M.Sc - Microbiology - Alagappa University

M.Sc., Microbiology

234

ALAGAPPA UNIVERSITY KARAIKUDI

SYLLABUS UNDER CBCS (w.e.f.2011
-
12)


M.Sc., MICROBIOLOGY
–

PROGRAMME STRUCTURE


Sem

Course

Cr.

Hrs./

Week

Marks

Total

Subject
Code


Name

Int.

Ext.



I




1MMI1C1

Core
–

I
–

de湥ra氠䵩cr潢楯o潧y

4

6

25

75

100

1MMI1C2

Core
–

II
–

B楯捨i浩獴sy

4

6

25

75

100

1MMI1C3

Core
–

III
–

䵩捲潢楡氠ohy獩潬ogy

4

6

25

75

100

1MMI1P1

Core
–

IV
–

ia戠b潵牳e⁩渠䝥湥ra氠


Microbiology & Microbial Physiology

4

4

40

60

100

1MMI1P2

Core
–

V
–

ia戠b潵牳e⁩渠
B楯捨i浩獴sy


4

4

40

60

100

1MMI1E1/
1MMI1E2

Elective
–

I

–

c潯搠a湤n䑩ary
䵩捲潢楯o潧y
 爩⁍ 物湥
䵩捲潢楯o潧y

4

4

25

75

100



Total

24

30

--

--

600

II

1MMI2C1

Core
–

VI
–

䵯汥c畬慲 B楯i潧y a湤n
䵩捲潢楡氠䝥湥瑩cs

4

6

25

75

100

1MMI2C2

Core
–

VII
–

䕮癩牯湭b湴n
氠l
䅧A楣畬瑵牡氠䵩c牯扩潬r杹

4

6

25

75

100

1MMI2P1

Core
–

VIII
–

ia戠c潵牳e⁩渠
䵯汥M畬慲⁢楯 ogy⁡湤n䵩捲潢楡氠
䝥湥瑩cs

4

6

40

60

100

1MMI2P2

Core
–

IX
–

ia戠b潵牳e⁩渠
䕮癩牯湭b湴慬n⁁杲楣畬瑵牡氠
䵩捲潢楯o潧y

4

4

40

60

100

1MMI2E1/
1MMI2E2

Elective
–

II
–

fmoⰠI楯ia晥ty⁡湤n
B楯整桩捳
潲⤠䍯浰畴e爠䅰灬楣A瑩潮o
C⁂楯
-
f湦n牭r瑩cs

4

4

25

75

100

1MMI2E3/
1MM12E4

Elective
–

III
–

B楯
-
乡n潴散桮潬潧y
⡯(⤠B楯獴a瑩獴scs

4

4

25

75

100



Total

24

30

--

--

600

III

1MMI3C1

Core
–

X
–

f浭畮潬ugy

3

5

25

75

100

1MMI3C2

Core
–

XI
–

䵥摩ca氠䵩c牯扩潬潧y

3

5

25

75

100

1MMI3C3

Core
–

XII
–

oec潭扩湡湴⁄乁
呥c桮潬hgy

3

4

25

75

100

1MMI3P1

Core
–

XIII
–

ia戠c潵牳e⁩渠
f浭畮潬ugy…⁍e摩捡氠
䵩捲潢楯o潧y

3

4

40

60

100

1MMI3P2

Core
–

XIV
–

ia戠b潵牳r⁩渠牄乁
呥c桮潬
潧o

4

4

40

60

100

1MMI3E1/
1MMI3E2

Elective
–

IV
–

䵯汥M畬a爠rax潮潭y
a湤⁐hy汯geny ⡯(⤠B楯晥牴楬rze爠r湤n
B楯ia湵牥⁔ec桮潬hgy

4

4

25

75

100

M.Sc., Microbiology

235

1MMI3E3/
1MMI3E4

Elective
–

V
–

Disease Diagnosis
Technology (or) Entrepreneurship in
Microbiology

4

4

25

75

1
00



Total

24

30

--

--

700

IV

1MMI4C1

Core
–

XV
–

Industrial Microbiology

4

6

25

75

100

1MMI4P1

Core
–

XVI
–

Lab course in
Industrial Microbiology

4

6

40

60

100

1MMI4PR

Core
–

XVII
–

Project Work

10

18

25

75

100


Total

18

30

--

--

300


Grand Tota
l

90

120

--

--

2200


M.Sc., Microbiology

236

I YEAR
–

I SEMESTER

COURSE CODE: 1MMI1C1


CORE
COURSE
I
–

GENERAL MICROBIOLOGY


U
nit

I

History, Classification of microorganisms:

Ha
eckel’s three
–
kingdom concept, Whittaker’s
Five
-
kingdom concept, Three
-
domain concept of Carl Woese.

Classification of V
irus and
Fungi, Classification of Bacteria according to Bergey’s Manual.


U
nit

II

Microscopy:

Simple, Compound, Dark
-
field, Phase contrast, Fluorescent and Electron
microscopes. (SEM & TEM), Confocal microscopy
–

Principles and their app
lications. Stains
and Staining techniques: Simple, Differential and Structural staining methods.


U
nit

III

Sterilization and Disinfection, Culture methods:

Auxenic and synchronous, aerobic and
anaerobic, Culture media and Nutritional types, Growth curve, G
eneration time and growth
kinetics. Factors influencing microbial growth. Preservation methods and Quality control.


U
nit

IV

Microbial Anatomy:
-

Prokaryotic cell structure & Organization, Cell membrane, Plasma
membrane, Cytoplasmic matrix, Inclusion bodies
, Ribosome, Nucleiod, Prokaryotic cell wall,
Capsule, Slime layers, S layers, Pili and Fimbriae, Flagella & Motility. Bacterial endospores.
Archaeal cell structures, Viruses, Properties of Viruses,
RNA & DNA Virus
, Virions &
Prions. Eukaryotic cell structu
re and its organelles.

Lichens and Microalgae:
-

Structural
organization and their properties.


U
nit

V

Modern Microbiology:

Molecular Taxonomy, 16S/18S rRNAs and its importance in
identification of microorganisms. Phylogenetic tree, Molecular tools in asse
ssing microbial
diversity, Metagenomics, Prebiotics and probiotics and their appl
ications, Microbial fuel cells


References

1.

Tortora, G.J., Funke B.R, and Case C.L. (2009).
Microbiology an Introduction
,
Benjamin Cummins, USA.

2.

Dubey, R.C. and Maheswari, D.K
. (2005).
A Textbook of Microbiology
, S.Chand
and Company Ltd., New Delhi.

3.

Prescott, L.M., Harley, J.P. and Klein, D.A. (2002).
Microbiology
, McGraw Hill
Publishers, Boston.

4.

Brock, T.D., Smith, D.W. and Madigam, M.T. (2002).
Biology of Microorganisms

(Four
th Edition) Prentice Hall International, London.

5.

Stanier, R.Y., Ingraham, J.L., Wheels, M.L. and Painter, P.R. (1999).
General
Microbiology
, Mac Millan Educational Limited, London.

6.

Boyd, R.F. (1998).
General Microbiology
, Mosby College Publishing, St. Lou
is.

7.

Nester, E.W., Roberts, C.V. and Nester, M.T. (1995).
Microbiology
, A Human
Perspective. IWOA, U.S.A.

8.

Pelzcar, M.J., Chan, E.C.S. and Kreig, N.R. (1993).
Microbiology
, McGraw Hill Inc.,
New Delhi.

M.Sc., Microbiology

237


I YEAR
–

I SEMESTER

COURSE CODE:

1MMI1C2


CORE
COURSE

I
I

–

BIOCHEMISTRY

U
nit

I

Biochemistry:
-

Structure and properties of water. Buffering in biological systems.
Biomolecules:
-

Amino acids, Proteins, Carbohydrates, Lipids and Nucleic acids
–

structure
and its biological role. Vitamins and Hormones: Chemistry
and Physiological role.


U
nit

II

Structure and diversity of biological membranes:
-

Mechanisms of membrane transport
(simple diffusion, facilitated transport, active and secondary active transport). Mitochondrial
and Microsomal electron transport chain

and
Oxidative phosphorylation.


U
nit

III

Thermodynamic quantities and laws:
-

A
pplications of free energy functions; ATP as the
main carrier of free energy in biological systems; biological oxidation
-
reduction reactions.


U
nit

IV

Metabolism and its regulation:
-

Carbohydrate metabolism
–

Glycolysis, Gluconeogenesis,
Pentose phosphate pathway, TCA cycle; Lipid metabolism
–

oxidation of fatty acid (

,


and


oxidation), biosynthesis of fatty acid, TG, PL and cholesterol; amino acid and nucleotide
metabolism (de no
vo and salvage pathway).


U
nit

V

Enzyme nomenclature and IUB classification. Catalytic power and specificity of enzymes.
Enzyme kinetics, general properties of enzymes and coenzymes. Enzyme regulation
(Allosteric and covalent modification). Clinical and in
dustrial applications of enzymes.
Immobilization of enzymes and its application. Enzyme engineering, abzyme and Ribozyme.


References

1.

