II Course Code: PMI301 T P C CIA-1 CIA-2 CIA-3 CIA-4 · CIA-3 CIA-4 Lab Theory Lab 10 10 - 50 - - 3Hrs. evolution, ecology issues theory. the concepts of environmental microbiology

Year: Second Year

Course: Evolution, Ecology and Environmental Microbiology

Teaching

Scheme

(Hrs/Week)

Continuous Internal Assessment (CIA)

L T P C CIA-1 CIA-2

4 0 - 4 10 20

Max. Time, End Semester Exam (Theory)

Prerequisite • Introduction and basic concepts

• Preliminary awareness of environmental

Objectives

1 To understand the history and development of evolutionary

2 To understand the evolutionary origin of biochemical disorders.

3 To create general understanding of ecological niche and its importance

4 To familiarize the students with

5 To describe environmental issues and apply the knowledge for developing sustainable

approach to address the challenges of field.

Unit

Number

1 History and development of evolutionary theory

Neo-Darwinism: Spontaneous mutation controversy, evolution of

mutation,

types of selection, levels of selection, group selection and selfish gene.

Sociobiology, kin selection, evolutionary stability of cooperation, sociality and

multicellularity in microorganisms , Game theory, Evolution and stability of

sex, sexual selection, parasite theory of sex and sexual selection. Co

evolutionary strategies, hostparasite co

molecular clocks, phylogeny and molecular distances, Molecular evolution:

origin of life, the origin of new genes

ageing, evolutionary trade offs, r and k selection,

2 Evolutionary origin of biochemical disorders

Speciation in sexual and asexual organisms, origin and stability of

diversity of secondary metabolites

Gut Microbiology: Gut Brain access., Fecal Microbial Transplant

3

Community ecology: community structure, benevolent interactions (control

within the microbial communities of rhizosphere), antagonistic

School of Science

M.Sc. Microbiology

Semester: I

Evolution, Ecology and Environmental Microbiology Course Code:

Internal Assessment (CIA) End Semester

Examination

2 CIA-3 CIA-4 Lab Theory Lab

10 10 - 50 -

End Semester Exam (Theory) - 3Hrs.

Introduction and basic concepts evolution, ecology

Preliminary awareness of environmental issues

To understand the history and development of evolutionary theory.

To understand the evolutionary origin of biochemical disorders.

To create general understanding of ecological niche and its importance

To familiarize the students with the concepts of environmental microbiology.

environmental issues and apply the knowledge for developing sustainable

approach to address the challenges of field.

Details

History and development of evolutionary theory

Darwinism: Spontaneous mutation controversy, evolution of




x, sexual selection, parasite theory of sex and sexual selection. Co

evolutionary strategies, hostparasite co-evolution, Neutral evolution and


origin of life, the origin of new genes and proteins. Evolution of life histories,

ageing, evolutionary trade offs, r and k selection,

Evolutionary origin of biochemical disorders: The case of insulin resistance.

Speciation in sexual and asexual organisms, origin and stability of

diversity of secondary metabolites

Gut Microbiology: Gut Brain access., Fecal Microbial Transplant

: community structure, benevolent interactions (control

within the microbial communities of rhizosphere), antagonistic interactions,

Semester: III

Course Code: PMI301

Total

100

the concepts of environmental microbiology.

environmental issues and apply the knowledge for developing sustainable

Hours

Darwinism: Spontaneous mutation controversy, evolution of rates of




x, sexual selection, parasite theory of sex and sexual selection. Co-

evolution, Neutral evolution and


and proteins. Evolution of life histories,

12

: The case of insulin resistance.

Speciation in sexual and asexual organisms, origin and stability of diversity, 12

: community structure, benevolent interactions (control

interactions,

12

(competition, antibiosis, predation etc.). Rhizosphere, rhizoplane, siderophore,

flavonide from plants, lectines, octapine, nipotine, indole acetic acid.

Mycorrhiza: Host-fungus specificity, host fungus interactions, rhizosphere

environment and recognition phenomenon, interaction of mycorrhizal fungi

with

non-host plants, functional capability.

Marine ecosystem: Environment of marine bacteria, bacterial growth in sea

and its regulation by environmental conditions, modeling of growth and

distribution of

marine micro plankton, mechanism of dissolved, organic matter production

(DOM), strategies of organic matter utilization and microbial utilization of

organic

matter in sea.

4 Wastewater Treatment

Wastewater treatment system (unit

equalization, mixing, flocculation, flotation, granular medium filtration,

adsorption.

Chemical precipitation, gas transfer, disinfection, dechlorination

Biological: (aerobic and anaerobic, suspended and attached growth

Working treatment systems and their analysis (reactions and kinetics, mass

balance analysis, reactor types, hydraulic character of reactors, selection of

reactor type,) Critical operating parameters like DO, hydraulic retention time,

mean cell residence time, F/M ratio etc. Malfunctioning of treatment systems

due to shock loading, hydraulic loading etc. and remedial measures adapted.

5 Effluent disposal, control and reuse. Water pollution control, Regulation and

limit for disposals in the la

reuse of

treated effluents and solid wastes.

