Course Contents FOR MSc Microbiology - Thapar University

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12 Φεβ 2013 (πριν από 4 χρόνια και 8 μήνες)

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Approved by the 74
th

meeting of the Senate(Feb 19, 2011)


DEPARTMENT OF BIOTECHNOLOGY AND ENVIRONMENTAL SCIENCES


SCHEME OF COURSES FOR

MSc (
Microbiology
)


First Semester


S. No.

Course No.

Course Name

L

T

P

Cr

1.

PMA101

Basic Mathematics

(For medical group)


2

1

0

2.5

2.

PMY

101

General Biology ( for Non
-
medi
cal group)

2

1

0

2.5

3.

PMY
102

Prokaryotic and Eukaryotic Microbial
Diversity

3

0

2

4.0

4.

PMY
103

Microbial Physiology and Metabolism

3

0

3

4.5

5.

PMY
104

Microbial Genetics

3

0

3

4.5

6.

PMY
105

Bio
-
Techniques

3

0

3

4.5

7.

PMY
106

Virology

3

0

2

4.0



T
otal

17

1

1
3

24.
0


Second Semester





S. No.

Course No.

Course Name

L

T

P

Cr

1.


PMY
201

Biophysics and Biostatistics

3

0

2

4.0

2.


PMY
202

Pharmaceutical Microbiology

3

0

2

4.0

3.


PMY
203

Recombinant DNA Technology

3

0

3

4.5

4.


PMY
204

Food & Dairy Microbiology

3

0

2

4.
0

5.


PMY
205

Immunology

3

0

2

4.0

6.


PMY
206

Industrial Microbiology

&
Biotechnology

3

0

3

4.5



Total

18

0

14

25.
0


Third Semester


S. No.

Course No.

Course Name

L

T

P

Cr

1.

PMY
301

Microbial Ecology
&

Environmental
Microbiology

3

0

2

4.0

2.

PMY
302

Bioprocess Technology

3

1

2

4.5

3.

PMY
303

Agriculture Microbiology

3

0

2

4.0

4.

PMY
304

Medical & Diagnostic Microbiology

3

0

2

4.0

5.

PMY
305

Bioinformatics

3

0

2

4.0

6.

PHU301

Entrepreneurship a
nd IPR

3

1

0

3.5

7.

PMY
391

Summer Assignment

0

0

0

2.0



Total

18

2

1
0

2
6
.
0



Approved by the 74
th

meeting of the Senate(Feb 19, 2011)


Fourth Semester


S. No.

Course No.

Course Name

L

T

P

Cr

1.

PMY
491

Seminar

0

0

0

2.0





2.

PMY
492

Major Research Project

0

0

0

12.0



OR


3.

PMY
493

Minor Research Project

0

0

0

4.0

4.

PMY
401

Plant
-
Pathogen

Interaction
s

3

0

2

4.
0

5.

PMY
402

Protein Engineering & Enzyme
technology

3

0

2

4.0



Total

0/6

0

0/
4

1
4
.0






Only students with CGPA higher than 6.5 in the first year, will be eligible for
Major Research
Project
.



Total Number of Credits:
89.0


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMA101 BASIC MATH
EMATICS


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2.5

Prerequisite(s): None


Real Number Systems:

Linear and quadratic equations
-

Permutations and combinations, Bionomial theorm,
Complex numbers.

Differentiation:

Limit, continuity and differentiability, Differentiation of sta
ndard functions, Product rule
quotient rule, Applications of derivatives, Cartesian graphing using first and second order derivatives.

Integration:

Integration by parts, Substitution and Partial fraction, Properties
-

Definite integrals and
applications to

area of regions.

Differential equations:

Solution of differential equations of first order and second order differential equations
with constant coefficients.

Determinants and Matrices:

Properties of determinants, Elementary operations, Rank of a Matrix,
Row
reduced echelon form, Solution of system of linear equations, Matrix inversion using row reduction method.

Coordinate geometry:

Systems of Co
-
ordinates in two Dimension, distance formula area of triangle, locus,
slope of line, various forms of equatio
ns of a line, equation of circle (Standard and general form).



Recommended Books

1.

Hal

HS and Knight S
R, Higher Algebra, Laxmi Publications (2000).

2.

Thomas GB and Finney R
L, Calculus and Analytical Geometry, Pearson Education (2007)

9
th

ed
.

3.

Simm
ons GF
, Diffe
rential equations, McGraw Hill (200
6
).

4.

Narayan S,

Differential and Integral Calculus, S. Chand (2005).

5.

Krishnamurthy VK, Mainra VP and Arora JL
, An Introduction to Linear Algebra. A
ffiliated

East
-
West
Press. (
1976
).


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
101 GENERAL BIOLOGY


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4.5

Introduction:

Definition of biology and its various branches, Origin of life, Molecular basis and characteristics
of life, Levels of Biological Organization.


Diversity of Living World:

Microbes, Plant Kingdom and its classification, Animal Kingd
om and brief
description of non
-
chordates and Chordate phyla, Typical features of animal life.


Cellular and Structural organization:

Prokaryotes and Eukaryotes, Basic structure of plant and animal cells,
Organization of plant and animal tissues, Plant mor
phology and anatomy.


Growth and Development:

Basics ofcellular division, Processes of mitosis and meiosis, Mendel’s Laws of
Inheritance, Patterns of inheritance


Incomplete dominance, Multiple alleles, Co
-
dominance, Lethal genes,
Polygenic inheritance, S
ex linked inheritance.


Plant Physiology:

Plant Growth, Transportation of fluids, Mineral nutrition, Photosynthesis in higher plants,
Plant growth, Respiration, Plant growth harmones, Reproduction in Plants.


Animal and Human Physiology:

Digestion and abso
rption, Breathing and exchange of gases, Body fluids and
circulation, Excretion, Neural control and coordination, Chemical coordination and integration, Animal
reproduction.


Recommended Books

1.

Bhatia KN and Tyagi MP
, Elementary Biology, Trueman Book Compan
y (2005).

2.

Dhami PS, Srivastava HN and Chopra G
, A Textbook of Biology, Pradeep Publications (2007).

3.

Campbell NA and Reece JB
, Biology, Pearson
-
Education Inc. (2005).


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
10
2

PROKARYOTIC AND EUKARYOTIC MICROBIAL DIVERSITY


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Pre
-
requi
site(s): None


Introduction:
Introduction

to

Microbial world, Historical development, biogenesis vs abiogenesis; prokaryotes
and eukaryotes; Bacterial
, Archeal and Eucaryl

diversity
; Universal tree of life; Distribution, abundance and
ecological niche of m
icrobes;
Biogeochemical cycling.
Classification,

occurrence, diversity, characteristic
features, significance of different groups of archaebacteria (Crenarchaeota, Euarchaeota, Korarchaeota,
Nanoarchaeota).


Eub
acteria:

General discussion on the occurrence
, diversity, characteristic features, significance and potential
applications of various groups of bacteria according to Bergey’s Manual of Systematic Bacteriology;
conventional and molecular systematics; types of bacterial classification systems, new appr
oaches to bacterial
taxonomy
.


Fungi:

Fungal systematics and diversity based on molecular and biochemical approaches; Endophytic fungi:

colonization, adaptation and applications of endophytic fungi; Mycorrhiza
-

ecto and endomycorrhizae; Biology
of arbuscul
ar mycorrhizal fungi: signaling, penetration and colonization inside roots, culturing and benefits,
agriculturally important toxigenic fungi.


Algae:

Classification and diversity of algae, cyanobacteria
; characteristic features of important groups; range o
f
thallus organization; life cycle and reproduction; photosynthetic pigments; economically important algae and
microalgae.


Protozoa:

Classification;
Structure

and morphological forms; habitat and nutrition; Important human and plant
diseases caused by pro
tozoans.


