20110124161222 m sc microbial biotechnology

PANJAB UNIVERSITY CHANDIGARH- 160 014 (INDIA) (Estted. under the Panjab Univerasity Act VII of 1947-enacted by the Govt. of India)

FACULTY OF SCIENCE

SYLLABI

FOR

M.Sc. MICROBIAL BIOTECHNOLOGY

1st to 4th SEMESTER

EXAMINATION 2011-2012

---:O:---

M.Sc. 1st year (1st Semester)

Total Credits= 30

Total Marks = 750

M.Sc. 1st year (2nd Semester)

Total Credits= 30

Total Marks = 750

Code

Theory Practical S. No. Course/Paper

Course No. Marks Course No. Marks

Credits

1. Microbial Biodiversity

and Physiology MBT-101T 100 MBT-101 P 50 6

2. Immunology and

Immunotechnology MBT-102T 100 MBT-102 P 50 6

3.

Genetics and

Recombinant DNA

Technology

MBT-103 T 100 MBT-103 P 50 6

4. Molecular Biology MBT-104 T 100 MBT-104 P 50 6

5. Bioprocess

Engineering MBT-105 T 100 MBT-105 P 50 6

Code



Credits

1. Medical

Microbiology MBT-201 T

100 MBT-201 P 50 6

2.

Microbial

Biochemistry and

Enzymology

MBT-202 T

100

MBT-202 P 50 6

3.

Industrial

Microbiology-1

(Health, Food,

Enzymes)

MBT-203 T

100

MBT-203 P 50 6

4. Bioinformatics MBT-204 T 100 MBT-204 P 50 6

5.

Intellectual Property

Rights (IPR) &

Bioethics

MBT-205 T

100

MBT-205 P 50 6

M.Sc. 2nd year (3rd Semester)

Total Credits= 22

Total Marks = 550

M.Sc. 2nd year (4th Semester)

Total Credits= 18

Total Marks = 450

Consolidation of Marks and Credits

Sr. No. Class Total Marks Total No. of Credits

1. M.Sc. 1st Yr 1500 60

2. M.Sc. 2nd Yr 1000 40

Grand Total

2500

100

Code



Credits

1.

Advances in

Microbial

Biotechnology

(Genomics,

Proteomics,

Metabolomics)

MBT-301 T 100 MBT-301 P 50 6

2.

Industrial

Microbiology-II

(Environment,

Biofuels, Chemicals,

Biomass)

MBT-302 T 100 MBT-302 P 50 6

3. Bioinstruments and

their Applications MBT-303 T 100 MBT-303 P 50 6

4. Tutorials MBT-304 T 100 MBT-304 P -- 4

Code



Credits

1. Journal club MBT-401 T 100 MBT-401 P -- 4

2. Dissertation MBT-402 T 350 MBT-402 P -- 14

Centre for Microbial Biotechnology (CMBT)

Syllabus

for

M.Sc. MICROBIAL BIOTECHNOLOGY

2011-2012

Semester I

1. MBT-101: Microbial Biodiversity and Physiology

2. MBT-102: Immunology and Immunotechnology

3. MBT-103: Genetics and Recombinant DNA Technology

4. MBT-104: Molecular Biology

5. MBT-105: Bioprocess Engineering

Semester II

1. MBT-201: Medical Microbiology

2. MBT-202: Microbial Biochemistry and Enzymology

3. MBT-203: Industrial Microbiology-1 (Health, Food, Enzymes)

4. MBT-204: Bioinformatics

5. MBT-205: Intellectual Property Rights (IPR) & Bioethics

Semester III

1. MBT-301: Advances in Microbial Biotechnology (Genomics, Proteomics, Metabolomics)

2. MBT-302: Industrial Microbiology-II (Environment, Biofuels, Chemicals, Biomass,

Protocols)

3. MBT-303: Bioinstruments and their Applications

4. MBT-304: Tutorials

Semester IV

1. MBT-401: Journal club

2. MBT-402: Dissertation.

MBT-101: Microbial Biodiversity and Physiology

Total Marks: 100 (Exam-80 + Int. Asses.-20)

Objective: To expose the students to (i) the diversity of microbes, (ii) growth & nutrient

requirements (iii) unique metabolic pathways.

Exam Pattern: Five questions to be attempted from a total of nine questions, which will be

divided into five units. Each unit will comprise of two questions and students

would be required to attempt one question from each unit. The last unit will

comprise of objective type/short notes covering the complete syllabus.

Unit -I 1. Relevance of microbiology as a field of Biotechnology.

2. Historical milestones in Microbiology and Biotechnology

3. Structures and functions of Escherichia, Staphylococci & Saccharomyces.

4. Control of microbes by the use of physical and chemical agents.

Unit – II

5. Biodiversity of

(a) Archaea

(b) Bacteria

(c) Fungi

(d) Algae

(e) Viruses

6. Microbial ecology: Biogeochemical cycling, Microbes in marine & freshwater

environments, Microbes in terrestrial environment, Microbial interactions

Unit – III

7. Nutritional requirements of microbes

8. Bacterial growth and its kinetics.

9. Chemostat, Turbidostat, Synchronous growth.

10. Mechanisms involved in transport of nutrients in microbes

Unit - IV

12. Unique pathways of microbial metabolism: ED, PK pathways; Respiration; Fermentations;

Amphibolic pathways; Anaplerotic reactions.

13. Bacterial cell wall biosynthesis

14. Photoautotrophy, Chemolithotrophy, Methylotrophy, Calvin cycle

Practicals:

Total Marks: 50 Int. Asses.-10. Based on the performance of the students during the practical

Exam. – 40 (Practicals - 20, Synopsis – 05, Notebook – 05, Viva voce – 10)

1. Use of basic instruments in Microbiology (Light microscope, pH meter, Autoclave,

Laminar flow chamber, Centrifuge, Spectrophotometer).