Current industrial wastewater treatment and disposal processes ( Textile,

dyestuff, diary, paper and pulp manufacturing industries)

Course Outcome

Students should able to

CO1 Student will be able to demonstrate an understanding

CO2 Student will be able to demonstrate the basic

CO3 Student will be able to demonstrate the basic idea and applications

CO4 Student will be able to

issues

CO5 Student will be able to

solving approach.


flavonide from plants, lectines, octapine, nipotine, indole acetic acid.

fungus specificity, host fungus interactions, rhizosphere

nd recognition phenomenon, interaction of mycorrhizal fungi

host plants, functional capability.

: Environment of marine bacteria, bacterial growth in sea




Wastewater Treatment:

Wastewater treatment system (unit process): Physical screening, flow


Chemical precipitation, gas transfer, disinfection, dechlorination

Biological: (aerobic and anaerobic, suspended and attached growth processes.)




residence time, F/M ratio etc. Malfunctioning of treatment systems


Effluent disposal, control and reuse. Water pollution control, Regulation and

limit for disposals in the lakes, rivers, oceans, and land. Direct and indirect

treated effluents and solid wastes.


dyestuff, diary, paper and pulp manufacturing industries)

Student will be able to demonstrate an understanding of evolution of life on earth.

Student will be able to demonstrate the basic understanding of ecological system.

Student will be able to demonstrate the basic idea and applications of ecosystem

Student will be able to develop a sense of understanding to deal with

Student will be able to use the knowlegde of techniques and develop the problem


fungus specificity, host fungus interactions, rhizosphere

nd recognition phenomenon, interaction of mycorrhizal fungi

: Environment of marine bacteria, bacterial growth in sea




process): Physical screening, flow


processes.)




residence time, F/M ratio etc. Malfunctioning of treatment systems


12

Effluent disposal, control and reuse. Water pollution control, Regulation and

kes, rivers, oceans, and land. Direct and indirect


12

Total 60

evolution of life on earth.

ecological system.

of ecosystem

to deal with environmental

develop the problem-

Resources

Recommended

Books

1. Strickberger M. W. (2000).

2. Macan, T. T. (1974).

3. Richards, B.N. (1987).

Scientific & Technical, New York.

Reference Books

1. Ridley Mark (2004). Evolution. Blackwell Science Ltd.

2. Meadows, P. S. and J. I. Campbell. (1978). An introduction to Marine

Science. Blackie & Son Ltd., Glasgow.

3. Tchobanoglous G. and F. L. Burton. (1991). Wastewater Engineering,

Treatment, Disposal and Reuse. 3rd Ed., Metcalf and Eddy (Eds). Tata

Mac Graw Hill Publishing

1. Strickberger M. W. (2000). Evolution. Jones & Bartelette Publications.

2. Macan, T. T. (1974). Freshwater Ecology. Longman Group Ltd., London,.

3. Richards, B.N. (1987). Microbiology of Terrestrial Ecosystems

Scientific & Technical, New York.

Ridley Mark (2004). Evolution. Blackwell Science Ltd.

Meadows, P. S. and J. I. Campbell. (1978). An introduction to Marine

Science. Blackie & Son Ltd., Glasgow.

Tchobanoglous G. and F. L. Burton. (1991). Wastewater Engineering,


c Graw Hill Publishing Co. Ltd. New Delhi.

. Jones & Bartelette Publications.

. Longman Group Ltd., London,.

Terrestrial Ecosystems. Longman

Meadows, P. S. and J. I. Campbell. (1978). An introduction to Marine

Tchobanoglous G. and F. L. Burton. (1991). Wastewater Engineering,


Year: Second Year

Course: Microbial technology and Genetic E

Teaching

Scheme

(Hrs/Week)


L T P C CIA-1 CIA-2

4 0 - 4 10 20


Prerequisite • Introduction and basic concepts

Objectives

1 To impart the knowledge of microbial technology

2 To familiarize the students with

products of biological origin

3 To introduce the concepts of genetic engineering and its application

4 To apply the knowledge for mitigation of various social

5 To develop research driven approach for better understanding of

biological processes

Unit

Number

1

Bioreactor design and

a. Designing of bioreactors

dimensional ratios of

aspects such as working

b. The configuration (placement)

and the different types

and propellers, and the

c. Immobilized cell reactors

d. Batch, Fed�batch and

Applications, advantages

2

Process Variables and

a. Process Variables:

i.Aeration � Theory of

kinetics (Oxygen Uptake

determination of KLa.

ii.Agitation � Functions

different types of impellers.

iii.Fermentation broth

Concept of Newtonian

School of Science

M.Sc. Microbiology

Semester: I

Microbial technology and Genetic Engineering Course Code:

Continuous Internal Assessment (CIA) End Semester

Examination

2 CIA-3 CIA- 4 Lab Theory Lab

10 10 - 50 -


Introduction and basic concepts microbial applications in industry

impart the knowledge of microbial technology

To familiarize the students with the fundamental processes of fermentation for production of

products of biological origin

introduce the concepts of genetic engineering and its application

for mitigation of various social issues

develop research driven approach for better understanding of

Details

and operation :

bioreactors � Design aspects CSTRs: The

of the outer shell, and the operational

working volume, baffles and impellers.