Laboratory Work:

Microscopy
,

Staining

techniques of microbial spores,
flagella, Gram Staining,

Micrometry, i
isolation

and pure culture techniques for bacteria, fungi and algae from water and soil,

Streaking,
Autoclaving, Dilution plate, viabl
e counts and

enrichment

culture

techniques
,

Isolation and identification and
study of
c
yanobacteria from soil / paddy field,
Isolation of thermo
philes, acidophiles

and
halophiles
,

Isolation
and Staining of Vesicular Arbuscular Mycorrhizae from soil
,
MPN
.



Recommended Books

1.

Stainer RY, Ingraham JL, Wheelis ML and Palmer PR, General Microbiology, MacMillan (2003)

2.

Barsanti L and Gualtieri P, Algae: Anatomy, Biochemistry and Biotechnology, Taylor and Francis
(2006)

3.

Tortora GJ, Funke BR and

Case CL, Microbio
logy: An introduction with Mastering Microbiology
,10/E

Benjamin Cummings

(2010)

4.

Madigan MT, Martinko JM, Stahl DA

and

Clark DP, Brock Biology of Microorganisms, 13/E
,
Benjamin Cummings

(2010)

5.

Landracker EM, Fundamentals of the Fungi,
4/E , Benjamin Cumming
s (1996)

6.

Garrity GM,

Bergey’s manual of Systematic Bacteriology (1984)


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
10
3

MICROBI
AL PHYSIOLOGY AND ME
TABOLISM


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Prerequisite(s): None

Introduction:

Introduction to microbial physiology
,
macromolecular

synthesis
,

m
easurement

of growth,
growth physiology, cell division
,
growth

yield
,
kinetics
.

Microbial Nutrition
:

uptake; transport across the membranes and cell wall (diffusion, passive diffusion, active
transport, group
translocation and iron uptake),
d
rug export systems
,

amin
o acid transport
, Type I
-
Type VI
secretory systems.

Enzymes and Carbohydrate Metabolism:

Enzyme and Enzyme Kinetics
,
g
lycolysis, PPP,
e
ntner
-
d
oudroff
pathway,
c
itric acid cycle;
s
ynthesis of polysaccharides, peptidoglycan and biopolymers as cell components
;
p
entose phosphate pathway; oxidative and substrate level phosphorylation, gluconeogenesis, glyoxylate cycle,
fermentation of carbohydrates, homo and heterolactic fermentation
,

metabolomics.

Nitrogen Metabolism:

Amino acid biosynthesis and utilization
,

ly
sine and glutamine overproduction
,

stringent
response,

polyamine biosynthesis and regulation;
regulation of nitrogen fixation, nitrification, de
-
nitrification
and ammonifying bacteria,
p
athway of nitrate assimilation in photosynthetic and non
-
photosynthet
ic systems,
transamination and deamination reactions.

Photosynthesis:

Absorption of light, photosynthetic and accessory pigments,

(chlorophyll, bacteriochlorophyll,
carotenoides, phycobilliproteins)
,

o
xygenic and anoxygenic photosynthesis in prokaryotes, e
lectron transport
chain
,

phosphorylation
,

c
alvin cycle
,

effect of light, temperature, pH and CO
2

on photosynthesis
,

p
hotosynthetic yield and
p
hotorespiration.

Lipid & Hydrocarbon Metabolism:

composition of microorganisms
,

biosynthesis and degradation of l
ipids
,

lipid accumulation in microbes
,

hydrocarbon utilization,
f
atty acid oxidation
-

alpha, beta and omega oxidations
,

e
nergy

yields from fatty acid oxidation
,

o
xidation of unsaturated fatty acids and fatty acids with odd numbered
carbon atoms;
PHA synthe
sis and degradation

Nucelotide Metabolism:

Purine and pyrimidine biosynthesis, regulation of purine and pyrimidine biosynthesis,
inhibitors of nucleotide synthesis

Physiological Adaptation and Stress Metabolism:

Introduction to two component system, regula
tory systems
during aerobic
-
anaerobic shifts: Arc, Fnr, Nar, FhlA regulon, response to phosphate supply: The Pho regulon;
Quorum sensing: A and C signaling system, sporulation in
Bacillus subtilis
, control of competence in
Bacillus
subtilis;
Heat
-
Shock res
ponses; pH; homeostasis; osmotic homeostasis; Siderophores.


Laboratory Work:
Evaluation of bacterial growth in liquid media:
d
iauxic growth curve,

Effect of water
activity on microbes of different environment, Determination of carbon, Nitrogen and Mineral

requirements for
Microbial growth, IMViC tests
,
Measurement of SOD in bacteria under different physiological conditions,
c
atalase activity, Amylase activity,
c
aseinolytic activity, glucose uptake by bacteria and fungi


Recommended Books

1.

Moat AG, Foster J
W and Spector MP, Microbial Physiology , 4/E, John Wiley and Sons (2002)

2.

Nelson DL and Cox MM,
Lehninger Principles of Biochemistry
5/E
, W.H. Freeman and Company
(2008)

3.

Berg JR, Tymoczko CZ and Stryer L, Biochemistry,

6/E,
W.H. Freeman and Company

(2006)

4.

G
ottschalk G, Bacterial Metabolism
, Springer,
(
1986
)

5.

Cladwell DR, Microbial Physiology and Metabolism,2/E Star(2002)


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY

104 MICROBIAL GENETICS


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Genomic Organization Of Microbes:
Structure of Prokaryotic and Eukaryotic gen
ome,
C
-
value, and C
-
value
paradox
; DNA replication
-

general principles; different modes of replication, proof reading, continuous and
discontinuous synthesis, Synthesis of leading and lagging strands, s
pecific features of replication in Prokaryotes
and Eu
karyotes, action of topoisomerases, telomere maintenance and chromatin Assembly, Single stranded
DNA replication, Relationship between DNA replication and cell cycle, DNA copy number maintenance strand
elongation and termination,
Superhelicity in DNA,

I
nhibitors of DNA replication.

Recombination

and Repair of DNA:
DNA repair and recombination, DNA Mismatch Repair, Double Strand
Break Repair,
Reciprocal and non reciprocal, mechanism of recombination; Holiday model, Fox model,
Enzymatic mechanism of recomb
ination,
Recombination as a molecular biology tool.

Transcription and Translation Machinery:
Transcription machinery of prokaryotes, various transcription
enzymes and cofactors, initiation, elongation and termination, sigma factors, Transcription machinery

of
eukaryotes, various forms of RNA polymerase and cofactors, initiation, elongation and termination, promoters,
enhancers, silencers, activators, effect of chromatin structure, regulation of transcription; Transport of RNA
within eukaryotic cell, RNA
processing; splicing; capping and polyadenylation
,

transcriptional gene regulation;
the genetic code and protein structure; Mechanisms of translation in prokaryotes and eukaryotes; initiation
complex; ribosomes and tRNA
,

elongation and termination

factor
s,

in

vitro
translation systems
,

polycis
tronic/
monocistronic synthesis, r
egulation of translation; inhibitors of translation
,

RNA instability
,

Protein
modification
,

folding
,

chaperones
,
transportation
,
Signal
h
ypothesis
,
protein degradation
;

Genetic
recombination:
Genetic recombination processes: Role of rec proteins in homologous recombination,
Conjugation: Discovery, F+, F
-

and Hfr cells, types of Hfr; F+ and F
-

and Hfr and F
-

genetic crosses,
mechanisms of conjugation, conjugational transfer of re
sistance transfer factors,
transformation and
transduction,
Genetic mapping, Plasmid
r
eplication and
i
ncompatibility,
c
ontrol of copy number, Transposons
-

insertional sequences and composite
,

Transposable element
,

Classes of transposable elements, nomencla
ture of
transposable elements; insertion sequences (IS elements), Transposons(composite structure and complex
transposons structure) mechanism of transposition
,
mutations: UV and Chemical induced and their mechanism
.