2. Staining of bacteria, yeast and fungi.

3. Purification of mixed cultures by streaking technique

4. Determination of viable count

5. Correlation of viable counting and optical density of cultures

6. Isolation of microbes from environment

7. Bacteriophage screening

8. Preparation of complex and synthetic medium.

9. Sterilization of liquid and solid items.

10. Storage of microbes

Suggested readings:

1. Microbial Biotechnology by A. R. Alagawadi, P. U. Krishnaraj, K. S. Jagadeesh, S.

Kannaiyan. (2006) Publisher: Alpha Science Intl Ltd; First edition (2006), ISBN-10:

8173197253 ISBN-13: 978-8173197253.

2. Microbial Diversity: Form and Function in Prokaryotes by Oladele Ogunseitan, (2004)

Publisher: Wiley-Blackwell. ISBN-13: 978-0632047086

3. Introduction to Biotechnology by William J. Thieman and Michael A. PalladinPo (2003)

Publisher: Benjamin Cummings; First edition ISBN-10: 0805348255 ISBN-13: 978-

0805348255

4. Biodiversity of Microbial Life: Foundation of Earth's Biosphere by James T. Staley and

Anna-Louise Reysenbach (2001) Publisher: Wiley-Liss; First edition ISBN-10:

0471254339 ISBN-13: 978-0471254331

5. Genetics and Physiology of Microbes by Rajan S. Sundara (2003), Publisher: Anmol

Publications Pvt Ltd ISBN-10: 8126113677 , ISBN-13: 978-8126113675

6. Microbial Physiology, 4th Edition by Albert G. Moat, John W. Foster, Michael P. Spector,

and Michael P. Sector (2002) Publisher: Wiley-Liss; 4th

edition, ISBN-10: 0471394831

ISBN- 13: 978-0471394839

7. Advances in Microbial Physiology by Robert K. Poole (2002), Publisher: Academic Press;

1st edition ISBN-10: 0120277468, ISBN-13: 978-0120277469

MBT-102: Immunology and Immunotechnology


Objective: To expose the students to (i) the basics of immune system (ii) the response of humans

to foreign bodies (iii) the techniques involved in immunoassays (iv) vaccines





Unit-I

1. Immune cells and immune organs, adaptive and innate immunity.

2. B cell biology: Development, selection, B cells as central players of humoral immunity.

3. T cell biology: Development, thymic education, TCR rearrangement, basic functions of

cells during immune response, T cells subsets.

4. Immunoglobulins: Structure and functions of Immunoglobulins, Immunoglobulin

rearrangement, molecular genetics of BCR generation

5. Antigens complement system, haptens, adjuvants.

Unit-II

6. Antigen presenting cells (APCs): Dendritic cell (DC), importance of DCs in adaptive

immune response, role of B cells and macrophages as APCs, non-professional APCs, cell

biology of antigen processing and presentation.

7. Major Histocompatibility Complex (MHC): Structure, function and immunogenetics of

MHC, MHC-TCR interactions.

8. Immune Homeostasis: Homeostasis, migration, tissue redistribution of lymphocytes, site

specific immune response.

9. Chemokine, cytokine and cell signaling: Their roles in activation and differentiation of

cells of immune system, importance in response to pathogens.

10. Nuclear receptors for macrophage and T cell plasticity, nuclear receptors and antigen

processing and presentation, nuclear receptors and immune cell effector repertoire.

Unit-III

11. Antigen-antibody reactions, interaction, cross reactions, precipitation and agglutination.

12. Radioimmunoassay, ELISA, Western blotting.

13. Hybridomas and Monoclonal antibodies.

14. Recent advances in immunological tools for diagnosis of diseases.

Unit-IV

15. Tolerance and autoimmunity, allergy and hypersensitivity-mediated diseases.

16. Immune response to infectious diseases: Responses to different class of pathogens such as

intracellular bacteria, viruses and extracellular and intracellular parasites.

17. Vaccines and their types: killed and live, sub unit, recombinant, multivalent, DNA, edible

vaccines. Microbe-resistant transgenic plants

18. Antibodies as immunotherapeutic, cytokine therapy

19. Cancer: immune-surveillance, tumor antigens, immunological intervention.

Practicals:


Exam. – 40 (Practical - 20, Synopsis – 05, Notebook – 05, Viva voce – 10)

1. Animal handling

2. Routes of injections

3. Drawing blood from animals

4. TLC and DLC for blood samples.

5. Determination of cell number (viable/non-viable).

6. Ficoll density gradient, separation of cell types.

7. Raising antibodies in animals.

8. Immunoassays

Suggested readings:

1. Kuby Immunology by Thomas J. Kindt, Barbara A. Osborne, and Richard A. Goldsby Publisher:

(2006) . W. H. Freeman; 6th edition. ISBN-10: 1429202114, ISBN-13: 978-1429202114

2. Basic Immunology, Abul K. Abbas and Andrew H. Lichtman (2006) Publisher: Saunders; 2nd

edition. ISBN-10: 1416029745, ISBN-13: 978-1416029748

3. Roitt's Essential Immunology (Essentials) by Peter Delves, Seamus Martin, Dennis Burton, and

Ivan Roitt (2006), Publisher: Wiley-Blackwell; 11th edition ISBN-10: 1405136030, ISBN-13: 978-

1405136037 4. Immunobiology by C. Janeway (2004) Publisher: Garland Science; 6

th edition. ISBN-10:

0815341016, ISBN-13: 978-0815341017

MBT-103: Genetics and Recombinant DNA Technology


Objective: To expose the students to (i) genetics of microbes (ii) permanent changes in the

genetic material (iii) techniques involved in the cloning of genetic elements





Unit-I

1. Significance of genetic recombination

2. Homologous genetic recombination (Transformation, Transduction, Conjugation)

3. Heterologous genetic recombination (IS, Tn, Mu phage)

4. Natural Plasmids and their types, Role of plasmids in transfer of genes

Unit II

5. Mutations: Fluctuation test, Replica plating

6. Physical and chemical mutagens

7. Types of mutations

8. DNA Repair mechanisms

Unit – III

9. Host restriction/modification, Enzymes involved in gene cloning

10. Plasmids as gene cloning vectors, Commercial vectors

11. Strategies involved in cloning of gene(s).

12. Construction of genomic, cDNA and meta-genomic libraries

Unit – IV

13. DNA sequencing

14. PCR and its applications and modifications

15. Phage display technology and its applications.

16. Yeast two-hybrid system, Combinatorial library

Practicals:



1. Isolation of chromosomal DNA

2. Isolation of plasmid

3. Preparation of competent cells

4. Transformation and Electroporation

5. Restriction digestion (complete and partial) of DNA

6. Cloning and expression of a gene in E.coli

7. Amplification of DNA by PCR

Suggested readings:

1. Modern Microbial Genetics by Uldis N. Streips and Ronald E. Yasbin. (2002) Publisher: Wiley-

Liss; 2nd

edition, ISBN-10: 0471386650 ISBN-13: 978-0471386650

2. From Genes to Genomes: Concepts and Applications of DNA Technology by Jeremy W. Dale and

Malcolm von Schantz. (2007), Publisher: Wiley-Interscience; 2nd

edition ISBN-10: 0470017333,

ISBN-13: 978-0470017333 3. Gene and Genome Technology: Principles and Applications of Recombinant DNA and Genomics

by Sandy Primrose and Richard Twyman. (2007) Publisher: Blackwell Publishing Limited ISBN-

10: 140515666X ISBN-13: 978-1405156660 4. Principles of Gene Manipulation and Genomics by Sandy Primrose, Richard Twyman, Bob Old,

and Giuseppe Bertola. (2006) Publisher: Blackwell Publishing, Incorporated; 7th edition ISBN-10:

1405135441 ISBN-13: 978-1405135443 5. Manipulation and Expression of Recombinant DNA, by Sue Carson and Dominique Robertson.

(2005) Publisher: Academic Press; 2nd

edition, ISBN-10: 0120884186, ISBN-13: 978-0120884186

6. Gene Cloning and DNA Analysis: An Introduction by T. A. Brown. (2001) Publisher: Blackwell

Publishing, Incorporated; 4th edition ISBN-10: 063205901X ISBN-13: 978-0632059010

7. Recombinant DNA Technology by O.S. Reddi (2000), Publisher: Allied Publishers Pvt. Ltd. ISBN-

10: 8170239958

MBT-104: Molecular Biology


Objective: To expose the students to the mechanism of (i) DNA replication (ii) DNA

transcription (iii) protein synthesis (iv) regulation of gene expression (v) signal

transduction





Unit – I

1. DNA and its various forms, super coiling of DNA, DNA melting, repetitive sequences, cot

and rot curves, C value paradox, DNA protein interaction, DNA super coiling.

2. Unit of DNA replication, enzymes involved in replication, origin and replication fork,

fidelity of replication.

3. Replication of bacterial chromosome

4. Replication of eukaryotic chromosomes.

Unit-II

5. RNA synthesis and processing: transcription factors and machinery, formation of initiation

complex, transcription activator and repressor, RNA polymerases, capping, elongation, and

termination, RNA processing, RNA editing, spilicing, and polyadenylarion, structure and

function of different types of RNA, non coding RNA, RNA transport.

Unit – III

6. Protein synthesis and processing: Ribosome structure, genetic code, aminoacylation of

tRNA, tRNA-identity aminoacyl tRNA synthetases, formation of initiation complex,

intiation factors and their regulation, elongation and elongation factors, termination,

translation proof-reading, translational inhibitors, Post- translational modification of

proteins.

7. Control of gene expression at transcription and translation level:

Unit – IV

8. Cell signaling: signal transduction pathways and their regulation, bacterial two-component

systems, bacterial chemotaxis and quorum sensing.

9. Role of microbes in cancer, apoptosis, antimicrobial peptides as cancer therapeutic.

10. Gene silencing strategies

Practicals:



1. Tm value of DNA

2. Spectrophotometric analysis of DNA

3. Protein purification by Gel exclusion chromatography

4. Protein purification by Ion-Exchange chromatography

5. Protein purification by Affinity chromatography

6. Separation of proteins on non-denaturing gels.

7. Separation of proteins on denaturing gels.

Suggested readings:

1. Molecular Biology of the Gene, by James D. Watson, Tania A. Baker, Stephen P. Bell, and

Alexander Gann (2007), Publisher: Benjamin Cummings; 6th edition ISBN-10: 080539592X ISBN-13: 978-0805395921

2. Fundamental Molecular Biology by Lizabeth A. Allison (2007), Publisher: Wiley-Blackwell; 1st

edition ISBN-10: 1405103795 ISBN-13: 978-1405103794

3. Molecular Biology by Robert F. Weaver (2007) Publisher: Mcgraw-Hill College; 4th edition ISBN-

10: 0072995246 ISBN-13: 978-0072995244

4. Cell and Molecular Biology: Concepts and Experiments by Gerald Karp (2007) Publisher: Wiley;

5th edition ISBN-10: 0470042176 ISBN-13: 978-0470042175

5. Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, and Martin Raff

Publisher: Garland Science; 5th edition, ISBN-10: 0815341059 ISBN-13: 978-0815341055

MBT-105: Bioprocess Engineering


Objective: To expose the students to the (i) bioreactor and its types (ii) production of bioactive

molecules /cells in a bioreactor (iii) purification of bioactive molecules (iv)

fermentation processes





Unit – I

1. Introduction to a bioreactor design. Control panels of a bioreactor. Types of bioreactors.

Kinetics of growth product formation and substrate utilization.

