Biotech 551

Cell and Developmental Biology

2+1=3

Unit I

Cell Theory & Methods of Study

Microscope and its modifications – Light, phase contrast and interference, Fluorescence, Confocal, Electron (TEM and SEM), Electron tunneling and Atomic Force Microscopy, etc.

Membrane Structure and Function

Structural models; Composition and dynamics; Transport of ions and macromolecules; Pumps, carriers and channels; Endo- and Exocytosis; Membrane carbohydrates and their significance in cellular recognition; Cellular junctions and adhesions; Structure and functional significance of plasmodesmata.

Unit II

Organelles

Nucleus – Structure and function of nuclear envelope, lamina and nucleolus; Macromolecular trafficking; Chromatin organization and packaging; Cell cycle and control mechanisms; Mitochondria – structure, organization of respiratory chain complexes, ATP synthase, Structure-function relationship; Mitochondrial DNA and male sterility; Origin and evolution; Chloroplast– Structure-function relationship; Chloroplast DNA and its significance; Chloroplast biogenesis; Origin and evolution.

Unit III

Endo-membrane System and Cellular Motility

Structure and function of microbodies, Golgi apparatus, Lysosomes and Endoplasmic Reticulum; Organization and role of microtubules and microfilaments; Cell shape and motility; Actin-binding proteins and their significance; Muscle organization and function; Molecular motors; Intermediate filaments; Extracellular matrix in plants and animals.

Unit IV

Cellular Movements and Pattern Formation

Laying of body axis planes; Differentiation of germ layers; Cellular polarity; Model plants like Fucus and Volvox; Maternal gene effects; Zygotic gene effects; Homeotic gene effects in Drosophila; Embryogenesis and early pattern formation in plants; Cell lineages and developmental control genes in Caenorhabditis.

Unit V

Differentiation of Specialized Cells

Stem cell differentiation; Blood cell formation; Fibroblasts and their differentiation; Cellular basis of immunity; Differentiation of cancerous cells and role of proto-oncogenes; Phase changes in Salmonella; Mating cell types in yeast; Surface antigen changes in Trypanosomes; Heterocyst differentiation in Anabaena; Sex determination in Drosophila.

Plant Meristem Organization and Differentiation

Organization of Shoot Apical Meristem (SAM); Organization of Root Apical Meristem (RAM); Pollen germination and pollen tube guidance; Phloem differentiation; Self-incompatibility and its genetic control; Embryo and endosperm development; Heterosis and apomixis.

Practical

Cell Biology

Microscopy – Bright field, dark field, phase contrast, fluorescence microscopy, visit to Electron microscope and Confocal microscope facilities.

Histology – Hand-sectioning of stem and leaf, saffranin and fast green staining.

Microtomy - fixing of tissues, dehydration, wax-embedding, sectioning and staining.

Mitosis – Onion root tips

Meiosis – Insect testes/plants

Biotech 552

Plant Biology/Plant Developmental Biology – Phsiological and molecular basis

2+0=2

Contents of Pl Phsiol 502 (Cross listing)

