and nature of proteome. Proteins - amino acids,
peptides and polypeptides. Protein structure – primary, secondary, tertiary and quaternary,
peptides as conformational determinants. Protein structure determination - X-ray and NMR.
Unit-II
Protein/Peptide separation techniques: Purification- solubility, size, charge and affinity
chromatography. Separation- single and two-dimensional gel electrophoresis, highperformance liquid chromatography and reverse-phase chromatography. Detection– staining
and immunoblot.
Unit-III
Protein characterization: Mass spectrometry– fundamentals, mass spectrometry ionization
techniques, mass analyzers– MALDI-TOF, MS-MS, LC-MS-MS; SDS-PAGE and in-gel
digestion, sample introduction, peptide fragmentation. Mass-spectrometry data: basics,
spectra; Sequence data: databases, tools and resources; Mass-spectrometry search engines:
Mascot and protein prospector. Mass spectra analysis– identification, molecular weight,
pI determination for intact protein; determination of peptide sequence, peptide sequencing
and identification using tandem mass spectrometry.
Unit-IV
Functional diversity of proteins: characteristics features, post-translational modifications–
identification, analysis of glycopeptides by mass spectrometry, proteome expression analysis
- heat shock proteins; protein array and its application. Clinical, biomedical and
biotechnological applications of proteomics.
Practicals
 Isolation and quantification of proteins
 Separation of proteins by electrophoresis
 Purification of proteins by chromatography
 Molecular weight determination of proteins
 Identification of proteins and glycoproteins
 Expression and analysis of heat shock proteins
32
BTE-105
Cancer Biology
32 Hours
Unit-I
Cancer Biology: the basics
Introduction, historical perspective, classification, Carcinogenesis, cancer initiation,
promotion and progression, Cancer cell cycles, Genomic instability, Apoptosis, Genes and
proteins as players in apoptosis, DNA viruses/ cell immortalization.
Unit-II
Cancer Genes I: Oncogenes and signal transduction
Cellular proto-oncogenes, oncogene activation, Growth factors, growth factor receptors,
signal transduction , Transcription, Transcription factors and cancer, Retroviral oncogenes,
Tumor suppressor, Tumor suppressor gene pathways, DNA methylation, epigenetic
silencing of suppressor genes.
Unit-III
Understanding Cancer as a Disease: natural history of cancer development
Free radicals, antioxidants and Metabolic oxidative stress and cancer, Epidemiology of
selected cancers, Gene rearrangements, detecting oncogene abnormalities in clinical
specimens, Cell: cell interactions, cell adhesion, angiogenesis, invasion and metastasis,
Antiangiogenic therapy of cancer.
Unit-III
Current concepts in cancer therapy
Strategies of anticancer chemotherapy, Strategies of anticancer gene therapy/translating
therapies from the laboratory to the clinic, Gene discovery in cancer research, cancer genome
anatomy project , Cancer immunity and strategies of anticancer immunotherapy, stem cells
and their applications in cancer therapy.
Practicals
 Immunological measurement of Growth factors in normal and tumor cells.
 Counting microvessel density in tumor tissues.
 Staining of normal and tumor cells for tumor suppersor gene p53.
 Methods to study apoptosis. Bcl to Bax ratio.
 Angiogenesis and antiangiogenesis assays.
33
BTE-106
Biological Control
32 Hours
Unit-I
Biological control – Definition, History, Scope, advantage of Biocontrol over chemical
pesticide, Classical biological control, Biocontrol agents– Arthropods, – dragon fly,
Lacewings, Beetles, flies, true bugs, ants, wasps, thrips, mantids and spiders, Roundworms –
Nematodes, Protozoan, Fungi– Hirsutella, Verticillium, Trichoderma spp., Bauveria spp.,
Bacteria – Bacillus turingensis, Bacillus phaericus, Pseudomonas spp., Rhizobium,
Azotobacter, Agrobacterium etc., Mycoplasma, Virus – Nucleopolyhedrosis virus.
Unit-II
Preharvest biological control– Insects, Nematodes, Protozoan, Fungi, Bacteria, Mycoplasma,
Virus and Weeds. Post harvest biological control – rodents, insects, molds etc.