2. Operation of bio-reactors.

Unit – II

3. Mass and Heat Transfer in Bioreactors: Aeration and Agitation in Bioreactors, Concept of

mass transfer correlation and scale up.

Unit – III

4. Up Stream Process (USP): Inoculum development, Media composition, Sterilization etc.

5. Down Stream Process (DSP): Cell disruptions, Flocculation, Filtration, Ultra filtration,

Centrifugation, Ultracentrifugation, Chromatographic methods, two phase aqueous

separations, solvent – solvent extraction, centrifugation, pre treatment, crystallization etc.

Unit – IV

6. Fermentations and Fermentative processes like Submerged, Solid state, Batch, Fed Batch,

Continuous system etc.

7. Hygiene and safety in fermentation laboratory/processes.

Practicals



1. Components and Operation of a Bioreactor

2. Batch fermentation in conical flask

3. Production of the enzyme/s in shake flask

4. Solid state fermentation

Suggested readings:

1. Biotransformations and Bioprocesses (Biotechnology and Bioprocessing Series). Mukesh Doble,

Anil Kumar Kruthiventi and Vilas Ganjanan Gaikar (2004). Publisher: CRC; 1st edition, ISBN-10:

0824747755, ISBN-13: 978-0824747756.

2. Bioprocess Engineering Basic Concepts (2002).Publisher: Prentice Hall; 2nd ISBN-10:

8120321103 ISBN-13: 978-8120321106. 3. Principles of Fermentation Technology. P.F. Stanbury, A.Whitaker and S. Hall. (2001)

4. Bioprocess Engineering: Basic Concepts. Michael L, Shuler and Fikret Kargi (2001). Publisher:

Prentice Hall PTR; 2nd edition ISBN-10: 0130819085, ISBN-13: 978-0130819086. 5. Solid-State Fermentation Bioreactors: Fundamentals of Design and Operation. David A. Mitchell,

Nadia Krieger, and Marin Berovic (June 2006). Publisher: Springer; 1st edition ISBN-10:

3540312854, ISBN-13: 978-3540312857. 6. Bioreactors for Tissue Engineering: Principles, Design and Operation. Julian Chaudhuri and

Mohamed Al-Rubeai (2005). Publisher: Springer; 1st edition.

7. Multiphase Bioreactor Design. Joaquim M.S. Cabral, Manuel Mota and Johannes (2001).Publisher:

CRC ISBN-10: 0415272092, ISBN-13: 978-0415272094.

MBT-201: Medical Microbiology


Objective: To expose the students to (i) various types of diseases caused by microbial pathogens

(ii) pathogenic mechanisms of microbes (iii) antimicrobial chemotherapy (iv)

epdiomology of important diseases





Unit – I (Pathogenesis, Chemotherapy)

1. Overview of a) Normal microflora of humans and its importance, b) Specific and Non-

specific defense mechanisms.

2. Pathogenesis of microorganisms: Host parasite relationships, pathogenesis of bacterial

diseases, pathogenesis of viral diseases, toxigenesis, host defense against microbial

invasion, microbial mechanism for escaping host defenses.

3. Antimicrobial chemotherapy: Characteristics of anti microbial drugs, determination of anti

microbial activity, anti bacterial drugs, anti viral drugs, anti fungal drugs, anti protozoon

drugs.

4. Development and transfer of drug resistance in microbes.

Unit – II (Bacterial infections)

5. Air-borne bacterial diseases (TB, Diphtheria, Pertusis, Streptococcal, etc.)

6. Food/Water – borne bacterial diseases (Botulism, Gastroenteritis, Cholera, Salmonellosis,

Shigellosis, Traveler’s diarrhea ; Sepsis and septic shock)

7. Direct - contact diseases (Gas gangrene, GBS, Conjunctivitis, Leprosy, Peptic ulcer,

Staphylococcal, STB, Tetanus, Trachoma)

8. Arthropod - borne bacterial diseases (Typhus, Lyme, Plague, Q fever etc.); Zoonotic

diseases (Anthrax, Brucellosis) ; Dental infections (Dental plaque, Dental Decay,

Periodontal diseases.

Unit – III (Viral infections)

9. Air-borne viral diseases (Chicken pox, Small pox, Measles, Mumps, Influenza)

10. Direct - contact diseases (AIDS, Sores, Common cold, CMV, Genital herpes, Leukemia,

Infectious monoucleosis, Hepatitis, Warts)

11. Food/Water – borne viral diseases (Gastroenteritis, Hepatitis, polio)

12. Zoonotic viral diseases; (Rabies, VHF); Arthropod - borne diseases (Encephalitis, RVF,

Yellow fever); Prion diseases.

Unit – IV (Other infections, Epidemiology)

13. Over view of human diseases caused by Fungi and Protists especially Malaria,

Leishmaniasis, Amebiasis, Giardiasis.

14. Brief introduction to discomforts caused by Algae

15. Epidemiological terminology, Morbidity rate, Mortality rate, Prevalence rate; Recognition

of an infectious diseases in a population; Recognition of an epidemic; infectious disease

cycle; Virulence and the mode of transmission

16. Emerging and reemerging infectious diseases/pathogens; Control of epidemics; Global

travel and health considerations; Nosocomial infections.

