With Effect From June-2009
MB204 Genetic Engineering and Bioinformatics for Microbiology 100 Marks
MB205 Bioprocess, Biochemical Engineering and Fermentation Technology 100 Marks
MB206 Pharmaceutical, Clinical, Omics and Nano Inter Phasing Microbiology 100 Marks
Practical – I 150 Marks
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Total: 450 Marks
Genetic Engineering And Bioinformatics
Section I
Unit 1 Cloning in E. coll
1. Genetic transfer in bacteria transformation, transduction and conjugation; Molecular basis recombination in bacteria
2. Cutting and joining DNA molecules;
3. Basic biology of piasmid and phage vectors
4. Cosmids, phasmids and other advanced vectors
5. Cloning strategies
6. Manipulation of gene expression in Prokaryotes
Unit2 Cloning in other than E. coll
1. Cloning in bacteria other than E. coli
2. Engineering plants: Cloning in plants,
3. Transgenic Plants: Commercial exploitation, Ethics Ethical issues
4. Engineering animal cells: Cell culture, Traninfection of animal cells, Viruses as vectors, Selectable markers and gene amplification in animal
cells, Expressing genes in animal cells, Engineering animals .
5. Transgenic animals: Commercial exploitation, Ethical issues
6. Microarray technology for DNA and Protein
Unit 3 Advances in Molecular biotechnology
1. Understanding genes, genomes, "otheromes'
2. Introduction and basic concept of systems biology
3. Introduction to synthetic biology
4. Directed Mutagenesis and Protein engineering
5. Regulating and Patenting Molecular Biotechnology
6. Ethical issues related to Genetic engineering technology
Section II
Unit 4 Sequence Analysis
1. Various file formats for bio-molecular sequences: GenBank, FASTA.GCG, MSF, NBRF-PIR etc.; Basic concepts of sequence similarity, identity
and homology
2. Scoring matrices: basic concept of a scoring matrix, Matrices for nucleic acid and proteins sequences, PAM and BLOSUM series, principles
based on which these matrices are derived.
3. Database Searches: Sequence-based: BLAST & FASTA
4. Pairwise sequence alignments: basic concepts of sequence alignment, Needleman & Wunsch, Smith & Waterman algorithms for pairwise
alignments
5. Multiple sequence alignments (MSA): The need for MSA, basic concepts of various approaches for MSA (e.g. progressive, hierarchical etc.);
Introduction to CLUSTALW and PileUp ; concept of dendrogram and its interpretation.
6. Sequence patterns and profiles: Basic concept and definition of sequence patterns, motifs and profiles, various types of pattern
representations viz. consensus, regular expression (prosite-type) and profiles; PSI-BLAST,
Unit 5 Applied Bioinformatics
1. Taxonomy and phytogeny: molecular evolution; nature of data used in Taxonomy and Phytogeny, Definition and description of phytogenetic
trees and various types of trees.
2. Computational Gene finding and Primer designing
3. Comparative genomics: Basic concepts and applications (Baxevanis)
4. Functional Genomics : Sequence-Based Approaches ; Microarray-Based Approaches ; Comparison of SAGE and DNA Microarrays (Jin)
5. 3-D structure visualization and simulation: Visualization of structures using Rasmol/Protein explorer, SPDB.; Basic concepts in molecular
modeling: different types of computer representations of molecules
6. Classification and comparison of protein 3D structures: Purpose of 3-D structure comparison and concepts! Introduction to FSSP. VAST and
DALI, Fold Classes.
Unit 6 Structural bioinformatics
1. Secondary structure prediction: overview of secondary structure of protein ; Computation methods for secondary structure prediction :
Chou Fasman, GOR etc.
2. Tertiary Structure prediction: Fundamentals of the methods for 3D structure prediction (sequence similarity / identity of target proteins of
known structure, fundamental principles of protein folding etc.) Homology Modeling; fold recognition, threading approaches, and ab-initio
structure prediction methods
3. RNA Structure Prediction: Introduction; Types of RNA Structures; RNA Secondary Structure Prediction Methods; Ab Initio Approach;
Comparative Approach;
