M

M.Sc. Syllabus for the session 2000-2001

The Department offers an one-year full-time MS course in Microbiology. An Honours degree in Microbiology or an equivalent degree is required as an entry qualification. The course aims to give detailed knowledge and understanding of important aspects of Microbiology, as currently applied in industry, health and medicine science, environment management and biotechnology, as well as in advanced research as applied to microbiology and biotechnology.

Students studying for MSc degree will be required to take a total of 6 units. Each unit consists of at least 60 lecture‑hour and bears 100 marks. Similarly, for each half‑unit course, there will be at least 30 lecture‑hour corresponding to 50 marks. There shall be one mid‑term and one term final examination for each course. Twenty percent of the total marks of each theoretical course shall be allocated for the mid‑term and 80% for the term final.

There shall be two groups of examinees: Group A (Non‑Thesis) and Group B (Thesis). Group A (Non‑thesis) students shall undertake and appear for written examinations in ten half‑unit theoretical courses of their choice, a half‑unit viva‑voce, and a half‑unit research project. During the course the students in non‑thesis group shall deliver at least one seminar related to their work and this will be examined by means of extended essays.

Group B (Thesis) students should undertake and appear for written examination in eight half‑unit theoretical courses of their choice, a half‑unit viva‑voce, a half‑unit seminar and a full‑unit dissertation. The students should prepare a short dissertation on a topic, which is individually chosen but must be offered by a teacher of the Department. Department will provide all laboratory facilities to the students, and often must be sent to other research laboratories for carrying out their research work with which the Department has collaborative research projects. The thesis students should attend a series of seminars on relevant topics and should present at least two seminars, one at ate interim period and another after the completion of their work. The dissertation should be prepared at the end of all theoretical courses and it should be submitted within four months after completion of their theoretical examinations. The examiners elected by the respective Examination Committee will assess the seminar course and will arrange for dissertation examination.

Course Information

501 Environmental Biotechnology

502 Enzyme & Protein Biotechnology

503 Molecular Genetics

504 Genomics & Bioinformatics

505 Immunopathology & vaccine Development

506 Bacterial Pathogenesis & Molecular Epidemiology

507 Bioprocess Technology

508 Microbiological Safety of Processed Foods & Beverages

509 Extremophiles

510 Biomass & Biofuel

511 Molecular Virology & Oncology

512 Molecular Systematics & Microbial Evolution

513 Dissertation (Thesis group)

514 Seminar

515 Project & Seminar (Non thesis group)

516 Viva voce

*Group A (Non-Thesis Group) and Group B (Thesis Group) students shall select respectively any ten and any eight theoretical courses (Microbial. 501 to 512). Except Dissertation (Course no. 513), all course are half unit.

Microbiol. 501 (Group A& B) 1/2 unit

Environmental Biotechnology

1. Environmentally transmitted pathogens: Various types of bacterial pathogens including opportunistic ones: their transmission, survival and pathogenicity; types of parasites‑, emerging pathogens, viruses.

2. Risk assessment: The concept of risk assessment, the process of risk assessment: hazard identification‑, exposure assessment, dose response, assessment, risk characterization, microbial risk assessment.

3. Microorganisms and metal pollutants: Sources of metals. metal bioavailability in. the environment, metal toxicity effects on the microbial cells, mechanisms of microbial metal resistance and detoxification; the benefits of metal‑microbial interactions; innovative microbial approaches to the remediation of metal contaminated aquatic system with special reference to arsenic, chromium and lead.

4. Biosensors: Recent developments in biosensors and their use; characteristics of biosensors: biochemical application of biosensors in environmental and clinical pollution detection.

5. Nonculturable microorganisms in the environment: Concept of viable but nonculturable cells (VBNC), present status of VBNC molecular genetic m1hods for detection and identification of VBNC; implication and significance of VBNC in environment and health.