(placement) of impellers in a vessel

types of impellers (types of turbines

their combinations)

reactors and air�lift reactors – Design and operation.

and Continuous operation:

advantages and limitations of each type.

and Monitoring:

of oxygen transfer in bubble aeration, Oxygen transfer

Uptake Rate –OUR; Oxygen Transfer Rate OTR; Ccrit),

KLa.

Functions of agitation. Flow patterns with

impellers.

broth rheology and power requirements for agitation

Newtonian and nonNewtonian fluids, effect of broth rheology

Semester: III

Course Code: PMI302

Total

100

s in industry

the fundamental processes of fermentation for production of

develop research driven approach for better understanding of the applications of

Hours

operation.

12 L

transfer

Ccrit),

itation –

rheology on

12 L

heat, nutrient and oxygen

Aeration number: working

b. Monitoring of process

Use of various types of

monitoring environme

O2), Basic principles

3

Microbial Processes:

for the following: iv.

Microbial enzymes (Chitinase).

Use of immobilized cells

Microbial Growth cha

a.Concept of primary

associated) metabolites

b.Kinetics of growth and

efficiency etc.)

c.Effect of type of growth

pellet form, mycelial

exopolysaccharides) affects

also cell proliferation

cells. At least one example

s in any suitable fermentation

4

Use of fungi in industry

i. Biofertilizers, Bioremediation

ii. Food industry, biosensors

Animal cell culture technology

a. Recombinant forms

b. Recombinant vaccines(protein

c. Recombinant enzymes(lipase,

d. Monoclonal antibodies

e. Nucleic acid�based

5

Genetic Engineering

Recombinant DNA technology:

Proteomics, DNA fingerprinting, Modern techniques: Use of RFLP, AFLP,

RAPD and Satellites in mapping of genes

Gene technology: Gene

genome libraries, cDNA

screening • Site directed

•Cloning and manipulating

• Gene transfer to host

•Genetically modified

plants and animals.

Applications of recombinant

Concept and meaning

oxygen transfer, Reynold’s number, Power number,

working out examples using different softwares

process variables:

of sensors and biosensors for

environmental parameters (pressure, pH, temperature, DO

of operation, types of biosensors

: Upstream, Fermentation and Downstream Processing

Antibiotics (Rifamycin)

(Chitinase). iii. Exopolysaccharides (Pullulan)

cells / enzymes to produce protease

characteristics and product formation

(growth associated) and secondary (growth non

metabolites and their control,

and product formation (growth rate, yield coefficient,

growth on fermentation: The type of growth (mycelia

mycelial filamentous form, free cell, cells producing

affects mass transfer of nutrients, oxygen and heat;

proliferation can be affected by shearing of

example of each type may be explained to show these

fermentation.

industry like agriculture and environmental applications:

Bioremediation and Biological control.

biosensors and fuel cells

technology to produce:

forms of natural proteins (insulin, erythropoietin),

vaccines(protein: HIV, hepatitis B and DNA: HIV,

enzymes(lipase, restriction endonuclease),

antibodies

based products (introduction to gene therapy)

Genetic Engineering

Recombinant DNA technology: Basic and applied aspects, Genomics and


RAPD and Satellites in mapping of genes

Gene cloning strategies: preparation of gene,

cDNA libraries, PCR cloning and alternatives. Library

directed mutagenesis and protein engineering,

pulating large fragments of DNA; YAC, BAC, HAC

host cells. •Expression vectors

modified animals and plant , applications of these transgenic

recombinant DNA technology

ng of genome projects and their applications.

number,

DO and DC

rocessing.

ii.

iv.

non�

coefficient,

(mycelia

heat; as

these effect

12 L

applications:

HIV, malaria),

12 L

Basic and applied aspects, Genomics and


Library

HAC

transgenic

12 L

Total 60

Course Outcome


CO1 Student will be able to describe fundamentals of biological processes.

CO2 Student will be able to explain the fermentation process

CO3 Student will be able to understand the design and types of bioreactor

CO4 Student will be able to apply the knowledge to for production and recovery of bio

products

CO5 Student will be able to understand principles and applications of genetic

engineering

Resources

Recommended

Books

1. Bioreactor

Butterworths

2. Doran Pauline

Press.

3. Lydersen

Engineering:

Sons Inc.

4. Ratledge

Ed. Cambridge

ples and

5. James D.

Michael

Gene, 5th

Publishing,

6. Lewin’s

7. Malom Campbell

Proteomics

8. S.B Primrose

9. Walker J.M.,

Biotechnology,

Reference

Books

10. Molecular

Press, U.K.

11. Lydersen

Bioprocess

Wiley and

12. Operational

Butterworths

13. Shuichi

14. Stanbury

Student will be able to describe fundamentals of biological processes.

Student will be able to explain the fermentation process

Student will be able to understand the design and types of bioreactor

to apply the knowledge to for production and recovery of bio

Student will be able to understand principles and applications of genetic

Bioreactor Design and Product Yield (1992), BIOTOL series,

Butterworths Heinemann.

Pauline (1995) Bioprocess Engineering Principles,

Lydersen B., N. a. D’ Elia and K. M. Nelson (Eds.) (1993)

Engineering: Systems, Equipment and Facilities, John Wiley

Inc.

