Microbial Biotechnology - Punjabi University Patiala

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M
.Sc.
(
Microbial Biotechnology
)

Part
-
I (Semester I & II)


F
or 20
11
-

1
2 &

201
2
-
1
3 Session


SEMESTER
-

I

P
-
I

Microbiology and Immunology

P
-
II

Microbial Genetics

P
-
III

Microbial Biochemistry

P
-
IV

Analytical Techniques


PRCTICAL

PAPER



1
: PERTAINING TO THEOR
Y PAPER

PI & PII.

PRACTICAL

PAPER



2
:
PERTAINING TO THEORY PAPER
PIII & PIV.


2
ND

SEMESTER

P
-
V


MICROBIAL METABOLISM

P
-
VI


GENETICS AND METABOLIC ENGINEERING

P
-
VII


BIOPRO
CESS AND FERMENTATION ENGINEERING

P
-
VIII


ENZYMOLOGY AND ENZYME TECHNOLOGY


PRCTICAL

PAPER


3: PERTAINING TO THEORY PAPER PV & PVI.

PRACTICAL PAPER


4: PERTAINING TO THEORY PAPER PVII & PVIII.


M.Sc. (Microbial Biotechnology)

Part
-

II(Semester III & IV)

For 2011
-
12 Session



3
RD

SEMESTER

P
-
IX


INDUSTRIAL MICROBIOLOGY


I (HEALTH, FOOD

AND

METABOLITES)

P
-
X


INDUTRAIAL MICROBIOLOGY

II (ENVIRON
M
ENTAL

BIOFUELS,
CHEMICALS AND BIOMASS)

P
-
XI


BIOSTATAISTICS AND COMPUTER APPLICATIONS

P
-
XII


BIOSAFETY, BIOETHICS AND INTELLECTUAL PROPERTY RIGHTS



PRACTICAL


5:
PERTAINING TO THEORY PAPER, P


IX & P
-
X

PRACTICAL


6:

PERTAINING TO THEORY PAPER, P
-
XI & P
-

XII


4
TH

SEMESTER

P
-
XIII


ENTERPRENEURSHIP,

PROJECT MANAGEMENT AND QUALITY

ASSURANCE

P
-
XIV


BIOINFORMATICS AND COMPUTATIONAL BIOLOGY


PRACTICAL

PAPER



7,


PERTAINING TO THEORY PAPER, P
-
XI
II & P
-

XIV

DISSERTATION



M
.Sc. (Microbial Biotechnology)

Part
-
I (Semester I
)

For 2011
-

12 & 2012
-
13 Session


Paper


I

Microbiology & Immunology


M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%



(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two question
s from respective sections of the syllabus and carry 15 marks each. Section E will
consist of 10 short answer type questions which will cover the entire syllabus uniformly and will
carry 20 marks in all.

Instructions for the candidates

01.

Candidates are req
uired to attempt one question each from sections A, B, C and D of the
question paper and the entire section E.

02.

The use of scientific calculators is allowed.






Section
-

A

01.

Introduction and history of Microbiology: Microscopy
-

light microscopy,
fluorescen
t microscopy, electron microscopy
, P
hase contrast

02.

Microbial g
roups: Prokaryotes & E
ukaryotes
: structure, function & classification.

03.

Viruses: Bacteriophages, cyanophages, plant & animal viruses


A brief account.


Section


B

01.

Pure culture techniques: isolat
ion & maintenance
of microbes, strain improvement
& media optimization

02.

Microbial Growth characteristics: growth curve, kinetics of Growth, Factor
s
affecting growth, measurement

of growth.

03.

Microbial spoilage: Toxins, microbial infections, a brief ac
count including

prevention and control.


Section


C

01.

Introduction to immunology, Historical Background, innate immunity
,

adaptive

immunity, cells & organ of the immune system
,
antigens, Antibodies,

02.

Cell mediated immune response and its mechanis
m
:

H
um
o
ral response & its
mechanism. Complement system.

03.

Transplantation
, MHC, auto immunity, Hypersensitivity
.


Section


D

01.

Hybridoma

techniques & monoclonal antibody production, Applicatio
n of
monoclonal antibodies
.

02.

Vaccine development & production and
immune
-
potentiation.

03.

Techniques of cell mediated and humoral immune response.



Suggested Readings

(Latest Editions)
:


1.

Betty Forbes, Daniel Sahm, Alice Weinfield, Bailey


Scott’s Diagnostic
Microbiology, 12
th

Edition Mosby, 2007

2.

Gerald Collee J
,

Andrew G

Fraser, Barrie P

Marmion, Mackie and McCartney’
s
Practical Medical Microbiology , Elsevier . 2006

3.

Elmer W Koneman et al
.
, Koneman’s Color Atlas and Text Book of Diagnostic
Microbiology, 6
th

Edition Lippincott Willams and Wilkins, 2005

4.

Patrick R. Murray, K
en S. Rosenthal, Michael A Pfalle
r. Medical Microbiology ,
5ht ed. (Philadelphia:

Elsevier/ Mosby , 2005

5.

Harvey, R.A.
, P.C. Champe, and B.D. Fisher.

Microbiology 2
nd

Edition
,
LIPP
INCOTTS’S ILL
USTRATED REVIEWS (Philadelphia : Lippincott.
Williams & Wilkins,

2007)

6.

Text Book of Bacteriology


N
.

C. Day & T
.

K
.

Day

7.

Parasitology


K.D. Chatterjee.

8.

Text Book of Microbiology


Chakarbourty.

9.

Bacteriology / Mycology / Virology :

10.

Microbiology


Prescott
, et. al

11.

Micr
obiology


Bernard D. Davis, et
. al

12.

Immunology , A.
Goldsby , J, Kindt, Osborne, 4ht Edition 2000, W.H. Freeman.

13.

Immunology & Immunopatholog by Stewart.

14.

Cellular and Molecular Immunology by Abul K. Abbas et al.

15.

Text Book of immunology by Barret.

16.

Essentia
l immunology by Roitt. Brostoff,

Male
,

Harcourt Brace
& Company (5
th

Edition)
,

Mosby (6
th

Edition ).

17.

Immunology by Kuby by Richard A Godlsby , Thomas J. Kindt. Barbara A.
Osborne, Freeman & Company Mosby Publishers.

18.

Molecular Biotechnology by Bernard R. Glick & Jack . J. Pasternak.

19.

Immunology by Kuby.


P
ape
r
-
II

Microbial Genetics


M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%


(
Theory and Practicals separately
)

Instructions fo
r the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two questions from the respective sections of the syllabus and carry 15 marks each. Section E
will consist of 10 short answer type ques
tions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidates are required to attempt one question each from sections A, B, C and D of the
question paper and the entire section E.

2.

The use of

scientific calculators is allowed.







Section


A

1.

Genome Organization:
-

Types of genetic material : DNA
-

A, B
-
,Z, and triplex
DNA, RNA, organizati
on of

bacteriophage genomes
-
Ph
iX174, lambda, T4, Mu,
fine structure of chromatin, bacterial and eukaryoti
c
genome
organization : Role
of nuclear matrix in chromosome organization and function: Matrix binding
prot
eins.

2.


Heterochromatin and Euchromatin
:
DNA melting an buoyant
density:

DNA re
-
association kinetics (Cot curve analysis): Repetitive and unique seque
nces:
Satellite DNA;
Nucleosome phasing: DNa
se I hypersensitive regions:

3.

Genome Replication and Repair:
-

Replication initiation, elongation and
termination in prokaryotes and eukaryotes; Enzymes and accessory proteins:
Fidelity: Polymerase chain reaction
, Replication of single stranded circular DNA:
Gene stability DNA repair


enzymes: Photo reactivation: Nucleotide excision
repair: Mismatch correction: SOS repair.





Section


B

4.

Prokaryotic and Eukaryotic Transcription:
Prokaryotic Transcription:
Trans
cription Unit; RNA polymerase, Promoters, Operators, Regulatory elements,
Initiation: Termination


Rho
-

dependent and i
ndependent : Anti


termination.

