Friday, 20 September 2013

MTI - 506 BIOINFORMATICS (II)

UNIT 1: Introduction to Biological Databases
Database : Types, Overview of Biological Databases and Information retrieval
from biological databases for example (Nucleic acid databases: Genbank, Protein
Databases- Swissprot) Sequence Formats, Sequence storage, Sequence
submission to sequence Database.

UNIT 2: Pairwise Sequence Alignment
Alignment Types: Local alignment, Global alignment, Scoring matrices- PAM,
BLOSUM, Gaps, Types of Gaps. Dot Plots. Dynamic programming Approach:
Needleman and Wunsch Algorithm, Smith and waterman Algorithm, Viterbi
Algorithm, Heuristic Approach: BLAST, FASTA.

UNIT 3: Multiple Sequence Alignment:
Exhaustive Algorithm- Divide and Conquer alignment, Heuristic Algorithm:
Progressive Alignment- ClustalW, Tcoffee, Iterative Alignment- PRRN, Block
based method- Match-Box, DIALIGN2

UNIT 4: Introduction to Protein Structure Prediction
Secondary structure prediction for Globular and Trans-membrane proteins, 3DProtein
Structure file format: PDB, mmCIF, MMDB, Methods of Tertiary
structure prediction: Threading and fold recognition methods, Homology
modeling, Fold recognition databases.


MTI - 505 GENETIC ENGINEERING - I

UNIT 1: Introduction to Genetic Engineering
Scope and history, Handling of DNA, RNA Restriction Enzymes, radioactive
isotopes and other corrosive, carcinogenic and inflammable chemicals/ reagents

UNIT 2: Requirement of genetic engineering
Isolation and purification of nucleic acids from living cells. DNA isolation:
Preparation of total cell DNA from animal and plant, Preparation of Plasmid
DNA, preparation of Bacteriophage DNA. RNA isolation: Total Cellular RNA,
Cytoplasmic and NuclearRNA, Poly ( A+) RNA

UNIT 3: Enzymes in recombinant DNA technology
Nucleases, Ligases, Poylmerases, DNA modifying enzymes, Topoisomerases,
Restriction endonucleases

UNIT 4: Cloning Vectors:
Nomenclature, properties of good vector. Vectors for E. coli: Plasmid and plasmid
based vectors: BAC, Phagemids, cosmids and expression, Virus based vectors:
M-13, Lambda and PAC. Vectors for eukaryotes: Yeast based vectors : 2micro m
plasmid, YEp, YAC, Vectors for plants : Ti plasmid and Ri Plasmid Ca MV,
vectors for Animals - SV-40, Retrovirus vectors and Vaccinia/ Bacculo virus

UNIT 5: In Vitro construction of recombinant DNA molecules
Creation of r-DNA, Gene Libraries – Genomic DNA and c DNA Cloning
techiniques, Selection of clones based on antibiotic, insertional inactivation,
hybridization, PCR and antibody.

UNIT 6: Methods of DNA transformation in bacteria, plants and animal cells
Salt based method, Electroporation, Genegun, Liposome mediated, Transfection

MTI - 504 INTERMEDIARY METABOLISM II

UNIT 1: Lipid metabolism and disorders
Oxidation of saturated and unsaturated fatty acids, β oxidation. role of a carnitine,
ketogenesis and utilization. Biosynthesis of fatty acids, Metabolism of
Triglycerides Phospholipids and Sphingolipids, cholesterol biosynthesis,
regulation, transport, excretion, reverse cholesterol transport, formation of bile
acids, lipoprotein metabolism. Disorders of lipid metabolism – plasma lipids and
lipoproteins, abnormalities -hypo and hyper cholesterolemia, lipidosis, clinical
inter relationship of lipids. Clinical inter-relations ships of lipids (sphigolipidosis,
multiple sclerosis) ,lipoproteins and apolipopeoteins, Inherited metabolic lipid
disorders – Taysach’s disease, Niemannpick’s disease,ganglisidosis ,hypo and
hyper lipo proteinemia.

UNIT 2: Protein Metabolism and disorders
General reactions –transamination, deamination, decarboxylation, ammonia
formation urea cycle, metabolic breakdown of aminoacids to amphibolic
intermediates, conversion of aminoacids to specialized products – serotonin,
aminobutyric acid,dopamine, epinephrine ,norepinephnine ,melanin ,creatinine
and creatine, biosynthesis of non-essential aminoacids, key role of glutamate
dehydrogenase in nitrogen metabolism. Disorders of protein metabolism –
hperammonemia, phenylalaninemia, alkptonuria, phenylketonuria,
homocystinuria,cysteinemia,tyrosinemia and related disorders of aminoacidurias,
Hartnups disease.