Ratledge C and Kristiansen B eds. (2001) Basic Biotechnology

Cambridge Univ. Press. Cambridge B. R. Glick, J.J.

applications of recombinant DNA, 3rd Ed., ASM

D. Watson, Tania Baker, Stephen P. Bell, Alexander

Levine, Richard Loswick (2004) Molecular Biology

5th Edition, Pearson Education, Inc. and Dorling

Publishing, Inc.

Genes XI, (2014) Jones and Bartelett Publishers

Campbell and L. J. Heyer, Discovering genomics,

Proteomics and Bioinformatics, 2nd Ed., Pearson Publication,

Primrose and R M Twyman 2006 7th edition. Blackwell

J.M., Rapley R. (eds.) Molecular Biology and

Biotechnology, 4thEd., 2009, Royal Society Press, U.K.

Molecular Biology and Biotechnology, 4th Ed., 2009, Royal

U.K.

Lydersen B., N. a. D’ Elia and K. M. Nelson (Eds.) (1993),

Bioprocess Engineering: Systems, Equipment and Facilities,

and Sons Inc.

Operational Modes of Bioreactors, (1992) BIOTOL series,

Butterworths Heinemann.

Shuichi and Aiba. Biochemical Engineering. Academic

Stanbury and Whittaker. Fermentation technology

Student will be able to describe fundamentals of biological processes.

Student will be able to understand the design and types of bioreactor

to apply the knowledge to for production and recovery of bio-

Student will be able to understand principles and applications of genetic

series,

Principles, Academic

(1993) Bioprocess

Wiley and

Biotechnology 2nd

J.J. Pasterneck, Princi

ASM press.

Alexander Gann,

Biology of the

Kindersley

Publishers Inc.

genomics,

Publication, 2009.

Blackwell publishing

U.K.

Royal Society

(1993),

Facilities, John

series,

Press. 1982

Year: Second Year

Course: Immunology

Teaching

Scheme

(Hrs/Week)


L T P C CIA-1 CIA-2

4 0 - 4 10 20


Prerequisite • Introduction

Objectives

1 To familiarize the student with the basics of immune system and its role in disease

outcome

2 To understand the cellular and molecular basis of immune responsiveness.

3 To describe the function of the immune system in both maintaining health and

contributing to disease.

4 To understand immunological response, its activation and regulation

5 To develop research oriented approach by transferring the knowledge of immunology

into applications.

Unit

Number

1

Introduction Overview of Immune system:

History and scope of Immunology,

Types of immunity,

Hematopoiesis

Cells and organs of the immune system: primary and secondary lymphoid

organs: structure and function.

2

Generation of B cell and T cell responses

Antigens: structure and properties, factors affecting the immunogenicity,

properties of B and T-

Antibody: structure, properties, types and function of antibodies, antigenic

determinants on immunoglobulin; isotypes, allotypes, and idiotypes, molecular

mechanism of antibody diversity and class switching.

Organization and expression of immunoglobulin genes

Cell mediated immunity and its mechanism

School of Science

M.Sc. Microbiology

Semester: I

Course Code:


Examination

2 CIA-3 CIA-4 Lab Theory Lab

10 10 - 50 -


Introduction to basic concepts and terms of immunology

To familiarize the student with the basics of immune system and its role in disease

understand the cellular and molecular basis of immune responsiveness.

To describe the function of the immune system in both maintaining health and

contributing to disease.

To understand immunological response, its activation and regulation

develop research oriented approach by transferring the knowledge of immunology

Details

Overview of Immune system:

History and scope of Immunology,

of the immune system: primary and secondary lymphoid

organs: structure and function.

Generation of B cell and T cell responses Antigens: structure and properties, factors affecting the immunogenicity,

- cell epitopes, haptens, mitogens, super antigen, adjuvants



mechanism of antibody diversity and class switching.

nization and expression of immunoglobulin genes

Cell mediated immunity and its mechanism

Semester: III

Course Code: PMI303

Total

100

to basic concepts and terms of immunology.

To familiarize the student with the basics of immune system and its role in disease

understand the cellular and molecular basis of immune responsiveness.

To describe the function of the immune system in both maintaining health and

To understand immunological response, its activation and regulation

develop research oriented approach by transferring the knowledge of immunology

Hours

of the immune system: primary and secondary lymphoid

12 L

Antigens: structure and properties, factors affecting the immunogenicity,

haptens, mitogens, super antigen, adjuvants



12 L

Course Outcome


CO1 Student will be able to understand the concepts of immunology

CO2 Student will be able to understand cellular and molecular mechanism involved in

immune response

CO3 Student will be able to describe the roles of immunity for defeating diseases.

CO4 Student will be able to demonstrate a capacity for problem

responsiveness.

CO5 Student will be able to apply this scientific knowledge of the field for developing

applications

3

Immune Effector Mechanisms

Major histocompatibility complex: organization of MHC genes, types and

function of MHC molecules, antigen presentation,

Complement system: components, activation pathways, regulation of activation

pathways and role of complement system in immune response.

Cytokines: types, structure and functions, cytokines receptors, cytokine

regulation of immune receptors.