6. Pollution control biotechnology: Use of commercial blends of microorganisms and enzymes in wastewater treatment; immobilized cells in the waste treatment; potential application of recombinant DNA technology in waste treatment,

7. Xenobiotic degrading bacteria and their catabolic genes in bioremediation: In situ analysis of microbial community and activity in bioremediation, DNA-based methods; RNA based methods. genetic finger printing techniques, recent development of methods increasing specificity of detection,

Books Recommended

1. Waste Water Microbiology. Wiley GB.

2. Microbial Biotechnology. Glazer AN & Nikaido H.

3. Environmental Microbiology. Maier RM.

4. Biotreatment System. vol. 2. Wise DL.

5. Nonculturable Microorganisms in the Environment. Colwell RR & Grimes DJ.

6. Molecular Approaches to Environmental Microbiology. Pickup RW & Saunders JR.

7. Microbial Ecology. Atlas RM & Bartha R.

Microbiol. 502 (Group A& B) 1/2 unit

Enzyme & Protein Biotechnology

1. Proteins: The scope of protein biotechnology; the range of industrially significant proteins‑. proteins employed in healthcare industry; protein sources; microorganisms as a sources of proteins; Plants as a sources of industrially important proteins; animal tissue as a protein source; conformational stability of proteins; recombinant protein technology; protein engineering.

2. Enzyme: Industrial approach to enzyme production; development of new enzyme preparations; biochemical applications of enzymes; medical uses of enzyme; the use of enzymes as catalyst in organic chemistry, restriction endonucleasc; biochemical processing; industrial and technical uses of enzymes; application of enzymes in food industry; use of enzymes in the extraction of natural products. detoxifying enzymes,, enzymes based detergents; use of enzymes as cleansing agents; enzymes in the leather industry; enzymes in the textile industry: enzymes in the paper manufacture; enzymes in the antibiotics; miscellaneous uses of biocatalysts.

Books Recommended

1. Protein Biotechnology. Walsh G & Headon D.

Protein Biotechnology: Isolation, Characterization and Stabilization. Frank F. Protein En&mring;. Principles and Practice. Cleland JF & Craik CS.
Hand Book of Enzyme Biotechnology. Wiseman A.
Biotechnological Applications of Proteins and Enzymes. Bobak Z & Sharon N.

Microbiol. 503 (Group A& B) 1/2 unit

Molecular Genetics

1. Regulation of Gene Expression in Eukaryotes: Spatial and temporal regulation: Ways of regulating eukaryotic gene expression: controlled transcription of DNA. alternate splicing of RNA. cytoplasmic control of mRNA stability, Induction of transcriptional activity by environmental and biological factors‑, Molecular control of transcription; Gene expression and chromosome organization: molecular organization of uanscriptionaby active DNA, gene splicing. DNA methylation & imprinting, gene amplification. Activation & inactivation of whole chromosome.

2. Studying Gene Expression & Function: Transcription of cloned gene, Identifying protein binding sites an a DNA. molecule, identifying and studying the translation product of a cloned gene: hybrid‑arrest translation (HRT) & hybridarrest translation (HART), analysis of protein by in vitro mutagenesis; Studying protein‑protein interaction: phage display. yeast two hybrid system.

3. Signal Transduction: Carriers and channels of membrane: G protein mediated activation & inhibition of target protein: Protein tyrosine kinase‑mcdiated phosphorylation cascades, The Ras/MARK pathway, Activating MAP kinase pathways. Cyclic AMP & activation of CREB; The JAK-STAT pathway, TGFB signals through Smdds; Signal transduction pathway in enteric bacteria (eg. Shigella).

4. Identification of Genes Responsible for Human Diseases: Tag-Sachs mutation; Huntington's disease; Cystic fibrosis.

5. Human Gene Therapy: Somatic cell gene therapy and germ‑line gene therapy. Gene function inicrniption therapy: antisense RNA & ribozymc. Therapeutic use of anti‑sense oligonuclcotidc: pre‑transcriptinal & posttrinscriptional inactivation of mRNA, Gene therapy & cancer: Ethical issues raised by gene therapy.

Book Recommended:

1. Genetics: From Genes to Genomes. Hartwell LH. Hood L. Goldberg ML.

Reynolds AE, Silver LM & Veres RC.

2. Gene Cloning and DNA Analysis: An Introduction. Brown TA.

3. Principles of Genetics, 2 edn. Snustad DP & Simmons MJ.

5. Gene VII. Lewin B.

Microbiol. 504 (Group A& B) 1/2 unit

Genomics & Bioinformatics

1. Introduction: Microbial gnome; The human genome; Importance of genome project: Genomics: structural genomics & functional genomics; Post‑genomics; Bioinformatics; Transcriptome; Proteome & proteornics.