4. Molecular docking: Fundamentals of docking small and macromolecules to proteins and nucleic acids.
5. Review of Bioinformatics resources for microbiology
6. Contemporary development in Molecular Biotechnology and Bioinformatics ( Selected Review / Research paper/ Scientific article)
Unit 1 Bioprocess Microbiology
1. Introduction: Scope of Biotechnology and Industrial Microbiology : Nature of Biotechnology and Industrial Microbiology; Characteristics of
Industrial Microbiology; Patents and Intellectual Property Rights in Industrial Micrcoiotogy and Biotechnology; The Use of the Word
'Fermentation' in Industrial Microbiology; Organizational Set-up in an Industrial Microbiology Establishment
2. Screening for Productive Strains and Strain Improvement in Biotechnokxjical Organisms: Sources of Microorganisms Used in Biotechnology;
Selection from naturally occurring vanants; Manipulation of the genome of industrial organisms in strain improvement
3. Metabolic Pathways for the Biosynthesis of Industrial Microbiology Products: The Nature of Metabolic Pathways; Industrial Microbiological
Products as Primary and Secondary Metabolites; Trophophase-kfophase Relationships in the Production of Secondary Products; Role of
Secondary Metabolites in the tftysiology of Organisms Producing Them; Pathways for the Synthesis of Primary and Secondary Metabolites
of Industrial Importance; Carbon Pathways for the Formation of Some Industrial Products Derived from Primary Metabolism; Carbon Pathways
for the Formation of Some Products of Microbial Secondary Metabolism of Industrial Importance.
4. Overproduction of Metabolites of Industrial Microorganisms: Mechanisms Enabling Microorganisms to Avoid Overproduction of Primary
Metabolic Products Through Enzyme Regulation; Derangement or Bypassing of Regulatory Mechanisms for the Over-production of Primary
Metabolites; Regulation of Overproduction in Secondary Metabolites; Empirical Methods Employed to Disorganize Regulatory Mechanisms in
Secondary Metabolite Production
5. Growth Kinetics: Introduction; Kinetics of batch culture; Disadvantages of batch culture; Advantages of continuous culture ; Growth kinetics
for continuous culture; Material balance for CSTR: Rate of product formation, Growth kinetics, biomass and product yields, YX/S and YP/S,
Biomass balances (cells) in a bioreactor, Material balance in terms of substrate in a chemostat, Modified chemostat. Fed batch culture
6. Industrial Media and the Nutrition of Industrial Organisms : The Basic Nutrient Requirements of Industrial Media; Criteria for the Choice of
Raw Materials Used in Industrial Media; Some Raw Materials Used in Compounding Industrial Media; Growth Factors; Water Some Potential
Sources of Components of Industrial Media, Carbohydrate sources, Protein sources; The Use of Plant Waste Materials in Industrial
Microbiology Media: Saccharification of Polysaccharides, Starch, Cellulose, hemi-celluloses and Ikjnin in plant materials
Unit 2 Bioprocess and Biochemical engineering
1. Bioreactor : Introduction; Background; Bioreactor for batch type fermentation : The Aerated Stirred Tank, Anerobic Batch, Airlift
bioreactors, Bubble column. Surface or Solid State; Bioreactor Configurations for Fed-batch Cultivation and Continuous fermentations;
Calculation for bioreactor Heat transfer Design equations for CSTR fermenter, Monod model for a chemostat; Temperature effect on rate
constant; Scale- up of stirred-tank bioreactor
2. Sterility in Industrial Microbiology : Introduction; The Basis of Loss by Contaminants; Physical and Chemical Methods of Achieving Sterility :
Hot plates; High temperature sterilization; Dry heat sterilization; Sterilisation with filtration; Microwave sterilization; Electron beam
sterilization; Chemical sterilization; Batch sterilization; Continuous sterilization; The sterilization of the fermentor and its accessories; Media
sterilization; Viruses (Phages) in Industrial Miaobiology
3. Dissolved Oxygen Measurement and Mixing: Introduction; Measurement of dissolved oxygen concentrations; Oxygen transfer rate (OTR);
Respiration quotient (RQ); Agitation rate studies
4. Gas and Liquid System (Aeration and Agitation): Introduction; Aeration and agitation; Effect of agitation on dissolved oxygen; Air sparger
Oxygen transfer rate in a fermenter. Mass transfer in a gas-liquid system; Gas hold-up; Agitated system and mixing phenomena;
Characterisation of agitation; Types of agitator Gas-liquid phase mass transfer (Oxygen transport, Diameter of gas bubble formed DO)
5. Material and Elemental Balance: Introduction; Growth of stoichiometry and elemental balances; Energy balance with example of continuous
ethanol fermentation; Conservation of mass principle with example of Acetic acid fermentation process
6. Fermentation Process Control: Introduction; 8ioreactor controlling probes; Characteristics of bioreactor sensors; Temperature measurement
and control; DO measurement and control; pH/Redox measurement and control; Detection and prevention of the foam; Biosensors
Unit 3 Downstream Processing, Scale up and economics
1. Extraction of Fermentation Products: Solids (Insolubles) Removal: Filtration, Centrifugation, Coagulation and flocculation, Foam fractionation,
Whole-broth treatment; Primary Product Isolation: Cell disruption, Liquid extraction (Continuous extraction column process, rotating disk
contactors), Dissociation extraction, Adsorption (Ion-exchange, Langmuir isotherm, Freundlich isotherm and Fixed-ted), Precipitation;
Purification: Chromatography, Carbon decolorizatic Crystallization; Product Isolation: Crystalline processing, Drying
2. Membrane Separation Processes: Introduction; Types of membrane; Membrane processes; Nature of synthetic membranes; General
membrane equation; Cross-flow microfiltration; Ultrafiltration; Reverse osmosis; Membrane modules.
