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RGPV M.Tech Biotechnology 1st Semester (Grading System) Syllabus

Tuesday, January 22

                                             MBT101 - ENGINEERING MATHEMATICS 

Differentiation; Integration; Maxima and minima; First and second order differentiation; Linear equation with constant and variable coefficient. Probability- Axiomatic definition; Addition theorem; Conditional probability; Bayes’ theorem; Random variable; Mathematical expectation; Theoretical distribution- Binomial, Poisson, Normal and Standard normal distribution

Statistics- Measures of central tendencies and distribution; Coefficient of variation; Sampling parameter; Static and standard error; Census and Sample methods; Method of sampling (Probability and non probability sampling).

Testing of hypothesis; Null and alternative hypothesis; TypeI and typeII errors; Level of significance; Large sample test; Test of significance of single and two sample means; Test of significance of single and two proportion.
Small sample tests- F test; T test (Paired, unpaired); Chi square test goodness of fit.

Correlation (Partial and Multiple correlation); Regression (Sample linear, non linear and multiple regression); Analysis of variance (One way and Two way).    

Mole concept, Determination of mole wt. by gram molecular volume relationship, problems based on mole concept, Solutions, colligative properties, Methods of expressing concentrations, strength, Normality, Molarity & Molality, ppm. Standardization of solutions, Colloids, pH, buffer systems, dissociation constant, pK value, Preparation of standard solution of acids and bases, problems related to acid base titrations, volumetric experiments-acidimetry, alkalimetry, permanganometry, dichrometry, iodometry., Methods of plotting Enzyme Kinetics Data, Effects of pH and temperature on Enzyme stability and activity.


a) Preparation of standard acid (succinic acid) and alkali and their standardization.
b) Preparation of various solutions (normal, molar, and percent) and ppm/ppb by serial dilutions.

                                MBT102- CELL AND MOLECULAR BIOLOGY  

Cell cycle and Genome Organization
Genome Organization in prokaryotes and eukaryotes - DNA content and C-value paradox - methods to measure DNA content variation - Various types of DNA sequences – simple sequences, repetitive sequences, Junk DNA or selfish DNA, tandem gene clusters, satellites Variety of DNA structures: double helix, Z-DNA, B-DNA, Mechanism of DNA replication: prokaryotes and eukaryotes, Overview of the cell cycle, Factors involved in cell cycle, Mitosis, Meiosis, cell cycle control, cell check points.

Module –II  
Replication and Cell Signaling Mechanisms
DNA replication models,  mode of action, DNA damage, DNA repair and recombination, Organization structures and function of ribonucleoproteins; Photoreactivation; Nucleotide excision repair; Mismatch correction; SOS repair; Recombination: Homologous and non- homologous; Site specific recombination; Chi sequences in prokaryotes; Gene targeting; Gene disruption; Signal transduction, primary and secondary messengers, involvement of G proteins, protein kinases, serine, threonine and tyrosine kinases, mechanism of signaling by steroids, cell death.

Module – III  
Prokaryotic & Eukaryotic Transcription
Prokaryotic Transcription; Regulation of transcription, Termination-Rho-dependent and independent, Attenuation; Transcriptional regulation-Positive and negative; Operon concept-lac, trp, ara, his, and gal operons; Transcriptional control in lambda phage; Anti-termination, Transcript processing; Processing of tRNA and rRNA Eukaryotic 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 posttranscriptional gene silencing

Module – 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; Catalytic RNA.
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; Genetic code in mitochondria; Transport of proteins and molecular chaperones; Protein stability; Protein turnover and degradation.

Module – V  
Diverse type of oncogenesis
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;  DNA virus/ cell immortalization ,Oncogenes as transcriptional activators. Strategies of chemotherapy and gene therapy against cancer; translating therapies from laboratory to clinic; Gene discovery in cancer research, Mechanisms of diverse type of cancers.  
Case studies.