Biotech 553

Molecular Biology

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Unit I
Genome organization
Organization of bacterial genome; Structure of eukaryotic chromosomes; Role of nuclear matrix in chromosome organization and function; Matrix binding proteins; Heterochromatin and Euchromatin; DNA reassociation kinetics(Cot curve analysis); Repetitive and unique sequences; Satellite DNA; DNA melting and buoyant density.
Unit II
DNA Structure; Replication; Repair & Recombination
Structure of DNA - A-,B-, Z- and triplex DNA; Replication: initiation, elongation and termination in prokaryotes and eukaryotes; Enzymes and accessory proteins; Fidelity; Replication of single stranded circular DNA; Gene stability and DNA repair- enzymes; Photoreactivation; Nucleotide excision repair; Mismatch correction; SOS repair; Recombination: Homologous and non-homologous; Site specific recombination.
Unit III
Prokaryotic & Eukaryotic Transcription
Prokaryotic Transcription; Transcription unit; Promoters- Constitutive and Inducible; Operators; Regulatory elements; Initiation; Attenuation; Termination-Rho-dependent and independent; Anti-termination; Transcriptional regulation-Positive and negative; Operon concept-lac, trp, ara, his, and gal operons; Transcriptional control in lambda phage; Transcript processing; Processing of tRNA and rRNA Eucaryotic transcription and regulation; RNA polymerase structure and assembly; RNA polymerase I, II, III; Eukaryotic promoters and enhancers; General Transcription factors; TATA binding proteins (TBP) and TBP associated factors (TAF); Activators and repressors; Transcriptional and post-transcriptional gene silencing
Unit IV
Post Transcriptional Modifications
Processing of hnRNA, tRNA, rRNA; 5'-Cap formation; 3'-end processing and polyadenylation; Splicing; RNA editing; Nuclear export of mRNA; mRNA stability
Translation & Transport
Translation machinery; Ribosomes; Composition and assembly; Universal genetic code; Degeneracy of codons; Termination codons; Isoaccepting tRNA; Wobble hypothesis; Mechanism of initiation, elongation and termination; Co- and post-translational modifications; Transport of proteins and molecular chaperones; Protein stability; Protein turnover and degradation
Unit V
Mutations; Oncogenes and Tumor suppressor genes
Nonsense, missense and point mutations; Intragenic and Intergenic suppression; Frameshift mutations; Physical, chemical and biological mutagens; Transposition - Transposable genetic elements in prokaryotes and eukaryotes; Mechanisms of transposition; Role of transposons in mutation; Viral and cellular oncogenes; Tumor suppressor genes from humans; Structure, function and mechanism of action of pRB and p53 tumor suppressor proteins; Activation of oncogenes and dominant negative effect; Suppression of tumor suppressor genes; Oncogenes as transcriptional activators.

Biotech 554

Lab on Molecular & Plant Biology   

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Plant Biology
1. Plant DNA extraction, digestion of DNA with restriction enzymes, agarose       gel electrophoresis.
2. Polymerase chain reaction to amplify a plant gene.
3. Homogenization of leaves, sub-cellular fractionation by differential     centrifugation, SDS-PAGE analysis of proteins.
4. RNA extraction, Agarose gel electrophoresis of RNA, RT-PCR analysis of a     plant gene.
Molecular Biology
1. Plasmid DNA isolation and DNA quantitation: Plasmid minipreps,     Restriction digestion
2. Preparation of competent cells, Transformation of E.coli with standard        plasmids, Calculation of transformation efficiency.
3. Purification of DNA from an agarose gel, DNA Ligation with plasmid    vectors.
4. Cloning of genomic DNA in standard plasmid vectors
5. Confirmation of the insert, Miniprep of recombinant plasmid DNA,     Restriction mapping
6. Polymerase Chain reaction by using standard 16srRNA eubacterial primers
7. RFLP analysis of the PCR product.