Laboratory Work:

Isolation of Genomic

DNA from
E. coli,
Isolation of RNA and its quantification, Isolation
and purification of plasmids from bacteria by agarose gel electrophoresis,

Replica plating technique for transfer
of bacterial mutants, Genetic recombination (Conjugation) in Bacteria ,

Selection of Diploids in
Aspergillus
nidulans,
Ordered and random ascospore analysis in
Neurospora crassa,
Induction of mutation
.


Recommended Books

1.

Maloy SR, Cronan JE Jr. and

Freifelder D, Microbial Genetics, 2/E, Narosa Publishing House (Reprint
2009)

2.

Trun NJ

and

Trempy JE, Fundamental Bacterial Genetics, Wiley Blackwell (2004)

3.

Strieps UN and

Yasbin RE, Modern Microbial Genetics, 2/E, Wiley Publishers (2002)

4.

Sundarajan S, Microbial Genetics 1/E, Anmol Publications (2003)

5.

Snyder L
and

Champness W, Molec
ular Genetics of Bacteria, 3/E, ASM Press (2007)
a



Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
105 BIO
-
TECHNIQUES


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Prerequisite(s): None





Sampling and Bioanalytical Sample Preparation Techniques:

Sample Processing, Fixation,
Extraction and
p
urification of bio
-
macromolecules.

Bioanalytical Techniques:

Separation of biomolecules, Chromatographic techniques
-

Principles and
Applications, Column, Thin
-
layer, Paper, Ion
-
exchange and Affinity Chromatography, High performance liquid
chromatography (HPLC), Gas Chromatography (GC), High performance thin
-
layer chromatography (HPTLC),
Detection and Interpretation.

Electrophoretic Techniques:

Theory and application of electrophoresis, Polyacrylamide gel electrophoresis,
Isoelectric focusi
ng, Capillary electrophoresis, Microchip electrophoresis, 2D gel Electrophoresis.

Centrifugation Techniques:

Theory and principle of sedimentation, Centrifuges and their uses, Preparative
and analytical centrifugation, Rotors types and safety aspects of ce
ntrifugation.

Spectrophotometric Techniques:
E
lectromagnetic radiations, Radiation and matter, Theory and applications
of UV
-
VIS, IR, Fluorescence, Atomic absorption spectrophotometry.

Spectroscopy Techniques:
Electro spin resonance (ESR), Nuclear magneti
c resonance (NMR) spectroscopy,
X
-
ray diff
raction, Mass spectroscopy (MS), Circular Dichorism


Radioisotope Techniques:

Radioactivity and radioisotopes, Detection and measurement of radioactivity and
Cerenkov counting, Applications in biological sciences
-

Analytical, diagnostics and metabolic studies, Safety
aspects of radioactive handling.

Microscopy:

Theory and principles of microscopy, Light, Dark field, Fluorescent, UV microscopy, TEM,
SEM, Confocal microscopy, Atomic force microscopy, Microtomy, Ultra
microtomy, Freeze fracturing, Flow

cytometry
.


Laboratory
W
ork
:

Paper chromatography, Thin layer chromatography (preparative, analytical, reverse phase),
Column chromatography,
Gel and Affinity Chromatography,
Gas chromatography, HPLC, UV
-
Vis
spectroscopy,

Atomic absorption spectroscopy, Microscopy, PAGE, SDS
-
PAGE, Agarose Gel electrophoresis.



Recommended Books

1.

Harrison RG, Todd P, Rudge SR and Petrides BB,

Bioseparations: Science and Engineering, Oxford
University Press (2006).

2.

Wilson K and Walker
J
, Principles and Techniques of Biochemistry and Molecular Biology, Cambridge
University Press (200
5
)

6
th

ed
.

3.

McHale JL
, M
olecular Spectroscopy, Prentice
Hall (199
8
).

4.

Marimuthu R
, Microscopy and Microtechniques. MJP Publishers (2008).


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)




PMY
106

VIROLOGY


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3

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2

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Prerequisite(s): None





Classification of Viruses:

Virus classification, properties of viruses, virus str
ucture
,
b
rief history of virology
highlighting the significant contributions of scientists to the development

of microbial, plant and animal
virology; modern classification of viruses and bacteriophages .

Virological Techniques:

Techniques for visualization and enumeration of viral particles,
assays for virus
estimation
, characterization of viral products expr
essed in infected cells,
d
iagnostic virology,
g
eneral methods
of propagation of animal and plant viruses; purification of viruses using centrifugation, chromatography and
electrophoresis techniques, their assay and comparison of the sensitivity of assay me
thods; methods employed
in identification of viruses i.e structural and functional genomics.


Virus Replication Strategies:

Principal events involved in replication: Adsorption, penetration, uncoating
nucleic acid and protein synthesis, intracellular traff
icking, assembly, maturation and release, viral
-
host
interaction, Host response to viral infection.


Replication Pattern of specific viruses:

Replicative strategies employed by animal DNA viruses. Replicative
strategies employed by animal RNA viruses. Iden
tification of virus prototypes associated with different virus
replication schemes;
Salient features of
important viruses namely Herpes

virus, Poliovirus, Influenza virus,
VSV, SV40 and Adeno Virus, Poxviruses, Hepatitis Viruses, coronaviruses, Retroviruse
s,
Subviral pathogens
:
HDV, Prions, Viroids


Phage Genetics:

T4 phage
-

structure, life cycle, genetic map and DNA replication. Lamda temperate phage:
Structure, genetic map, lytic and lysogenic cycle, lysogenic repression and phage immunity, Lambda regulon
,

applications of phages in microbial genetics.


Viral Pathogenesis:

Stages of infection,
Salient features of some
viral diseases
-
epidemiology, transmission,
infection, symptoms, risk,
T
ransformation and oncogenesis,
E
merging viruses

and their evolution
.


Anti
-
viral strategies
-
prevention and control:

Host specific and nonspecific defense mechanisms involved in
resistance to and recovery from virus infections
,

r
ole of interferon in viral infections
,

c
ontributions of various
host defense mechanisms in viral
infections
,

v
iral
c
hemotherapy:
n
ucleoside analogs, reverse transcriptase
inhibitors, protease inhibitors, History of vaccines especially smallpox and polio. New methods: subunit
vaccines, anti
-
idiotype and DNA vaccines.


Laboratory Work:

Plaque assay for

Bacteriophages,
study of helical and icosahedral viruses by models,
c
ultivation
and
e
numeration of Bacteriophages, Isolation of coliphages from sewage and testing for plaque formation by infecting
susceptible bacterial culture
,
Isolation of phages from
sewage
.


Recommended Books

1.

Dimmock NJ, Easton

AJ and

Leppard K, Introduction of to Modern Virology, 6/E
, Wiley
-

Blackwell
(200
1
)

2.

Carter JB and

Saunders VA, Virology : Principles and Applications, John Wiley and Sons (2007)

3.

Wagner EK, Hewlett MJ, Bloom DC
and Camerini C, Basic Virology, 3/E, Blackwell Publishing (2008)

4.

Flint

SJ, Enquist LW, Racaniello VR and

Skalka AM, Principles of Virology, 3/E, ASM Press (2009)

5.

Knipe DM, Howley PM and

Griffin DE, Fundamental Virology, 4/E, Lippincot Williams & Wilkins
(2
001)


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
201 BIOPHYSICS AND BIOSTATISTICS


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Prerequisite(s): None






BIOPHYSICS

Interactions in biological systems:

Intra and intermolecular forces, Electrostatic interactions and Hydrogen
bonding interactions, Disulfide bridges,

Hydrophobic and hydrophilic molecules and forces, Water and weak
interactions.

Theories and Applications:

Debye
-
Hückel theory, Monte Carlo method, Molecular Dynamics method.