Lab on Cell & Molecular Biology   
1. Isolation and Quantitation of cellular macromolecules (DNA, RNA and Protein) .
2. cDNA Synthesis
3. Transformation and Preparation of competent cells.
4. Antibiotics sensitivity test on microbial cultures
5. Agarose gel electrophoresis of DNA fragments.
6. SDS PAGE for resolution of proteins.
7. Elution of DNA from an agarose gel.
8. Preparation of metaphase Chromosome.
9. Karyotyping and banding Pattern (G-banding).
10. Preparations of blood smear for study of sex chromatin.

                                  MBT103 -BIOPROCESS ENGINEERING   

Module I  
Fundamentals of Bioprocess engineering  
Microbial growth, Factors affecting growth, Growth kinetics and metabolism, Stoichiometry: Material and energy balance calculations, Transport phenomenon (mass and energy transfer).

Module II  
Introduction to bioreactors: General design information; Selection of bioprocess equipment (upstream and downstream); Specifications of bioprocess equipment; Batch and Fed-batch bioreactors, Continuous bioreactors; Bioreactor operation; Sterilization; Aeration; Sensors; Instrumentation; Culture-specific design aspects: plant/ mammalian cell culture reactors.

Module III  
Upstream processing   
Effect of scale on oxygenation, mixing, sterilization, pH, temperature, inoculums development, Media Formulation, nutrient availability and supply; Strain improvement; Bioreactor scale-up based on constant power consumption per volume; mixing time; impeller tip speed (shear), mass transfer coefficients; Process economy.

Module IV  
Bioseparations / Downstream Processing  
Biomass removal and disruption: Filtration; centrifugation; distillation; adsorption; Extraction (solvent, aqueous two phase, super critical), Chromatographic Techniques(Ion exchange, gel filtration, affinity, HPLC, TLC, GC); Cell disruption (Physical, chemical, enzymatic); Membrane based purification (Ultrafiltration, Reverse Osmosis, Dialysis), Process configurations (packed bed, expanded bed, simulated moving beds); Precipitation (Ammonium Sulfate, solvent); Electrophoresis (SDS-PAGE, isoelectric focusing, 2D-gel, capillary);
Crystallization; Drying.  

Module V  
Description of industrial processes  
Microbial processes for production of organic acids (citric acid, acetic acid), amino acids (Lysine, isoleucine, glutamic acid, Arginine), antibiotics (Penicillin, Cephalosporin C, actinomycin), alcohol, enzymes. Recombinant protein production in microbes e.g. recombinant insulin; Waste treatment, Process economics.  
Case studies.

Lab on Bioprocess Engineering  
1. Microbial growth and product formation kinetics.
2. Conventional filtration.
3. Effects of inhibitor on microbial growth.
4. Enzyme immobilization techniques.
5. Bioconversion using immobilized enzyme preparation.
6. Bioconversion in batch.
7. Mixing and agitation in fermenters.
8. Protein precipitation and its recovery.
9. Membrane based filtration-ultra filtration in cross flow modules and micro filtration.
10. Enzyme purification and estimation of enzyme kinetics.  

                                   MBT104 -CELL & TISSUE CULTURE 

Culture Technique: Animal 
Structure of animal cell; History of animal cell culture; Basic requirements for animal cell culture; Cell culture media and reagents; Animal cell, tissue and organ cultures; Primary culture, secondary culture; Continuous cell lines; Suspension cultures; Somatic cell cloning and hybridization; Transfection and transformation of cells.

Applications of culture techniques: Animal 
Commercial scale production of animal cell, Stem cells and their application; Application of animal cell culture for in vitro testing of drugs; Testing of toxicity of environmental pollutants in cell culture; Application of cell culture technology in production of human and animal vaccines and pharmaceutical proteins.

Culture Techniques: Plant
Totipotency, Cyto-differentiation; Organogenesis; Somatic embryogenesis; Regulation and applications; Artificial seed production; Micropropagation; Somaclonal variation; Androgenesis and its applications in genetics and plant breeding; Germplasm conservation and cryopreservation, Virus free culture and its applications.

Plant Tissue Culture: Protoplast Culture and Somatic Hybridization 
Protoplast isolation; Culture and usage; Somatic hybridization - methods and applications; Cybrids and somatic cell genetics and its application, cytoplasmic sterility, secondary metabolite production.