Biotech 561

Tissue Culture & Transgenic Technologies  

2+0=2

Unit I
Totipotency; Tissue culture media; Plant hormones and morphogenesis; Direct and indirect organogenesis; Direct and indirect embryogenesis; Cell suspension culture; Micropropagation – shoot tip culture, somatic embryos, artificial seeds; Applications of tissue culture; Virus elimination by shoot tip culture; Wide hybridization and embryo culture; Anther culture and dihaploids.
Unit II
Large-scale cell suspension culture; Production of alkaloids and other secondary metabolites; Protoplast culture, Plant cell wall structure and cell wall hydrolyzing enzymes; Protoplast isolation and purification; Protoplast viability test; Protoplast fusion; Somatic hybrids; Cybrids.
Unit III
Direct transformation of protoplasts using PEG; electroporation; Transformation by particle bombardment; Assembly of particle gun; Microprojectile preparation and bombardment; Chloroplast transformation by particle bombardment
Unit IV
Agrobacterium biology; Ti plasmid-based transformation; crown gall and hairy root disease, Ti and Ri plasmids, T-DNA genes, borders, overdrive, chromosomal and Ti plasmid virulence genes and their functions, vir gene induction, mechanism of T-DNA transfer; Ti pasmid vectors, vir helper plasmid, super virulence and monocot transformation, binary vector; Floral dip transformation; Promoters and polyA signals; Protein targeting signals; Plant selectable markers; Reporter genes; Positive selection; Selectable marker elimination; Transgene silencing; Strategies to avoid transgene silencing.
Unit V
Genetic engineering of crops; Commercial status of transgenic plants; Herbicide resistance, glyphosate, sulfonyl urea, phosphinothricin, atrazine; Pest resistance, Bt toxin, synthetic Bt toxin; Protease inhibitor; GNA and other lectins; α-amylase inhibitor; nematode resistance; Genetic engineering for male sterility- Barnase-Barstar; Delay of fruit ripening; polygalacturanase, ACC synthase, ACC oxidase; Improved seed storage proteins; Improving and altering the composition of starch and plant oils; Golden rice for β-carotene accumulation; Production of antibodies and pharmaceuticals in plants; Bio-safety concerns of transgenic plants.

Biotech 562

  Genetic Engineering   

2+0=2

   Unit I
Basics Concepts
DNA Structure and properties; Restriction Enzymes; DNA ligase, Klenow enzyme, T4 DNA polymerase, Polynucleotide kinase, Alkaline phosphatase; Cohesive and blunt end ligation; Linkers; Adaptors; Homopolymeric tailing; Labeling of DNA: Nick translation, Random priming, Radioactive and non-radioactive probes, Hybridization techniques: Northern, Southern and Colony hybridization, Fluorescence in situ hybridization; Chromatin Immunoprecipitation
Unit II
Cloning Vectors
Plasmids; Bacteriophages; M13 mp vectors; PUC19 and Bluescript vectors, Phagemids; Lambda vectors; Insertion and Replacement vectors; EMBL; Cosmids; Artificial chromosome vectors (YACs; BACs); Expression vectors; pMal; GST; pETbased vectors; Protein purification; His-tag; GST-tag; MBP-tag etc.;  Plant based vectors, Ti and Ri as vectors, Yeast vectors, Shuttle vectors

Unit III
Cloning Methodologies
Insertion of Foreign DNA into Host Cells; Transformation; Construction of libraries; Isolation of mRNA and total RNA; cDNA and genomic libraries; cDNA and genomic cloning; Expression cloning; Jumping and hopping libraries; Southwestern and Far-western cloning; Protein-protein interactive cloning and Yeast two hybrid system; Phage display; Principles in maximizing gene expression
Unit IV
PCR and Its Applications
Primer design; Fidelity of thermostable enzymes; DNA polymerases; Types of PCR – multiplex, nested, reverse transcriptase, real time PCR, touchdown PCR, hot start PCR, colony PCR, cloning of PCR products; T vectors; Proof reading enzymes; PCR in gene recombination; Deletion; addition; Overlap extension; and SOEing; Site specific mutagenesis; PCR in molecular diagnostics; Viral and bacterial detection; PCR based mutagenesis, Mutation detection: SSCP, DGGE, RFLP, Oligo Ligation Assay (OLA), MCC (Mismatch Chemical Cleavage, ASA (Allele-Specific Amplification)
Unit V
Sequencing methods; Enzymatic DNA sequencing; Chemical sequencing of DNA; Automated DNA sequencing; RNA sequencing; Chemical Synthesis of oligonucleotides; Principle and application of gene silencing; Gene knockouts and Gene Therapy