2. Protocols of Detection of Polymorphisms: DNA Sequence Polymorphisms; RFLP‑based protocol; PCR‑based protocol; ASO protocol; SSCP protocol; RAPD protocol; Protocols for detection of microsatellite, minisatellite, deletion, duplication & other insertion, & complex haplotypc; Karyotypc analysis; DNA arrays on microchips.

3. Mapping Genome by Genetic and Physical Techniques: Genetic & physical maps; Markers for genetic maps; Approaches to genetic mapping; High density linkage maps; RFLP and microsatellite maps: Cytogenetic maps, Clone banks; Restriction mapping; Long‑range physical maps: FISH mapping, STS mapping; Positional cloning: chromosome walks & chromosome jumps.

4. Strategies for Assembly of a Contiguous DNA Sequence: Sequence assembly by the shotgun approach; Sequence assembly by the clone contig approach; The direct shotgun approach.

5. Sequencing Phase of the Human Genome Project: Cloning and separation of large DNA fragments; Yeast artificial chromosome (YAC) & bacterial artificial chromosome (BAC) cloning systems.

6. Post‑Genomics: Locating genes in DNA sequence: gene location by sequence inspection, experimental technique for gene location, Determining the function of an unknown gene: computer analysis of gene function, assigning gene function by experimental analysis; Activity of a protein coded by an unknown gene; Comparative genomics as a aid to gene mapping and in the study of human disease genes.

7. Identification of Gene Functions in Bacteria: Transcriptional reporter fusion (replicon ori); Mutagenesis strategies—site-directed, transposon, viral transduction: Linkage, cloning & rapid sequencing of the gene in question.

8. Bioinformatics: Definition; Sequence comparison by computational analysis and gene bank retrieval, Pattern matching and automatic discovery; Protein motif and putative function; 2,3 D protein structure (computer model), Protein threading and protein folding: Determination of homology and protein identification; Genome cartography and genome annotation; Evolution and phylogeny, Analysis of gene expression; Metabolic pathways and regulatory network.

Book Recommended:

1. Genetics: From Genes to Gcnomes. Hartwell LH, Hood L, Goldberg ML, Reynolds AE, Silver LM & Veres RC.

2. Gene Cloning and DNA Analysis: An Introduction, 4th edn. Brown TA.

3. Biotechnology. Genomics and Bioitiformatics. 2 d edn., vol. 5b. Rehm H-J & Reed G.

4. Principles of Genetics, 2 d edii. Snustad DP & Simmons MJ.

5. Genome. Brown TA.

6. Genome 2. Brown TA.

7. Gene VII. Lewin B.

8. Gene. Lewin B.

9. Molecular Biotechnology. Glick & Pasternak.

10. Molecular Biology and Biotechnology. Mayers RA.

11. DNA Sequencing Protocols. GT Win & Griffin AM.

Microbiol. 505 (Group A & B) 1/2 unit

Immunopathology & Vaccine Development

1. Inactivation and activation of biologically active molecules. Mechanism of antibody mediated inactivation and activation (hormone, receptor, ligand); Neutralizing antibodies-- cause and effect, Protective functions of inactivating antibodies.

2. Cytotoxic and cytolytic reaction: Mechanism of cytolytic reactions: Immunohaematologic disease: erythrocyte, leukocytes, platelets; Detection of circulating cytotoxic antibodies: Protective and pathologic effects in infectious diseases.

3. Granulomatous reactions: Nature of ganulomatous. Granulomatous disease: Infectious diseases‑bacterial and parasitic.

4. Inflammation: Nonimmune and immune inflammation, Immune specific protection against infections. Interaction of immune mechanism in infectious disease‑, Evasion of immune defense mechanisms:

5. Antibody engineering: Antibody gene cloning, Recombinant antibody gene expression; Applications of engineered antibodies.

6. Vaccination: Designing of vaccines, attenuated vaccine, conjugate vaccine, subunit vaccine, DNA based and other vaccines.

7. Vaccine Strategy: Experimental vaccines for botulism, anthrax, malaria, pneumonia, cholera, typhoid, hepatitis and tumors.