Protein Structure and Conformation:

Configuration and confirmation, Nonbonded and

dipolar interaction,
Protein and polypeptides
-

secondary and tertiary structures, Conformational analysis, Ramachandran plot,
Hydration of proteins.

Nucleic Acid Structure and Confirmation:

Backbone torsional angle, Sugar confirmation, Base
-
pairing and
b
ase stacking, DNA and RNA conformational structures.

Biological Membranes:

Membrane transport and fluidity, Concepts in multiple equilibrium.

BIOSTATISTICS

Introduction:
Biology and statistics, Variables and data, Sampling and sampling errors in biological

data,
Sampling techniques, Probability and distribution.

Hypothesis Testing:
Test of hypotheses, One and two sample analysis, Paired sample analysis, Non
-
parametric
statistics and limitations. Confidence limits and tests of confidence, Single, Two and Mul
ti
-
factorial analysis,
Non
-
parametric Analysis of Variance, Multiple comparison tests


Tukey, Newman
-
Keul, Scheffe tests,
Goodness of fit test.

Regression and correlation analysis:

Simple, linear and multiple regression, Simple and multiple correlation.

Design of Experiments and Data Presentation:
Response Surface Methods, Cantor Plots, Survivalship
curves, Graph plotting and significance of Curves, Data representation.


Laboratory Work
:
MS Excel and Graphpad Prism software, Data entry and graphical repr
esentation, Equation
formulation and analysis for sample testing, correlation and regression, ANOVA, Multiple comparisons,
Survivalship tests.

Electrophysiology, Optical tweezers, Ultrasonic imaging, Mass spectrometer, Viscosity measurements,
Computationa
l tools for macromolecular dynamics (Biomed Cache).



Recommended Books

1.

Rosne, B, Fundamentals of Biostatistics, Cengage Learning (200
5
).

2.

Za
r
, JH, Biostatistical Analysis, Pearson Education (200
9
)

5
th

ed
.

3.

Daun M, Molecular Biophysics, Oxford University Pre
ss (1999).

4.

Glaser R, Biophysics, Springer (200
4
).


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
202 PHARMACEUTICAL MICROBIOLOGY


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0

3

4.5

Prerequisites: None

Antibiotics and synthetic antimicrobial agents:
Antibiotics and synthetic antimicrobial agents
(Aminoglycosides, β
-
lacta
ms, tetracyclines, ansamycins, macrolide antibiotics), Antifungal antibiotics,
antitumor substances, Peptide antibiotics, Chloramphenicol, Sulphonamides and Quinolinone antimicrobial
agents, Chemical disinfectants, antiseptics and preservatives.

Mechanism
of action of antibiotics:
Mechanism of action of antibiotics (inhibitors of cell wall synthesis,
nucleic acid and protein synthesis, Molecular principles of drug targeting, Bacterial resistance to antibiotics,
Mode of action of non


antibiotic antimicrobi
al agents. penetrating defenses


How the antimicrobial agents
reach the targets (cellular permeability barrier, cellular transport system and drug diffusion)

Microbial production and Spoilage of pharmaceutical Products:
Microbial contamination and spoila
ge of
pharmaceutical products (sterile injectibles, non
-

injectibles, ophthalmic preparations and implants) and their
sterilization as per USP and IP, manufacturing procedures and in process control of pharmaceuticals, other
pharmaceuticals produced by mic
robial fermentations (s
treptokinase, streptodornase).

Regulatory practices, biosensors and applications in Pharmaceuticals:
Financing R&D capital and market
outlook. IP, BP, USP, government regulatory practices and policies, FDA perspective, Rational drug
design,
Immobilization procedures for pharmaceutical, applications (liposomes); macromolecular, cellular and synthetic
drug carriers, application of microbial enzymes in pharmaceuticals.

Quality Assurance and Validation:
Good Manufacturing Practices (GMP)
and Good Laboratory Practices
(GLP) in pharmaceutical industry, Regulatory aspects of quality control, Quality assurance and quality
management in pharmaceuticals ISO, WHO and US, certification, Sterilization control and sterility testing (heat
sterilizati
on, D value, z value, survival, curve, Radiation, gaseous and filter sterilization), Chemical and
biological indicators, Design and layout of sterile product manufacturing unit.

Laboratory Work
:

Bioassay of chloremphenicol by plate assay method or turbidio
metric

a
ssay method;
Treatment of bacterial cells with cetrimide, phenol and detection of leaky substances such as potassium ions,
aminoacids, purines, pyrimidines and pentoses due to cytoplasmic membrane damage, To determine MIC,
MBC

of Beta
-
lactam/amin
oglycoside/

tetracycline/ansamycins; Sterility testing by
Bacillus
stearothermophilus;

Sampling of pharmaceuticals for microbial contamination and load (syrups,

suspensions,
creams) as per USP/IP; Determination of D value, Z value for heat sterilization in

pharmaceuticals;
In vitro

antimicrobial susceptibility testing methods, Determination of antimicrobial activity of a chemical compound
(
T
hymol) to that of phenol under
s
tandardized experimental conditions i.e phenol coefficient.

Recommended Books

1.

Easter M
C, Rapid microbiological methods in the pharmaceutical industry, Interpharm/CRC Press (2003)

2.

Hugo WB

and

Russel AD, Pharmaceutical Microbiology, 6/E, Blackwell Scientific (1998)

3.

Hugo WB,
Denyer SP, Hodges NA, Gorman SP and

Hugo
WB,
Russell’s Pharmaceutical

Microbiology
7/E, Wiley
-
Blackwell

(2004)

4.

Baird RM,
Handbook of microbiological quality control:
pharmaceuticals and medical devices
, Taylor &
Francis (2000)

5.

Doorne
H
, A Basic P
rimer on Pharmaceutical Microbiology,
Davis Horwood International Publishers,
L
imited (DHI)

(2
004
)



Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
203 RECOMBINANT DNA TECHNOLOGY


L

T

P

Cr


3

0

3

4.5

Prerequisites: None

Molecular c
loning

Techniques
:
Various

h
osts for molecular cloning
,

restriction endonucleases and other
commonly used enzymes & their applications, di
fferent
cloning

techniques, c
loning vectors
-
plasmids, phages
lambda and M13, phagemids, cosmids, P1 phage, PACs, BACs and YACs, selection and screening of
the
recombinant
clones.

Construction of cDNA and genomic DNA libraries:
Vectors used in the construct
ion of cDNA
&

genomic
DNA libraries, construction of cDNA and genomic DNA libraries, Screening expression libraries
-
colony
hybridization and colony PCR, Enriching for clones in cDNA libraries by positive selection and subtractive
hybridization, Identifyin
g genes in complex genomes by direct selection of cDNA and exon trapping.

Advanced molecular techniques:
P
ulsed field gel electrophoresis of DNA, Northern and Southern blotting,
RFLP analysis, DNA analysis in disease diagnosis and taxon
omy,
Polymerase Cha
in Reaction:

Concept of
PCR, thermophilic enzymes,

d
esigning
of
primers
, different t
ypes of PCR
-

Gradien
t; Touchdown PCR;
Multiplex PCR, Cloning PCR products,


RT
-
PCR, 5’ and 3’ RACE, qPCR, Real Time PCR using

various
reagents & primers
,
mRNA
Differentia
l Display
,

RAPD fingerprinting of micro
-
organisms
,
DNA sequencing
by Sanger’s method
-
t
raditional and cycle sequencing,

Physical mapping
of BAC clones, STS mapping, shotgun
sequencing,

c
lone
-
by
-
clone shotgun sequencing of genome
,
preparation of BAC/YAC libr
ary, map construction

&

clone selection, genome annotation
s

at nucleotide, protein
&

process level
s
, Comparative genome sequencing
of micro
-
organisms
to identify and categorize SNPs, various molecular techniques for studying DNA
-
protein &
protein
-
protein i
nteractions, high throughput analyses.