Practicals:



1. Collection, handling and storage of clinical samples

2. Culture identification of bacteria (E.coli, Salmonella, Shigella, Staphylococcus,

Streptococcus)

3. Culture identification of fungi (Candida, Aspergillus)

4. Identification of pathogens by PCR technology

5. Antibiotic sensitivity of clinical pathogens

Suggested Readings:

1. Medical Microbiology, by Geo. F. Brooks. (2007) Publisher: McGraw-Hill Medical; 24

th edition.

ISBN-10: 0071476660, ISBN-13: 978-0071476669,

2. Medical Microbiology by Patrick R. Murray, Michael A. Pfaller, Ken S. Rosenthal, and Patrick R. Murray (2005). Publisher: Mosby; 5

th edition ISBN-10: 0323033032, ISBN-13: 978-0323033039

3. Review of Medical Microbiology by Patrick R. Murray and Ken Rosenthal (2005). Publisher:

Mosby; 1st edition ISBN-10: 0323033253 , ISBN-13: 978-0323033251

4. Medical Microbiology & Immunology by Warren E. Levinson (2004) Publisher: McGraw-

Hill/Appleton & Lange; 8th edition. ISBN-10: 0071431993, ISBN-13: 978-0071431996

MBT-202: Microbial Biochemistry and Enzymology


Objective: To expose the students to (i) macromolecular interactions (ii) structure and functions

of biomolecules (iii) enzymes: their functions, regulation and industrial applications





Unit - I

1. Buffers and physiological buffers.

2. Thermodynamics and Principles of thermodynamics, free energy, enthalpy and entropy.

3. Macromolecular interactions: van-der waal’s, hydrogen bonding, ionic, hydrophobic,

covalent etc.

4. Structure and functions of Carbohydrates, Proteins, Lipids, Nucleotides, DNA, RNA, and

Vitamins

Unit – II

5. Metabolism of Carbohydrates (Glycolysis, TCA, HMP, Gluconeogenesis)

6. Metabolism of Lipids (Fatty acid metabolism, Phospholipid metabolism, Cholesterol

biosynthesis)

Unit – III

7. Metabolism of protein (Digestion of proteins, General reactions of amino acids, Fate of

carbon skeletons of amino acids, Regulation of amino acid biosyntheses)

8. Electron transport chain, Oxidative phosphorylation

Unit – IV

9. Enzymes: General distinctive features, nomenclature and industrial applications

10. Enzyme kinetics

11. Allosteric enzymes

12. Feed back inhibition and Feedback repression mechanisms

13. Multienzyme complexes: advantage and examples

14. Biocatalysis-Definition, chirality, advantages/disadvantages of biocatalysis over chemical

catalysis, different types of biocatalysis

Practicals:



1. Qualitative and quantitative assay of Sugars

2. Qualitative and quantitative assay of Proteins

3. Qualitative and quantitative assay of Lipids

4. Qualitative and quantitative assay of Nucleic acids

5. Assay of enzymes

6. Substrate specificity and efficiency of enzymatic catalysis

7. Kinetics of enzyme catalyzed reactions

8. Effect of pH and temperature on enzyme activity

9. Enzyme immobilization

Suggested readings:

1. Enzyme Kinetics and Mechanism by Paul Cook. (2007) Publisher: Garland Science; 1st edition

ISBN-10: 0815341407 ISBN-13: 978-0815341406

2. Enzymatic Reaction Mechanisms by Perry A. Frey and Adrian D. Hegeman (2006), Publisher:

Oxford University Press, USA; 1st edition ISBN-10: 0195122585 ISBN-13: 978-0195122589 3. Enzyme Kinetics: A Modern Approach by Alejandro G. Marangoni (2002) Publisher: Wiley-

Interscience; 1st edition ISBN-10: 0471159859 ISBN-13: 978-0471159858

4. Introduction to Biocatalysis Using Enzymes and Microorganisms by S. M. Roberts, Nicholas J. Turner, Andrew J. Willetts, and Michael K. Turner (1995) Publisher: Cambridge University Press

ISBN-10: 0521430704 ISBN-13: 978-0521430708

MBT-203: Industrial Microbiology- I (Health, Food, Enzymes)


Objective: To expose the students to (i) Industrially important metabolites produce by microbes

especially in the areas of health, food and enzymes (ii) immobilization of

enzymes/cells





Unit I

1. Primary and Secondary metabolites of industrial importance.

2. Techniques involved in screening/detection of industrially important metabolites from

microbes.

3. Pyruvate as the hub molecule

Unit II

4. Biosynthesis and fermentation process involved in

(a) Health & Pharma- Antibiotics (Penicillin, Streptomycin,), Alkaloids (ergot, lysergic acid),

Biotransformations (Steroids, chirals), Therapeutic proteins (Interferons, Insulin,

Streptokinase, Erythropoietin).

(b) Food and Beverages- Beer, Wine, Whisky, Vinegar, Probiotics, Traditional fermented

foods, Food additives: Vitamins, Bioflavors

Unit – III

5. Microbial Enzymes - Pharma related enzymes, Detergent enzymes, Processing of starch

and related carbohydrates, Fruit juice production, Textile & leather manufacture,

Treatment of wood pulp, Organic synthesis, Diagnostics

Unit – IV

6. Immobilization of enzymes and cells: Parameters for choosing a matrix for immobilization,

types of methods for immobilizations. Applications of immobilization techniques.

Practicals:



1. Screening of microbes for production of industrially important enzymes.

2. Optimization of conditions for optimal production of enzyme: - Media composition,

Incubation temperature, Aeration, Incubation time.