Donald Voet and Judith G.Voet, (2004),
Biochemistry
, John Wiley and Sons, USA.

2.

Jeremy M.Berg, John L.Tymoczke and Lubert S
tryer, (2002),
Biochemistry
,
W.H.Freeman and Company, USA.

3.

Nelson D.L,M.M.Cox, (2000),
Lehninger Principles of Biochemistry
, Macmillan
worth Publishers.

4.

Geoffrey A.F, J.Beckett, S.H.Halker and P.H.Rae, (2004), Lecture Notes on Clinical
Biochemisry, Blackwe
ll Science, UK.

5.

Mallikarjuna Rao M., (2002), Medical Biochemistry, New Age International (P) Ltd
Publishers, India.

6.

Voet, D. J., Voet J.G and Pratt C. W. (2008).
Fundamental of Biochemistry
:
Life at
molecular level
, Wiley publishers, USA

7.

Berg, J.M., Tomocz
ko J.L. and. Stryer L. (2008).
Biochemistry
, W. H. Freeman
publisher, USA.

8.

Lehninger, A., Nelson, D. L. and. Cox, M.M. (2008).
Lehninger Principles of
Biochemistry
, W.H. Freeman, USA.


♣♣♣♣♣♣♣♣♣♣

M.Sc., Microbiology

238

I YEAR
–

I SEMESTER

COURSE CODE:

1MMI1C3


CORE
COURSE

I
II

–

MICROBIAL PHYSIOLOGY


U
nit

I


Basic aspects of bioenergetics:
-

E
ntropy, enthalpy, electron carriers, artificial electron
donors, inhibitors, uncouplers, energy bond, phosphorylation.


U
nit

II


Brief account on photosynthetic and accessory pigments:
–

C
hloro
phyll,
bacteriochlorophyll, rhodopsin, carotenoids, phycobiliproteins. Oxygenic and anoxygenic
photosynthesis, autotrophic generation of ATP. Fixation of CO
2
. Calvin cycle: C3 and C4
pathway.


U
nit

III


Respiratory metabolism, oxidative and substrate leve
l phosphorylation, Pasteur effect;
fermentation of carbohydrates: homo and heterolactic fermentations.


U
nit

IV


Microbial differentiation, Sporulation:
-

Endo and Exospores, Endospore formation in
Bacillus

sp. Exospore formation in
Streptomyces
: Sporulatio
n in fungi:
Aspergillus

sp.,
Penicillium

sp. Formation of specialized structures: akinetes, cyst and heterocyst.


U
nit

V


Extremophils:
-

Survival at extreme environments
–

starvation, adaptive mechanisms in
thermophilic, alkanophilic, osmophilic and psychr
ophilic organisms. Chemotaxis,
Bioluminescence: Mechanisms, advantages. Quorum sensing
–

Cell signaling
–

mechanism
and applications.


References


1.

Caldwell D.R., (1995),
Microbial Physiology and Metabolism
, Wm.C.Brown
Publishers, USA.

2.

Gottychalk G.,
Bacter
ial Metabolism
, (Latest edition) Springer
–

Verlag, Bertin.

3.

Moat A.G, J.W.Foster,
Microbial Physiology
, (Latest edition) John Wiley & Sons,
New York.

4.

Prescott, L.M., Harley, J.P. and Klein, D.A. (2002).
Microbiology
, McGraw Hill
Publishers, Boston.

5.

Salle,
A.J. (1999).
Fundamentals of Bacteriology
, Hill Publishing Company Limited,
New Delhi.


♣♣♣♣♣♣♣♣♣♣


M.Sc., Microbiology

239

I YEAR
–

I SEMESTER

COURSE CODE:

1MMI1P1


CORE
COURSE

I
V

–

LAB

COURSE

IN

GENERAL

MICROBIOLOGY

&


MICROBIAL

PHYSIOLOGY



1.

Lab safety method and Regulations.

2.

P
rinciples and methods of sterilization.

3.

Preparation of media : Nutrient broth, Nutrient agar, slants, soft agar

4.

Pure culture technique
–

Pour plate, Spread plate & Streak plate.

5.

Measurement of microbes

–

Micrometry.

6.

Motility determination

–

Hanging drop m
ethod.

7.

Enumeration of bacterial /

yeast cells

–

Viable count, Total count.

8.

Enumeration of bacteria / fungi from environmental samples
–

Direct and Indirect
methods (Haemocytometer & Total viable counts).

9.

Staining methods: Simple, Negative, Acid fast, Gram

staining, Spore, Flagella,
Capsule and Metachromatic granular staining. Staining of fungus
–

Lacto phenol
cotton blue staining.

10.

Measurement of growth
–

Direct count, Viable count
–

Growth curve, Determination
of growth rate and generation time.

11.

Effect of
pH, Temperature and Salinity on bacterial growth.

12.

Anaerobic Cultivation
–

RCM, T
h
ioglycolate broth and Anaerobic jar methods


References


1.

Cappuccino J.G, N.Sherman, (2002),
Microbiology: A Laboratory Manual,

Addison
–

Wesley.

2.

Atlas R.M, A.E.Brown and L.C.Pa
rks, (1995),
Laboratory Manual of Experimental
Microbiology,

Mosby, St.Louis.

3.

Kannan K., (2002),
Laboratory Manual in General Microbiology
, Panima
Publishers.

4.

Holt J.G, N.r.Krieg, (2000),
Bergey’s Manual of Determinative Bacteriology
, Ninth
edition Lippinc
ott Williams & Wilkin Publishers.

5.

Aneja K.R., (2002),
Experiments in Microbiology, Plant pathology, Tissue culture
and Mushroom Production technology
, Third edition.
New age international
Publishers.




♣♣♣♣♣♣♣♣♣♣










M.Sc., Microbiology

240

I YEAR
–

I SEMESTER

COURSE CODE:

1MMI1P2


CORE
COURSE

V

–

LAB COURSE IN BIOCHEMISTRY



1.

Colorimeter and its applications:
-

Verification of Beer
-
Lambert’s law using colored
solution CuSo
4
. Estimation of Carbohydrate (Phenol
-
sulphuric acid

method), Protein
(Lowry’s method), nucleic acid
–

DNA (Diphenylamine method) and RNA (Orcinol
method).

2.

pH meter and preparation of buffers (Phosphate and acetate buffer).

3.

Acid base titration:
–

pKa value determination
–

Determination of [H
+
] ion
concentrat
ion.

4.

Separation and identification of sugars and amino acids by paper and thin layer
chromatography.

5.

Enzymes:
-

Production of amylase, purification of the enzyme (Ammonium sulphate
precipitation, Dialysis and g
el permeation chromatography), D
etermination of

Km and
Vmax, molecular weight determination by using SDS
-
PAGE.


References


1.

Rodney and Royer, (2004),
Modern Experimental Biochemistry
, Pearson education,
India.

2.

Jayaraman J., (1996),
Laboratory Manual in biochemistry
, fifth edition, New Age
International

Publisher, New Delhi.

3.

Sawhney S.K., R.Singh, (2001),
Introductory Practical Biochemistry
, Narosa
Publishing House, New Delhi.

4.

Wilson K, J.Walker, (2000),
Principles and Techniques of Practical Biochemistry
,
Cambridge University Press.

5.

Sadasivam S, A.Manic
kam, (1997),
Biochemical Methods
, New Eye International
Pvt Ltd, India.

6.

Palanivelu P., (2000),
Laboratory Manual for Analytical Biochemistry and
separation techniques
,
Madural Kamaraj University.

7.

Plemmner D.T., (1997),
An Introduction to Practical Biochemi
stry
, TATA
McGraw Hill Publications co. Ltd, New Delhi.


♣♣♣♣♣♣♣♣♣♣





M.Sc., Microbiology

241

I YEAR
–

I SEMESTER

COURSE CODE:

1MMI1E1


ELECTIVE COURSE
I (A)
–

FOOD & DAIRY MICROBIOLOGY



U
nit

I


Food as substrate for microorganisms:
-

Importance of microorganisms in food
microbiology

–

molds, yeasts and bacteria
–

general characteri
stics
–

classification and
importance. Factors influencing microbial growth in food
–

Extrinsic and intrinsic factors.


U
nit
II


Principles of food preservation.
Asepsis:
-

Removal of microorganisms, Anaerobic conditions,
Preservation by Heat processing
–

H
igh temperature, Thermal
death of microorganisms: D
and Z

Values, Low temperature
–

Chilling and Freezing, Drying, Food additives, Chemicals
(Orga
nic acids and esters, Nitrite, Sulfur dioxide, Benzoic acid, P
arabens, Probionates, natural
preservatives, etc

Canning, and by Radiation (Microwave, UV, Ionizing radiation). (anaerobic
conditions, high temperatures, low temperatures, drying).


U
nit

III


Contamination and spoilage:
-

Cereals, sugar products, vegetables, fruits, meat and meat
products, milk and milk
products
–

Fish and sea foods
–

poultry
–

spoilage of canned food.
Detection of spoilage and characterization.