Unit-III
Mechanism involved in biocontrol organism mediated disease protection- Parasitism,
Antagonism, Induction of Systemic resistance (ISR), Strategies to improve the biocontrol
ability of selected microorganisms – genetical modification, development of consortia,
addition of elicitors, application strategies.
Unit- IV
Mass multiplication, Toxicological studies, Formulations, shelf-life period, storage,
Application methodologies, Field trials, Transfer of technology, Intellectual property rights
(IPR). Other methods to improve biocontrol ability - Pheromones, Plant extract, Plant
resistant to pests, Cultural methods, Planting time, Cultivation, Harvesting, Irrigation and
water management, Sanitation, Crop rotation, Genetic methods.
Practicals






Isolation of rhizobacteria
Characterization of rhizobacteria for plant growth promoting traits
Characterization of rhizobacteria for disease suppression traits
Morphological, physiological and biochemical characterization of rhizobacteria
Mass multiplication
Preparation of bioformulations.
34
BTE-107
Molecular Marker Technology
32 Hours
Unit I: Introduction. Biomarkers - Morphological, biochemical and molecular markers;
Importance of molecular markers; Molecular and protein polymorphism; Naturally occurring
polymorphism in DNA sequences – Base pair deletion, substitution, additions or patterns;
Application – germplasm characterization, genetic diagnosis, characterization of
transformants, study of genome organization and phylogenetic analysis. Molecular markers
for genome analysis: kinds of molecular markers - protein markers – merits and demerits and
their applications in different fields of molecular biology; isozyme marker – merits and
demerits, their application in molecular biology.
Unit II: Molecular markers in plant breeding: Genetic molecular markers – Introduction
and developments, direct mapping, in silico mining; Application of genetic molecular
markers – trait mapping, functional diversity, inter-specific and inter-generic transferability,
genetic resource management, transgenic crops, fingerprinting of cultivars, Plant variety
protection act etc; Comparison of Genic molecular markers (GMMs) and Random molecular
markers (RDMs). Molecular assisted selection (MAS) for biotic / abiotic stress and
quantitative traits.
Unit III: Genetic marker database-SNP, SSR, Conserved orthologue set (COS); An ideal
DNA marker – Non-PCR based technology – RFLP, Minisatellites or Variable Number of
Tandem Repeats (VNTR); PCR-based markers – RAPD, AFLP, Minisatellites, PCR
sequencing, microsatellites or simple sequence repeats (SSR), Inter simple sequence repeats
(ISSR), Sequence characterized amplified region (SCAR), Single strand conformation
polymorphism (SSCP), Denaturing gradient gel electrophoresis (DGGE), Inter-simple
sequence repeats (ISSR), Single nucleotide polymorphism (SNP). Comparative qualities of
DNA marker techniques, genomic abundance, level of polymorphism, codominance of
alleles, reproducibility; comparison of commonly used markers. Application of RT-PCR.
Unit IV: Application of molecular markers in animal breeding and diagnosis of
animal/human diseases- Genomic organization, current status of genome maps of livestock
and humans. DNA markers and their application – RAPD, RAPD, SNP, DNA sequences,
DNA finger printing; Transgenesis and methods of gene transfer – super ovulation and
embryo transfer techniques. Pharmacogenomics - Genetic markers – early drug development,
clinical development, molecular diagnostics.
Practical
 Extraction of protein from different plants and fungi
 Study variation through electrophoresis (SDS-PAGE & Native PAGE)
 Isozyme analysis (Peroxidse, Esterase, Catalase)
 Isolation of DNA from different plants and fungi
 Study of RAPD markers
 Microsatellite markers
 Other PCR based markers viz., SCAR, SCAP
35
BTE-108
Medicinal Plant Biotechnology
32 Hours
Unit -I
Introduction - Plants, genes, genomes, epigenomes and Biotechnology; Plants as sources of
medicines; The engineering of medicinal plants: Prospects and limitations, Genetic
transformation and production of transgenic plants, Pathway engineering and combinatorial
biosynthesis, Bioprocessing, Plant propagation, Phytochemistry.