G
ene expression

studies & o
verexpression of recombinant proteins:

Gene expression analysis by Northern
Blotting, RT
-
PCR, EST analysis, reporter gene application, enzymatic and bioluminescent reporters,

Functional
ch
aracterization of promoters
,
transcriptomics
-
principles & techniques
, DNA

microarrays (cDNA arrays and
oligo arrays),
Over expression

and tagging of recombinant proteins in
E.coli,
driven by
inducible
/controllable
promoters, expression in

B. subtilis
,
Over expression
vector
systems in
the yeasts
,

baculovirus
&

mammalian
cell over expression systems.

Laboratory W
ork
:
Bacterial transformation, Isolation of plasmid/bacteriophage

& genomic

DNA, Restriction
analysis of DNA, Cloning in plasmid vectors, Const
ruction and screening of gene library, Different PCR
techniques, Gene expression in
bacterial hosts

and

a
nalysis of gene products, Reporter gene assay.

Recommended Books:


1.

Primrose SB and Twyman RM,

Principles of Gene Manipulation and Genomics,

Blackwell
Publishing
(2006).

2.

Lewin B,
Genes VIII,

International Edition, Pearson Education (2004).

3.

Alberts B, Johnson A, Lewis J, Raff M
, Roberts

K, and Walter P,
Molecular Biology of the Cell,

5th Edition,
Garland Science Publishing (2008).

4.

Balasubramanian, D, Bry
ce, CFA, Dharmalingam K, Green J, and Jayaraman, K, Concepts in
Biotechnology, Universities Press (2007).

5.

Satyanarayana U, Biotechnology, Books and Allied (P) Ltd. (2005).

6.

Fritsch J and Maniatis

EF,

Molecular Cloning A laboratory Manual,

Cold Spring Harbor

Laboratory
(1999).







Approved by the 74
th

meeting of the Senate(Feb 19, 2011)


PMY

204 FOOD & DAIRY MICROBIOLOGY


L

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Cr


3

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2

4.
0

Prerequisite(s): None

Introduction :
Basic components of food
,
Factors influencing microbial survival and growth in food: Extrinsic
and intrinsic factors; important micr
obes involved in spoilage of food, meat, poultry, vegetables and dairy
products; microbial deterioration of cereals, pulses, fish and sea
-
foods during storage.

Food chemistry
: Flavours, generation of flavours by microbes, colours, synthetic and natural foo
d colours,
antinutritional components in food, allergenic components in food, additives sweeteners and chemicals generated
during processing, chemical and biological preservatives, their mode of action.

Microbial Toxins:
Bacterial and mycotoxins, microbia
l toxins, chemical nature of important toxins; their role in
food poisoning; physiology and mechanism of action, modification and detoxification; prevention and control of
toxin contamination.

Microbial biomass and Single cell proteins:
Uses of microbes in

meats and poultry products, vegetables
etc.
Use of microbial enzymes in food; low calorie sweeteners, flavour modifiers; Food additives; food quality
monitoring, biosensors and immune assays. Indian fermented foods, mushrooms and food value of mushrooms,
food conversions: Lactic acid conversions, soyabean conversions and cereal products.

Role of microbes in milk and dairy products:
Microbiological examination of milk, standard plate count,
direct microscopic count and reductase test, composition of milk,
sources of contamination of milk, types of
microbes in milk, pasteurization of milk, ability of milk to cause disease; Manufacture of cheeses, butter, yoghurt
and fermented milk.

Functional foods
: Probiotics, prebiotics and nutraceuticals; characteristics
of probiotic microorganisms,
production of probiotic foods and nutraceuticals, factors affecting functionality of probiotic, prebiotic and foods
containing nutraceuticals, consumer perception of functional foods.

Principles of Food preservation:
Spoilage m
icroorganisms in food
,
basic principles
,
preservation by use of
high temperature, low temperature, drying and desiccations, chemical preservatives and additives, preservation
by radiation, alternatives to conventional preservation methods.

Food quality& S
afety:
International and national guidelines, traceability in food chain, HACCP, GMP,
adulteration and bioterrorism, GLP and biosafety guidelines


Laboratory exercises:

Detection of food borne pathogens and selected spoilage bacteria, recovery of heat
injured pathogens from
processed foods, D & Z value tests, quality tests for raw milk, simulated survival studies of surrogate pathogens
in food, assessment of risk using prediction based models, assessment of synthetic preservatives , detection of
microb
ial toxins, estimation of nutraceuticals, vitamins and sweeteners, preparation of fermented dairy foods,
evaluation of probiotic characteristics of standard probiotic cultures, preparation of probiotic diary/non dairy
food, substantiation of health cla
ims of probiotic cultures(
in vitro

only).


Recommended books

1.

Adams M R, Mo
ss M O, Food Microbiology
, 3
/
E,

RSC Publishing
, Cambridge (
2008
).

2.

Jay JM, Loessner MJ, Golden DA, Modern Food Microbiology, 7/E, Springer (2007)

3.

Forsythe S, The Microbiology of Safe

Food, 2/E, John Wiley & Sons (2010)

4.

Montville TJ, Matthews KR, Food Microbiology: An Introduction, 2/E, ASM Press (2008)

5.

Robinson R
K,

Dairy Microbiology

Handbook
,
3/E, John Wiley & Sons (2002)




Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
205 IMMUNOLOGY


L

T

P

Cr


3

0

2

4.0

Prerequis
ites: None

Immune System:
Introduction and overview, General features of immune response, Clonal selection
hypothesis, Lymphoctes, Macrophages, Dendritic cells, Other non
-
lymphoid cells, Primary and secondary
lymphoid tissues and organs.

Antigens and Ant
ibodies
: Factors responsible for immunogenicity, Epitopes, Adjuvants, Superantigens,
Structure and function of immunoglobulins, Immunoglobulin superfamily, Monoclonal antibodies,
Immunoglobulin genes, generation
of antibody
diversity.

Antigen
-
antibody Reac
tions
: Molecular mechanism of Antigen
-
Antibody binding, Precipitation reaction,
Agglutination,
Immuno
-
electrophoresis,
Immunoflorescence, ELISA, Western
-
blotting.

B
-
Cell and T
-
Cell Activation
: Antibody responses, Cell interactions in antibody response, B c
ell activation,
Synthesis and secretion of immunoglobulins, T
-
cell receptor, T
-
cell maturation, Activation, Differentiation.

Major Histocompatibility Complex
: Histocompatibility genes, Genomic map of H
-
2 comples in mouse, HLA
complex in humans, Structure o
f MHC molecules, MHC
-
peptide interaction, Minor Histocompatibility loci,
Antigen processing and presentation.

Cytokines and Regulation
: Common properties of cytokines, Cytokine types, Molecular mechanism of
regulation, Biological activities of cytokines, P
ro
-
inflammatory cytokines, Chemokines, Cytokine diseases and
therapies.

Tolerance and Autoimmunity
: Tolerance, Mechanism of self tolerance, Autoimmunity
, Complement systems,
hypersensitive

reactions, Immunopathologies, AIDS and other immune
-
deficiencies
,

T
ransplantation
-

Tissue
and organ grafting, Cancer and the immune system
.

Antibody and Cell
-
mediated Effector Responses:
CTL, NK, DH, Immune responses to infection, vaccines,
Leukocyte recirculation and inflammation, Neutralization, Opsonization, ADCC
.



L
aboratory
W
ork
:

Blood film preparation and identification of cells,
lymphoid

organs and their microscopic
examination, Immunization and collection of serum, Immuno
-
diffusion, Western blotting, ELISA,
Immunodiagnostics (with commercial kits)

radial and dot
ELISA
, Animal Handling
.



Recommended Books

1.

Delves PJ and

Roitt IM, Roitt's Essential Immunology, 11/E, Wiley
-
Blackwell (2006)

2.