Biotech 572

Bioinformatics and Biocomputation  

2+1=3

 Unit I
Introduction theory and Biology
Definitions; History; Contentions with education; Agriculture; Medicine; Structural biology & Pharmaceutical industry; Scope of bioinformatics; Concepts of entropy; Shannon’s formula; equi-probability and independence-application to DNA and protein; Introduction to computers and high performance computing (HPC)
Unit II
Databases
a. Sequence database: Concepts of database; Key features of database system; History; Database management systems; Database types; Introduction to query language; Index; Forms and Reports.
b. Structure databases: Biological databases: plant, animal, microbial, viral and organism databases and biodiversity; Sequence and structure databases; Advanced concepts and approaches in database construction and management; Knowledge discovery and data mining; Introduction to Protein Data Base (PDB); Nucleic acid databases at NCBI.
Unit III
Genetic algorithms, sequence alignment and search Introduction to genetic algorithms; Concepts and approaches; Alignment algorithms: global, linear space, map and multiple sequences; Evolutionary basis of sequence alignment; Score matrices; Statistical significance of alignment; Low-complexity regions; Repetitive elements; Motifs and patterns; Multiple and progressive alignment methods; Hidden Markov Model (HMM) and threading theory; Database similarity searching; FASTA and BLAST; Dynamic programming
Unit IV
Phylogenetic analysis: Elements of phylogenetic models; Phylogenetic data analysis; tree building and tree
evolution.
Unit V
Comparative structural and functional genomics: Genome and Comparative Genome sequencing-methods and platforms; Nature of raw genome sequence data, Expressed sequence tags (ESTs), SAGE, MPSS and 454 sequence gene tags, Polymorphism, DNA chips and comparative genomics; Genome annotation-approaches and concepts; Genome-wide maps from large community of data; Use of sequences in drug design and prediction of forms; Cluster analysis; Neural networks and artificial intelligence.
Practical
Post sequence analysis, introduction to genomic data and data organization, comparative genome organization, comparative genome analysis and post-genomic biology. Homologous sequences and scoring matrices. Sequence comparison and multiple sequence alignments. Homologous search algorithms: BLAST, FASTA and SENSEI. Sequence to trees, metabolic reconstruction. Integration of sequence and metabolic data. Homologous modeling-protein structure prediction. Related software packages 

Biotech 591

M.Sc.Seminar

1+0=1

Biochem 501

Biochemistry                   (Contents of Biochem 501)

3+1=4

Biochem 551

Techniques in biochemistry                    (Contents of Biochem 551)

3+1=4

GP 501

Principles of Genetics                             (Contents of GP 501)

2+1=3

Stat 511

Statistical methods of applied sciences (Contents of Stat 511)

3+1=4

Lib 501

Literature and technical writing(Contents of Lib 501)

1+0=1

Biotech 601

Gene Cloning

1+1=2

Theory: Advent of gene cloning-tools and techniques-vehicles, plasmids and phages-purification of DNA from living cells-total cell, plasmid and phage DNAs-polymerase chain reaction (PCR) for DNA amplification; pulsed-field electrophoresis for separation of large DNA molecules; manipulation of DNA-purification of enzymes involved; introduction of DNA into host cells and selection; cloning vectors for E. coli, fungi, yeast, higher plants and mammalian cells-Strategies for obtaining the clone of choice-direct selection-selection from gene library; methods of clone identification-restriction mapping-study of cloned gene expression and sequencing; cloning PCR or AFLP product after electrophoresis-positional cloning-uses of gene cloning in research; applications in biotechnology.
Practical: Culturing of plasmid borne bacteria/lambda phage-extraction of plasmid/lambda DNA-restriction analysis of vector DNA-elution of insert of designed DNA product-ligation of exogenous DNA-transformation of E. coli-screening for transformants-mass multiplication of transformant-analysis of transformant DNA. 