Transcriptional regulation


Positive and negative:

5.

Eukaryotic Transcription Process:
Transcriptional
RNA polymerases,
transcription factors, regulatory elements, RNA polymerase structure and
assembly ;RNA polymerase I, II, III; eukaryotic promoters and enhancers;
General Transcription factors: Activators and repressor

6.

Transcript Processing:
-

Processing o
f tRNA and rRNA; co
-

transcriptional and
post


transcriptional modifications; 5’ Capping polyadenylation, nuclear export
of

mRNA, mRNA stability, Splicing; RNA editing,

Catalytic RNA
s
.






Section


C

7.

Translation:
-

Prokaryotic and Eukaryotic Translation

process: Genetic code.
degeneracy of genetic code, altered genetic code
-

mitochondria, Termination
codons;

Isoaccepting tRNA; Wobble hypothesis
.

8.


Ribosome
,

tRNAs, mechanism of prokaryotic and eukaryotic translation
processes; initiation, elongation and t
ermination, the translation machinery, co
-

translational and post
-

translational modifications of proteins; Transport of
proteins and molecular chaperones; Protein
folding,
stability; Protein turnover and
degradation

9.

Regulation of gene expression in proka
ryotes and eukaryotes:
-

regulatory
signal elements, hLh motifs, activators and inhibitors of protein synthes
is, the
operon concept, Lac, Tr
p Ara,, His operons, positive, negative and compound
control, Attenuation, quorum sensing, spatial and temporal reg
ulation of Gene
expression in eukaryotes.

DNA
M
ethylation & Imprinting.




Section


D

10.

Mutations: Oncogenes and Tumor suppressor genes:
-

Nonsense, missense and
point mutations; intragenic and Intergenic suppression; Frame shift mutations;
Physical, ,chemic
al and biological mutagens; Transposition


Transposable
genetic elements in prokaryotes and eukaryotes; Mechanisms of transposition;
Ro
le of transposons in mutation .

11.

Viral and Cellular oncogenes; Tumor suppressor genes from humans; Structure,
function an
d mechanism of action of pRB and p53 tumor suppressor proteins;
Activation of oncogenes and dominant negative effect; Suppression of tumor
suppressor genes; Oncogenes as transcriptional activators.


12.

Gene Disruption and Gene Targeting:
-

Homologous Recombin
ation: Holliday
junction, FLP/FRT and Cre/Lox recombination gene targeting, gene disruption
Rec A and other recombinases; Antisense and Ribozyme Technology; Molecular
mechanism of antisense molecules, inhibition of splicing, polyadenylation and
translation
, disruption of RNA structure and capping, strategies for designing
ribozymes and antisense RNA, Application of Antisense and ribozyme
technologies in medical science.



Suggested Readings

(Latest Editions)
:

1.

Biotechnology


Fundamentals of Microbial Genet
ics and Genetic Engineering (Vol. 12)
by R.H. Rehm and G. Reed, Veriag Press, NY, 1992.

2.

Gene Cloning by T.A. Brown, Van Nesterland and Rainold, NY, 1996.

3.

Genes VII by B. Lewin, John Wiley & Sons, NY,

4.

Genetic Fundamentals & Genetic Engineering by H.R. Rehm

and G. Reed, Vol
-
12 VCH,
1993.

5.

Genetics for Microbes by A. Brainbridge, Balckkis & Sons Ltd. New York, 1987

6.

Molecular Biology by D. Grialder, Narosa Publishing House, New Delhi, 1989

7.

Molecular Biology of the Cell by B. Alberts, D. Bray, J.Lewis , M. raft,

K. Ropbertis and
J. Watson, Gerland Publish ICE, 1988.

8.

Molecular Cloning (Vol. 1,2, & 3) J. Sambrook, E.F. Fristsch and T. Maniatis, Cold
Spring, Harbor, NY, 1989

9.

Microbial Biotechnology by D. Drilder, Narosa Publishing House New Delhi, 1989

10.

Molecular Bio
technology : Principles & Applications of recombinant DNA by Bernard
R.Click and Jack J. Pasternak, ASM Press, Washington, D.C. 1997.

11.

Principles of Gene Manipulation by R.W. Old and S. B. Primrose, Blackwell Scientific
Publications, 1997.

12.

Principles of Gen
etic by Gardner and D.P. Snusted, John Wiley & Sons, NY, 1988.

13.

Recombinant DNA by J.D. Watson, J. Tooz and K. Kurtz, Scientific American Books,
NY, 1988

14.

Recombinant DNMA Methodology by R. Wu, L. Grossman and K. Maidenme (ed.)
Academic Press, San Diegd, 198
9

15.

Micrbial Genetics
-

1997 Freifielder.

16.

Molecular Genetics


T.A. Brown Van Nesteorland & Raink , New York, 1997

17.

Genes to Clones


Winnacker, 1997.


P
aper
-
III

Microbial Biochemistry


M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%


(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A
, B, C and D will have
two questions from the respective sections of the syllabus and carry 15 marks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions

for the candidates

1.

Candidates are required to attempt one question each from sections A, B, C and D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.



Section


A

1.

Chemical basis of life :
Composition of living
matter ; Water


properties, pH,
pK, acids, bases, Buffers, weak bonds, covalent bonds, ionization and
hydrophobicity; Emergent properties of biomolecules in water; Biomolecular
hierarchy; Macromolecules; Molecular assemblies; atomic and molecular
dimensi
ons, space filing and ball and stick models.

2.

Biological Macromolecules (Amino acids and Proteins) :
-

Amino acids and
peptides; classification , chemical reaction and physical properties; Peptides and
covalent structure of proteins.

3.

Elucidation of primary
and higher order structures; Evolution of protein structure,
hierarchy in structure ; Structure
-

function relationships in model proteins like
ribonuclease A, myoglobin, hemoglobin, chymotrypsin etc; Tools to characterize
expressed proteins; Ramachandran m
ap.






Section

B

4.

Sugars:
-

Sugars; mono, di and polysaccharides; Suitab
i
lity in the context of their
different functions


cellular structure, energy storage, signaling; Glycosylation of
other biomolecules
-

glycoproteins and gycolipids,

5.

Lipids:

classifi
cation, structure and properties of important members of storage
and membrane lipids; lipoproteins
.

6.

Lipo
-
proteins, Glycoproteins, Glycolipids etc.







Section
-

C

7.

Biological Macromolecules (Nu
cleic acids and heterocyclics):

Types, structural
features, m
ethods for compositional analysis of Nucl
e
osides, nucleotides, nucleic
acids; structure, diversity, and function; Heterocyclic compounds and secondary
metabolites in living systems; pigments, isoprenoids

8.

Vitamins:

Water s
oluble and fat soluble vitamins.
Ho
rmones :
-

hormones, their
structures and functions
.


9.

Enzymes
Introduction and scope, enzymes coenzymes, Nomenclature,
Mechanism of Catalysis, Chemical and Physical properties of enzyme; general
principles of catalysis; Quantitation of enzyme activity and ef
ficiency; Enzyme
characterization and Michaelis
-

Menten kinetics; Relevance of enzymes in
metabolic regulation, activation , inhibition and covalent modification ; Single
substrate enzymes; Inhibitors and activators; Multi
-
substrate systems; Effect of
pH
and temperature; Allosteric enzymes.






Section
-
D

10.

Enzymes:
Introduction and scope, enzymes coenzymes, Nomenclature,
Mechanism of Catalysis, Chemical and Physical properties of enzyme; general
principles of catalysis; Quantitation of

enzyme activity and e
fficiency.

11.


Enzyme characterization and Michaelis
-

Menten kinetics; Relevance of enzymes
in metabolic regulation, activation, inhibition and covalent modification; Single
substrate enzymes; Inhibitors and activators; Multi
-
substrate systems; Effect of
pH a
nd temperature; Allosteric enzymes.

12.