U
nit

IV


Food born infection and intoxication:
-

Bacterial and nonbacterial
–

with examples of
infective and toxin types
–

Brucella, Bacillus, C
lostridium, Escherichia, Salmonella,

Shigella,
Staphylococus, Vibrio, Yersinia
; Nematodes, Protozoa, Algae, Fungi and Viruses. Food born
outbreaks laboratory testing procedures; Prevention measures
–

Food sanitation in
manufacture and retail trade; Food co
ntrol agencies and its regulations, Plant sanitation
–

employees health standards
–

Waste treatment
–

disposal
–

quality control.


U
nit

V


Food fermentation:
-

Bread, Cheese, V
inegar, fermented vegetables, fermented dairy
products, experimental and industri
al production methods. Spoilage and defects

of fermented
dairy products
–

O
riental fermented foods, their quality standards and control. Genetically
modified foods.


References


1.

Adams, M.R. and Moss M.O., (1995),
Food Microbiology
, Royal Society
Publicatio
ns, Cambridge.

2.

Frazier, WC and Westhoff Dc, (1998),
Food Microbiology
, Tata McGraw Hill
Publishing Company Limited, New Delhi.

M.Sc., Microbiology

242

3.

Principles of Fermentation Technology (1995) by Stanbury, PF., Whitekar, A and
Hall, S.J., Pergamon Press.

4.

Banwart, GJ, (1989),
B
asic Food Microbiology
, CBS Publishers and Distributors,
Delhi.

5.

Hobbs BC and Roberts D, (1993),
Food Poisoning and Food Hygiene
, Edward
Arnold (A Division of Hodder and Stoughton) London.

6.

Robinson, RK, (1990),
Dairy Microbiology
, Elsevier Applied Sciences,

London.

7.

James M.Jay, (2003), Modern Food Microbiology, CBS publishers & Distributors,
New Delhi.


♣♣♣♣♣♣♣♣♣♣




M.Sc., Microbiology

243

I YEAR
–

I SEMESTER

COURSE CODE:

1MMI1E2


ELECTIVE COURSE
I (B)
–

MARINE MICROBIOLOGY



U
nit
I


Classification of microbes:
-

C
onventional and modern methods. Typical structure of
bacteria, fungi, algae, protozoa and viruses.
Marine microorga
nisms:
-

collection,
preservation, enumeration (total

and viable counts), isolation of
culture and identification
based on

morphological, physiological and biochemical characteristics. Interna
tional and
national collection c
entres.



U
nit
II


Extremophiles:
-

Thermopiles, basophiles, halophiles, psychrophiles, acid

–

alkalinophiles,
oligotroph, toxitolerant, xerotolerant, endolith
–

Extremophiles and thei
r environment,
biodiversity.
Genomics of extremophiles, phylogeny of extremophiles, 16
S
RNA
classification

in mitochondrial DNA genome, RAPD, RFLP studies, cloning of commercially
important extremozymes, comparative genome organisation of extremophiles and mesophiles
.


U
nit
III


Microbiology of degradation of xenobiotic environment:
-

E
cological considerations,

decay
behaviour, degradative plasmids, hydrocarbons, oil pollution, surfactants, pesticides,
B
ioremediation:
-

Factors affecting bioremediation
–

role of microbes in the marine nutrient
cycles
–

diseases of marine organisms and its impact on marine biodive
rsity.


U
nit

IV


Brief account of photosynthetic and accessory pigments:
-

C
hlorophyll
–

bacteria
l

chlorophyll
–

carotenoids
–

rhodopsin, phycobilliprotein, carbohydrates, anabolism

–

autotrophy

–

photosynthesis

–

autotrophic generation of ATP, fixation of
CO
2

–

Calvin cycle
–

C
3

and C
4

pathway. Respiratory metabolism

–

Embden Meyerhoff pathway

–

Enter Doudroff
pathway

–

Glycoxylate pathway, Kreb’s cycle

–

Oxidative and substrate level of
phosphorylation

–

Reverse TCA cycle.


U
nit

V

Molecular nature of mutati
on, mutagens.
Gene transfer mechanism:
-

Transformation,
Transduction, Conjugation, and T
ransfection.
Plasmids:
-

F factor, description and their use in
genetic analysis

–

plasmid as a vector for gene cloning

–

rep
lication of selected plasmids,
T
ransposon an
d their use in genetic analysis.
DNA sequencing methods:
-

dideoxy and
chemical methods, sequence analysis, automates sequencing.
Bar coding of marine
organisms:
-

Genome sequencing and physical mapping of genome.





M.Sc., Microbiology

244

R
eferences


1.

Dube, H.C., (1994).
A text
book of fungi, bacteria and viruses.

Vikas Publishing
House, New Delhi.

2.

Dale,

J.W. (1994).
Molecular genetics of Bacteria
.. John Wiley and Stones.

3.

Pelczar, M. JR. E.C.s. and Chan and Noel, R. K. (2006).
Microbiology
. Tata McGraw,
Hill. Co. fifth Edition, N
ew Delhi.

4.

Presscott, L.N., Harley, J.P. and Klein, D.A. (1999).
Microbiology
. W.C. Brown
Publishers.

5.

Stanier, R.Y., Ingharam J.L. Wheelis, M.L. Painter, P.R. (1986).
General Waste water
engineering Treatment, Disposal and Reuse
. Metcaff and Eddy. Inc., Tat
a Mc Grew
Hill, New Delhi.




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M.Sc., Microbiology

245

I YEAR
–

II SEMESTER

COURSE CODE: 1MMI2C1


CORE VI
–

MOLECULAR BIOLOGY AND MICROBIAL GENETICS


U
nit

I

Identification of DNA as genetic material:

(Griffith, Avery and MacLeod, Hershey and
Chase experiments). Gene
tic nomenclature, Mutants and Mutations
–

Types of mutants,
Isolation and characterization of mutants, Revertants and Reversion; Genetic analysis of
mutants.


U
nit

II

Mutations and mutagenesis:

Spontaneous mutations, Mutagenesis by Base analog mutants,
Che
mical mutagens (nitrous acid, hydroxylamine, alkylating agent), mutagenesis by
intercalating agents and UV.

DNA damage and repair:

DNA damage by UV, alkylating
agents, cross linkers. Mechanism of repair

–

photoreactivation, excision repair,
recombinational

repair. The SOS and adaptive responses and their regulation.


U
nit

III

Transformation:

C
ompetent cells
–

regulation, general process,

Transduction:

generalized
and specialized transduction,

Conjugation:

Hfr and triparental mating.
Transposable genetic
ele
ments
:

Introduction, discovery, Insertion sequences. Compound transposons and Complex
transposons
–

Tn10, Tn5, Tn3 and retrotransposons.


U
nit

IV

Bacterial DNA replication. Biology of bacteriophage

. Lytic growth of phage


and phage
production, recombina
tion in the


life cycle.


U
nit

V

Transcription, Translation, Post
-
translational modifications.
Regulation of gene expression:

The Operon concept
–

(
i
) lac and (ii)

trp; stringent response.


References

1.

Maloy S.R, J.E.Cronan, and D.Friefelder, (1994),
Mirco
bial Genetics
, Jones and
Bartlett Publishers, Sudbury, Massachusetts.

2.

Malacinski G.M, D.Friefelder, (1998),
Essentials of Molecular Biology
, Jones &
Bartlett Publishers.

3.

Hunter, L. E. (2009).
The Process of Life
-

An Introduction to Molecular Biology
,
The M
IT press, USA

4.

Lee, C.H. (2009).
Applied Molecular Biology
, Kompass books, USA.

5.

Weaver, R.F. (2008).
Molecular biology
, McGraw Hill higher education, USA.

6.

Alberts, B., Johnson, A., Lewis J., Raff, M., Roberts, K, and.Walter, P. (2007).
Molecular Biology of
the Cell,

Garland publishing Inc, New York.

7.

Allison, L. A. (2007).
Fundamental Molecular Biology,

Wiley
-

Blackwell, London.

8.

Karp, G. (2007).
Cell and Molecular Biology
-

Concepts and Experiments,

John
Wiley and Sons, Inc. New York.

9.

Watson, J.D., Hopkins, N.
H., Roberts, J.W., Steitz, J.A., Weiner, A.M. (1998).
Molecular Biology of the Gene
, fourth Edition, Benjamin/ Cummings Publishing
Company.

M.Sc., Microbiology

246

I YEAR
–

II SEMESTER

COURSE CODE: 1MMI2C2


CORE VII

–

ENVIRONMENTAL AND AGRICULTURAL
MICROBIOLOGY


U
nit

I


Ecosystem
:

Ecological hierarchy

–

Ecological succession of microorganism

–

Homeostasis

–

Adaptive mechanism among microorganisms

–

interaction between microbes, plants and
animals.

Microbes in marine and fresh water environment
–

Eutrophication

–

food chain water
borne
pathogens

–

indicator organism

–

Microbiology of Domestic water

–

Microbial water
Quality
–

water purifications, Aeromicrobiology


U
nit

II


Waste water (sewage and industrial effluents) treatments:

Primary, Secondary (Trickling
Filter, Activated Sludg
e) and Tertiary treatments. Anaerobic treatment of industrial effluents:
Hydrolysis, Fermentation and Methonogenesis. Conventional methods of waste water
treatment (Aerobic and Facultative ponds, AMS, Thin film technique and Sand filter).
Advanced emerging

and B
iotechnological treatments of industrial effluents (Biotower, RBC,
Fluidized bed Reactors and Column Reactor).