Biotech 602

Metabolic pathway Engineering

1+0=1

Theory: Plant cell development and metabolism, manipulation of metabolic partitioning in transgenic plants; manipulation of plant development-flower development, fruit ripening, seed storage proteins, seed oil composition and production; genetic engineering of polyamine metabolism; genetic engineering of metabolic pathway in medicinal plants like Catharanthus, Atropa belladona etc.; manipulation of chalcone synthase pathway; transgenic plants for the production of biodegradable plastics; metabolic pathway engineering in cotton  biosynthesis of polyhydroxy butyrate fibres; molecular pharming-transgenic plants for the production of recombinant antibodies, vaccines etc. 

Biotech 603

Molecular Marker Technology

2+1=3

Theory: Composition of genome - molecular dissection of genome-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 -  DNA markers, different kinds-hybridization based, PCR based markers; methods of high-throughput marker genotyping; genome selection, linkage mapping-development of mapping populations, F2s, backcrosses, NILs, RILs and DH lines- choice of mapping population- linkage map construction; applications of markers in mapping of agronomically important traits;  marker assisted selection (MAS) in backcross and heterosis breeding; foreground and background selection; MARS, MAS for gene introgression and pyramiding: MAS for specific traits with examples; application of molecular markers in characterization and management of plant genetic resources-choice of molecular marker for germplasm characterization-examples of markers used in genetic resource management; applications of molecular markers in detection of GMOs, IPR etc.
Practical: Isolation of plant DNA, spectrophotometric and gel quantitation, restriction digestion, agarose gel electrophoresis, hybridization, autoradiograph development (conventional X-ray film and phosphorimager); extraction of proteins and their characterization through SDS-PAGE and isozyme analysis; analysis of DNA markers-RAPD, RFLP, AFLP, SSR, STS and SNP markers-other PCR based markers.  

Biotech 604

Advances in plant cell and tissue culture technology

2+1=3

Theory : Plant cells, tissue and their systems-structure of reproductive and vegetative organs-cell division and Influence on growth and development-nutrition of plant tissues-growth limiting factors; plant growth regulators; mode of action, effects on in vitro culture and regeneration; high frequency regeneration and morphogenesis-somatic embryogenesis-molecular aspects-cell suspension culture-cell culture techniques regeneration techniques, totipotency-recalcitrance-plant cell cloning-cell plating- in vitro mutagenesis-production of secondary metabolites-batch culture-single cell culture, histo- and immunochemical techniques, cytogenetic analysis of plant cells-fluorescence staining-autoradiography-protoplast-genetic manipulation and protoplast-fusion-cybrids and hybrids-molecular approaches-in vitro toxicity testing related to mutagens-large scale clonal propagation of plants; applications-haploidy breeding, ploidy manipulation-somaclonal and gametoclonal variation, wide hybridization and embryo rescue, in vitro fertilization-cryopreservation and germplasm conservation-storage-artificial seed production and applications-automation in in vitro culture-prospects.
Practical: Establishment and maintenance of callus and suspension cultures-identification of embryogenic and non-embryogenic calli-embryoids-cell suspension characterization-somatic embryogenesis-haploid induction and characterization-protoplast isolation and fusion techniques-hybrid identification-embryo rescue-multiple shoot induction and calli regeneration-establishment-molecular approaches.

Biotech 605

Commercial Biotechnology

1+1=2

Theory: Microbial technology-fermentation process-fermentors-types-design of equipments-products recovery-methods of production and improvement through biotechnological tools- bioconversion types-applications-industrial production of nucleosides-nucleotides-enzymes-xylanases, heat stable b-glucanase-phytase-antibiotics- biofertilizers-biopesticides-regulation of B. thuringiensis protein production-single cell proteins; pharmaceutical proteins-downstream processing of proteins-human blood proteins and human lysosomal proteins expression in transgenic plants-commercialization of transgenic plants producing pharmaceutical proteins-expression of antibody in plants for immunotherapy-microbial control of environmental pollution.
Practical: Isolation and characterization of antibiotic-producing microorganisms-microbial production of IAA/GA-fermentors-design and operation-fermentation techniques for biofertilizers/ biopesticides production-microbial enzymes of industrial importance-immobilization techniques-selection of Thermus aquaticus and multiplication-production of Taq polymerase-production of single cell protein. 