Organization of Biomembrane and Cell Wall:
-


Properties of lipid aggregates,
micelles, liposome’s, structure and properties, membrane proteins and their
function, fluid mosaic model, membrane mediated transport, membrane

equilibrium and permeability, chemical, physical composition and biosynthesis of
cell wall components.

Suggesting Reading

(Latest Editions)

:

1.

Fundamentals of Enzymology. N.Price, and L. Stevens, 1999. 3
rd

Edition. Oxford
University Press Inc. New York

2.

Fu
ndamentals of Biochemistry, 3
rd

Edition by D. Voet, J.G.Voet, C.W. Pratt.
2004, John Wiley and Sons, New York.

3.

Principles of Biochemistry, A.L. Lehninger. D.L. Nelson and M.M. Cox, 4ht
Edition. W.H. Freeman and Company, 2004

4.

Biochemistry, G. Zubay, 4
th

Ed
ition, 1998. Brow Dubuque, Lowa,

5.

Biochemistry, L. Stryer, 5ht, Edition.2002. W.H. Freeman and Co.

6.

Harper’s Biochemistry, R.K. Murray, D.K Grammer, P.A. Mayes, V.W. Rodwell,
25
th

Edition. 2000. Appleton and Lange.

7.

Enzymes


Dixon & Webb.

P
aper
-

IV


Analyti
cal Techniques

M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%




(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two questions from the respective sections of the syllabus and carry 15 mar
ks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidates are required to attempt one question each from sections A, B, C and
D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.









Section


A

1.

Basic Techniques:
-

Buffers, Methods of Cell Disintegration: Physical chemical
& biolog
ical

methods, detergents and membrane proteins; Dialy
sis, Ultrafiltration
and other membrane techniques.

2.

Spectroscopy Techniques & X
-

ray diffract
ion
:
-

UV, Visible and Raman
Spectroscopy: Theory and application of Circular Dichroism, Fluorescence,
NMR, PMR, ESR, Plasma Emission spectroscopy MA
L
DI
-
TOF; Mass
spectrometry.

3.

X
-
ray diffraction






Section


B


4.


Chromatography Techniques

T
L
C

and Paper chromatography; methods for
macromolecule separation


Gel permeation, Ion exchange; hydrophobic;
Reverse
-
phase and Affinity chromatography.

5.

HPLC and FPLC,

Criteria

of protein purity.

6.

Electrophoretic techniques :
-


Theory and application of Polyacrylamide and
Agarose gel electrophoresis; Capillary electrophoresis;; Disc gel electrophoresis;
Gradient electrophoresis;

2D
Gel
Electrophoresis


Pulsed field gel electroph
oresis
.








Section


C

7.

Centrifugation :
Basic Principles; Mathematics
and

theory (RCF, Sedimentation
coefficient etc); Types of centrifuge
-

Microcentrifuge, High speed
and

Ultracentrifuges; Preparative centrifugations; Differential
and

density gradie
nt
centrifugation; Application (Isolation of cell components); Analytical
centrifugation ; Determination of molecular weight by sedimentation velocity
and

sedimentation equilibrium methods.

8.

Radioactivity:
-

Radioactive
and

stable isotopes; Pattern and rate
of radioactive
decay; Units of radioactivity; Measurement of radioactivity; Geiger
-

Muller
counter; Solid
and

Liquid scintillation counters (Basic principle, instrumentation
and

technique); Brief idea of radiation dosimetry; Cerenkov radiation.

9.

Autoradiog
raphy :
Measurement of

stable isotopes; Falling drop method ;
Applications of isotopes in biochemistry; Radiotracer techniques; Distribution
studies ; Isotope dilution technique; Metabolic studies; Clinical application ;
Radioimmunoassay.






Section


D

10.

Techniques used in Functional Genomics;
-


Protein sequencing methods,
Nucleic acid sequencing techniques Maxam
-

G
i
lbert and Sanger’s dideoxy
method, automated sequencing PCR,
Flourescent
In


situ hybridization
,

Blotting methods; Southern, Northern, West
ern, Dot Blotting.

11.

Advanced Techniques:
-

Protein crystallization, Theory and methods; API


electrospray, DNA

and

peptide Synthesis
.

12.


Enzyme and cell immobilization techniques.


Suggest
ed

Readings

(Latest Editions)

:

1.

Biotechnology


Fundamentals of Micr
obial Genetics and Genetic Engineering
(Vol. 12) by R.H. Rehm and G. Reed Veriag Press, NY 1992

2.

Genes VII by B. Lewin, John Wiley & Sons, NY, 2001

3.

Genetic Fundamentals & Genetic Engineering by H.R. Rehm and G.Reed , Vol 12
VCH, 1993.

4.

Genetics for Microbes
by A. Brainbridge, Balckkis & Sons Ltd. New York, 1987.

5.

Molecular Biology by D. Grialder, Narosa Publishing House, New Delhi, 1988.

6.

Molecular Biology of the Cell by B. Ablerts. D. Bray, J. Lewis, M.Raft, K.
Rolbertis and J Watson, Gerland Publish ICE, 1988

7.

Molecular Cloning (Vol. 1,2, & 3) Sambrook, E.F. Fristsch and T. Maniatis, Cold
Spring Harbor, NY, 1989

8.

Microbial Genetics by D. Drilder, Narosa Publishing House , New Delhi, 1989

9.

Molecular Biotechnology: Principles & Applications of Recombinant DNA by
Be
rnard R. Click and Jack J. Pasternak, ASM Press, Washington, D.C. 1997.

10.

Principles of Genetic by Gardner and D.P. Snusted, John Wiley & Sons, NY,
1988.

11.

Recombinant DNA by J.D. Watson, J. Tooz and K. Kurtz, Scientific American
Books, NY, 1988

12.

Microbial Gene
tics


1997 Freifielder.

13.

Molecular Genetic


T.A.Brown Van Nesteorland & Raink, New York, 1997

14.

Molecular Biology and Biotechnology, J.M. Walker and E.B. Gingold, 3
rd

Edition
1993. Royal Chemistry Society.

15.

Molecular Cell Biology, Lodish, Berk, Zipursky, 4
th

Edition. 2000. W.H.
Freeman.

16.

Cell and Molecular Biology, Gerald Karp, 3
rd

Edition, 2002, John Wiley and
Sons.

17.

Advanced Molecular Biology, M. Twynmen, 1999. Viva Books Pvt. Ltd.

18.

Cell and Molecular Biology by De Robertis, E.D.P. De Robertis, E.M.F Latest
ed
n., B.I. Waverly Pvt. Ltd, New Delhi.

19.

Chromatin & Gene Regulation by B. M. Turner, 1
st

Edition , Wiley


Blackwell,
2002
.

20.

Freifelder D,Physical Biochemistry . Application to Biochemistry and Molecular
Biology, 2
nd
Edition W.H, .Freeman & Company , San Fran
sisco, 1982.

21.

Keith Wilson and John Walker, Principles and Techniques of Practical
Biochemistry , 5
ht

Edition Cambridge University Press, 2000

22.

D.Holme & H. Peck, Analytical Biochemistry , 3
rd

Edition , Longman,1998.

23.

R. Scopes. Protein Purification


Princip
les & Practices, 3
rd

Edition, Springer
Verlag,1994

24.

Selected readings from Methods in Enzymology, Academic Press.


Practical I:
pertaining to

Theory Paper I and II


Max. Marks: 100





Practical Time: 60 hours

Time: 4 hours


1.

Isolation of Chromosomal DNA
from
E. coli

2.

Isolation of Chromosomal DNA from plant cells

3.

Isolation of plasmid DNA

4.

Determination of Tm and % (G+C) of DNA

5.

Spectrophotometric analysis of DNA/protein & RNA

6.

Agarose gel electrophoresis of DNA

7.

Use of basic instruments in Microbiology (Light

microscope, pH meter,
autoclave, Laminar Flow chamber, Deionized water purification systems,
centrifuge, electronic balance, Spectrophotometer).

8.

Staining of bacteria, yeast and fungi.

9.