Immune response to infectious diseases: viral infection, bacterial infection,

protozoan diseases, helminthes related diseases.

4

The Immune System in Health and Disease

Hypersensitivity: type I, II, III and types IV hypersensitivity.

Immunodeficiency diseases: primary and secondary immunodeficiency.

Autoimmunity: organ specific autoimmune diseases, mechanism of

autoimmune diseases and therapeutic approaches.

Transplantation immunology: immunologic basis of graft rejection, clinical

manifestation of graft rejection and clinical transplantation.

Cancer immunology: tumor antigen, immune response to tumor, oncogene and

induction, cancer immunotherapy.

5

Applications of Immunology:

Antigen- antibody interaction: avidity and affinity measurements, detection of

antigen- antibody interaction by precipitation, agglutination, RIA, and ELISA,

Western Blotting, Immunofluorenscence, Flow cytometry.

Vaccines: Active and passive immunization, vaccine schedule, whole organism

vaccine, subunit vaccine, vaccine, DNA vaccine, recombinant vaccine, subunit

vaccines

Hybridoma technology: murine monoclonal antibody production, principle of

selection, characterization and app

research.

Antibody engineering: Chimeric and Humanized monoclonal antibodies.

Student will be able to understand the concepts of immunology

Student will be able to understand cellular and molecular mechanism involved in

Student will be able to describe the roles of immunity for defeating diseases.

Student will be able to demonstrate a capacity for problem-solving about immune

Student will be able to apply this scientific knowledge of the field for developing

Immune Effector Mechanisms Major histocompatibility complex: organization of MHC genes, types and

function of MHC molecules, antigen presentation,


pathways and role of complement system in immune response.


regulation of immune receptors.

se to infectious diseases: viral infection, bacterial infection,

protozoan diseases, helminthes related diseases.

The Immune System in Health and Disease Hypersensitivity: type I, II, III and types IV hypersensitivity.



autoimmune diseases and therapeutic approaches.

tion immunology: immunologic basis of graft rejection, clinical

manifestation of graft rejection and clinical transplantation.


induction, cancer immunotherapy.

Applications of Immunology:

antibody interaction: avidity and affinity measurements, detection of

antibody interaction by precipitation, agglutination, RIA, and ELISA,

Western Blotting, Immunofluorenscence, Flow cytometry.

e and passive immunization, vaccine schedule, whole organism



selection, characterization and applications in diagnosis, therapy and basis


Student will be able to understand cellular and molecular mechanism involved in

Student will be able to describe the roles of immunity for defeating diseases.

about immune

Student will be able to apply this scientific knowledge of the field for developing

Major histocompatibility complex: organization of MHC genes, types and



se to infectious diseases: viral infection, bacterial infection,

12 L

Hypersensitivity: type I, II, III and types IV hypersensitivity.



tion immunology: immunologic basis of graft rejection, clinical


12 L

antibody interaction: avidity and affinity measurements, detection of

antibody interaction by precipitation, agglutination, RIA, and ELISA,

e and passive immunization, vaccine schedule, whole organism



lications in diagnosis, therapy and basis


12 L

Total 60

Resources

Recommended

Books

• Jacquelyn G. Black (2013) Microbiology: Principles and

Explorations, 6th Edition, John

• Microbial Diversity: Form and Function in Prokaryotes,

Published Online: 30 NOV 2007.

DOI: 10.1002/9780470750490.ch1

• Ridley Mark (2004). Evolution. Blackwell Science Ltd.

• Breed and Buchanan. Bergey’s Manual of Determinative

Bacteriology. 8

• Breed and Buchanan. Bergey’s Manual of Determinative

Bacteriology. 9

• Breed and Buchanan. Bergey’s Manual of Systematic

Bacteriology. 2

Reference

Books

• Sykes, G. and F. A. Skinner (Eds). Actinomycetales:

Characteristics and Practical Importance. Society for Applied

Bacteriology Symposium Series No. 2, Academic Press. 1973.

• Jacquelyn G. Black (2013) Microbiology: Principles and

Explorations, 6th Edition,

• Lodder J. (1974). The Yeasts: A Taxonomic Study, North

Holland Publishing Co. Amsterdam.

Jacquelyn G. Black (2013) Microbiology: Principles and

Explorations, 6th Edition, John Wiley & Sons, Inc.,

Microbial Diversity: Form and Function in Prokaryotes,

Published Online: 30 NOV 2007.

DOI: 10.1002/9780470750490.ch1

Ridley Mark (2004). Evolution. Blackwell Science Ltd.

Breed and Buchanan. Bergey’s Manual of Determinative

Bacteriology. 8th Edition, 1974.

Breed and Buchanan. Bergey’s Manual of Determinative

Bacteriology. 9th Edition, 1982.

Breed and Buchanan. Bergey’s Manual of Systematic

Bacteriology. 2nd Edition, (Volumes. 1 – 5) (2001 – 2003).

Sykes, G. and F. A. Skinner (Eds). Actinomycetales:



Jacquelyn G. Black (2013) Microbiology: Principles and

Explorations, 6th Edition, John Wiley & Sons, Inc.,

Lodder J. (1974). The Yeasts: A Taxonomic Study, North

Holland Publishing Co. Amsterdam.