Murphy KP,
Murphy KM, Travers P, Walport M and

Janeway C, Immunobiology,7/E,

Garland
Science(2008)

3.

Elgert DK, Immunology: unders
tanding the immune system, 2/E, John Wiley and Sons(2009

)

4.


Go
ldsby RA, Kindt TJ, Osborne BA and

Kuby J, 6/E, W H Freeman & Co

(
2006
)

5.

Richard C and
Geoffrey

S,

Immunology: a short course, 6/E, Wiley
-
Blackwell

(
2009
)


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
206

INDUSTRIAL

MICROBIOLOGY

& BIOTECHNOLOGY


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3

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3

4.5

Prerequisites: None

Introduction to industrial microbiology:
Sources of industrially important microbes, screening techniques, strain
development, types of fermentation and fermenters, process optimization, and rec
ent developments in fermentation
technology
, culture maintenance and preservation of

industrially important

microorganisms.

Fermentation economics:
Basic o
bjective for successful economically viable fermentation process, cost break down for
well establishe
d fermentation processes, market potential of the products, cost aspects of various stages in the processes
development including effluent treatment

Production aspects:
M
icrobial production of alcohols: vinegar, wine and alcohol, industrial production of s
olvents
-
glycerol, acetone, and butanol, production of citric acid and glutamic acid , production of amylase and proteases; industrial

production of antibiotics: Penicillin and Cephalosporin; enzyme immobilization and applications, Microbial production of
V
itamin B
2
and B
12 ,

microbial production

of
r
ecombinant products (insulin,

somatostatin, thaumatin, interferon); vaccine

production,


microbial polyester and polymers and biotransformations
,
Microbial nanosensors; Whole Cell ( enzyme and
protein based)
biosensors and their applications.


Laboratory Work
:
Isolation of antibiotic/ amino acid/organic acid producing microbes and their preservation, Batch
fermentation
for

Citric acid production, recovery and estimation of citric acid; Production of any vita
min and its
quantification by bioassay, Penicillin production and estimation of penicillin,
Strain improvement for enhancing citric acid
production.



Recommended books

1.

Blatz RH, Davies JE and

Demain AL, Manual of Industrial Microbiology and Biotechnology
, 3/E, ASM
Press (2010)

2.

Waites MJ, Morgan NL, Rockey JS and

Higton, G, Industrial Microbiology: An introduction, 7/E,
Wiley
-
Blackwell (2008)

3.

Barredo JL, Microbial processes and products, Humana Press (2005)

4.

Glazer AN and

Nikaido H, Microbial Biotechnology:

Fundamentals of Applied Microbiology,2/E, WH
Freeman and Co (2007)

5.

Moo
-
Young M, Cooney CL

and Humphery AE, Comprehensive B
iotechnology
: The Principles,
Applications and Regulations of Biotechnology in Industry, Agriculture a
nd Medicine
, Pergamon Press
(19
85).





Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
301
MICROBIAL ECOLOGY
& ENVIRONMENTAL MICROBIOLOGY


L

T

P

Cr


3

0

2

4.
0

Prerequisites: None

Introduction:

Introduction and historical context, Origin and evolutionary record of life,
Microbe: microbe
interactions, Microbe: plant/animal

interactions,
Population ecology, Microbial community structure:
benevolent interactions (control within the microbial communities of rhizosphere), antagonistic interactions,
(competition, antibiosis, predation etc.).

Ecological Adaptations:

Occurrence,
diversity, adaptations and potential applications of oligotrophs,
thermophiles, psychrophiles, barophiles, organic solvent and radiation tolerants, metallophiles, acidophiles,
alkaliphiles and halophiles;
Biogeochemical cycling, Quantitative ecology: numbe
rs and biomass, Quantitative
ecology: metabolic activity, Molecular microbial ecology, Metagenome analysis
, Biofilms.

Marine ecosystem:

Environment of marine bacteria, bacterial growth in sea and its regulation by
environmental conditions, modeling of grow
th 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
,
bioremediation of heavy metals, pesticides, PAH and role of
GMO’s in population
abatement.

Brief history and development of environmental microbiology:
History and development of microbial
ecology highlighting significant contributions of microbiologists and emergence of environmental
microbiology, and significant
applications of microbes in solving environmental pollution problems

Biodegradation and Biogeochemical cycling:
Microbial degradation of lignocellulosic substances, keratin and
chitin and Xenobiotics i.e of pesticides; hydrocarbons; clean up of sites pollu
ted with oil spills, heavy metals
and chlorinated solvents; biological treatment of effluents of sugar, pulp and paper industry

W
aste disposal and management:

Microbes in solid waste and sewage treatment systems, disinfection of
potable water supplies; Mic
robial water safety; Microbial assessment of water quality; Standards for tolerable
levels of fecal contamination, Bioaugmentation and Biostimulation,

Biomining and Microbially enhanced Oil Recovery (MEOR):

Recovery of minerals and metals from ores i.e
bio
leaching, Use of microbes for the recovery of oils from oil wells.


Laboratory Work
:
Isolation and identification sewage micro flora;
To study the microbiological quality of
water samples from different sources

and
calculate their relative abundance and f
requency of occurrence
; To
study the decolorization of distillery or textile industrial waste;
Determination of BOD of water from tap and
effluent.


Recommended books

1.

Barton LL and

Northup DE, Microbial Ecology, John Wiley & Sons (2008)

2.


Fry

JC, Giuliano
L and

Golyshin PN, Aquatic Microbial ecology: thematic issue Elsevier, 2003

3.

Maier RM, Pepper IL and

Gerba CP, Environmental Microbiology, 2/E, Academic Press (2009)

4.

Mitchell RG

and

Ji
-
Dong, Environmental Microbiology, 2/E, Wiley
-
Blackwell (2010)

5.

Hurst CJ

and

Crawfold RL,
Manual of Environmental M
icrobiology, 3/E, ASM Press (2007)







Approved by the 74
th

meeting of the Senate(Feb 19, 2011)


PMY
302 BIOPROCESS TECHNOLOGY


L

T

P

Cr


3

1

2

4.5

Prerequisites: None






Introduction and Basic Concepts:
Units and dimensions,
Principles of bioprocesses, advantages
over
chemical process, bioprocess control, types of reactors and
the relation between chemical and biochemical
process.

Sterilization Concepts:
Sterilization principles and practices, Media sterilization, thermal
-
death batch and
continuous sterilization sy
stems, Sterilization of air fibrous filters, Design of continuous sterilization.

Cell and Enzyme kinetics:
Cell number and Cell mass calculations, Material and Energy balance,

Continuous
and batch fermentation, Microbial growth kinetics, Growth and non
-
gro
wth synthesis, Cell and enzyme
immobilization, Production of biomass and important extracellular products, Product synthesis kinetics,
Submerged and solid state fermentation.

Bioreactor Studies:
Study of Batch, CSTF (Continuous stirred tank fermenter) and
Plug flow reactor (PFR),
Calculations for steady state substrate, Product concentration, External and internal feedback system, Airlift
bioreactors
, UASB reactors.

Aeration and Agitation:
Aeration and agitation systems for bioreactors and their design, Mas
s transfer in
microbial system, Gas liquid transfer, Biological heat transfer, Energy and material balance.

Down stream processing
: Product isolation and recovery, Disruption of microbial cells, Filtrations, Reverse
osmosis, Spray drying methods, Quality c
ontrol and bioprocess economics
-
Scale
-
up considerations of
bioprocesses, Freeze drying.


Laboratory Work

:
To study different types of bioreactors, Fermenter sterilization, Medium preparation,
sterilization and checking sterility by thermal death kinetics
, Surface culture fermentation to study the
production of lactic acid using sucrose and lactose as the raw material, Production of citric acid, Growth
kinetics for some industrially useful organism, Immobilization of cell on a matrix, Estimate the mass tra
nsfer
coefficient in a fermenter by sulphite oxidation method, Study solid state fermentation, Production of yeast
cells, Industrial visits.