3. Wine fermentation

4. Purification of antimicrobial metabolites from a microbe.

Suggested readings:

1. Food Microbiology: Fundamentals and Frontiers. Doyle (2007). Publisher: American Society

Microbiolgy; 3rd edition ISBN-10: 1555814077, ISBN-13: 978-1555814076. 2. Food Microbiology: An Introduction. Montville (2005). Publisher: American Society Microbiolgy;

1st edition ISBN-10: 1555813089, ISBN-13: 978-1555813086.

3. Environmental Microbiology: A Laboratory Manual. Ian L. Pepper and Charles P. Gerba(2004). Publisher: Academic Press; 2nd edition ISBN-10: 0125506562, ISBN-13: 978-0125506564.

4. Advances in Food & Nutrition Research. Steve Taylor (2003). Publisher: Academic Press; 1st

edition ISBN-10: 0120164477, ISBN-13: 978-0120164479.

5. Environmental Microbiology. Raina M. Maier, Ian L. Pepper, and Charles P. Gerba(2000). Publisher: Academic Press; 1st edition ISBN-10: 0124975704, ISBN-13: 978-0124975705.

6. Applied Dairy Microbiology. Elmer H. Marth and James Steele (2001).Publisher: CRC; 2nd edition

ISBN-10: 082470536X, ISBN-13: 978-0824705367. 7. Peter F Drucker. Innovation and Enterpreneurship. Harper & Row, 1985

8. Prasanna Chandra- Projects: Preparation Appraisal and Superimplementation. Tata Mc-Graw-Hill

Co. Ltd

9. J.D. West & F.K. Levy. A management guide to PERT/CPM, Prentice Hall, India

MBT-204: Bioinformatics


Objective: To expose the students to (i) basic understanding of computers (ii) computational

tools developed for understanding of genetic material and proteins





Unit – I (Computer skills)

1. Important components and functions of a computer.

2. Computer languages: History and generation of languages

3. Importance of Bioinformatics in microbiology/ biotechnology

4. Perl language and programming

Unit – II (Biological databases)

5. Database- introduction, Primary, Secondary and Tertiary databases. Type and kind of

databases. Literature search (PUBMED and MEDLINE).

6. Nucleic acid (GenBank, EMBL etc.). Structural databases- PDB, PDBsum, NDB, CATH,

SCOP etc. Motifs and Pattern Databases- PROSITE, Pfam, etc.

7. Protein databases (SWISS PROT, UNIPROT etc.). Structural databases- PDB, PDBsum,

NDB, CATH, SCOP etc. Motifs and Pattern Databases- PROSITE, Pfam, etc.

8. Sequence retrieval (SRS, Entrez) and Data submission.

Unit – III (Sequence analysis)

9. Sequence alignment- introduction and concepts, Local and Global alignment concepts.

10. Similarity and Percent identity score (open, extended gap penality). Multiple sequence

alignment - introduction and concepts. Types of multiple sequence alignment techniques.

Description of major softwares (MSA, CLUSTALW, PILEUP).

11. Database Scanning and Sequence similarity searches. Algorithm of FASTA. Description of

BLAST algorithm. Various BLAST programs (BLASTP, BLASTN).

12. Protein Structure: Classification, Structure Analysis, Secondary structure predictions,

Comparative modeling.

Unit – IV (Genome analysis) 13. Introduction to genomes. Sequencing techniques. Sequencing of whole genomes.

14. Next Gen Sequencing. Assembling of Genomes from Short Reads.

15. Concept of Metagenomics. Types of repeats and repeat finding techniques. Structure of

genes. Prediction of gene in prokaryotic and eukaryotic genomes. Prediction of promoter

prediction in E. coli and in eukaryotes.

16. Description of major gene prediction methods.

Practicals:



1. Sequence (DNA & Protein) alignments

2. Genome sequence studies

3. Designing ideal primers for amplification of genetic material

4. Deciphering 3-D structure of proteins.

5. Designing inhibitors of enzymes

Suggested readings:

1. Understanding Bioinformatics by Marketa Zvelebil and Jeremy Baum (2007) Publisher: Garland

Science; 1st edition ISBN-10: 0815340249, ISBN-13: 978-0815340249

2. Essential Bioinformatics by Jin Xiong (2006) Publisher: Cambridge University Press; 1st edition

ISBN-10: 0521600820, ISBN-13: 978-0521600828 3. Bioinformatics: Sequence and Genome Analysis by David W. Mount (2004). Publisher: Cold

Spring Harbor Laboratory Press; 2nd

edition ISBN-10: 0879697121 ISBN-13: 978-0879697129

4. An Introduction to Bioinformatics Algorithms (Computational Molecular Biology) by Neil C. Jones

and Pavel A. Pevzner (2004) Publisher: The MIT Press; 1st edition ISBN-10: 0262101068, ISBN-

13: 978-0262101066

5. Bioinformatics: A Biologist's Guide to Biocomputing and the Internet by Stuart M. Brown

(2000). Publisher: Eaton Publishing Company/Biotechniques Books ISBN-10: 188129918X, ISBN- 13: 978-1881299189

MBT-205: Intellectual Property Rights (IPR) & Bioethics


Objective: To expose the students to (i) understanding of patents (ii) filing of a patents (iii)

ethical and social issues in biotechnology





Unit - I

1. Introduction: General Introduction

2. Patent Claims, the legal decision-making process

3. Ownership of Tangible and Intellectual Property.

4. Basic requirements of patentability, patentable subject matter, novelty and the Public

Domain; Non-obviousness

5. Special issues in Biotechnology Patents: Disclosure Requirements, Collaborative research,

competitive research, Plant Biotechnology

Unit - II

6. Foreign Patents

7. Patent Litigation: Substantive Aspects of Patent Litigation, Procedural Aspects of Patent

Litigation

8. Recent Development in Patent System and Patentability of Biotechnology invention IPR

issues of the Indian Context

9. IPR Regime in the Digital Society; Copyright and Patents; International Treaties and

Conventions; Business Software Patents; Domain Name Dispute and Resolution.