Purification of mixed cultures by streaking technique

10.

Determination of
viable count

11.

Correlation of viable counting and optical density of cultures

12.

Isolation of microbes from environment (soil, water, skin bread, milk)

13.

Isolation of extremophiles from environment

14.

Bacteriophage screening

15.

Preparation of complex and synthetic m
edium

16.

Sterilization of liquid and solid items

17.

Storage (short & long term) of microbes

18.

Collection, handling and storage of clinical samples

19.

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

20.

Culture identifica
tion of fungal pathogens (
Candida, Aspergilllus
)

21.

Identification of pathogens by PCR technology

22.

Antibiotic sensitivity of clinical pathogens

23.

Animal handling

24.

Routes of Injections

25.

Drawing blood from animals

26.

TLC and DLC for blood samples.

27.

Determination of cel
l number (viable/non
-
viable)

28.

Ficoll density gradient separation of cell types.

29.

Raising antibodies in animals.

30.

Immunoassays.

31.

Collection, handling and storage of clinical samples




Practical II: for Paper III and IV

Max. Marks: 100





Practical Time: 60 h
ours

Time: 4 hours




Qualitative and quantitative assay of sugars



Qualitative and quantitative assay of proteins



Qualitative and quantitative assay of lipids



Qualitative and quantitative assay of nucleic acids



Separation of proteins on non
-
denaturing gels.



Separation of proteins on denaturing gels



Gel exclusion chromatography



Ion
-
Exchange chromatography



Affinity chromatography



Operation of HPLC



Operation of IR



Operation of NMR



Operation of Atomic absorption spectroscopy



Demonstration of Polyacrylamide gel e
lectrophoresis



Demonstration of 2D
-

gel electrophoresis

M
.Sc. (Microbial Biotechnology)

Part
-
I (Semester I
I)

For 2011
-

12 & 2012
-
13 Session


P
aper
-

V

Microbial Metabolism


M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks
: 35%


(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and

D will have
two questions from the respective sections of the syllabus and carry 15 marks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the c
andidates

1.

Candidates are required to attempt one question each from sections A, B, C and D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.







Section
-

A

1.

Carbohydrate metabolism: glycolysis, biochemistry of
alcohol and lactic acid
fermentation.

2.

Citric acid cycle, pentose phosphate pathway, EDP pathway,

3.

Disaccharide and polysaccharide metabolism, gluconeogenesis, regulation of
carbohydrate metabolism.

Section


B

4.

Oxidative phosphorylation / respiration: electr
on transport chain, Photorespiration,
microsomal electron transport.

5.

Biochemistry of lipid metabolism; biosynthesis and catabolism of acids regulation
of fatty acid metabolism.

6.

Neutral lipids, phospholipids cholesterol, glycolate cycle.



Section


C

7.

Amin
o acid metabolism; biosynthetic families of amino acids, ammonia ion
assimilation into amino acid by glu and gln, regulation acid synthesis.

8.

Degradation of amino acids ; oxidative deamination of glutamate, carbon atom
degradation, amino acid is major metab
olic intermediates, C
3,
D
4,
, and C
5
families,
amino acid degradation to succinyl CoA, Leucine , Phenyl alanine and tyrosine
degradation.

9.

Urea cycle, nitrogen fixation and nitrogenase complex.

Section


D

10.

Nucleotide metabolism; Purine and Pyrimidine nucleot
ide Biosynthesis, synthesis
of deoxyribonucleotides,

11.

D
egradation of purines, regulation of nucleotide metabolism.

12.

Photosynthesis: Photosynthetic pigiments, cyclic and monocyclic electron flow,
oxygen evolution system, Calvin cycle, C3, C4, mode of photosy
nthesis.

RECOMMENDED READING

(Latest Editions)

:

1.

Biochemistry by Voet, D and J.G. Voet, John Wiley and Co. 1990

2.

Lehinger Principles of Biochemistry , 3
rd

Edition. By David L. Nelson and Michael
M. Cox Printed in India by Repubic Press Pvt. Ltd. New Dehli
For Machmillen
Press/Publishes 2000

3.

Biochemistry by Stryer, LK, CBS Publishers and Distribution, New Delhi, 1995.

4.

Catherine Desktop Molecular Modellar3, by James M.C. Carbbe, John R. Abbey
and Oxford University Press.

5.

Fundamentals of Nitrogen Fixation, by
Postage J.R. Cambridge University Press,
Oxfords, 1982.

P
aper
-

VI

Genetic and Metabolic Engineering


M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%



(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two questions from the respective sections of the syllabus

and carry 15 marks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidates are required to attempt one question each from sect
ions A, B, C and D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.







Section


A

1.

Tools of Genetic Engineering
: Scope and history of Genetic Engineering, Tools
in genetic engineering, DNA modifying enzymes,
restriction endonucleases,
reverse transcriptase, RNaseA, RNase H, alkaline phosphatatase, Polynucleotide
kinase, SI Nuclease, exonucleses; DNA polymerases, Klenow enzyme, T4 DNA
polymerases.

2.

DNa ligase; Cohesive and blunt end ligation, Linkers, Adaptors,
Homopolymeric
tailing; labeling of DNA; Nick translation, Radioactive and non
-

radioactive
probes, Hybridization techniques ; Northern, Southern and colony hybridization,
Fluorescence in situ hybridization; Chemical Synthesis of DNA.

3.

Vectors used in Gene C
loning
; plasmids
-

pBR322; Bacteriophages, lambda;
M13 mp vectors; pUC19 and Bluescript vectors, phagemids; Insertion and
Replacement vectors; Cosmids; Artificial chromosome vectors (YACs’ BACs)
Yeast vectors, Shuttle vectors.

Section


B

4.

High Expression Ve
ctors
; Principles in maximizing gene expression, Properties
of expression vectors; pMal; GST; pET


based vectors ; Protein purification ; His


tag; GST
-

tag; MBP
-

tag etc. inclusion bodies; Methodologies to reduce
formation of inclusion bodies, ch
i
meric
constructs, processing of recombinant
proteins; Purification refolding and characterization of recombinant proteins

5.

Cloning Methodologies
; Insertion of Foreign DNA into Host Cells ;
Transformation; Construction of libraries; Isolation of mRNA and total RN
A;
cDNA and genomic libraries; cDNA and genomic cloning;

6.

Expression cloning
; Jumping and hopping libraries; Southwestern and
Farwestern cloning ; Protein


protein interactive cloning and Yeast two hybrid
system; Phage display ;


Section
-

C

7.

PCR and its A
pplications

; Primer design ; Fidelity of thermostable enzymes;
DNA polymerases; Types of PCR
-

multiplex, nested, reverse transcriptase, real
time PCR, touchdown PCR, hot start PCR, colony PCR, Proof reading enzymes
and SOEing; PCR in molecular diagnostics
;

8.

Mutagenesis and Protein engineering:
PCR based mutag
enes
is
,

Site
-

Directed
Mutagenesis and Protein Engineering.

9.

Selection and Identification of Recombinant Organisms
: Direct and indirect
methods, methods of Recombinant screening and selection; immunolog
ical
methods; Sequencing methods; Enzymatic DNA sequencing ; Chemical
sequencing of DNA ; Automated DNA sequencing ; RNA sequencing;



Section
-

D

10.


Application of Genetic Engineering
: Expression of industrially important
products in bacteria yeast
.

DNA ma
rker technology, DNA foot printing and DNA
fingerprinting.

11.

Generically engineered biotherapeutics and vaccines and their manufacturing,
Potential risks and guidelines on R
-

DNA (NIH, DBT and FDA guidelines)

12.

Metabolic Engineering

:
-

Metabolism, metabolic
flux analysis, strategies to
increase/alter metabolite flow, metabolic control analysis; Importance of
metabolic Engineering : Completion of partial pathways giving novel products
(
Erwinia herbicola),

transfer of entire biosynthetic pathway (Trp biosynthes
is to
E.coli

and overproduction of Trp in C
glutamicum
), Creating new products
(indigo and melanin in
E coli
) , redirecting metabolite flow (Increased Thr in
bacteria and Lys in crops; Increased CephC production); Metabolic engineering of
PHAs and Caroteno
ids.