Biotech 606

 Advances in genetic engineering for stress tolerance    

3+0=3

Theory: Importance of biotic and abiotic stresses in crop production; biotic stress responses; molecular biology of plant-pathogen interactions; role of programmed cell death in defense; molecular biology of Rhizobium and Agrobacterium- plant interactions; genetic engineering in stress management- gene isolation techniques-isolation and characterization of resistance genes to biotic stresses (fungal, bacterial and viral diseases); insect resistance genes-plant derived-enzyme inhibitors -protease inhibitors, trypsin inhibitors-α-amylase inhibitors, lectins, terpenes and terpenoids; genes of non-plant origin- Bacillus thuringiensis endotoxins-mode of action-cry genes-classification and properties, other toxin genes, genes derived from entomophagous viruses; effect of transgenic plants on pest biology and development; genetic engineering for nematode resistance; genetic engineering for herbicide resistance;  abiotic stress -water, (excess and low), temperature (chilling & heat), salinity, problem soils; stress tolerance mechanisms; genetic engineering for abiotic stress management; N2 fixing genes-nif genes-Pyramiding of genes and their expression-problems of expression. 

Biotech 607

 Bio-safety and Patent Laws

1+0=1

Theory: Biological risk assessment-biosafety guidelines for genetically modified microorganisms (GMM)/Plants(GMP)-risk assessment and contained use of GMM and GMPs-guidelines for research activities-import and shipment-quality control of biologicals produced by rDNA technology-guidelines for environmental release of GMM and GMP-safety in the contained use and release of transgenic animals-mechanism of implementation of biosafety guidelines-at institutional, national and international level-DBT guidelines-acts and treaties related to biosafety of GMM and GMPs-public awareness perception and acceptance of products of biotechnology-global scenario of transgenic microorganisms and plants-intellectual property rights-patent laws at national and international level-ethical issues related to biotechnology products-ecological risks of engineered microorganisms and remedies.

Biotech 608

Transgenic plant technology

2+1=3

Theory: Plant genomes-their organisation-variation in genome size-cytosine methylation-methylation-sensitive restriction endonucleases-organization of genome into chromosomes-tandem array of repeats-telomeres-centromeres-origins of replication-cytoplasmic organelle DNA-evolution of repetitive sequences; plant transformation systems-classification-evolution of the systems-expression signals and vectors-selectable marker and reporter genes-Agrobacterium-mediated transfer-direct gene transfers-vectors for transformation-molecular genetics of T-DNA transfer from Agrobacterium to plants-comparison of vector-mediated and vector-free methods; recombinant DNA technology for enhanced gene expression, use of promoter elements from heterologous sources, plant pathogens as sources of restriction enzymes, promoter elements, retention signals, use of endoplasmic retention signals, KDEL sequences, TMV W-elements for optimized gene expression; transgene transcription-role of post-transcriptional control in transgenic gene design-accumulation of solid proteins in the endomembrane system of plants-downstream processing of proteins from transgenic plants-transgene stability-gene tagging in transgenic plants-analysis of transgenic plants-standard molecular techniques for the analysis of transgenic plants; patents and transgenic plants-release of transgenic plants: regulations and developments.
Practical: Agrobacterium plant transformation vector construction using CAMBIA vectors-vector design and construction for biolistic method-gene transfers using both the methods-isolation of genomic DNA from transgenic plants-isolation of total RNA from plant tissues-PCR analyses for transgene detection-southern analyses for transgene detection-northern analyses for transgene detection-western analyses for transgene detection. 

Biotech 691

 Doctoral Seminar

1+0=1

Biotech 692

 Special Problem

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