Recommended Books

1.

Shuler ML

and Kargi
F
,
Bioprocess Engineering: Basic Concepts,
Prentice
-
Hall (200
1
)

2
nd

ed
.



2.


Stanbury PF
, Principles of Fermentation Technology, Book News, Inc. (19
92
)

2
nd

ed
.

3.

Vogel
HC
an
d Haber
CC
,
Fermentation and Biochemical Engineering Handbook,
Noyes Publications (
2001
)

2
nd

ed
.

4.

Bailey JE and Ollis DF
, Biochemical Engineering Fundamentals, McGraw
-
Hill (1986).

5.

Wang

DC and Humphrey

L, Fermentation and Enzyme Technology, John Wiley (1989).


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
303 AGRICULTURAL MICROBIOLOGY


L

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P

Cr


3

0

2

4.
0

Prerequisites: None





Soil Microbiology:
Soil as a habitat for microorganisms; Soil enzymes, Soil water & microbial activity, Soil
microflora, soil fertility and management of agricultural soils, rhizosphere, phylloplane and rhizoplane
microbes & their interaction with plan
ts.

Plant pathogenesis:
role of toxins and enzymes; Fungal , bacterial and viral diseases of plants: Rusts of wheat,
linseeds; late blight of potato; red rot of sugarcane; Citrus canker, blight; Leaf curl of Papaya, vein clearing of
lady’s finger

Bioferti
lizers:
Biofertilizers; Rhizobium
-
taxonomy, physiology, host
-
Rhizobium
interaction, mass cultivation;
Associative and non symbiotic association
-
Azospirillum, Azotobacter
, Cyanobacteria; Mycorrhiza: Host
-
fungus
specificity, host fungus interactions, rhizo
sphere environment and recognition phenomenon, interaction of
mycorrhizal fungi with non
-
host plants, functional capability
-

plant nutrition and stress tolerance; Commercial
production of biofertilizers, formulations and BIS specifications; their applicati
ons and limitations for Indian
agriculture.

Biopesticides:
Microbiology of plant surfaces; Principles of biological control; microbial control of pests
-

bioinsecticides; biofungicides and bioherbicides; commercial production of biopesticides with reference

to
Bacillus thuringiensis
; integrated pest management, their applications and limitations for Indian agriculture;
v
iral control of insect pests : Nuclear polyhedrosis visuses (NPV) and cytoplasmic polyhedrosis viruses (CPV).

Composting and Green Manure:

M
icrobiology of composting and compost enrichment, and green manuring;
reclamation of barren lands, production of biogas and alcohol from agricultural wastes.


Laboratory Work
:

Isolation and identification soil micro flora
;
Isolation, culturing and seed in
oculation of
Rhizobium

and testing of nodulation ability and beneficial effects, Isolation and testing the efficiency of various
biofertilizers like
Rhizobium, Azotobacter, Azospirillum
, Isolation of mycorrhiza from soil, isolation from plant
pathogenic ba
cteria and fungi
, Isolation of microbes from compost.


Recommended books

1.

Rai MK, Handbook of M
icrobial Biofertilizers, Routledge,
(
2006
)

2.

Rangaswami G, Bagyaraj DJ, Bagyaraj DG, Agricultural Microbiology, 2/E, PHI Learning Pvt. Ltd
(2004)

3.

Elsas
JD, Jansson

JK, Trevors JT, Modern soil microbiology, 2/E, CRC Press/ Taylor & Francis (2007)

4.

Insam H, Riddech N,

Klammer S, Microbiology of C
omposting, Springer (2002)

5.

Khetan SK, Microbial Pest Control, Marcel Dekker (2000)


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
304
MEDICAL

& DIAGNOSTIC MICROBIOLOG
Y


L

T

P

Cr


3

0

2

4.
0

Prerequisite(s): None

Introduction:

Early discovery of pathogenic microorganisms, Host
-
parasite relationship governing the
infection and establishment of disease, factors affecting virulence, normal microflora of human body; norm
al
flora of skin, respiratory, gastrointestinal, genital tract, role of resident flora, mode of spread of infection

,
invasiveness, role of aggressins, hyaluronidase, coagulase, fibrinolysins or kinase; depolymerizing enzymes
mucinase, lipases, proteases,
nucleases, collagenase, neuraminidase, depolymerising enzymes, organotroisms,
variation and virulence
.

Sources of infection
:
Opportunistic and true pathogens, establishment and spreading of infections,

Pathogenicity,
Mode of spread of infection: Respirato
ry, skin, wound and burn infection, venereal infections,
alimentary tract infection, arthropod borne blood infections, laboratory infections, nosocomial infections,
preventive and curative measures for diseases.

Pathogenic bacteria:


Salient features and d
iagnosis of
Pneumococcus, Neisseria
,
Corynebacterium,
Clostridium
,
Proteus
, Shigella, Salmonella
,
Vibrio, Mycobacterium, Staphylococcus, Pseudomonas,
Pasteurella, Yers
i
nia, Brucella;

Actinomycetes, Rickettsiaeae,
C
h
lamydiae
,

Spirochaete

and Microbial
biofi
lms.

Pathogenic fungi:
Classification of medically relevant fungi
,

Collection of clinical samples and laboratory
diagnosis of important human fungal diseases: Candidiasis; Dermatophytosis; Aspergillosis; Otomycosis;
Cutaneous and subcutaneous mycoses; Syst
emic mycoses; Opportunistic mycoses; Antifungal agents (specific
to disease to included in course).

Parasitology:
Important diseases caused by intestinal and urogenital protozoa:
Entamoeba
;
Giardia
;
Trichomonas
; Blood and tissue protozoa;
Plasmodium;Trypan
osoma
;
Leishmania
.


Clinical Microbiology:
Collection and transport of clinical specimens and serological testing for important
pathogens (bacterial, viral and fungal)
,

Laboratory diagnosis of bacteria, fungi, parasites & viruses
.


Laboratory Work
:

Isolati
on of transient and pathogenic microflora from Skin and oral cavity, in vitro
antimicrobial susceptibility testing of topical disinfectants and antibiotics, evaluation of mouth rinses in
reduction of microflora in the oral cavity
,
Isolation and identificat
ion of microorganisms from sputum, throat,
nose, ears swabs and urine samples; Isolation and enumeration of bacteria from
saliva, t
o study pathogenicity of
Staphylococcus aureus
by coagulase test;
Preparation of Antigens, control sera for serological tests
.
;
Laboratory
diagnosis of important human diseases
:

Tuberculosis,

Typhoid (
WIDAL
)
,

venereal

diseases
(
VDRL
).


Recommended Books

1.

Murray P.R
., Pfaller M.A., Tenover F.C., and

Yolken R.HClinical Microbiology, ASM Press
(2007)

2.

Forbes BA, Sahm DF, Weissfeld A
S, Bailey WR, Bailey’s and Scott’s Diagnostic Microbiology 12/E
,
Elsevier Mosby
(2007)

3.

Greenwood D,

Medical Microbiology
4/E,

I.K. Inter
national (2004)

4.

Kayser FH,
Medical M
icrobiology, Thieme (2004)

5.

Mims CA, Medical M
icrobiology, 3/E, Mosby (2004)


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
202 BIOINFORMATICS


L

T

P

Cr


3

0

2

4.0

Prerequisites: None


.

Biological Databases
: Biodiversity information, Sequence databases, Protein and nucleic acid databases,
Structural and cluster data, Basics of sequence analysis, Similarity searches an
d related algorithms, Comparison
and scoring, Statistical interpretations, Motifs and domains.