10. IT Act, 2000 : Aims and Objectives; Overview of the Act; Jurisdiction; Role of Certifying

Authority; Regulators under IT Act; Cyber Crime-offences and Contraventions; Grey

Areas on IT Act.

Unit - III

11. Public acceptance issues for biotechnology: Case studies/experiences from developing and

developed countries.

12. Biotechnology and hunger: Challenges for the Indian Biotechnological research and

industries.

13. The Cartagena protocol on biosafety

Unit - IV

14. Biosafety management: Key to the environmentally responsible use of biotechnology.

15. Ethical implications of biotechnological products and techniques.

16. Social and ethical implication of biological weapons

Practicals:



1. Searching of National Patent databases

2. Drafting of National Patent applications

3. Searching of International Patent databases

4. Drafting of International Patent applications

Suggested readings:

1. Law of intellectual property. Myneni, S.R. (2001). Asia Law House, Hyderabad. 2. Intellectual property law. Davis, Jennifer (2001). Butterworths, London

3. Intellectual property: patents, copyright, trade marks and allied rights. Cornish, W.R. (2001).

Universal Law Publishing, Delhi. 4. Textbook on intellectual property rights. Acharya, N.K. (2001).Asia Law House, Hyderabad.

5. Intellectual Property rights in the WTO and Developing countries. Watal, J. (2001) Oxford

University Press, New Delhi. 6. Intellectual Property Bulletin.

MBT-301: Advances in Microbial Biotechnology (Genomics, Proteomics & Metabolomics)


Objective: To expose the students to recent trends in the field of microbial Genomics, Proteomics

& Metabolomics.





Unit – I

1. Introduction to Microbial genomes

2. Genome sequencing of different microbes and their importance

3. Techniques for genome research (chromosome walking, RFLP etc.)

4. Application of microbial genomic variability for utilizing in human welfare (applications)

5. Phylogenetic relationships between various genera of microbes

Unit – II

6. Sequences as Biological Information - Cells obey the Laws of Chemistry and Physics

7. Evolution by Genome Expansion and Reduction

8. Metagenomics

9. Methods to Compare Genomes

10. Evolution by Genome Expansion and Reduction

11. Archaeal Genomics

12. Microbial Genome Annotation

13. Genomics for pathogenic microbes – Search for better vaccines

Unit – III

14. Introduction to microbial proteomics

15. 2D gel profiling of various microbes

16. Microbial pathogenesis at the proteome level

17. Structural proteomics and computational analysis

18. Proteomics of Archaea

19. Proteome research for novel drug targets

20. Techniques for Proteome research (2 – D gel, MALDI – ToF, Protein purification work

station)

21. High throughput proteomic screening for novel enzymes

Unit – IV

22. Techniques for metabolic engineering

23. Gene manipulation of useful microbes

24. Production of valuable products by metabolic engineering

25. Strain improvement by metabolic engineering

26. Applications of metabolic engineering

Practicals:



1. Isolation of RNA.

2. Characterization of different types of RNA molecules

3. Construction of cDNA

4. Demonstration of 2-D gel electrophoresis

5. Demonstration of MALDI – ToF

6. Demonstration of DNA/Protein Microarray system

7. Practicals on Microbial Genomics/Proteomics/Metabolomics using computational tools

8. Comparison of genomes. Genome projects and sequence archive databases.

Suggested readings:

1. Microbial Proteomics: Functional Biology of Whole Organisms by Ian Humphery-Smith and Michael Hecker (2006) Publisher: Wiley-Interscience; 1

st edition ISBN-10: 0471699756, ISBN-13:

978-0471699750

2. Microbial Genomics and Drug Discovery by Thomas J. Dougherty and Steven J. Projan (2003)

Publisher: CRC; 1st ed. ISBN-10: 0824740416, ISBN-13: 978-0824740412

3. Metabolic Engineering by Sang Yup Lee and E. Terry Papoutsakis (1999) Publisher: CRC; 1st

edition ISBN-10: 082477390X, ISBN-13: 978-0824773908

4. Advances in Microbial Biotechnology by Rajhi Gupta, Jagjit Singh, T.N. Lakhanpal, and J.P. Jewari (1999) Publisher: A.P.H. Pub. Corp. ISBN-10: 8176480789, ISBN-13: 978-8176480789

MBT-302: Industrial Microbiology-II (Environment, Biofuels, Chemicals, Biomass,

Protocols)


Objective: To expose the students to (i) the benefits of microbes/their products in cleaning the

environment (ii) large scale production of useful microbial biomass (iii) production of

biofuels and chemicals (iv) useful protocols





Unit – I (Environment)

1. Waste water and effluent treatment,

2. Biodegradation of xenobiotics, Bioremediation, Biomining

3. Biodegradable plastics

4. Bioinsecticides

5. Microbes as N and P Biofertilizers

Unit – II (Biomass)

6. Manufacture of Baker’s yeast

7. Single cell protein production especially Spirulina

8. Mushroom cultivation especially Agaricus bisporus

9. Probiotics, Prebiotics, Synbiotics

Unit – III (Biofuels & Chemicals)

10. Biofuel production especially Ethanol, Butanol, Methane, Hydrogen,

Electricity, Biodiesel

11. Organic acids especially Amino acids (glutamic acid, lysine), Citric acid, Acetic acid,

Lactic acid

12. Microbial exopolysaccharides

Unit – IV (Protocols)