Suggested Reading
(Latest Editions)

:

1.

Biotechnology


Fundamentals of Microbial Genetics and Genetic Engineering
(Vol. 12) by R.H. Rehm and G. Reed, Veriag Press, NY, 1992.

2.

Gene Cloning by T.A. Brown, Van Nesterland and Rainold, NY, 1996.

3.

Genes
VII by B. Lewin, John Wiley & Sons, NY,

4.

Genetic Fundamentals & Genetic Engineering by H.R. Rehm and G. Reed, Vol
-
12 VCH, 1993.

5.

Genetics for Microbes by A. Brainbridge, Balckkis & Sons Ltd. New York, 1987

6.

Molecular Biology by D. Grialder, Narosa Publishing

House, New Delhi, 1989

7.

Molecular Biology of the Cell by B. Alberts, D. Bray, J.Lewis , M. raft, K.
Ropbertis and J. Watson, Gerland Publish ICE, 1988.

8.

Molecular Cloning (Vol. 1,2, & 3) J. Sambrook, E.F. Fristsch and T. Maniatis,
Cold Spring, Harbor, NY, 1
989

9.

Microbial Biotechnology by D. Drilder, Narosa Publishing House New Delhi,
1989

10.

Molecular Biotechnology : Principles & Applications of recombinant DNA by
Bernard R.Click and Jack J. Pasternak, ASM Press, Washington, D.C. 1997.

11.

Principles of Gene Manipul
ation by R.W. Old and S. B. Primrose, Blackwell
Scientific Publications, 1997.

12.

Principles of Genetic by Gardner and D.P. Snusted, John Wiley & Sons, NY,
1988.

13.

Recombinant DNA by J.D. Watson, J. Tooz and K. Kurtz, Scientific American
Books, NY, 1988

14.

Recombi
nant DNMA Methodology by R. Wu, L. Grossman and K. Maidenme
(ed.) Academic Press, San Diegd, 1989

15.

Micrbial Genetics
-

1997 Freifielder.

16.

Molecular Genetics


T.A. Brown Van Nesteorland & Raink , New York, 1997

17.

Genes to Clones


Winnacker, 1997.

18.

Metabolic En
gineering by S. Y. Lee and E.P. Popoutsakis (Eds.) M. Dekekr, NY,
USA.

19.

Metabolic Engineering by G. N. Stephanopoulous, A.A. Aristidon, J. Neilson,
Academic Press, USA.

Paper


VII

Bioprocess and Fermentation Engineering



M. Marks: 80







Lectures to b
e delivered: 60

Time allowed: 3 hours

Pass Marks: 35%


(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of fi
ve sections A, B, C, D, and E. Section A, B, C and D will have
two questions from the respective sections of the syllabus and carry 15 marks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidates are required to attempt one question each from sections A, B, C and D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.





Section


A

1.

Intro
duction: Fundamentals of bioprocess development.

2.

Bio
-
reactor design, Designing criteria of a bioreactor, types of bioreactors.

3.

Bioprocess c
o
ntr
o
l and monitoring; In line and on line Instruments /
probes in process control
,

computer control in bio
rea
ctors.

Section


B

4.

Sterilization in bior
eactors: kinetics of batch, continuous and fibrous filter
ste
riliz
ation.

5.

Aeration and Agitation: Agitation is sha
ke

flask as tube rollers, factor
affecting agitation as aeration in sha
ke

flasks, Fluid R
heology.

6.

Transport p
henomenon is bioreactors: Mass transfer co
-
e
fficient (k for
gases, li
quids, Determination of KL
a by vario
us methods, factors affecting
kL
a , heat transfer coefficient Dimensionless groups.

Section


C

7.

Scale


UP : Scale up of

bioprocess

8.

Fermentation econo
mics: cost determination i
n

bioprocess
es,

capital
i
nvestment

and

raw materials etc.

9.

Mathematical modeling: mathematical modeling in bioprocesses.

Section


D


10.

Pilot and industrial scale bioreactors
-

design and development.

11.

Neural networking: neural netwo
rking in bioprocesses.

12.

Downstream processing in bioreactors: filtration, centrifugation,
extraction, solid
-
liquid extraction, liquid
-
liquid extraction
, finishing steps
in bioproduct development.


RECOMMENDED READING

(Latest Editions)

:

1.

Biochemical Engi
neering by A. Aiba, A.E. Humphery and N.F. Mkili University of
Tokyo, 1973.

2.

Biotechnology Vol : 1, 2 and 7 by Moo Young, Pergamoon Press, NY, 1985.

3.

Comprehensive Biotechnology Vol. 2 by Moo Young, Pergamnon Press, NY, 1985.

4.

Fundamentals of Biotech
nology by P. Prave, F. Eaus, W. Sitting and D.A. Sukatech,
ECH Weinheim, 1987.

5.

Biochemical Engienering Fundamentals by J.E. Bailley and D.F. Ollis, McGraw Hill
Co., NY, 1986.

6.

Methods in Industrial Microbiology by B. Sikyata, Ellis Horwood Ltd., Londo
n,
1983.

7.

Principles of Fermentation Technology by P.F. Stanbury and A. Whitaker,
Pergamnon Press, NY, 1984.

8.

Principles of Microbial and Cell Cultivation by S.J. Pirt. Black Well Scientific
Publications, London, 1983.

Paper


VIII

Enzymology and Enzy
me Technology


M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%


(
Theory and Practicals separately
)

Instructions for the pape
r setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two questions from the respective sections of the syllabus and carry 15 marks each. Section E
will consist of 10 short answer type questions whic
h will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidates are required to attempt one question each from sections A, B, C and D of the
question paper and the entire section E.

2.

The use of scientifi
c calculators is allowed.





Section


A

1.

Introduction to enzyme
s

and

how it works, Specificity of Enzyme: Basic
concept
and

types. Physical structure of enzyme


the monomeric and
oligomeric enzymes. Concept of Active Site
-

Ogston’s experiment, Lock and
K
ey and Induced Fit hypotheses.

2.

Kinetics of Enzyme activity
-


Introduction of Chemical Kinetics
,

Kinetics of
Single substrate enzymes catalysed reactions


Wilhelmy’s and Brown’s
work, Henri and Michaelis and Menten derivations, Briggs and Haldane
Modificat
ion,

3.

Signif
icance of the M
-
M equation and K
m. Modification of the M
-
M equation


Lineweaver


Burk, Eadi
e

Hofstee, Hanes

and Eisenthal & Cornish
Bowden;

Kinetics of multi


substrate reactions. Sigmoidal Kinetics


Hill and
Adair equations for co
-
operativ
ity.


Section


B


4.

Basic concept of catalysis


activation energy barrier and the transition state
theory. Catalytic mechanisms in Chemistry and in Enzymes


acid


base,
covalent and electrochemical reactions.

5.

Factors enhancing the catalytic efficiency
of enzymes proximity and
orientation, oribital steering, distortion and strain.

6.

Functional group involved in the catalytic mechanisms


a) Amino acid b)
Cofactors


prosthetic groups, coenzymes, co
-

substrates, c) metal ions in
enzyme function


their ro
le, metal activated and metallo enzymes, ternary
complexes.


Section
-

C

7.

Regulation of Enzyme Function:
Models proposed to explain the mechanism
of functioning (MWC and KNF) structural aspects of asparatate: carbamoyl
transferase, role of allosteric enzyme
s in metabolic regulation (feedback
inhibition).

8.

Enzymes in organized systems and their role in control of function
:

Multienzyme systems


basic concepts, significance and types with examples,
S
tructural aspects of pyruvate dehydrogenase and fatty acid syn
thetase.

9.

Isoenzymes


basic concepts, types with examples and their significance to
the cells and to the medical field.

Section


D

10.