UNIT 3: Metabolism of Nucleotides and disorders
Purine and pyrimidine nucleotide biosynthesis and catabolism regulation of
purine and pyrimidone nucleotide biosynthesis. Disorders of nucleotide
metabolism

UNIT 4: Metabolism of porphyrins
Biosynthesis and Degradation of porphyrins, heme , bile pigment formation,
transport and excretion.Porphyrias.

UNIT 5: Integration of metabolism
Inter-relationship of carbohydrate, protein and fat metabolism – role of acetyl
CoA. and TCA cycle in the inter-relationship, interconversion of major
foodstuffs. Regulation of intermediary metabolism .

MTI - 503 BIOPROCESS TECHNOLOGY

UNIT 1: Introduction to Fermentation process.
Upstream Process, Downstream Process, Range of fermentation process,
Component parts of fermentation process

UNIT 2: Media for Industrial fermentations

Medium Sterilization. Batch Sterilization: Continuous sterilization, Fermentor
Sterilization, Feed Sterilization, Filter sterilization

UNIT 3: Bioreactor Design

Construction material, Aeration and agitation, Sampling/ Feed port, Valves and
steam traps

UNIT 4: Growth kinetics and stolchiometry
Batch Culture, Continuous culture, Fed Batch Culture
Stolchiometric calan: Elemental Balance, Yield coefficient

UNIT 5: Types of Reactor
Stirred tank reactor, Acetators and Cavitators, Air Lift Reactor, Bubble Column
Reactor, Packed Bed Reactor, Fluidized Bed Reactor, Photobioreactor

UNIT 6: Solid state Fermentation
Bioreactors in solid state fermentation.

UNIT 7: Process monitoring and control.
Physical and chemical sensors for medium and gases, Online/ Offline sensors

UNIT 8: Microbial interactions
Effluent treatment, Process Economics, Scale up procedure from lab scale to pilot

scale

MTI – 502 COMMERCIAL ASPECTS OF BIOTECHNOLOGY

UNIT 1: Food and Beverages 
Dairy products- cheese (Swiss, Cheddar and Camembert),
Beverages – Bear & wine, Citric Acid, Mushroom, SCP – Spirulina and Yeast,
Glutamic Acid, Acetic Acid, Oriental fermented foods & beverages (Koji, Meso,
Soy sauce), Bakery products (Bread), Sweetners, Microbial polysac charides
(Xanthon, Gellan).

UNIT 2: Agricultural Biotechnology 
Biofertilizers: Types, process of manufacture and applications,
Biopesticides: Bacterial, fungal and viral- production and applications,
Aerobic and anaerobic treatment of agricultural wastes,
Composting and Vermicomposting.

UNIT 3: Health related products
Vit. B12, Blood products- Factor VIII, Streptokinase, Anticoagulants, therapeutic
proteins- Human GH, Interferons, Interleukins, insulin, erythropoietin, Nerve
growth factor, synthetic Vaccines.

UNIT 4: Secondary Metabolites 
Antibiotics:- Penicillin, streptomycin, actinomycin, cephalorphorin

UNIT 5: Biotransformation 
Basic Concepts, Products , Steroids biotransformation.

UNIT 6: 
GMP , QC and Marketing aspects of biotechnology

MTI-501 Advanced Analytical Techniques

UNIT 1: Atomic absorption spectrometry
Introduction to Spectrometric Methods, Introduction to Optical Atomic
Spectroscopy, Atomic Absorption and Fluorescence Spectroscopy, Atomic
Emission Spectroscopy, Atomic Mass Spectroscopy, Atomic X-Ray

UNIT 2: Molecular absorption spectrometry
Introduction to UV/Visible Molecular Spectroscopy with application, Molecular
Luminescence Spectroscopy, Introduction to Infrared Spectroscopy with
application, Raman Spectroscopy, NMR with applications such as MRI,
Molecular Mass Spectroscopy and X ray crystallography.

UNIT 3: Separation Techniques: Chromatography
Introduction to Chromatographic Separations, Gas Chromatography, HPTLC,
HPLC, GC-MS, LC-MS with applications

UNIT 4: Separation Techniques: Electrophoresis
Introduction to Electrophoretic separations, Acrylamide, Starch, Gelatin, agarose
gels, IEF, capillary isoelectrofocussing, 2D electrophoresis, pulse fiend
electrophoresis, Capillary Electrophoresis and Capillary Electrochromatography.

UNIT 5: Specialized techniques
MALDI-TOF-MS, Alternative methods for ionization such as SELDI, ESI, CI,
FAB etc MS-MS analysis( Tandom MS).