13. Good Lab Practices guidelines

14. Good Manufacturing Processes guidelines

15. Guidelines for use of recombinant microbes

16. Important Biotech companies of India and the World

Practicals:



1. Estimation of BOD levels of a water sample

2. Isolation of P-solubilizers from the soil

3. Estimation of P-solubilizing activity of P-solubilizer

4. Isolation of Lactobacilli from milk/ curd

5. Production of bacteriocin by probiotics

6. Effect of temperature on the preparation of curd from milk

7. Effect of type of milk on the preparation of curd from milk

Suggested readings:

1. Food Microbiology: Fundamentals and Frontiers by Doyle (2007) Publisher: American Society

Microbiolgy; 3rd

edition ISBN-10: 1555814077 ISBN-13: 978-1555814076 2. Food Microbiology: An Introduction by Montville (2005) Publisher: American Society

Microbiolgy; 1st edition. ISBN-10: 1555813089 ISBN-13:978-1555813086

3. Environmental Microbiology: A Laboratory Manual by Ian L. Pepper and Charles P. Gerba (2004)

Publisher: Academic Press; 2nd

edition ISBN-10: 0125506562 , ISBN-13: 978-0125506564 4. Advances in Food & Nutrition Research by Steve Taylor (2003) Publisher: Academic Press; 1

st

edition ISBN-10: 0120164477, ISBN-13: 978-0120164479

5. Environmental Microbiology by Raina M. Maier, Ian L. Pepper, and Charles P. Gerba (2000) Publisher: Academic Press; 1

st edition ISBN-10: 0124975704, ISBN-13: 978-0124975705

6. Applied Dairy Microbiology, by Elmer H. Marth and James Steele (2001) Publisher: CRC; 2nd

edition ISBN-10: 082470536X, ISBN-13: 978-0824705367

MBT-303: Bioinstruments and their Applications


Objective: To expose the students to the variety of instruments used in the study of

Microbial Biotechnology.





Unit - I

1. Microscopy: Light microscope, Field Microscope, Florescent microscope, Phase contrast

microscope, AAS, AFM, SCM, TEM, and SEM, Tunnel microscope.

2. Spectrophotometer: UV and Visible

3. Mass spectroscopy, Infrared and Raman spectroscopy. CD spectroscopy, NMR, ESR.

Unit - II

4. Centrifugation: Theory and its applications to biological systems, centrifuges, rotors,

angle/swing out/vertical, buoyant density centrifugation.

5. Electrophoresis: Theory, different methods of electrophoresis for proteins and nucleic

acids.

Unit – III

6. Chromatography: GC, Paper Ch, TLC, HPLC, FPLC, GCMS, LCMS

7. Crystallography and X-Ray diffraction, Electron diffraction, Neutron diffraction.

8. Radioisotope techniques: radiotracers GM Counter, Proportional and Scintillation

counters, autoradiography, MALDI-ToF

Unit – IV 9. Protein purification workstation

10. Flow Cytometery

Practicals:



1. Operation of Microscopes: TEM, and SEM.

2. Running TLC; Rf value using TLC

3. Operation of Centrifuges (microfuge and high speed centrifuge and ultracentrifuge).

4. Operation of GC, HPLC

5. Operation of MS, LCMS, NMR.

Suggested Readings: 1. Advances in Chromatography. Eli Grushka and Nelu Grinberg (2007). Publisher: CRC: 1

st edition.

ISBN-10: 1420060252, ISBN-13: 978-1420060256, Volume 46.

2. Understanding NMR Spectroscopy. James Keeler (2005). Publisher: Wiley; 1st edition ISBN-10:

0470017872, ISBN-13: 978-0470017876.

3. Physical Principles of Electron Microscopy: An Introduction to TEM, SEM, and AEM. Ray F. Egerton (2005). Publisher: Springer; 1

st ed.. ISBN-10: 0387258000, ISBN-13: 978-0387258003.

4. Fundamentals of Light Microscopy and Electronic Imaging. Douglas B. Murphy (2001). Publisher:

Wiley-Liss; 1st edition ISBN-10: 047125391X, ISBN-13: 978-0471253914.

5. Principles and Techniques of Practical Biochemistry. Keith Wilson & John Walker(2000). Cambridge University Press.

6. Introduction to Spectroscopy. Donald L. Pavia, Gary M. Lampman, and George S. Kriz (2000).

Publisher: Brooks Cole; 3rd edition. ISBN-10: 0030319617, ISBN-13: 978-0030319617.

MBT-304: Tutorials


Objective: (i) To cover up the academic deficiencies of students (ii) To expose the students to

those parts of Microbial Biotechnology which have not been covered in the syllabus (iii) Invited

lectures from experts.

Exam Pattern: The question paper will be set from the lectures delivered in the Tutorials.

Predominantly the pattern of questions will be either MCQ or short notes.

The course will consist of lectures on current issues pertaining to Microbiology,

Biotechnology and other important topics in the field of biological sciences. The lectures

will be delivered by the students/faculty/scientists of teaching/research institutes, industrial

personals and government bodies etc.

MBT-401: Journal Club


Objective: This course will help the students to know the type of research going on various

countries. It will also help the students in preparing, delivering and defending a ‘talk’.

The Int. asses. will be made from the attendance and the interaction of the student in the Journal

Club meetings.

Students will be asked to deliver a talk on articles from reputed Journals.

MBT-402: Dissertation

Total Marks: 400

Objective: To prepare the students as how to carry out independent research work

Each student will be given an independent research project. The evaluation will be

based on the presentations, knowledge of the topic of research, quality of the compiled

Dissertation.

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