Enzymes in Medical Diagnosis


Lactate dehydrogenase, malate
dehydrogenase, Fructose
-
6
-
biphosphatase, acid and alkaline ph
osphatase,
Glucose 6 phosphate dehydrogenase.

11.

Enzyme therapy


cancer, Genetic disease, clotting disorders, Neonatal
jaundice, surgery, toxicity, artificial cells, enzyme carriers, enzyme probe.

12.

Industrial applications


catalysts in the manufacturing and

other conversion
processes immo
bi
li
zation of enzyme in bioprocess as analytical tools (enzyme
electrode).

Suggested Readings

(Latest Editions)

:

1.

Enzyme Nomenclature


International Union of Biochemists (IUB), Academic
Press.

2.

Understanding Enzymes


Trevor

Palmer, Ellis Horwood Publications.

3.

Fundamentals of Enzymologoy


N.C. Price and L. Stevens, Oxford University
Press.

4.

Enzymes
-

P. Boyer, Academic Press.

5.

The Enzymes


M. Dixon and E.C. Webb.

6.

Advances in Enzymology


Series edited by N.O. Kaplan, Academic

Press.

7.

Enzyme Structure and Mechanism


A. Fersht, Freeman , USA.

8.

Enzyme Biotechnology


Tripathi.

Practical III:
Pertaining to

Theory papers

V and VI

1.

Isolation of microbes from environment (soil, water, skin bread, milk)

2.

Isolation of extremophiles fro
m environment

3.

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

4.

Antibiotic sensitivity of clinical pathogens

5.

Preparation of competent cells

6.

RAPD on bacterial DNA

7.

Isolation and estimation of DNA from bacter
ia/ yeast / fungi /
bacteriophage

8.

Isolation and estimation of RNA / mRNA from bacteria/ yeast/ fungi

9.

Restriction digestion (complete and partial) of DNA

10.

Cloning and expression of a gene in

E. coli

11.

Amplification of DNA by PCR

12.

Southern Hybridization

13.

Isola
tion of DNA, RNA and plasmids and staining with ethidium bromide.

14.

10
Electrophoretic separation of DNA fragments and their recovery from gel
slabs.

11.

Performance of Southern and Northern blotting.

15.

Transformation of
E. coli

with plasmids by chemical and elect
ro
p
oration.

16.

Purification of mRNA by using immobilized technique.

17.

Mapping of restriction sites on a plasmid.

18.

Cloning using restriction enzyme generated cohesive/blunt ends.

19.

Sequencing of DNA fragement with Maxam
-
Gillbert method.

20.

Qualitative and Quantitative

analysis of Proteins and Nucleic acids by U.V.
Spectrophotometer.

21.

Determination of protein in pressence of nucleic acid by spectrophotometer
method.

Practical IV:

Pertaining to Theory

Paper VII and VIII

Max. Marks: 100





Practical Time: 60 hours

Time
: 4 hours


12.

Screening of microbes for production of industrially important enzymes.

13.

Optimization of conditions for optimal production of enzyme: Media
composition, Incubation temperature, Aeration, Incubation time.

14.

Assay of enzymes (amylases, lipases, prote
ases)

15.

Effect of pH and temperature on enzyme activity

16.

Substrate specificity and efficiency of enzymatic catalysis

17.

Enzyme/cell immobilization in different matrices


18.

Protein purification by Gel exclusion chromatography

19.

Protein Purification by Ion
-
Exchange c
hromatography

20.

Protein Purification by Affinity chromatography

21.

Introduction to laboratory scale bioreactor, its fabrication and evaluation of
performance

22.

Isolation of useful microorganisms from natural samples

23.

Growth of microorganisms and estimation of Mono
d parameters

24.

Batch, fed batch and continuous cultures: Estimation of Monod parameters, Pure
and mixed cultures, Production of secondary metabolites in synthetic and
complex industrial media

25.

Determination of KLa value


M
.Sc. (Microbial Biotechnology)

Part
-
I (Semester I
II
)

For 2011
-
12 Session

P
aper
-
IX

Industrial Microbiology


1 (Health, Food, Enzymes)


M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%



(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two questions from the respective sections of the syllabus a
nd carry 15 marks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidates are required to attempt one question each from sectio
ns A, B, C and D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.







Section


A

1.

Primary and Secondary metabolites of industrial importance,

2.

Techniques involved in screening / detection of industrially impor
tant metabolites
from microbes

3.

Biosynthesis and fermentation process involve in: Rol
e of Bioproducts as
Neutraceuti
cs : Mycoproteins, Phycoproteins, High Fructose syrups.

Section


B

4.

Antibiotics (Penicillin, Streptomycin,

Tetracycline), Alkaloids (ergot, l
ysergic
acid),

5.

Biotransformations (Steroids, chirals), Vaccines (BCG, DPT, polio, hepatitis)

6.

Therapeutic Proteins (Inter
f
erons, Insulin
, Streptokinase, Erythropoietin
)
Bacteriophages.

Section


C

7.

Fermentative production of Beer, wine, whisky organic acids
-

citric, lactic, acetic
acids, vinegar.

8.

Production of Cheese, Yoghurt, Probiotics, Traditional Fermented foods

9.

Food Additives: lipids, vitamins, flavours.

Section
-

D

10.

Pharma
and

Therapeutic enzyme
s


11.

Enzymes in detergent

12.

Enzymes in textile & leather indu
stries.

Suggested Readings

(Latest Editions)

:

1.

Publisher: American Society Microbiology, 3
rd

edition (J2007) ISBN


10,
1555814077 ISBN
-
13:978
-
1555814076, Food Microbiology: Fundamentals and
Frontiers by Dolye.

2.

Publisher : American Society Microbiology, 1
s
t

Edition (2005) ISBN


10
1555813089 ISBN
-

13 : 978
-
1555813086, Food Microbiology : An Introduction
by Montville

3.

Publisher: Academic Press: 2
nd

edition (2004) ISBN


10: 0125506562, ISBN


13: 978
-
01255016564, Environmental Microbiology: a Laboration Man
ual by Ian
L. Pepper and Charles P. Gerba.

4.

Publisher: Academic Press: 1
st

edition (2003) ISBN


10: 0120164477, ISBN
-
13;
978
-
0120164479, Advances in Food & Nutrition Research by Steve Taylor.

5.

Publisher: Academic Press: 1
st

edition (2000) ISBN


10: 0124975
704, ISBN
-

13:
978


01254975705, Environmental Microbiology by Raina M. Maier. Ian I.
Pepper and Charles P. Gerba.

6.

Publisher : CRC 2
nd

edition (2001) ISBN


10 : 082470536x, ISBN
-

13, ; 978
-
0824705367, Applied Dairy Microbiology , by Elmer H. Math and Jam
es Steele.

P
aper
-
X

Industrial Microbiology


II (Environment, Biofuels, Chemicals, Biomass)



M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%



(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two questions from the respective sections of the syllabus and ca
rry 15 marks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidates are required to attempt one question each from sections A,

B, C and D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.







Section
-

A

1.

Bioremediation
:

Types and sources of pollution


Inorganic, organic and biotic.
Clinical example of air, water and land pollutions.
Environmental impact of
pollution and measurement methods. Composting of organic wastes, microbial
bioremediation of oil spills.

2.

Waste water treatment


sewage treatment and common industrial effluent
treatment. Concept of bioremediation (in


situ and ex



situ); Bioremediation of
toxic metal ions


bisorption and bioaccumulation principles. Concept of
phytoremediation. Microbial biotransformatioln of pesticides and xenobiotics .

3.

Bio
-
leaching
:
Microbial leaching of ores


direct and indirect mechanisms.

B
iodegradation of Polyaromatic hydrocarbons, Desulphurization of coal,
Biodesulfurization of petroleum.


Section


B

4.

Classification , Characteristics and conversion methods of bio
-

mass and solid
wastes,Bio


mass combustion
:

Principles
and

mechanism, fur
naces and their
design.

5.

Chemical conversion of bio


mass and agricultural waste into pulp, paper,
various other products and chemicals. Conversion of agricultural wastes into
energy chemicals.