U
nit

III


Biodegradation and bioremediation

–

Solid waste management:

Landfills, Composting
and Earthworm treatment. Recycling and proces
sing of organic residues, Biodegradation of
Xenobiotic compounds. Organisms involved in degradation of chlorinated hydrocarbons,
substituted simple aromatic compounds, polyaromatic hydrocarbons, pesticides and
surfactants. Microbial treatment of oil pollut
ion.


U
nit

IV


Environment of soil microorganism:

Role of microorganisms in the formation of soil

–

Role of microbes in soil fertility. Biogeochemical cycles

–

Carbon, Nitrogen, Phosphorous
and Sulphur cycles. Biological nitrogen fixation
–

diazoprophs
–

f
ree living, aerobic,
symbiotic bacteria and cyanobacteria. Microbial interactions, interaction of microbes with
plants and insects.


U
nit

V


Plant diseases:

symptoms, disease cycle and control measures
–

Bacterial diseases, Blight of
rice, Citrus canker an
d wilt of potato. Viral diseases, Vein clearing disease, Tungro disease of
rice, TMV and CMV. Fugal diseases
,

rust of wheat, smut of sugarcane, wilt of cotton, tikka
leaf spot in groundnut.
Biofertilizers:

M
icrobes used as biofertilizers, Mass multiplicati
on,
field application and crop response.
Biopesticides:

bacterial, fungal and viral
. Recent
advances in biological pest control.


M.Sc., Microbiology

247

References


1.

Alan Scragg, (1999),
Environmental Microbiology,

Longman.

2.

Gareth M.E
vans & Judith C.Furlong
John, (2003),
Environm
ental Biotechnology
–

Theory& Application
, wiley & Sons Ltd.

3.

Subba Rao, N.S., (1995).
Soil Microorganisms and plant growth
. Oxford & IBH
Publishing Co., Pvt. Ltd., New Delhi.

4.

Rangasami G. and D.J.Bagyarai (1993).
Agricultural Microbiology
. Second Edition,
Prentice
-
Hall of India Private Limited, New Delhi.



♣♣♣♣♣♣♣♣♣♣



M.Sc., Microbiology

248

I YEAR
–

II SEMESTER

COURSE CODE: 1MMI2P1


CORE COURSE VIII
–

LAB COURSE IN MICROBIAL GENETICS &
MOLECULAR BIOLOGY



1.

Single colony isolation and checking for genetic markers.

2.

Measurement of growth
-
one step growth curve using a T even phage.

3.

T
itration of phages (T4).

4.

Induction of Lambda Phage

5.

Induced mutagenesis UV.

6.

Isolation of antibiotic resistant mutants

7.

Isolation of auxotrophic mutants.

8.

Isolation of specialized transducing phage.

9.

Bacterial conjugation
–

transfer of drug resistant factor (Pl
asmid).

10.

Transposon mutagenesis of chromosomal and plasmid DNA.


References


1.

Miller, J.H. (1972).
Experiments in Molecular Genetics.


Cold Spring Harbor
Laboratory, Cold Spring Harbor, New York, 466 pp.

2.

Murray, R.G.F., wood, W.A. and Krieg, N.B, (1994).
Met
hods for General and
Molecular Bacteriology.


Washington, DC:

American society for microbiology.


3.

Freifelder D. 1987.
Microbial Genetics
. Boston: Jones and Bartlett Publishers.





♣♣♣♣♣♣♣♣♣♣




















M.Sc., Microbiology

249

I YEAR
–

II SEMESTER

COURSE CODE: 1MMI2P2


C
ORE IX
–

LAB COURSEIN ENVIRONMENTAL & AGRICULTURAL
MICROBIOLOGY


a)

Environmental Microbiology


1.

Bacterial examination of water (qualitative and quantitative).

2.

Membrane filtration technique.

3.

Enumeration of microorganism from air.

4.

Settle plate technique.

5.

Air sa
mpling technique.

6.

Isolation of bacteria and bacteriophages from sewage.

7.

Estimation of dissolved oxygen (DO), BOD and COD.


b)

Agricultural Microbiology


1.

Isolation of free
–

living nitrogen fixing bacteria from soil
–

Azotobacter.

2.

Isolation of Symbiotic nitrog
en fixing bacteria from root nodule
–

Rhizobium.

3.

Isolation of phosphate solubilizers, ammonifiers and denitrifers.

4.

Study of Mycorrhizae, Cyanobacteria and Azolla.

5.

Examination of Plant diseases:


Bacterial diseases

Fungal diseases



V
iral diseases


Blight o
f rice

Blast of ric
e


Banana

bunchy

top

virus

Citrus canker Smut o
f sugarcane


W
heat yellow mosaic virus

Wilt of potato Wilt of co
tton


Tobacco dwar
f of wheat




Redro
t of sugarcane


yellow Dwarf of wheat




Tikka leaf sp
ot of groundnut


Citrus variegation virus






Rice dwarf virus

References


1.

Cappuccino J.G, N.Sherman, (2002),
Microbiology: A Laboratory Manual
,
Addison
-
Wesley.

2.

Atlas R.M, A.E.Brown and Parks, Mosby, St. Louis, (1995),
Laboratory Manual of
Experimental Microbiology

3.

Kannan N.,
(2002),
Laboratory Manual in General Microbiology
, Panima
Publishers.

4.

Holt J.G,, N.R.Krieg, (2000),
Bergey’s Manual of Determinative Bacteriology.
Ninth Edition Lippincott Williams & Wilkin Publishers.

5.

Aneja K,R., (2002),
Experiments in Microbiology, Plant

pathology, Tissue culture
and Mushroom Production technology,

Third Edition.



♣♣♣♣♣♣♣♣♣♣

M.Sc., Microbiology

250

I YEAR
–

II SEMESTER

COURSE CODE: 1MMI2
E1


ELECTIVE COURSE II (A)
–

IPR, BIOSAFETY AND BIOETHICS


Unit I


Introduction. Important Definitions.
Establishment and functions of General Agreement on
Trade and Tariff (GATT) and World Trade Organizat
ions. WTO Summits. IBSC and RCGM.


U
nit
II


Trade Related Aspects of Intellectual Property Rights. Different types of intellectual property
rights
–

Patents, Trademark, Trade secret Copy right. Important microbiological examples of
patents, trademark, and

trade secret


U
nit
III


Rules governing patents. Case studies on patents (Super bug, Basmati rice, Turmeric, Neem,
etc.). Indian Patent Act, 1970 and its amendments.


U
nit
IV


Biosafety

–

Introduction. Different levels of biosafety. Guidelines for recom
binant DNA
research activities in microorganisms. Good Laboratory Practices (GLP). Containments

–

Types. Basic Laboratory and Maximum Containment Laboratory microbiology research.


U
nit
V


Bioethics

–

Introduction. General issues related to environmenta
l release of genetically
modified microorganisms. Ethical issues related to research in embryonic stem cell cloning.


References


1.

Recombinant DNA safety guidelines

(January1990), Department of Biotechnology,
Ministry of Science & Technology, Government
of India, New Delhi.

2.

Revised guidelines for research in Transgenic plants

(August 1998), Department of
Biotechnology, Ministry of Science & Technology, Government of India, New Delhi.

3.

Subbaram N., (2003),
Patents
, Pharma Book Syndicate, Hyderabad.

4.

Glick
, B.R., and Pasternack, (1998),
Molecular Biotechnology
, Second Edition, J.J.,
ASM Press, Washington, DC.

5.

Chawla H.S., (2001),
Introduction to Plant Biotechnology
, Oxford & IBH
Publishing Co. Pvt. Ltd.



♣♣♣♣♣♣♣♣♣♣



M.Sc., Microbiology

251

I YEAR
–

II SEMESTER

COURSE CODE: 1MMI2
E2


ELECTIVE COURSE II (B
)
–

COMPUTER APPLICATIONS &
BIOINFORMATICS


U
nit

I

Computer architecture:

Input and output devices
–

Memory devices
–

Types of modern
computing
–

Number Systems
–

Programming conc
epts
–

Introduction to Operating systems
like Windows, UNIX & LINUX
–

Computer Viruses
–

Overview and prevention.


U
nit

II

Computer Networks:

Topologies, Hardware and Network security
–

Internet basics
–

Protocols and Services
–

Database systems
–

Basic co
ncepts
–

Indexing and Hashing
–

Multimedia and Text databases


U
nit

III

An overview of bioinformatics tools:

Global Vs local alignment
–

Similarity searching
–

Principle and Algorithms
–

Pair wise alignment and Multiple alignment
–

Biological
Databases
–

Literature, Sequence and Structure
–

Finding and retrieving information from
databases.


U
nit

IV

Protein structure prediction:

S
econdary and tertiary and motifs
–

Proteomic tools at
ExPASy server
–

Protein structure comparison and classification
–

RNA str
ucture analysis
–

Plasmid mapping and Primer designing using programs from public domain
–

Structure
visualization softwares
–

Phylogenetics
–

Tree types and construction methods.