Year: Second Year

Course: Bioinformatics and Structural Biology

Teaching

Scheme

(Hrs/Week)


L T P C CIA-1 CIA-2

4 0 - 4 10 20


Prerequisite To understand the genomics and proteomics data for the disease diagnosis and

drug development

Objectives

1 To study the development and scope of bioinformatics

2 To study the various biological databases and its importance

3 To study the basis of proteomics

4 To study the genomics and phylogenetics analysis

5 To study the basic concepts of molecular modeling

Unit

Number

1 Introduction to Bioinformatics

History, development, scope, importance and application of Bioinformatics,

introduction of computer, internet and related programs for

e.g. WWW, HTML, HTTP, telnet, ftp etc., Internet resources of biological

data; Pubmed, Entrez, NCBI, NLM, NIH, EMBnet, Genomnet, DBGet,

EMBL, database retrieval. Concept of database, various types of biological

databases.

2 Biological sequence and structure databases

sequencing, cDNA libraries, submission of sequence to databases, sequence

formats, protein primary, composite, secondary sequence databases.

sequence databases

European molecular Biology laboratory (EMBL), DNA Databank of Japan

(DDBJ), GenBank, websites for protein sequence databases.

databases: Three-dimensional structure prediction, X

EM techniques, protein folding classe

Protein Data bank (PDB), Nucleic Acid Data Bank (NDB), Molecular

School of Science

M.Sc. Microbiology

Semester: I

and Structural Biology Course Code:


Examination


10 10 - 50 -


To understand the genomics and proteomics data for the disease diagnosis and

drug development

To study the development and scope of bioinformatics

To study the various biological databases and its importance

To study the basis of proteomics

To study the genomics and phylogenetics analysis

To study the basic concepts of molecular modeling

Details

Introduction to Bioinformatics:


introduction of computer, internet and related programs for file/data sharing




Biological sequence and structure databases: Protein and DNA


formats, protein primary, composite, secondary sequence databases.

sequence databases: Human genome project, Microbiome genome,


(DDBJ), GenBank, websites for protein sequence databases. Structural

dimensional structure prediction, X-ray, NMR and Cryo

EM techniques, protein folding classes, structure classification databases,


Semester: III

Course Code: PMI304

Total

100

To understand the genomics and proteomics data for the disease diagnosis and

Hours


file/data sharing




12 L

Protein and DNA


formats, protein primary, composite, secondary sequence databases. DNA

me genome,


Structural

ray, NMR and Cryo-

s, structure classification databases,


12 L

modeling Data Bank (MMDB).

3 Proteomics study: Protein sequence and structure information,

physicochemical properties of protein based on sequence, secondary

structure analysis, sequence comparison, pair

alignment, gaps, gap

structure prediction from sequence, Homology modeling; 3D protein

structure prediction from sequence, validation of protein model,

Ramachandran plot, significance of 3

using internet tools, protein folding classes.

4 Genomics study: Goals of the Human Genome Project, structural and

functional aspects of DNA and RNA, Central dogma, recombinant DNA

technology, next generation sequencing (NGS), designing primer for DNA

sequencing, Genome Mapping, Genome information

Nucleotide sequence analysis, Expressed sequence tag, DNA Microarray and

analysis, Gene identification: masking repetitive DNA, DNA database

search, codon-bias detection, identification of functional sites in the DNA.

Internet resources for gene identification.

elements of phylogeny, methods of phylogenetic analysis, phylogenetic tree

of life, phylogenetic analysis online tools.

5 Molecular Modeling

ordinate system; bond distance, bond angle, torsion angle, Van der Waals

and electrostatic interactions, Introduction of quantum mechanics, force

field, energy calculations, energy minimization and geometry optimization,

conformational search, Molecular

docking analysis, Computer aided drug design, ligand and structure based

approach. Introduction to molecular dynamics simulation, theory and

applications of MD simulations.

Course Outcome


CO1 Understand the history and development of Bioinformatics

CO2 Understand the use of biological databases and its use

CO3 Understand the proteomics data and how to analyze

CO4 Analyze the genomics data

CO5 Understand the basis of molecular modeling and molecular dynamics simulations

Resources

modeling Data Bank (MMDB).

: Protein sequence and structure information,


structure analysis, sequence comparison, pair-wise and multiple sequence

alignment, gaps, gap-penalties, scoring matrices, ClustalW. Secondary



Ramachandran plot, significance of 310

helix and loops, proteomics analysis

using internet tools, protein folding classes.

Goals of the Human Genome Project, structural and



sequencing, Genome Mapping, Genome information and special features,



bias detection, identification of functional sites in the DNA.

es for gene identification. Phylogenetic analysis: Evolution,


of life, phylogenetic analysis online tools.

Molecular Modeling: Introduction of molecular modeling approach, c




conformational search, Molecular docking and virtual screening, post



applications of MD simulations.

he history and development of Bioinformatics

Understand the use of biological databases and its use

Understand the proteomics data and how to analyze

Analyze the genomics data

Understand the basis of molecular modeling and molecular dynamics simulations

: Protein sequence and structure information,


wise and multiple sequence

penalties, scoring matrices, ClustalW. Secondary



helix and loops, proteomics analysis

12 L

Goals of the Human Genome Project, structural and



and special features,



bias detection, identification of functional sites in the DNA.