3. Advanced Downstream Processing in Biotechnology: Introduction; Protein products; Cell disruption; Protein purification; General problems,
associated with conventional techniques; Fluidised bed adsorption; Design and operation of liquid fluidised beds; Interfaced and integrated
fluidised bed/expanded bed system
4. Immobilized Enzymes and Immobilized Cells: Advantages of immobilized biocatalysts in general; Methods of immobilizing enzymes; Methods for
the immobilization of cells; Practical Application of Immobilized Biological Catalyst Systems; Bioreactors Designs for Usage in Biocatalysis ;
Immobilised cell reador(ICR) experiments and ICR rate model
5. Bioprocess Scale-up: Introduction; Scale-up procedure from laboratory scale to plant scale( Scale-up for constant KLa, for shear forces,
constant mixing time), Bioreactor design criteria ; CSTR chemostat versus tubular plug flow; Dynamic model and oxygen transfer rate in
activated sludge; Aerobic wastewater treatment
6. Fermentation economics
Section II
Unit 4 Primary metabolites production
1. Amino Acids: Introduction, Microbial string employed in aminoacid production, process control in amino acid fermentation, Production of
Glutamic Acid by Wild Type Bacteria, Production of Amino Acids by Mutants, Improvements in the Production of Amino Acids Using
Metabolically Engineered Organisms.
2. Production of Organic Acids: Citric, acetic lactic, Gluconic and Itaconic acid
3. Production of Microbial enzyme: Introduction, Development of new enzymes, Fermentation process, Recovery and finishing, Regulations and
specification, Survey of enzyme and application
4. Production of Beer, Wines and Spirits
5. Vitamin: Vitamin B12, Riboflavin, Carotenodis
6. Production of Fermented Foods: Introduction; Fermented Food from Wheat: Bread; Fermented Foods Made from Milk; Fermented Foods from
Com; Fermented Vegetables; Fermentations for the Production of the Stimulant Beverages: Tea, Coffee, and Cocoa; Fermented Foods
Derived from Legumes and Oil Seeds
Section I
Unit 1 Pharmaceutical Microbiology
1. Microbial aspect of Pharmaceutical processing : Microbial spoilage and prevention of pharmaceutical product; Principle and practice of
sterilization, Sterile pharmaceutical product , Factory and hospital hygeny and good Manufacturing practice
2. Drug Discovery: Targets and Receptors; Drug Discovery: Small Molecule Drugs
3. Drug Discovery: Large Molecule Drugs: Enzymes, Vaccines (Attenuated, DNA, Subunit, vector), Antibodies( Monoclonal antibodies),
Cytokines, Hormones, Gene Therapy, Stem Cells
4. Drug Development and Preclinical Studies; Clinical Trial : Overview, Role of microbiologist in CRO, GCP
5. Bio safety: Principle of bio safety , Laboratory Bio safety Level Criteria
6. Bioterrorism; Biomedical waste management
Unit 2 Clinical Microbiology
1. Overview of clinical laboratory diagnosis (Hematology, Cardiac, Renal, Liver testing's) ; Culturing of pathogens; Immunological Diagnostic
Procedure; Monoclonal Antibodies; DNA diagnosis systems; Molecular Diagnosis of genetic disease.