U
nit
V

DNA sequencing
–

DNA microarray
–

basic principles and databases
–

G
enomics and
Proteomics
–

Prediction of genes, promoters, splices sites and regulatory regions
–

Drug
designing and Commercial Bioinformatics.


References


1.

David W. Mount, (2001),
Bioinformatics. Sequence and Genome Analysis,

Cold
Spring Harbor Laboratory P
ress.

2.

Higginns
D and W. Taylor, (2000),
Bioinformatics. Sequence, Structure and
databanks
–

A Practical Approach
, Oxford University Press.

3.

Baxevanis A.D and B.F. Francis Ouellette, (2001),
Bioinformatics
–

A Practical
Guide to the Analysis of Genes and Pro
teins
, Wiley
–

Interscience.

4.

G. Gibson and S.V. Muse, (2002), A Primer of Genome Science, Sinauer Associates,
Inc. Publishers.

5.

S. Misener and S.A. Krawetz, (2000),
Methods in Molecular Biology
–

Bioinformatics. Methods and Protocols
, Humana Press.

6.

Attwood
T.K and D.J. Parry
-
Smith, (2001),
Introduction to Bioinformatics
, Pearson
Education Asia.

7.

Claverie J.M, C. Notredame, (2003),
Bioinformatics for Dummies,

wiley Publishing,
Inc

M.Sc., Microbiology

252

I YEAR
–

II SEMESTER

COURSE CODE: 1MMI2
E3


ELECTIVE COURSE II
I

(
A
)
–

BIONANOTE
CHNOLOGY


Unit I

Biotechnology to Bionanotechnology:

Bionanomachines
–

Modern bionano materials
–

protein, nucleic acid, lipids used for carrying information
–

polysaccharides use in special
structural roles
–

Present status of bionanotechnology.


Unit II

Molecular design for nanotechnology:

Recombinant DNA technology
–

X
-
ray
crystallography, NMR spectroscopy and electron microscopy, use in nanotechnology
–

Computer modeling to bionanomachines and computer assisted molecular design.


Unit III

Structural pri
nciples of Bionanotechnology:

Natural bionanotechnology design for specific
environment
–

Biomolecular structure as low materials
–

Hierarchical strategy in construction
of nanomachines
–

protein folding
–

self organization
–

molecular recognition
–

flexib
ility.


Unit IV

Functional principles of Bionanotechnology:

Information driven nano assembly
–

chemical
transformation
–

biomolecular sensing
–

self application
–

machine phase bionanotechnology.


U
nit
V


Future of Bionanotechnology
:

Problems in bionanotec
hnology
–

Abide finger problem
–

Sticky finger problem
–

role of enzyme to solve these problems
–

Core studies
–

nomotuble
synthesis, nanoscale assembler, nanozurveillance
–

ethical consideration
–

respect for life,
potential dangers, fuel


R
eference
s




D
avid S. Goosell, (2004),
Bionanotechnology
, Lessons from nature, John Wiley &
Sons Inc. publication.



David S. Goodsell, (1996),
Biomolecules and Nanotechnology
, Ancient Scientist, 88,
230
–

237.



Blundell T. L. and Johnson L. N, (1976),
Protein crystallogr
aphy
, New York.



Eisenberg. D & D. Crothers (1979),
Physical Chemistry with Applications to the
Life Sciences.

Benjamin Cummings, Menlo Park, California.



Ausubel, F. M., Breut R. Kingston R. E., Moore, D. D., Siedman, J. G., Smith, J. A.
and Struhl K, (1999
), Short protocols in Molecular Biology
, Fourth Edition. Wiley,
New York.




♣♣♣♣♣♣♣♣♣♣




M.Sc., Microbiology

253

I YEAR
–

II SEMESTER

COURSE CODE: 1MMI2
E4


ELECTIVE COURSE II
I

(
B
)
–

BIOSTATISTICS


U
nit
I

Introduction

to biostatistics. Numerical Summary Measures

–

Me
asures of Central Tendency
–

Mean, Median, Mode. Measures of Dispersion

–

Range, Interquar
tile Range, Variance and
Standard Deviation Coefficient of Variation. Grouped Data

–

Grouped Mean, Grouped
Variance. Chebychev's Inequality.


Unit
II

Data Presentation
–

Types of Numerical Data. Tables
–

Frequency Distributions, Relative
Frequency. Graph
s

–

Bar Charts, Histograms, Frequency Polygons, One
-
Way Scatter Plots,
Box Plots, Two
-
Way Scatter Plots, Line Graphs.


Unit
III

Confidence interval

–

The Standard Deviation, The Gaussian Distribution, The Confidence
Interval of a Mean,
Survival
Curves
.
Comparing groups with confidence intervals
–

Confidence Interval of a Difference between means, Confidence Interval for the Difference or
Ratio of Two Proportions.


U
nit
IV

Introduction to p values

–

What is a P value? Statistical significance and hypothesis testing,

Multiple comparisons
.

Probability,
Bayesian logic

–

Bayes' theorem in genetics. Population
genetics, gene pool, allele freque
ncy, genotype frequencies, Hardy
-
Weinberg equation,
implications of Hardy
-
Weinberg equation. Diagnostic Tests
–

Sensitivity and Specificity,
ROC Curves, calculations of prevalence.


U
nit
V

Simple correlation
–

correlation coefficient.
Regression
–

simpl
e linear regression. Basic idea
of significance test
–

hypothesis testing, level of significance.


References


1.

Jeffrey A. Witmer Myra L., (2002),
Statistics for the Life Sciences
, Third Edition,
Prentice Hall.

2.

Marcello Pagano


Kimberlee Gauvreau
, (2000),
Principles o
f Biostatistics, Second
Edition,
Brooks Cole.

3.

Stanton A. Glantz
,

(2001),
Primer of Biostatistics,
McGraw
-
Hill

4.

Bernard Rosner
,
(1999),
Fundamentals of Biostatistics,
Duxbury Press

5.

Beth Dawson


Robert G. Trapp


Beth Dawson


Robert Trapp
, (2004),
Basic & Clinical
Biostatistics (LANGE Basic Science),
McGraw
-
Hill.

6.

Harvey Motulsky, (1
995), Intuitive Biostatistics
,

Oxford University Press.


♣♣♣♣♣♣♣♣♣♣




M.Sc., Microbiology

254

II YEAR
–

I
I
I SEMESTER

COURSE CODE: 1MMI3C1


CORE
COURSE
X

–

IMMUNOLOGY


U
nit
I


Historical Perspective:

D
iscovery, early theories.
Types of immunity:

I
nnate and acquired
immunity. Cells and Organs of the immune system. Hematopoiesis, lymph
oid cells, cells of
the immune system, primary and secondary lymphoid organs of the immune system, B and T
cell
–

Maturation and differentiation. Clonal selection theory.


U
nit

II


Antigens:

Factors influencing immunogenicity, epitopes and haptens.
Immuno
globulin:

Structure, antigenic determinants, immunoglobulin classes, monoclonal antibodies.
Antigen
–
Antibody interaction
:

P
recipitation reactions, agglutination reactions, radioimmunoassay,
enzyme linked immunosorbent assay (ELISA), Western blotting, immu
nofluorescence and
immuno electron microscopy.


U
nit
III


Major histocompatibility complex (MHC):

Organization and inheritance, MHC molecules
and clones, genomic map of MHC genes, cellular distribution and expression, MHC and
susceptibility infectious dise
ases. Antigen processing and presentation
–

antigen presenting
cells and presenting pathways
–

cytosolic pathway and endocytic pathway.


U
nit
IV


Complement system:

the complement components, classical and alternate pathways,
regulation and biological sequ
ences of complements. Cell mediated and humoral effector
responses.
Hypersensitivity reactions:

Gell and Coomb’s cla
ssification, IgE mediated
(Type
–

I), antibody
–

mediated (Type
–

II), Immune complex mediated (Type
–

III) and T
DTH
–

mediated (Type
–

IV) hy
persensitivity.


U
nit
V


The immune system in health and diseases:

C
ytokines
–

properties, receptors, related
diseases and therapeutic uses.
Vaccines
:

A
ctive and passive immunization, whole organism
vaccines, recombinant vaccines, DNA vaccines, edible vacc
ines, synthetic peptide,
multivalent subunit and anti
-
idiotype vaccines. Immunological tolerance, Autoimmunity,
immunodeficiency, immune system in AIDS, transplantation immunology, Cancer and
immune system.


References


1.

Ivan M.Roit (1994), Essential Immuno
logy
–

Blackwell Scientific Publications,
Oxford

2.

Kuby J (1997), Immunology
–

WH Freeman and Company, New York

M.Sc., Microbiology

255

3.

Donal M.Weir, John Steward (1993) Immunology VII edition. ELBS, London,
Harward Publishing company.

4.

Coico R, and Sunshine, G. (2009).
Immunology: A Short Course
,

Wiley
-
Blackwell,
London

5.