: Evolution,


12 L

: Introduction of molecular modeling approach, co-




docking and virtual screening, post



12 L

Total 60

Understand the basis of molecular modeling and molecular dynamics simulations

Recommended

Books

1. Introduction to computational Biology by C. Stan Tsai

2. Essential Bioinformatics by Jin xiong

3. Introduction to Bioinformatics by Attwood and Parry

Reference Books

1.Molecular modeling of proteins by Andreas Kukol, Humana press

2.Introduction to computational biochemistry, by C.

WILEY & SONS, Inc., Publication.

3.Bioinformatics,

4.Introduction to Bioinformatics, Teresa K Attwood and David J Parry

smith.

5.Essential Bioinformatics, Jin Xiong, Cambridge University press.

6.Molecular modeling of proteins by Andreas Kukol, Humana press.

Introduction to computational Biology by C. Stan Tsai

Essential Bioinformatics by Jin xiong

Introduction to Bioinformatics by Attwood and Parry-Smith

Molecular modeling of proteins by Andreas Kukol, Humana press

Introduction to computational biochemistry, by C. Stan Tsai, A John

WILEY & SONS, Inc., Publication.

Bioinformatics, Sequence and Genome analysis by David Mount.

Introduction to Bioinformatics, Teresa K Attwood and David J Parry

Essential Bioinformatics, Jin Xiong, Cambridge University press.

Molecular modeling of proteins by Andreas Kukol, Humana press.

Smith

Molecular modeling of proteins by Andreas Kukol, Humana press

Stan Tsai, A John

Sequence and Genome analysis by David Mount.

Introduction to Bioinformatics, Teresa K Attwood and David J Parry-

Essential Bioinformatics, Jin Xiong, Cambridge University press.

Molecular modeling of proteins by Andreas Kukol, Humana press.

Year: Second Year

Course: Evolution, Ecology and Environmental Microbiology

Microbial technology and genetic engineering Laboratory

Teaching

Scheme

(Hrs/Week)


L T P C CIA-1 CIA-2

0 0 4 2 - -


Objectives

1 To acquire proficiency in

2 To impart the knowledge of fermentation techniques for production and recovery of bio

products

3 To train the students in genetic engineering techniques.

Sr.

No.

1 Water and soil sampling

2 Microbial population (Direct and indirect

3 Isolation of free-living and symbiotic N2

4 Isolation and enumeration of phosphate solubilising

degraders or pesticide degraders 5 Physico-chemical analysis of water

Chemical oxygen demand, Biological oxygen demand6 Determination of potability of water following MPN methods

and confirmatory tests of 7 Collection and identification of important bacterial/fungal strains of industrial importance

8 Media optimization for large scale production (effect of medium composition on any one

of the products 9 Antibiotic production, its recovery and

10 Alcoholic fermentation 11 Citric acid production in batch culture.12 Transformation and conjugation of bacteria13 PCR technique 14 Southern blotting

School of Science

M.Sc. Microbiology

Semester: I

Evolution, Ecology and Environmental Microbiology And

Microbial technology and genetic engineering Laboratory Course Code:


Examination


- - 50 - 50


To acquire proficiency in the field of ecology and environmental microbiology

To impart the knowledge of fermentation techniques for production and recovery of bio

To train the students in genetic engineering techniques.

Description

sampling

Microbial population (Direct and indirect methods)

living and symbiotic N2-fixing bacteria

Isolation and enumeration of phosphate solubilising /cellulose decomposing

degraders or pesticide degraders bacteria from different habitats (plate count method).

chemical analysis of water -pH, total and dissolved solids, Dissolved oxygen,

Chemical oxygen demand, Biological oxygen demand.

Determination of potability of water following MPN methods-MPN index, presumptive

and confirmatory tests of coliforms.

Collection and identification of important bacterial/fungal strains of industrial importance

Media optimization for large scale production (effect of medium composition on any one

Antibiotic production, its recovery and its purification

Citric acid production in batch culture.

Transformation and conjugation of bacteria

Semester: III

Course Code: PMI311

Total

100

the field of ecology and environmental microbiology

To impart the knowledge of fermentation techniques for production and recovery of bio

cellulose decomposing/ chitinase

bacteria from different habitats (plate count method).

pH, total and dissolved solids, Dissolved oxygen,

MPN index, presumptive

Collection and identification of important bacterial/fungal strains of industrial importance

Media optimization for large scale production (effect of medium composition on any one

Term Work:

Term Work assessment shall be conducted for the Project, Tutorials and Seminar. Term work is

continuous assessment based on

journal/record book, oral/viva, respectively

institute. At the end of the semester, the final grade for a Term Work shall be assigned based on

the performance of the student and is to be submitted to the University.

Notes

1 The regular attendance of

monitored and marks will be given accordingly (10

2 Good Laboratory Practices (

3 Timely Completion (10 Marks)

4 Journal / Record Book (10 Marks)

5 Oral / Viva (10 Marks)

Practical/Oral/Presentation:

Practical/Oral/Presentation shall be conducted and assessed jointly by at least a pair of examiners

appointed as internal and external

mark/grade sheet in the format as specified by the University, authenticate and seal it. Sealed

envelope shall be submitted to the head of the department or authorized person.