Biological Data Computation
: Datamining and data security, Identification of protein primary sequence,
Practical aspects of multiple sequence alignment, CLUSTALW
, MULTALIN, BLOCKS, ALSCRIPT, Macbox,
Phylogenetic analysis, Tree building, Evaluation of trees and blocks, Detection of functional sites, Repeat
analysis, AAcompledent and AAcompsin; Propsearch, Sequence, Physical property interpretation, nnPredict,
ssPre
d, SOPMA.

Modelling Softwares
: GCGsequence analysis, Oligoprimer analysis, Rasmol, Chemical Drawing Softwares,
Molpac, MDL systems, MOLSCRIPT, ALSCRIPT, TREEVIEW.

Machine Learning and Bioprogramming
: Development of Algorithms, Algorithms on strings, trees

and
sequences, Hidden Markov Models, Artificial Neural Networks.


Laboratory W
ork
:
Sequence analysis, Biodiversity informatics and phylogenetic analysis, Protein
visualization and structural elucidation, Comparative genomics and proteomics, Chemical graph
ic visualization
and informatics, Introduction to machine learning techniques


Perl based and Visual C++.



Recommended Books

1.

Dwyer RA, Genomic Perl: From Bioinformatics Basics to Working Code, Cambridge University Press
(2004).

2.

Leach AR, Molecular Model
ing: Principles and Applications, Pearson
-
Education (2001) 2
nd

ed.

3.

Mount DW, Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor Laboratory Press (200
1
).

4.

Higgins D and Taylor W, Bioinformatics: Sequence, Structure and Databanks


A Practical A
pproach,
Oxford University Press (2000).

5.

Bish
op MJ and Rawlings CJ, DNA and Protein Sequence Analysis
-

A Practical A
pproach
,

Oxford
University Press (1997).


Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PHU301 ENTREPRENEURSHIP AND IPR


L

T

P

Cr


3

1

0

3.5

Prerequisites: None


Entrepreneursh
ip:

Entrepreneurship and principles of entrepreneurial development, Qualities of an
entrepreneur, Functions and types of entrepreneur.

Project Management
: Formulation, Identification and selection based on size, Technological assessment,
Project cost and
market potential and marketing concepts.

Project Appraisals
: Technical reports and feasibility reports with commercial viability, Break
-
even analysis,
Depreciation, Sources of funding.

Financing:
Sources of finance, Initial capital, Capital structure, Ve
nture capital and Institutional finance.

Economics
: Demand
-
supply
-
pricing, Business ethics, Industrial laws,
Women entrepreneurs


Role, problems
and development.

Industrial Sickness
: Symptoms, control and rehabilitation of sick units.

Introduction to Inte
llectual Property
: Intellectual property and IPR, patent, copyrights, geographical
indications, trademarks, trade secret, Industrial designs, Patent law, Legislations covering IPR’s in India,
product planning and development, filing patent, provisional and

complete specification, patentable and non
-
patentable items, Valuation & business concerns.


Recommended Books


1.

Desai V
,
Dy
namics of Entrepreneurial Development and Management, Himalaya Publishing House
(2007).

2.

Singh I. and Kaur B
, Patent law and Entrepre
neurship, Kalyani Publishers (2006).

3.

Sateesh MK
, Bioethics and Biosafety, IK International (2008).



Approved by the 74
th

meeting of the Senate(Feb 19, 2011)



PMY
40
1 PLANT

PATHOGEN INTERACTIONS


L

T

P

Cr


3

0

2

4.0

Prerequisites: None




Concepts
and
physiology

of plant diseases:
What is a disease and w
hat causes disease, pathogenesis,
pathogenesis

in relation to environment, effect of microbial infections on plant physiology, photosynthesis,
respiration,

transpiration, translocation.

Biochemical basis of plant diseases:
Enzymes and toxins in plant disea
ses, phytoalexins.

Some important plant diseases and their etiological studies:
Crown gall, symptoms of viral diseases and
their

control, diseases of some important cereals, vegetables and crops.

Genetical basis of plant diseases:
Genetics of host
-
pathogen

interactions, resistance genes, resistance
mechanism

in plants.

Disease control:
Principles of plant disease control, physical and chemical methods of disease control,
biocontrol,

biocontrol agents
-

concepts and practices, fungal agents,
Trichoderma
as b
iocontrol agent,
biocontrol agents


uses

and practical constraints.

Molecular approach:
Molecular diagnosis, transgenic approach for plant protection, futuristic vision of
molecular

diagnosis, applications and constraints.

Disease forecasting:
History and

important milestones in disease control, disease forecasting and its relevance
in

Indian farming.

Recommended Books

1.
George N,

Plant Pathology,
Agrios: Academic press, New York,
4th ed.,
(
1969
)
.

2.
R.S. Mehrotra

RS,

Plant Pathology,

Tata McGraw

Hil
l Pu
blishing Company L
imited. New Delhi

(2003).

3.
Sigee DC, Bacterial Plant Pathology, Cell and Molecular A
spects, Cambridge University Press,

(
1993
)
.

4.

Dickinson

M, Molecular Plant P
athology
,

BIOS Scientific Publishers, London,
(
2003
)
.

5.
Basu, AN and Giri
BK,
The essentials of Viruses, Vectors and Plant diseases Wiley Eastern Limited,

(
1993
)
.















Approved by the 74
th

meeting of the Senate(Feb 19, 2011)


PMY
40
2

PROTEIN ENGINEERING AND ENZYME TECHNOLOGY


L

T

P

Cr


3

0

2

4.0

Prerequisites: None


Protein Engineering and Design:

Conformation of protein
s
-

Ramachandran plot, secondary, tertiary and
quaternary structure, domains, motifs and folds, Relationship between structure and function, Methods in
protein engineering and design


Physical, computational, biochemical and molecular techniques, Protein
engineering in lysozyme and pepsin class of enzymes, Chemical modifications of proteins, Design of peptides
and protein mimics.



Enzyme Technology:

Introduction, Enzyme production, Mechanism of enzyme action and specificity,
Identification of binding and
catalytic sites, Activation energy and transition state theory, Use of enzymes in
free solution and associated problems, Stabilization of soluble enzymes, Objectives of enzyme immobilization,
Methods of enzyme and cell immobilization
-
adsorption, entrapment
, direct covalent linkage, cross
-
linking,
Immobilized enzyme reactors
-

Batch, continuous and membrane reactors, Applications of immobilized
enzymes
-

Manufacture of commercial products and analytical purposes, Enzyme electrocatalysis
-

immobilization of e
nzymes onto electrodes, measurement of enzyme activity, regeneration of cofactors,
Enzymes as biosensors.



Laboratory work:

Introducing todifferent protein structure databases, Visualization 3
-
D protein structures,
Predicting physical properties of protei
ns, Analysis of secondary, tertiary and quaternary structure of proteins
from sequence information, Predicting domains, Active sites and protein
-
ligand interactions, Primary screening
for useful enzymes from microbes and other sources, Production, Purifica
tion and characterization of enzymes,
Determination of Vmax & Km, Enzyme immobilization by different methods, Chemical modification of
proteins.

Recommended Books

1.

Balasubramanian D, Bryce CFA, Dharmalingam K, Green J, and Jayaraman

R
, Concepts in Biotechno
logy,
Universities Press (2007).

2.

Berg

JM
, Tymoczko JL and Stryer L
,

Biochemistry, W H Freeman and Company (2002).

3.

Creighton TE, Protein
-
Structure and Molecular Properties, W.H. Freeman and Co. (1997).

4.

Friefilder D and Malacinsk
i
,GM, Essentials of Molecular

Biology, Panima Books (2006).

5.

Rastogi SC, Mendiratta N and Rastogi P, Bioinformatics
-

Methods and Applications, PHI (2006).

6.

Satyanarayana, U, Biotechnology, Books and Allied (P) Ltd. (2005).

7.

Smith JE, Biotechnology, Cambridge University Press (2006).