Applications of Plant tissue culture  
Role of tissue culture in agriculture, horticulture and forestry, Transgenic plants Technique of transformation– Agrobacterium mediated, Applications of transgenic plants. Edible Vaccines from plants – Banana, Watermelon.

Lab on Tissue Culture 
1. Aseptically media preparations.
2. Cryopreservation of cells and retrieval of cells.
3. Maintenance and development of cell passage.
4. Handling of secondary animal cell culture.
5. Identification of contaminants in animal cell culture.
6. Subculturing of continuous cell line growing in monolayer and suspension.
7. Construction and analysis of growth curve.
8. Isolation of primary cell culture.
9. Plant Protoplast Isolation.
10. Plant propogation through Tissue culture (shoot tip and Nodal culture).

                          MBT105 -GENOMICS AND GENETIC ENGINEERING 

Genetic engineering tools  
Restriction Enzymes; The range of DNA manipulative enzymes (Nucleases,  Ligases, Polymerases, Modifying enzymes, Topoisomerases); Cohesive and blunt end ligation (Linkers, Adaptors, Homopolymer tailing); Labeling of DNA (Radioactive and Non- radioactive); Plasmids; Bacteriophages; M13 mp vectors; pUC19 and Bluescript vectors, Phagemids; Lambda vectors; Cosmids; Artificial chromosome vectors (YACs; BACs); Animal Virus derived vectors SV-40; Expression vectors (pMal, GST, pET-based vectors); Protein purification (His-tag, GST- tag, MBP-tag); Inclusion bodies; Baculovirus vector system, Yeast vectors, Shuttle vectors; Principles in maximizing gene expression.

Module- II 
Genomic Analysis 
Insertion of Foreign DNA into Host Cells; Construction of libraries; Isolation of mRNA and total RNA; cDNA synthesis and cloning; genomic libraries; Expression cloning; jumping or hopping libraries; Southwestern and Farwestern cloning; Protein-protein interactive cloning and Yeast two hybrid system; Phage display;. Hybridization Techniques (Colony Hybridization, Fluorescence in situ Hybridization); DNA-Protein Interactions (EMSA-Electrophoretic mobility shift Assay; DNaseI footprinting, Chromatin Immunoprecipitation);

Module- III 
PCR and Its Applications 
Primer design; Fidelity of thermostable enzymes; Types of PCR (multiplex PCR, nested PCR, reverse transcriptase PCR, real time PCR, touchdown PCR, hot start PCR, colony PCR); cloning of PCR products; vectors for cloning; 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), PTT (Protein Truncation Test); Cloning vactors for direct cloning of PCR parts.

Post Genomic analysis 
Enzymatic DNA sequencing; Chemical sequencing of DNA; Automated DNA sequencing; RNA sequencing; Chemical Synthesis of oligonucleotides; Gene silencing techniques; siRNA & stRNA  technology; Micro RNA; Construction of siRNA vectors; Principle and application of gene silencing; Gene knockouts; Creation of knock out mice; Identification and classification using molecular markers- ribosomal typing/sequencing.

Module- V 
Genetic engineering applications
Gene therapy in Disease models (Cancer, Diabetes, AIDS, Thalassaemia); Somatic and germ- line therapy- in vivo and ex-vivo ; Suicide gene therapy; Gene replacement; Gene targeting; Transgenics; cDNA and intragenic arrays; Differential gene expression and protein array.
Case studies

Lab on Genetic Engineering 
1. Plasmid DNA isolation and DNA quantitation.
2. PCR amplification of genes and analysis by agarose gel electrophoresis.
3. Cloning using pUC18 and pBR 322.
4. Transformation of recombinant plasmid in to host .
5. Non-radioactive Random Primer labeling.
6. Blotting techniques: ( Southern, Western, Northern)
7. Southern hybridization with genomic DNA with non radioactive labeled probe detection.
8. RFLP analysis of the PCR product.
9. Introduction of DNA into mammalian c ells; Transfection techniques;
10. Preparation of genomic DNA library in plasmid vector.
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