Book Recommended

1. Immunology: lmmnunopathology and Immunity. Sell S.

2. Bacterial Pathogenesis: A molecular Approach. Salyers AA & Whitt DD

3. Molecular Immunology. Hatnes. BD & Glover DM.

4. Immunology Today. Elsevier Trends Journals

Microbiol. 506 (Group A& B) 1/2 unit

Bacterial Pathogenesis & Molecular Epidemiology

1. Pathogenesis with Special Reference to Molecular Basis: Shigellosis; Cholera; Bacterial ulcer in human, Meningitis and epiglotitis; Botulism; Gas gangrene; Anthrax; Toxic shock syndrome, Plague, Pelvic inflammatory disease, Haemophilus influenzae; Listeria monocylogenes.

2. Bacterial Resistance to Antibiotics: Mechanism of antibiotic resistance; Antibiotic tolerance: Transfer of resistance genes.

3. Infection Control. & Prevention: Epidemic versus endemic; Steps in epidemiologic evaluation. Role of the laboratory in epidemiologic evaluation: Potential problems related to laboratory activities in epidemiologic investigations.

4. Epidemiologic Analysis: Criteria for evaluating typing system; Phenotypic techniques: biotyping, antimicrobial susceptibility testing, serotyping, bacteriophage typing; MLEE; Genotypic techniques: plasmid analysis, REA of chromosomal DNA, Southern blot analysis of RFLPs, PFGE of chromosomal DNA, typing system applying PCR, PCR‑based detection of restriction sites, & nucleotide sequence analysis; Molecular typing of specific organisms; Application of microbial typing system; Implementing a molecular epidemiology laboratory.

1. Introduction: Importance & development of bioprocess technology. Upstream & downstream processing.

2. Methods for Biocatalysis and Biotransformations: Concepts and general features of biotransformations, Procedures, techniques & media for biotransformations, Reactions in solvent mixtures: addition of organic compounds to reaction mixtures; Equipments, automation. standardization, quality control & quality assurance. Optimization procedures, Examples of typical bioconversion procedures.

3. Scale Up of Microbial Processes: Criteria used for scale up: Important factors considering for development of microbial processes: physical, chemical. process & sterilization factors.

4. Processing of Food & Feed: Raw materials, microorganisms, processing, food value & economic importance of idli. ogi. dahi. tofu. tcmpch, animal & poultry feed.

5. Biocomposting processes: Introduction; Composting processes: Succession microorganisms. Bioelemental change, Application.

6. Recent Trend in Vinegar & Citric Acid Production Processes: Potential raw materials. Fermentation. recovery, future prospects of vinegar & citric acid.

7. Biopharmaceuticals: Gems for the biosynthesis of secondary metabolites, Antibiotic production & its modification, Metabolic engineering of antibiotic biosynthetic pathways, Biotransfarmation of steroids.

1. Introduction: Importance of safe food & beverage for health; Manufacture hygienic foods; Microbial indicators of safe foods.

2. Factors Influencing Microbiological Safety of Foods: Process equipment of plant design, Sanitation & cleaning; Food ingredients; Personal hygiene; Packaging; Storage; Transportation.

3. Food poisoning and Spoilage: Poisoning & spoilage problems; Control & monitoring programs; Detection method & Conventional, rapid, rapid end‑detection & specific detection techniques.

4. Management and Control of Food Safety: Sanitation & hygiene program; Control & inspection‑, Management of microbial ha7ards in foods‑. HACCP plans, RC, RM & RA; GNM & GHP; GRAS.

5. Investigation of Food‑borne Disease Outbreaks: Objectives, personnel involved, materials & equipment, & field of the investigation: Laboratory testing, interpretation & application of results; Preventing measure.

6. Food Laws and Regulations: Laws; Enforcement‑, Impact of regulations, Exports & imports.

1. Extreme Environment: Microbial adaptations to extreme environments: Extreme environment as a resource for novel microorganisms.

2. Biodiversity: Biodiversity at the molecular level: the domains, kingdoms and phyla of life; Microbiological perspective, The primary divisions of life: domain archaea; domain bacteria, domain eukary, Microbial diversity.

3. The Archaea: Phylogenetic overview, Kingdom Euryarchaea. Kingdom Crenarchaca; Hyperthermophilic archaca and microbial evolution.