Levinson, W. (2008).
Review of Medical Microbiology and Immunology, Tenth
Edition (LANGE Basic Science)
,

McGraw
-
Hill Medical, USA

6.

Chakravarthy, A.K. (2006). Immunology and Immunotechnology, Oxford University
Press India, New Delhi.

7.

Delves, P.
, Martin, S., Burton, D. and Roitt, I. (2006).
Roitt's Essential Immunology
,
Wiley
-
Blackwell, London



♣♣♣♣♣♣♣♣♣♣



M.Sc., Microbiology

256

II YEAR
–

I
I
I SEMESTER

COURSE CODE:
1
MMI3C2


CORE COURSE XI

–

MEDICAL MICROBIOLOGY


U
nit

I

History, Koch Postulates,
Normal Microbial flora,

Host Parasite Interactions

–

The process of
infection, Infections

–

source and types, Modes of Transmission, Microbial Virulence factors,

General approaches to clinical specimens, collection and transport of specimens for
microbiological examination, Infective syndromes, Strategy of Antimicrobial Chemotherapy,
Epidemiology and control of community infections.


U
nit
II

Morphology, Culture c
haracters, Pathogenicity, Laboratory diagnosis, control and Treatment
of following organisms.
Staphylococci, Streptococci, Pneumococcus, Neisseriae gonnoroae,
Corynebacteria, Mycobacteria tuberculosis, Clostridia, Bacillus

and non
–

spore forming
Anaerobes
.


U
nit
III

Morphology, Culture characters, Pathogenicity, Laboratory diagnosis, control and Treatment
of following organisms.
Escherichia, Klebsiella, Proteus, Salmonella, Shigella, Vibrios,
Pseudomonas, Campylobacter, Helicobacter and Legionella. Brucel
la, Bordetella, Y
ersinia,
Haemophilus, Listeria
and Spirocheates
–

Rick
ettsiae, Chlamydiae, Mycoplasma
and
Actinomycetes
.


U
nit

IV

Mechanism of pathogenesis and lab diagnosis of fungal diseases
:

Superficial Mycoses,
Cutaneous Mycoses, Subcutaneous Mycoses,

Systemic mycosis, Opportunistic Mycoses,
Mycotoxicosis. Mechanism of pathogenesis and lab diagnosis of Protozoology

–

Intestinal,
Blood and Tissue Protozoa.


U
nit
V

Influenza, Measles, Mumps, Chicke
n pox, Hepatitis A, B, C, D & E
, Poliomyelitis, AIDS,
Hum
an Papilloma virus, Rabies, Yellow fever, Dengue and Japanese Encephalitis, SARS,
Swine Flu. Hospital acquired infections, Common type of Hospital infections, their diagnosis
and control
–

Hospital waste disposal.


R
eferences


1.

Baron EJ, Peterson LR and Fi
negold SM (1994).
Bailey and Scott’s diagnostic
microbiology
. Ninth Edition
, Mosby Publications.

2.

Jawetz E, J.L. Melnic and E.A. Adelberg (2001).
Medical Microbiology
. Twenty
second Edition, McGraw Hill.

3.

Ananthanarayanan R. and Jayaram Panicker C.K. (199
4).
Textbook of Microbiology
.
Orient Longman.

4.

Chakraborthy, P. (1995).
A Textbook of Microbiology
, Ne
w Central Book Agency
Pvt. Ltd,
Calcutta.

5.

Panicker, C.K.J. (1993).
A Textbook of Medical Parasitology
, Third

Edition. Jaypee
Brothers.

M.Sc., Microbiology

257

II YEAR
–

III SEMES
TER

COURSE CODE:
1
MMI3C1


CORE COURSE

XII

–

RECOMBINANT DNA TECHNOLOGY


U
nit

I

Enzymes using in rDNA technology:

Restriction enzymes, DNA Polymerase,
Polynucleotide kinase, T
4

DNA ligase, Terminal deoxynucleotidyl transferase, Reverse
Transciptase, Nucl
eas
es:

Bal 31, S1 nucleases, DNase I, Ribonucleases, EXO III.
Thermostab
le DNA Polymerases used in PCR.


Unit

II

Cloning vectors and their applications:

a) Plasmids b) Bacteriophage
–

Lambda and M13
vectors c) Cosmids d) Phagemids e) Ti Plasmid Specialized ve
ctors & their uses

a) Expression vectors for Prokaryotes & Eukaryotes b) Gene fusion vectors c) Artificial
chromosomes
–

BAC, PAC, YAC, MAC and HAC.


U
nit

III

Principles of gene cloning:

Use of adapters & linkers in cloning
–

Shotgun cloning
–

Constructio
n of genomic and cDNA libraries
–

screening of recombinants
–

alpha
complementation
–

antibody screening
–

Labeling of nucleic acids
–

colony hybridization
–

southern hybridization
–

Western Blot
–

Northern Blot. DNA fingerprinting, footprinting, zoo
blot,

chromosome jumping, chromosome walking.


U
nit

IV

PCR:

Basic process
–

PCR Primer designing
–

optimization of PCR reactions
–

Variations in
PCR (Asymmetric PCR

/

Nested PCR

/

Inverse PCR, RT

PCR, RACE, Reverse Transe
PCR)
–

RAPD
–

Multiplex PCR
–

AFLP
–

App
lications of PCR in medicine, agriculture and
forensic science. DNA sequencing
–

enzymatic and chemical methods
–

Automated DNA
sequencing
–

cycle sequencing. Site
–

directed mutagenesis
–

oligo and PCR mediated.


U
nit

V

DNA chips and microarray gene scree
n technology, site directed mutagenesis, cell culture
based techniques, Genetic diagnosis, Applications in medical field biology, transgenic plants
and animals, Recombinant vaccines development, Gene therapy, molecular basis of genetic
diseases, genetic co
unseling.


R
efer
e
nce
s


1.

Primrose S.B, R.M. Twyman and R.W.Old, (2003),
Principle of Gene Manipulation

Blackwell scientific publications.

2.

Brown T.A., (2001),
Gene cloning and DNA Analysis. An Introduction
, Black well
scientific publication.

3.

Watson, J.D,

M.
Gilman, J.Witowski and Mark Zoller, (1992),
Recombination DNA
,
Scientific American books.

4.

Sambrook.J.,

Russell, D.W., (2001),
Molecular cloning: A Laboratory press
, cold
spring harbor, new York.

5.

Moo
-
young, (2004),
Comprehensive Biotechnology
, Robinson how
ell.


M.Sc., Microbiology

258

II YEAR
–

III SEMESTER

COURSE CODE: 1MMI3P1


CORE COURSE XIII

–

LAB COURSE IN
IMMUNOLOGY AND
MEDICAL MICROBIOLOGY



1.

Separation of serum

/

plasma.

2.

ABO Blood Grouping
–

Rh typing and cross matching.

3.

Agglutination tests.


a)

Haemagglutination and Haemag
glutination inhibition test.

b)

WIDAL
–

slide and tube test.

c)

Weil felix Test.

d)

RA test

e)

ASO test.

f)

CRP test.

g)

Beta
–

HCG test.

h)

TPHA test.


4.

Precipitation reaction
–

Ouchterlony’s Double Immundiffusion Test (ODD).

5.

Rapid Plasma regain test
–

VDRL Test.

6.

Complement Fi
xation test.

7.

ELISA
–

thyroid hormone analysis

8.

Serological Tests: Serodiagnosis of various viral diseases

9.

Haemaggluination (HA) and Haemagglutination inhibition (HAI) test


a)

Medical Microbiology


1.

Collection and transport of clinical specimens from sputum, p
us, urine, faeces, blood
and CSF.

2.

Culture techniques for sputum, pus, urine, faeces, blood and CSF.

3.

Biochemical identification of pathogenic bacteria from clinical specimens.


Staphylococcus sp.,

Escherichia sp.
,
Vibrio sp.
,

Streptococcus sp.
,

Klebs
iel
la sp.,



Pseudomonas




Proteus sp.
,

Shigella sp.
,

Salmonella sp.
,

Bacillus sp.
,




b)

Parasitology


1.

Examination of parasites in clinical specimens
–

Ova

/

cysts in faeces
–

Direct and
concentration methods
–

formal ether and zinc su
lphate methods
–

Saturated saline
technique.

a)

Entamoeba coli b)Entamoeba hist
olytica c)Giardia intestinalis


2.

Blood smear examination for malarial parasites.



M.Sc., Microbiology

259

c)

Mycology


1.

Collection and transport of clinical specimens, Direct microscopy: KOH and
Lactophenol

cotton blue preparations for skin scrapings.


2.

Isolation and identification of fungal pathogens from clinical specimens, their
biochemical and specific identification tests.


Clinical specimens

Fungi


1)

Nail/Skin scrap
ing


–


Dermatophytes.

2)

Corneal scraping


–

Aspergillus sp., Fusarium sp
.
,

3)

Blood




–

Candida sp.
,

4)

Urine




–

Candida sp
.,




-



d)

Virology


A. Staining of some viral inclusion bodies.


i) Rabies
–

Negri bodies.



ii)

CPE stained smears.