Metabolomics: Introduction, analytical methods, chromatography, GC, HPLC, Capillary
electrophoresis, TLC, Spectroscopy, MS, NMR spectrometry, Identification of metabolites.
Unit-II
Plant-associated microorganisms (Endophytes) as sources of bioactive natural products:
endophyte diversity, selection of plants, isolation, preservation and storage of endophytes;
fermentation media composition and conditions, use of precursors and elicitors, scale up,
examples of bioactive natural products from endophytes.
Unit-III
DNA profiles of plants: methodology of plant DNA profiling, DNA sequencing and
multilocus DNA profiles – Hybridization-based RFLP fingerprinting, PCR with arbitrary
primers, PCR with microsatellites – complementary primers, AFLP analysis; Locus-specific
microsatellite DNA markers; PCR-based RFLP analysis of organellar and nuclear genomes;
other DNA markers. Application of molecular markers in herbal drug technology.
Applications – Genotype identification, plant species, plant cultivars and accessions, In vitro
propagated plant material; Genetic diversity – variation and relatedness, amount and
distribution of variability in wild-growing plants, plant systematics; Gene tagging.
Unit-IV
Bioprospecting: The search for bioactives, assay systems; lead structures from nature,
Secondary metabolites - modes of action and utilization in medicine. Biotechnological
approaches for the production promising plant-based chemotherapeutics, cell cultures,
immobilization, feeding precursors, elicitors, in-situ product removal, biotransformation,
bioreactor and scale-up, biosynthetic pathway mapping and metabolic engineering.
Biosynthesis of podophyllotoxin, paclitaxel and camptothecin.
Engineered plants: Heterologous expression of plant natural product genes and pathways. Eg.
Alkaloids, isoprenoids, sesquiterpenes and diterpenes, taxol, artemissinin, carotenoids,
flavonoids; Production of therapeutic antibodies in plants, protein folding, assembly and
glycosylation, downstream processing, biosafety concerns, regulatory issues, ethical and
patent issues.
Practicals
 Identification of medicinal plants
 Isolation of bioactives
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Qualitative determination of phytochemicals
Anti-oxidant, Anti-diabetic, Anti-inflammatory, Anti-microbial assays;
Isolation of endophytes, identification, fermentation, separation of metabolites – TLC,
HPLC, assay-guided fractionation.
Extraction of protein from different plants and fungi
Study variation through electrophoresis (SDS-PAGE & Native PAGE)
Isolation of DNA from different plants and fungi
Study of RAPD markers
Microsatellite markers
Other PCR based markers viz., SCAR, SCAP
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BTE-109
Molecular Virology
32 Hours
Unit-I: Economic importance of viral diseases in plants, animals and humans; virus
classification, structure, replication and assembly; types of infection and effect, symptoms,
transmission; viral proteins and their functions; cell to cell and long distance movement of
plant viruses; viral transformation and oncogenesis; sub-viral infections – satellite viruses,
virusoids, viroids, defective viruses, mobile genetic elements, prions.
Unit-II: Genome organization and replication of DNA viruses - dsDNA viruses (Herpes
Simplex Virus), dsDNA viruses that use an RNA intermediate (Hepatitis B virus, Cauliflower
Mosaic virus), ssDNA viruses (Geminivirus, Parvorirus); RNA viruses – (+)ssRNA viruses
(Poliovirus, Tobamovirus, Potyvirus, Bromovirus), (-) ssRNA (Rhobdoviridae, Influenza
virus), (+)ssRNA viruses that use a DNA intermediate (Retrovirus), dsRNA virus (Reovirus);
Genome organization and replication of bacteriophages including Q replicase.
Unit-III: Viral interactions with the immune system – non-specific, cell-mediated and
serological immune response, apoptosis; evasion of immune surveillance, epitope mapping,
production of specific antisera, passive immunity.
Medical applications: Vaccines and immunotherapy, Adjuvants, Approaches to vaccine
development, tailoring of immune response to vaccination, alternative delivery systems;
antiviral drugs, cloning and gene therapy.