4. Different Types of Extremophiles: The extreme thermophiles; The extreme acidophilcs, The extreme alkalophiles., The extreme halophiles; The extreme barophiles.

5. Cultivation of Extremophilic Microorganisms: Various strategies applied for cultivation of extremophiles.

6. Extremozymes: Biocatalysts under extreme conditions, Extremophiles as a source of novel enzymes for industrial application: Screening strategies for novel enzymes: Heat‑stable amylase and glucoamylase, Thermostable cellulases, Thermostable xylanascs; DNA processing enzymes in PCR, High temperature reverse transcrition; Therniostable DNA ligase; Other theroactive enzymes of biotechnological interest. Themo stable glucose isomerases, Thermostable alcohol dehydrogenases; Biochemical basis of heat stability.

4. Biotechnology: A Multi Volume Comprehensive. Trcaticsc, vol. 10 (Special Processes). Rehm & Reed G.

6. Microbes in Action: Concept and Application in Microbial Ecology. Lynch JM & Hobbie JE.

1. Introduction: Importance of fuel energy: Fuels from nature: Basic bioenrgy interconversion; Formation biomass & its conversion to fuel.

2. Potential Biomass for Fuel Production: Types of natural biomasses: Land crops, aquatic plants & waste materials; Production of desirable biomass; Advantages & problems in utilization of biomass for fuel generation; Pretreatment of biomass for fuel production.

3. Bioconversion of Biomass to Methane: Biomass composition & methane production; Synthesis of methane under natural conditions, Potential microbes involved in methane generation; Man‑made processes: Methane from sanitary landfills, sewage, farm, industrial wastes & energy crops; Reactor design; Utilization of the methane as fuel.

4. Production of Fuel Ethanol from Biomass: Potential biomass and microorganisms for ethanol production. Problems in production of ethanol from agro‑industrial wastes; Development of technology of fermentation; Ethanol production from molasses by yeast; Ethanol production from cellulose by rumen bacteria; Ethanol production by Zymomonas mobilis; Future prospects of the industrial alcohol.

5. Production of Hydrogen from biomass: Potential substrates and microorganisms; Natural biosyntlicsis of hydrogen under natural habitats; Cell‑free system and combined system for production of hydrogen.

1. Persistence of Viruses: Patterns of virus infections‑, Mechanisms of viral persistence. Persistence of HSV. EPV & HIV in humans.

2. Viruses of' Special Interest: Dengue and Japanese encephalitis virus, Ebola virus infection. Severe acute respiratory syndrome (SARS) & SARS coronavirus, Other important viruses of recent epidemics.

3. Virus Evolution & Emerging Viruses: How do viruses evolve. Emerging viruses: Emergence of dengue virus infection in Bangladesh.

5. Cancer: Development of cancer; Spread of cancer‑. Molecular mechanisms of transformation by DNA and RNA viruses; Physical & chemical factors contribute to cancer development, Cancer therapy.

1. Origin of Life: Primitive earth, Evidence for microbial life on the early earth. Primitive organisms, Origin of modern eukaryotes.

2. Phylogenetic Analysis: Evolutionary chronometers: Molecular chronometers. rRNA sequencing methodology, Evolutionary distance: Generation of phylogenctic trees from RNA sequences, Signature sequences.

3. Phylogenetic Groups: Phylogenetic analyses of bacteria. archaea & eukarya; Chracteristics of the primary domains of life.

4. Conventional Bacteria Taxonomy: Classification. nomenclature & identification. Phenotypic characterization of bacteria: morphology, physiology. biochemical, antigenic structure & chemical composting. Identification & typing: Phenotypic identification: conventional epidemiological typing; Bacteriocin typing.

5. Numerical Taxonomy: Similarity & arrangement; Taxonomic structure; Strain selection; Test selection; Data coding; Computer analyses; Presentation & interpretation of results.

6. Molecular Taxonomy~ G+C ratio of DNA‑, NA hybridization; 16 rRNA oligonucleotide cataloguing; AP‑PCR; REP‑PCR; RFLP; RFLP1PCR‑, ribotyping, DNA fingerprinting, RAPd; DAF; AFLP DNA fingerprinting.