2. Overview and Current status of Anti HIV, Anti Malaria, Anti Tuberculosis and Anti Cancer treatment; Multidrug resistance : Introduction,
development, detection and treatment
3. New disease: SARS, bird flu, swine flu etc.
4. RNA Interference: Targeted Medicine
5. Overview of Artificial Cells
6. Pharmacpgenomics: Overview, concept and application of Individualized Therapy
Unit 3 Nanotechnology : Microbiology Inter phase
1. Introduction : BuckybaH Discovery; Nano scale concept
2. What makes Nano special; Nano science tools; Application of in Biology, medicine and environment
3. Microbial Nanoparticle Production
4. Magnetosomes: Nanoscale Magnetic Iron Minerals in Bacteria
5. Bacteriorhodopsin and its Potential in Technical Applications
6. Nanopartides as Non-Viral Transfection Agents
Unit 5 Production of Secondary metabolites and other
1. Microbial Polysaccharides and Polyesters: Polysaccharides, Xanthan Gum, Polyesters
2. Production of Antibiotics and Anti-Tumor Agents: Classification and Nomenclature of Antibiotics; General production methods; Penicillin,
Cephalosporins, Tetrcycline, Bacitracin production; Problem of Antibiotic Resistance; The Search for New Antibiotics; Combating Resistance
and Expanding the Effectiveness of Existing Antibiotics; Antj-Tumor Antibiotics; Newer Methods for Searching for Antibiotic and Anti-tumor
Drugs
3. Production of Ergot Alkaloids: Nature of Ergot Alkaloids, Uses of Ergot Alkaloids and their Derivates, Production of Ergot Alkaloids, Physiology
of Alkaloid Production
4. Microbial Production of Nucleocide and Nucebtides: Introduction, Methods for production
5. Single Cell Protein (SCP): Substrates for Single Cell Protein Production; Microorganisms Used in SCP Production; Use of Autotrophic
Microorganisms in SCP Production; Safety of Single Cell Protein; Nutritional Value of Single Cell Protein Yeast Production: Production of Baker's
Yeast; Food Yeasts; Feed Yeasts; Alcohol Yeasts; Alcohol feasts
Unit 6 Novel Microbial products
1. Production of Microbial Insecticides: Alternatives to Chemical Insecticides; Biological Control of Insects; Bacillus thuringiensis Insecticidal
toxin ; Production of Biological Insecticides; Bioassay of Biological Insecticides; Formulation and Use of Bioinsecticides; Safety Testing of
Bioinsecticides; Search and Development of New Bioinsecticides
2. Plant cell culture: Introduction, Plant Cell culture techniques, Cell suspension cultures
3. Probiotics: Concept, methods and application
4. Synthesis of commercial products by recombinant microorganism: Small Biological molecules, Antibiotics, Biopolymers
5. Bkxatalysis in Organic Chemistry: Nature and Use of Steroids and Sterols, Uses of Steroids and Sterols, Types of microbial transformations in
steroids and sterols, Fermentation conditions used in steroid transformation, Asymmetric Catalysis in the Pharmaceutical and Agrochemical
Industries
6. Contemporary development in Bioprocess, Biochemical engineering and Fermentation technology ( Selected Review / Research paper/
Scientific article)
Section II
Unit4 Protcomics: Microbiology
1. Holistic Biology of Microorganisms: Genomics, Transcriptomics and Proteomics
2. Tools and technique for genomics and proteomics
3. Exploring and Exploiting Bacterial Proteomes; Strategies for Measuring Dynamics: The Temporal Component of Proteomics; Quest for Complete
Proteome Coverage
4. Proteomics of Corynebacterium glutamicum: Essential Industrial Bacterium
5. Analyzing Bacterial Pathogenesis at Level of Proteome; Structural Proteomics and Computational Analysis of a Deadly Pathogen: Combating
Mycobacterium tuberculosis from Multiple Fronts
8. Genomics and Proteomics in Reverse Vaccines
Unit 5 Genomics: Microbiology
1. Bacterial Genomes for the Masses
2. Comparative Genomics for Microorganisms
3. Microbial Genome Sequencing and Annotation
4. Using the Genome to Understand Pathogenicity
5. Genomic Approaches to Antibacterial Discovery
6.
Microbial Communities: Core and Pan-Genomics
Unit 6 Advances in Molecular biology: Microbiology
1. Metagenomics: Concepts, tools and technique, application, review of metagenomics project
2. Origins of Bacterial Species; Evolution of Microbial Communities
3. Bacterial Taxonomies
4. Discovering New Pathogens
5. Microarrays for Bacterial Typing
6. Interspecies and Intraspebes Comparison of Microbial Proteins: Learning about Gene Ancestry, Protein Function, and Species Life Style;
Overview of Cellular Kinetic Modeling of the Microbial Metabolism