Notes

1 One experiment from the regular

2 Oral/Viva-voce (10 Marks).


continuous assessment based on attendance, good laboratory practice (GPL), timely completion,

journal/record book, oral/viva, respectively. It should be assessed by course



The regular attendance of the students during semester for practical course will be

rks will be given accordingly (10 Marks).

Good Laboratory Practices (10 Marks)

Timely Completion (10 Marks)

Journal / Record Book (10 Marks)


internal and external examiners by the University. The examiners will prepare the



One experiment from the regular practical syllabus will be conducted (40 Marks).


attendance, good laboratory practice (GPL), timely completion,

course teacher of the


practical course will be


The examiners will prepare the


practical syllabus will be conducted (40 Marks).

Year: Second Year

Course: Immunology and Bioinformatics and Structural Biology

Laboratory

Teaching

Scheme

(Hrs/Week)


L T P C CIA-1 CIA-

2

0 0 4 2 - -


Objectives

1 To train the students in immunological techniques

2 Queering and analyzing the proteomics and genomics data, and its use in the finding the cause

of disease and in the drug development

Sr. No.

1 Determination of phagocytic index2 ABO blood grouping3 Immuno-diffusion method

4 Immunoelectrophoresis technique5 Serological test- Widal test for titre determination6 ELISA for detection of antigen and antibodies.7 Introduction to scientific literature database at National Centre for Biotechnology

Information (NCBI) and querying the PUBMED literature database.

8 Getting the primary sequences of protein or DNA from protein database and

querying the protein/DNA sequence database. 9 Introduction of Basic local alignment search tool (BLAST).

10 Pairwise and multiple protein sequence analysis using the Clustal Omega. 11 Introduction of RCSB and querying, and analyzing the primary, secondary tertiary

and quaternary structure of protein using PyMol.

12 Three dimensional protein structure

technique. 13 Molecular docking of protein and ligand using AutoDock4.2 software. 14 Molecular dynamics simulation using GROMACS/AMBER.

School of Science

M.Sc. Microbiology

Semester: I

Immunology and Bioinformatics and Structural Biology Course Code:


Examination

CIA-

3

CIA-

4 Lab Theory Lab

- - 50 - 50


To train the students in immunological techniques

Queering and analyzing the proteomics and genomics data, and its use in the finding the cause

of disease and in the drug development

Description

Determination of phagocytic index

ABO blood grouping

diffusion method (Ouchterlony method)

Immunoelectrophoresis technique

Widal test for titre determination

ELISA for detection of antigen and antibodies./ dot ELISA

Introduction to scientific literature database at National Centre for Biotechnology


Getting the primary sequences of protein or DNA from protein database and

querying the protein/DNA sequence database.

Introduction of Basic local alignment search tool (BLAST).

Pairwise and multiple protein sequence analysis using the Clustal Omega.

Introduction of RCSB and querying, and analyzing the primary, secondary tertiary

and quaternary structure of protein using PyMol.

Three dimensional protein structure prediction using homology modeling

Molecular docking of protein and ligand using AutoDock4.2 software.

Molecular dynamics simulation using GROMACS/AMBER.

Semester: III

Course Code: PMI312

Total

100

Queering and analyzing the proteomics and genomics data, and its use in the finding the cause

Introduction to scientific literature database at National Centre for Biotechnology


Getting the primary sequences of protein or DNA from protein database and

Pairwise and multiple protein sequence analysis using the Clustal Omega.

Introduction of RCSB and querying, and analyzing the primary, secondary tertiary

prediction using homology modeling

Molecular docking of protein and ligand using AutoDock4.2 software.

Term Work:


continuous assessment based on Attendance, G

Completion, Journal/Record book and Oral. It



Notes

1 The regular attendance of the

and marks will be given accordingly (10

2 Good Laboratory Practices (

3 Timely Completion (10 Marks)

4 Journal / Record Book (10 Marks)

5 Oral / Viva (10 Marks)

Practical/Oral/Presentation:


appointed as internal and external

mark/grade sheet in the format as specified by the University


Notes

1 One experiment from the regular practical syllabus will be conducted (40 Marks).

2 Oral/Viva-voce (10 Marks).


based on Attendance, Good Laboratory Practice

Completion, Journal/Record book and Oral. It should be assessed by subject teache



the students during semester for practical course will be monitored

rks will be given accordingly (10 Marks).

Good Laboratory Practices (10 Marks)

Timely Completion (10 Marks)

Journal / Record Book (10 Marks)


internal and external examiners by the University. The examiners will prepare the





(GLP), Timely

should be assessed by subject teacher of the


practical course will be monitored


The examiners will prepare the

, authenticate and seal it. Sealed


Documents

II Course Code: PMI301 T P C CIA-1 CIA-2 CIA-3 CIA-4 · CIA-3 CIA-4 Lab Theory Lab 10 10 - 50 - - 3Hrs. evolution, ecology issues theory. the concepts of environmental microbiology