B. Viral cultivation methods.

i)

Egg inoculation (All routes) techniques.

ii)

Animal Tissue culture (Demonstration).


References


1.

Cappucino J.G, N.Sherman,(2002),
Microbiology: A Laboratory Manual
, Addison
–

wesley.

2.

A
tlas R.M, A.E. Brown and L.C. Parks, (1995),
Laboratory Manual of
Experimental Microbiology,
Mosby, St. Louis.

3.

Kannan N.,

(2002),
Laboratory Manual in General Microbiology
. Panima
Publishers.

4.

Sundararajan

T.
, (2002),
Microbiology Laboratory Manual
. IIT Che
nnai.

5.

Rose

N.R
,

R.G. Hamilton and B. Detrick, (2002),
Manual of Clinical Laboratory
Immunology

ASM Press.

6.

Weir, D.M. (1986),
Handbook of Experimental Immunology
, Fourth Edition,
volume I

–

IV, Blackwell scientific Publication.







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M.Sc., Microbiology

260

II YEAR
–

III SEMESTER

COURSE CODE:
1
MMI3P2


CORE COURSE
XIV
–

L
AB COURSE IN RECOMBINANT DNA
TECHNOLOGY




1.

Isolation of plasmid and chromosomal (bacterial) DNA.


2.

Quality and quantity checking of DNA by UV Spectrophotometer and Submarine
ag
arose gel electrophoresis.


3.

Gene cloning
–

Preparation of vector and passenger
–

Ligation
–

Preparation of
competent cells
–

Transformation of
E.coli

with recombinant plasmids.


4.

Selection of recom
binants by blue white selection


5.

PCR amplification
–

Demo.




Refrerences


1.

Sambrook.J., Russell, D.W, (2001),
Molecular Cloning: Laboratory Manual,
cold
spring harbor laborato
ry press, cold spring harbour, N
ew York.

2.

Bruce Birren
et al
, (1997),
Genome Analysis. A Laboratory Manual. Vol I
–

Analysing DNA
, Cold
Spring Harbor Laboratory Press.

3.

C. Hardin
et al,

(2001),
Cloning, Gene Expression, and Protein Purification.
Experimental Procedures and Process,

Rationale Oxford University Press.

4.

Reece R.J., (2004),
Analysis of Genes and Genomes,

John Wiley & Sons, Ltd.





♣♣♣♣♣♣♣♣♣♣

M.Sc., Microbiology

261

II YEAR
–

III SEMESTER

COURSE CODE:
1MMI3E1


ELECTIVE COURSE

I
V

(A)
–

MOLECULAR TAXONOMY A
ND
PHYLOGENY


U
nit

I


Introduction to M
icrobial taxonomy:

Morphological taxonomy, Biochemical taxonomy and
M
olecular taxonomy. Numerical taxonomy, positiv
e and negative aspects of each
taxonomical method
s
. Morphological phylogeny


U
nit
II

Chemotaxonomy:

Fatty acid;

protein fingerprinting, Isozyme typing, pigments &

polyamines. Biochemical phylogeny, Molecular Taxonomy

–

G + C content, DNA

–

DNA
hybridizatio
n, plasmid profiles, RFLP, RAPD, STRR & LTRR, Rep
–

PCR, rR
NA based
fingerprinting methods


U
nit

III

Types of rRNA, 16S rRNA &5S rRNA. Importance of 16S rRNA in microbial identification
and taxonomy. Methods of 16S rRNA /

rDNA fingerprinting
–

Isolation of

rRNA, RT
-
PCR,
Isolation of DNA, amplication of 16S rDNA using PCR, Sequencing of 16S rDNA using
chain termination method.


Unit

IV

Submission of rDNA sequences in GenBank

–

Bankit & Sequin guidelines, NCBI, EMBL &
DDBJ retrieving sequences, RNA structure
prediction, Restriction enzyme patterns.
Ribosomal Database project

–

Designing primers and probes. Sequence comparison,
alignment and data base searching

–

ClustalW, FASTA & BLAST, DNA barcoding.


U
nit

V

Introduction to molecular phylogeny:

T
ree terminolo
gy
, S
oftware programs for making
phylogenetic trees
–

MEGA, PHYLIP, Genetic Distance based RAPD, Cladogram, additive
trees and ultrametric trees, rooted and unrooted trees and tree shapes.


R
eferences


1.

Roderic D.M. Page, Edward C. Holmes

(1998). Molecular
evolution
: A phylogenetic
Approach. Blackwell publishing, USA.

2.

Principles
of Genome analysis
: A guide to Mapping sequencing DNA from different
organisms by S.B. Primrose.

3.

Microbial Genome methods by Keeneth W. Adolph (Hard cover
–

Oct 28.1996).

4.

Genome mapp
ing and Sequencing by Ian Dunham (Hard cover

–

Sep 1, 2003).

5.

Brendon Wren (Editor), Nick Dorrel (2002) Functiona
l Microbial Genomics (Vol
.
33)
(
Methods in Microbiology) Academic Press, UK.

6.

Primrose. S.B, Richard M. Twyman (2005). Principles of Genome Analy
sis and
Genomics, Blackwell Publishing, USA.



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M.Sc., Microbiology

262

II YEAR
–

III SEMESTER

COURSE CODE:
1MMI3E2


ELECTIVE COURSE

I
V

(B)
–

BIOFERTILIZER AND BIOMANURE
TECHNOLOGY


Unit I


Introduction
–

History, importance and present status of different types of

fertilizers and their
application to crop plants.
Biological fixation of nitrogen; Natural

cycles associated with
microorganisms
–

Carbon, nitrogen, phosphorus and sulphur.


Unit II


Cyanobacterial Biofertilizers
–

Nostoc, Anabaena, Gloeocaps and Scytonema as

biofertilizers;
Symbiotic association with Azo
lla; Multiplication of blue green algae and

their effect on
agricultural (rice) yields. Bacterial Biofertilizers; Free living forms
–

Azatobacter,
Azospirillum; Symbiotic forms
–

Rh
izobium
; Legume Association;

Pseudomonas
; Non
-
legume association.


Unit III



Fungal Biofertilizers
–

Ectom
ycorrhizal
association with pines; Vescicular

arbuscular
m
ycorrizal association (VAM)
–

Glomus
sp.,

Actimomycetes as Biofertilizers

–

Actinomycetes associations
–

Frankia
sp.
,


Unit IV


Biomanures
–

A general account of man
ures
–

Moulds; Composts
–

Farm yard

manure, oil
seed cakes, castor and neem; Green leaf manures
–

Glyciridia, Sesbania
and

Crotalaria
;
Agro
-
industrial wastes
–

Poultry manure and saw
-
dust; Compost; Vermi and

microbial
compost
–

Pure culture techniques, con
sortium; Types of compost pits;

Biodegradation of
organic components.


Unit V


Application of biofertilizers and biomanures
–

A combination of biofertilizer and

manure
applications with reference to soil, seed and leaf sprays. Laboratory and field

applica
tion;
Cost
-
benefit analysis of biofertilizer and biomanure production.



References


1)

Burns, R.C. and R.W.F. Hardy, (1975). Nitrogen fixation in bacteria and higher

plants.
Springer
–

Verlag, Bertin.

2)

Gallen and Chaplin, (1987). Introduction to Nitrogen fixa
tion. Elsvier

Publications.

3)

Harley, J.L. and S.E. Smith, (1983). Mycorrhizal Symbiosis. Academic Press,

London.

4)

Kumar, H.D, (1990). Introductory Phycology. Affiliated East
-
West Press Ltd.,

Madras.

5)

Marks, G.C. and T.T. Koslowski (Eds.), (1973). Ectomycorrhi
zae, Academic

Press,
London.

M.Sc., Microbiology

263

6)

Rao, N.S., G.S. Venkataraman and S. Kannaiyan, (1983). Biological N2 fixation,

ICAR
Publications, New Delhi.

7)

Sandera, F.E., B. Mosse and P.B. Tinke, (1975). Endomycorrhizae, Academic

Press,
London.

8)

Rao, N.S, (1980). Biofertiliz
ers in Agriculture. Oxford & IBH Publishing Co.,

Pvt.,
Ltd., Bombay.

9)

Thompson, L. M. and T. Fredrick, (1979). Soils and Soil Fertility. Tata Mc Graw
-
Hill
Publishing Co., New Delhi.

10)

Tilak, K.V.B.R, (1990). Bacterial Biofertilizers. IARI Publications, New De
lhi.

11)

Tirdale, S.L. Nelson, L. Werver and J.D. Becton, (1985). Soil fertility and

fertilizers.
Macmillan Publishing Co., New York.




♣♣♣♣♣♣♣♣♣♣

M.Sc., Microbiology

264

II YEAR
–

III SEMESTER

COURSE CODE:
1MMI3E3


ELECTIVE COURSE

V (A)
–

DISEASE DIAGNOSIS TECHNOLOGY



Unit I


Scope and relevance of Microbiology
–

Definition and concepts, Type of microorganism,
Distribution of microorganism in nature; Developm
ent of microbiology as a

scientific
discipline; General characteristics of microorganisms
–

General principles,

taxonomy,
classification and structural organization of bacteria, fungi, viruses, algae,

actinomycetes,
mycoplasma, and ricketssiae; Microscopy
–

Principles and application of

phase contrast, dark
field, fluorescent, and electron microscope; Micrometry

–

Basic

principles and applications.