6.

Utilization of Milling by

products of cereals, pulses and oth
er bearing materials
for foods, feed and chemicals production, Biomass as Baker’s yeast, SCPs,
Mushrooms.

Section


C

7.

Biomass and Bio


fuels: Plant biomass (Cellulose, starch, pectin, gum materials),
Animal biomass (chitin, milk whey, Slaughter house waste
s), Microbial biomass
(algal blooms


in fresh and sea waters, Fungal


Mushrooms, yeasts and bacterial
fermentation biomass wastes)

8.

Concepts of single cell proteins, probiotics and their application. Biomass feed
stocks to fermentation.

9.

Microbial producti
on of fuels; alcohols, hydrogen and methane. Microbial
production of polymers (xanthan gums)

Section


D

10.

Biofertilizers : Biofertilizers and their importance in corp productivity . Algal and
fungal (mycorrhizae) biofertilizers, Bacterial rhizobial , free
living N2 fixers and
phosphate solublizing bacteria, their significance and practice

11.

Biopesticides: Bacterial (Bt pesticides), fungal (Trichoderma). Viral biopesticides


Baculovirus, NPV insecticides.

12.


Production of biofertilizers and biopestici
des for l
arge scale application.
.


Suggested Readings

(Latest Editions)

:

1.

Publisher: American Society Microbiology, 3
rd

edition (J2007) ISBN


10,
1555814077 ISBN
-
13:978
-
1555814076, Food Microbiology : Fundamentals and
Frontiers by Dolye.

2.

Publisher : American Socie
ty Microbiology, 1
st

Edition (2005) ISBN


10
1555813089 ISBN
-

13 : 978
-
1555813086, Food Microbiology : An Introduction
by Montville

3.

Publisher: Academic Press: 2
nd

edition (2004) ISBN


10: 0125506562, ISBN


13: 978
-
01255016564, Environmental Microbiolog
y: a Laboration Manual by Ian
L. Pepper and Charles P. Gerba.

4.

Publisher: Academic Press: 1
st

edition (2003) ISBN


10: 0120164477, ISBN
-
13;
978
-
0120164479, Advances in Food & Nutrition Research by Steve Taylor.

5.

Publisher: Academic Press: 1
st

edition (2000)

ISBN


10: 0124975704, ISBN
-

13:
978


01254975705, Environmental Microbiology by Raina M. Maier. Ian I.
Pepper and Charles P. Gerba.

6.

Publisher: CRC 2
nd

edition (2001) ISBN


10 : 082470536x, ISBN
-

13, ; 978
-
0824705367, Applied Dairy Microbiology , by Elm
er H. Math and James Steele.

7.

Comprehensive Biotechnology (All volumes) Ed. Young. M.Y. Pub: Pergmon
Press.

P
aper



XI

Biostatistics and Computer applications

M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%



(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
tw
o questions from the respective sections of the syllabus and carry 15 marks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candi
dates are required to attempt one question each from sections A, B, C and D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.







Section


A

1.

Fundamental concepts in Biostatistics : applied probability: explora
tory data
analysis and statistical inference; Probability and analysis of one two way samples
: discrete and continuous probability models;

2.

Expectation and variance; Central limit theorem; Inference; Hypothesis; Critical
region and error probabilities.

3.

St
atistical Tools : Tests for proportion ; Equality of proportions; equality of means
of normal populations (variance known, variance unknown); Chi


square test for
independence ; P


value of the statistic; Confidence limits; Introduction to one
way and tw
o


way analysis of variance; Data transformations

Section


B

4.

Fundamentals of computers; Definition of computers, computer organization
memory, number systems, input and output devices.

5.

Types of computers, network computers, working with mainframe, person
al
computer

6.

Computer Networking: LAN, WAN, intranet, internet, TCP/IP, http, ftp, web
page, web site and World Wide Web, network securities, applications of
computers in biological sciences.





Section
-

C

7.

Operating Systems : Need of OS, its functions, fe
atures, functions of common
OS;

8.

Functions of OS:
Windows

9.

Functions of OS:

Linux.





Section
-

D

10.

Programming Languages: Programming Language C: character set, identifiers
and keywords data types,

11.

Operator and expression control statements, switch break,

continue statements

12.

Function arrays, pointers,

Suggested Readings

(Latest Editions)

:

1.

Wayen W. Biostatistics : A foundation for Analysis in the Health Sciences, 8
th
Edition, Wiley 2004

2.

Prem S. Mann, Introductory Statistics,
6
th

Edition , Wiely, 2006

3.

John

A. Rice: Mathematical Statistics and Data Analysis, 3
rd

Edition, John A.
Rice Duxbury Press, 2006

4.

Campbell and Heyer, Discovering Genomics, Proteomics, & Bioinformatics,
2
nd

Edition, Benjamin Cummings, 2002

5.

Cynthia Gibas and Per Jambeck, Developing Bioinf
ormatics Computer Skill,
1
st

Edition , O’Reilly Publication, 2001

6.

Object Oriented Programming in C ++, by Robert Lafore, Techmedia, 2002

7.

The C ++ Programming Language by Stroustrup, Addison Wesely, 2001

8.

Functions of OS : Windows

9.

Function of OS : Linux

P
aper
-
XII

Biosafety
, Bioethics & IPR


M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%


(
Theory and Practicals separately
)

Ins
tructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two questions from the respective sections of the syllabus and carry 15 marks each. Section E
will consist of 10 short answ
er type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidates are required to attempt one question each from sections A, B, C and D of the
question paper and the entire section E
.

2.

The use of scientific calculators is allowed.







Section


A

1.

Introduction: General Introduction to IPR (Patents, Plant Breeders’ rights)

Trade, Marks, Industrial design, trade secrets (or undisclosed informat
ion)
integrated circuit designs.

2.

Copyright

and right related to copyright
, Patent Claims, the legal decision


making process
.

3.

Ownership of Tangible and intellectual process, Basic requirements of
patentability, patentable subject matter, novelty and the public Domain : Non
-

obviousness, Special is
sues in Biotechnology Patents : Disclosure requirements,
Collaborative research, competitive research,
Microbial

biotechnology, Foreign
Patents.





Section


B

4.

Patenting Principle, International Standards & Pate
nt Validity (Neem and
Relaxins).

5.

Patent Liti
gation: Substantive aspects of patent litigation, Procedural aspects of
patent litigation.

6.

Recent Development in Patent System and Patentability of Biotechnology
invention IPR issues of the Indian context.





Section


C

7.

IPR Regime in the Digital Society;

International Treaties and Conventions:
Business software Patents, Domain Name Dispute and Resolution.

8.

Patenting of biological processes, patenting regulations in India, USA & Europe,
Buda pest treaty & convention.

9.

Public Acceptance issues for biotechnolo
gy: Case studies / experiences from
developing and developed countries,







Section
-

D

10.

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

Biosafety :
The Cartagena protocol on biosafety

11.

Biosafety management: K
ey to the environmentally r
esponsible use of
biotechnology,


12.

Ethical implications of biotechnological products techniques
,

Social and
ethical implication of biological weapons


Suggested Readings

(Latest Editions)

:

1.

Asia Law House, Hyderabad, 2001, Law o
f Intellectual property by Myneni.S.R.

2.

Butterworth’s London 2001. Intellectual property law by Davis. Jennifer

3.

Universal Law Publishing, Delhi 2001, Intellectual property: Patents trade marks
and allied rights by Cornish W. R.

4.

Sign KC : Intellectual Prope
rty Rights on Biotechnology , BCIL, New Delhi

Practical V:

Pertaining to theory papers

Paper IX and X

Max. Marks: 100





Practical Time: 60 hours

Time: 4 hours


1.

Yoghurt Fermentation

2.

Cheese Fermentation

3.

Wine fermentation

4.

Purification of antimicrobial m
etabolites from a microbe.

5.

Isolation and partial purification of industrially important enzymes

6.

Fermentative production of organic acids and ethanol

7.