Management of plant virus diseases – conventional methods, cross protection, transgenics,
antisense technology.
Unit-IV: Virus detection and diagnosis; Infectivity assays - sap transmission, insect vector
transmission, agro-infection; Ultracentrifugation, electron microscopy, serological methods,
immunoelectrophoresis in gels, direct double-antibody sandwich method, Dot ELISA,
Immunosorbent electron microscopy (ISEM), Polymerase chain reaction; DNA and
oligonucleotide microarray; Gene silencing, PTGS and TGS, viral suppressors of gene
silencing, RT-PCR, Multiplex ELISA/PCR, Diagnostic kits.
Practical: Growing on tests and indicator plant tests for plant viruses, ELISA, DIBA,TEM,
ISEM, RT-PCR, FTA, IC-RT-PCR, Kit-based diagnosis.
References:
Mandahar, C.L. (Ed.). Molecular Biology of Plant Viruses, 1999. Kluwer Academic
Publishers.
Harper, D.R.1994. Molecular virology - A medical perspectives Book, (1994) Bios scientific
publishers.
Roger Hull (Ed). 2002. Mathew Plant Virology. 4th Edition, AP.
Walkey D.G.A. (Ed). 1991. Applied Plant Pathology. Chapman and Hall.
Nayudu, M.V. 2008. Plant Viruses. Tata McGraw Hill
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BTE-110
Metabolomics
32 Hours
Unit-I
Plant Metabolomics: Developments and history of plant metabolomics, Nature and
prospecting of metabolism-related secondary plant products, tools and techniques, production
in culture: optimization; selection, hormonal kinetics for secondary metabolites, production,
mechanism and control.
Unit-II
Production of secondary metabolites: Induction, Alkaloids, antitumor compounds, food
additives, steroids and saponins, detoxification of secondary metabolites, production of
secondary metabolites by bioconversion, genetic transformation for production of secondary
metabolites, large-scale production in bioreactors, Metabolomics-assisted breeding.
Unit-III
Microbial metabolomics: Systems biology of microbial metabolism; microbe sensors, In
silico metabolomes, Food and Applied metabolomics, Biomarker discovery. Experimental
Approaches- Genome sequencing, Gene expression arrays, Nuclear Magnetic Resonance,
Mass spectroscopy, Capillary electrophoresis, Two dimensional gel electrophoresis, Gene
expression arrays, Pathway analysis, HPLC, Protein sequencing, Bench-scale fermentation,
AFLP/RLFP analysis.
Unit-IV
Pharmacometabolomics: personalized medicine and future of health system, Pathways
discovery and disease pathophysiology, Bioinformatics analysis of targeted metabolomics;
Environmental metabolomics, Bioactive compounds and Pharmacognosy, Clinical
Applications of Metabolomics, Nutrigenomics and Metabolomics, Novel Technologies for
Metabolomics, Data Handling for Metabolomics.
Practicals
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Tissue culture techniques for the production of secondary metabolites in medicinal
and aromatic plants: Stages of secondary metabolites production in vitro –
optimization, selection and stress conditions.
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Genetic Transformation for Production of Secondary Metabolites:
- Induction of hairy roots by Agrobacterium rhizogenes.
- Establishment of hairy root cultures.
- Markers for conformation.
- Elicitation of products accumulation: Abiotic and Biotic elicitors.
Extraction and Isolation of secondary metabolites
- from medicinal plants.
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-from medicinal plants associated with endophytes.
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Analysis of secondary metabolites
-Phenolics compounds
- Analysis of Alkoloids: Quantification of Reserpine, Ajmaline, and Ajmalicine
- Analysis of Flavonoids.
- Analysis of Terpenoids.
- Analysis of Food Additives: Colours – Anthocyanines, Betalaines, Crocin &
Crocetins and other capsaicinoids, sweeteners – Steviosides and Thaumatin
-Fingerprint Chromatographic Analysis by HPLC
Bioassays of secondary metabolites
Scavenging activity of natural Antioxidants (DPPH assay)
Analysis of sequential genetic regulations of β-carotene, betalaines and other selective
nutraceuticals by using specific primers in selected crop plants and microorganisms.
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