Unit II


Fixatives and fixation of smears, Stains
–

Definition, acidic, basic stains, simple

and
differentia
l staining, use and significance of stains in microbiology; Cultivation of

microorganism
–

Definition, concept, use and types of different culture media for

cultivation
of microorganism, pure culture techniques; Cultivation of anaerobes; control

of
microor
ganism
–

sterilization by physical an
d chemical methods, antiseptics.


Unit III


Binomial nomenclature: Outline classification of living organisms
–

Haekel,

Whittaker and
Woese system, normal micro flora in human body and their beneficial

effects; Lymphoid

organs and types of immunity; General principles of diagnostic

microbiology
–

Collection,
transport, and processing of clinical specimens, General

methods of laboratory diagnosis
–

Cultural, biochemical, serological, and molecular

methods.


Unit IV


Host

pathogen interaction
–

Virulence factors: General account of the following

diseases
–

Causal organisms, pathogenesis, diagnosis, prevention and therapy of typhoid,

cholera,
d
ysentery, whooping cough, tuberculosis, urinary tract infection, syphilis, ringwo
rm,

dermatophytes, malaria, small pox, measles, hepatitis, and AIDS. General account

of
nosocomial infections and prevention.


Unit V



Antimicrobial therapy in the diagnosis of diseases;
In vitro
diagnostic methods
–

Agglutination, precipitation, immunofl
oresence, ELISA, Skin test; Vaccines
–

Principles

underlying the preparation of live and attenuated vaccines. Synthetic peptide vaccines.

Immunization, its rationale, schedules and its importance in public health; Automation in

disease diagnosis; Ethical c
ommittee
–

Structure and

functions.


M.Sc., Microbiology

265

References


1)

Morag, C. and M.C. Timbury, (1994) Medical Virology (10th Edition). Churchill

Livingston,
London.

2)

Dimmock, N.J. and S.B. Primrose, (1994) Introduction to Modern Virology, (4
th

Edition).

Blackwell Scientifi
c Publications, Oxford.

3)

Conrat, H.F., P.C. Kimball, and J.A. Levy, (1994) Virology (3rd Edition).

Prentice
Hall, New Jersey.

4)

Maloy S.R., J.E. Cronan and D. Freifelder, (1998). Microbial Genetics. Jones and

Bartlett publishers.

5)

Robert G. W. and G. Allan, (1
994). Encyclopaedia of Virology, Vol. I, II &III

Academic Press inc. San Diego, CA 92101. Ed.




♣♣♣♣♣♣♣♣♣♣

M.Sc., Microbiology

266

II YEAR
–

III SEMESTER

COURSE CODE:
1MMI3E4


ELECTIVE COURSE

V (B)

–

ENTREPRENEURSHIP IN
MICROBIOLOGY


Unit I


Evolution of the concept of entrepr
eneur
–

Entrepreneurship: Definitions
–

co
ncept of
Entrepreneurship, development
–

need
–

role of resource, talent and spirit
–

process of
Entrepreneurship to socio
-
economic gains.


Unit II


Institutions and schemes of Government of India
–

Schemes and pr
ogrammes, Department of
Science and Technology schemes, Nationalized banks
–

other financial institutions
–

SIDBI,
NSIC, NABARD, IDBI, IFCI and ICICI.


Unit III


Skills for entrepreneurs
–

Communication skills, problem solving skills; Business plan
develo
pment; Market need
–

Market research, SWOT analysis, identifying competitors.
Financial plan
–

Financial support for business, business insurance, Marketing
–

Mix
-
product,
distribution, price, promotion and market goal setting.


Unit IV


Project
–

idea ge
neration
–

Sources of idea generation
–

Trade Fairs and Exhibitions
–

Project
identification
–

classification
–

project formulation
–

project appraisal. Composting of
domestic, agricultural and industrial wastes, vermicomposting.

SCP production; Mushroom
c
ultivation.


Unit V


Biofertilizers and biopesticides. Production of teaching kits (plasmid DNA isolation, serum
electrophoresis) and diagnostic kits (WIDAL test kits, ABO blood grouping kits).


References


1)

Nagendra S., (2008) Entrepreneurship and managem
ent Sanguine technical publishers

2)

Bhatia, B.S. and G.S Batra, (2003) Entrepreneurship and
small business management.
Deep
and deep publications

3)

Naidu, N.V.R, (2008) Management and entrepreneurship. I.K. International Pvt.

Ltd.

4)

Greene, (2000) Entrepreneursh
ip ideas in action. Thomson learning

5)

Tilak, K.V.B.R., (1990). Bacterial Biofertilizers. IARI Publications, New Delhi.

6)

Venkataraman, G.S. (1972). Algal Biofertilizers and Rice Cultivation. Today and

Tomorrow's Printers and Publishers, New Delhi.


♣♣♣♣♣♣♣♣♣♣

M.Sc., Microbiology

267

II YEAR
–

IV SEMESTER

COURSE CODE:
1
MMI4C1


CORE
COURSE
XV

–

INDUSTRIAL MICROBIOLOGY


U
nit

I


Introduction to Industrial Microbiology, Isolation, cultivation, preservation and improvement
of industrially important microorganisms. Screening methods for ind
ustrial microbes

–

detection and assay of fermentation products

–

classification of fermentation types

–

Substrates for fermentation. Mutation and recombinant DNA techniques for strain
development.


U
nit
II


Fermentors:

Basic functions, design and compone
nts

–

asepsis and containment
requirements
–

Body construction and temperature control

–

aeration and agitation systems

–

sterilization of fermentor, air supply and medium; aseptic inoculation methods

–

sampling
methods, valve systems
–

Monitoring and cont
rol devices. Types of fermentors.


U
nit
III


Fermentation:

Microbial growth kinetics,
Measurement of growth (cell number, direct and
indirect methods) growth and nutrient, growth and product formation, heat evolution, effect
of environment (temperature, p
H, high nutrient concentration) media formulation, bioprocess
kinetics of growth and substrate utilization in Batch, Fed batch and Continuous system.


U
nit

IV


Production of
F
ermentative products:
Microbial production of Antibiotics (Penicillin,
Streptomy
cin), Enzymes (Protease and Amylase) Organic acids (Citric acid and Acetic acid),
Vitamins (B
12,

B
2
)
,
Amino acids (Glutamic acid and Lysine), Ergot Alkaloids: Alcohol, Beer,
Wine

–

Exopolysaccharides

–

Food and Dairy products: Cream
, Yoghurt, Kafir, Kumiss
,
acidophilus milk and cheese

–

Single cell protein and food.


U
nit

V


Downstream Processing:

Recovery and purification of fermentation products

–

Removal of
microbial cells and other solid materials, foam separation, Precipitation, Filtration,
Centrifuga
tion, Cell Disruption

–

Physical, Chemical methods, Extractors, Chromatography,
Membrane process, Drying, Crystallization and W
hole broth processing.


References


1.


Kalaichelvan,
P.T. Arulpandi, I. (2007).
Bioprocess Technology
, MPJ

Publishers,
Chennai.

2.

Cru
egar, W. and Cruegar, A. (2000).
Biotechnology: A Textbook of Industrial
Microbiology

Fourth edition. Panima publishing corporation, New Delhi.

M.Sc., Microbiology

268

3.

Demain, A.L. and Davies, J.E. (1999).
Manual of Industrial Microbiology
and
Biotechnology.

ASM Press.

4.

Patel, A
.H. (1996).
Industrial Microbiology,

MacMillan India Ltd.,

5.

Stanbury, A.H., Whittaker, A. and Hall S.J. (1995).
Principles of fermentation
technology
, Second edition, Pergamon Press.

6.

Richard,

H. George, B., Hagemann, D.
and
Paul, L. (1993).
Industrial
Mi
coorganisms
-

Basic and Applied Molecular Genetics.
American Society of
Molecular Genetics. American Society of Microbiology, Washington.

7.

Casida, J.E. (1968).
Industrial Microbiology
, Wiley Eastern publication.





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M.Sc., Microbiology

269

II YEAR
–

IV SEMESTER

COURSE
CODE:
1
MMI4P1


CORE
COURSE
XVI

–

LAB COURSE IN INDUSTRIAL
MICROBIOLOGY



1.

Wine production

–

Alcohol Estimation, Sugar Estimation.

2.

Production and Quantification of

(i)

Alcohol

(ii)

Citric acid

(iii)

Protease

(iv)

Amylase

(v)

Lipase

3.

Immobilization te
chnique (sodium alginate method
)


R
eferences


1.

Demain, A.L and Davies, J.E (1999).
Manual of Industrial Microbiology and
Biotechnology
, ASM Press.




♣♣♣♣♣♣♣♣♣♣

M.Sc., Microbiology

270

II YEAR
–

IV SEMESTER

COURSE CODE:
1
MMI4
PR


CORE COURSE XVII

–

PROJECT WORK



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