Production of alcoholic beverages

8.

Medium optimization for bacterial growth by statistical method

10.

Biomass es
timation by different methods

11.

Isolation of Biofertilizer microbes by biological enrichment method

12.

Production of microbial biofertilizers and biopesticides

13.

Efficacy testing for biofertilizers (nodulation test for rhizobia) and
biopesticides

14.

Estimation of B
OD & COD

15.

Testing for microbiological quality of potable water (Coliform test)

16.

Microbial degradation of organic matter

17.

Testing for effect of chemical pesticides on soil microbial respiration

18.

Testing for microbial biodegradation of pesticides

Practical VI:

Pertaining to theory papers

Paper XI and XII


Max. Marks: 100





Practical Time: 60 hours

Time: 4 hours

1.
Searching of National Patent databases

2.
Drafting of National Patent application

3.
Searching of International Patent databases

4.
Drafting of International
Patent applications

5.
Generating Global Technology Strategic Report (GSTR)

6.
Other exercise related to theory course

7.
Representation of statistical data by


a) Histograms


b) Ogive curves


c) Pie diagrams

8. Determination of statistical averages/central tenden
cies

a) Arithmetic mean

b) Median


c) Mode

9. Tests of significance
-
Applicaton of following


a) Chi
-
square test

b) t
-
test



c) Standard error

10. Computer operations
-
getting acquainted with different parts of computer, DOS and
basics of operating systems

1
1. Creating files, folders and directories

12. Applications of computer in biology using MS
-
Office


a) MS word


b) Excel



c) Power point

13. Creating an e
-
mail account, sending and receiving mails.


M
.Sc. (Microbial Biotechnology)

Part
-
I (Semester I
V)

F
or 2011
-
12 Session


P
aper
-
XIII

Entrepreneurship, Project Management and Quality Assurance


M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%



(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two questions from the respective sections of the syllabus and carry
15 marks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidates are required to attempt one question each from sections A, B,
C and D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.









Section


A

1.

Entrepreneurship: Need scope and philosophy, Creativity and
Entrepreneurship.

2.

Entrepreneurship competencies and traits, factors affec
ting Entrepreneurship
development, Introduction to entrepreneurship
.

Barriers to entrepreneurship,
community and entrepreneurship
.

3.

F
unctions of entrepreneurship, classification of entrepreneurship.





Section


B

4.

Forms of Project Organization: Project Pla
nning
, Developing a Project,
Control.

5.


Human aspects of project management, per


requisites for successful project
implantation, project management of project network time estimation,
determination of critical path. Scheduling when resources are limited.

6.

PERT and CPM models network cost


system, venous techniques of market
survey.





Section


C

7.

Plant and equipment financial pr
ocedure and their significance.

8.

Books of accounts.

9.


Financial and fund flow analysis.





Section


D

10.

Introduction to quality: q
uality as
surance and testing of products

11.

E
lemental knowledge of marketing and Sales Management, Marketing
Str
ategies.

12.


P
ackaging
and
advertising.


Suggested Readings

(Latest Editions)

:


1.

Enter
p
re
neur
ship : Rajeev Ray (2000) Oxford University.

2.

Peter F Druck
er. Innovation and Entrepreneurship, Harper & Row , 1985

3.

Prasanna Chandra


Projects: Preparation Appraisal and
Superimplementation. Tata Mc
-

Graw


Hill Co. Ltd.

4.

Enterpreship Development Small Business Enterpreship (2004) Purnima
M. Charantimath.

5.

Project
Management Clofford F Gray, TATA Mc Graw Hill.

6.

The Management & Control Quality James R . Erans.


Paper


XIV

Bioinformatics and Computation Biology







M. Marks: 80







Lectures to be delivered: 60

Time allowed: 3 hours

Pass Marks: 35%



(
Theory and Practicals separately
)

Instructions for the paper setters

The question paper will consist of five sections A, B, C, D, and E. Section A, B, C and D will have
two q
uestions from the respective sections of the syllabus and carry 15 marks each. Section E
will consist of 10 short answer type questions which will cover the entire syllabus uniformly and
will carry 20 marks in all.

Instructions for the candidates

1.

Candidat
es are required to attempt one question each from sections A, B, C and D of the
question paper and the entire section E.

2.

The use of scientific calculators is allowed.







Section


A

1.

Introduction to Bioinformatics : what is bioinformatics use of computer

for
biological research

2.

Overview of web servers and software : NCBI, EBI, PDRB,

3.

Search engines: Pubmed, ENTREZ, Expasy and SRS.





Section
-

B

4.

Biological database : Genban
k, EMBL, EBI, DDBJ, PDRB,

5.

Primary and secondary database of Nucleic acid
:

G
enb
ank
, SCOR, and Protein

databases:
Swiss PROT,PIR.SCOP,CAT, prosite, PDB
.

6.

Composite database OWL, metabolic pathway database
: KEGG, Ecocyc,
MetaCyc





Section
-

C



7.

Computation Biology : Analysis of Nucleic acid and protein sequences, sequence
comparison
algorithm scoring schemes, BLOSUM, PAM 250

8.

Sequence and Genome analysis : Local alignment , global alignment, FASTA,
BLAST, (Blast P, Blast N, Blast X) and similarity searching scores and their
statistical interpretation.

9.

Functional genomics strategies fo
r generating EST and full length inserts, EST
clustering and assembly, statistical
analysis
of EST data microarray.




Section
-

D

10.

Functional Proteomics: Protein family and domain databases (PROSITE) Pfam,
SMART), algorithms for multiple sequence alignment

(CLUSTAL x and
CLUSTAL w) and comparison with sequence databases, Biological motifs
(PSSMs, HMMs) , finding protein


coding regions.

11.

Prediction of macromolecular structure ( protein secondary and tertiary structures)
and properties, software for displayi
ng macromolecular structures (Port Param,
PREDATOR )

12.

Protein modeling software: RASMOL, MOLMOL,INSIGHT,

EMBOSS, and
their applications.


Suggested Readings

(Latest Editions)

:

1.

Introduction to Bioinformatics By A. M. Lesk, Oxford University Press, USA,
200
5

2.

Bioinformatics Basics: application in biological science and medicine. By
Hooman Rashidi and L. K. Buehler, CRC Press, 2005.

3.

Proteins and Proteomics : a lab manual by R. J sompson , Cold Sprin Harbor, US,
2003

4.

Bioinformatics : Genes , proteins and Compu
ters by C A Orengo and J M
Thornton, Taylor and Francis, US 2003

5.

Bioinformatics Computing By Bryan Bergeron, Pearson Education, US 2002

6.

Bioinformatics sequence and genes analysis by Mount, D.A. 2001

7.

Bioinformatics methods and Protocols by Baxevanis, A. D.
2001

8.

Introduction to protein Architecture; The structural biology of proteins By A M.
Lesk, Oxford University Press, UK , 2000

9.

Bioinformatics : A practical guide Analysis of genes and proteins 2
nd

ed,

10.

Let Us C by Y. Kanitkar BPB Publications

11.

Computer Fun
damentals by P.K. Sinha















Practical Paper VII

Pertaining to Theory Paper:

XIII and XIV


Max. Marks: 100





Practical Time: 60 hours

Time: 4 hours


1. Retrieval of sequences using ENTREZ

2. Sequence analysis using BLAT, Align, Lalign

3. Multi
ple sequence alignment and Phylogenetic analyzing using Clustal, ClustalW

4. Studying 3D structure using RASMOL

5. Homology Modeling using Swiss PDB


Hb, Protease

6. Calculation of Phi and Psi angle
-

Hb, Protease

7. Docking: protein
-
protein; protein
-
smal
l molecules

8. Potential energy calculation of regular structures

9. To mutate protein and energy minimization using Swiss PDB viewer

10. Gene prediction


Gene D’cefer

11. Adhesion protein prediction


Sea path

12. Comparative proteomics and genomics


Pr
oteome calculator

13. Protein annotation


PLHost



Dissertation