M.Sc. (BIOTECHNOLOGY) PART-II(Semester III - Punjabi University ...

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Dec 3, 2012 (4 years and 7 months ago)

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SYLLABUS

M.Sc.
(BIOTECHNOLOGY) PART
-
II

(Semester III & IV)

2012
-
201
3 & 2013
-
14

SESSIONS


The course will consist of two semesters in the second year i.e., semester III and
IV. In semester III, there shall be four theory papers and two practical papers. In
the
semester IV, there shall be two theory paper
s

and one practical paper. In addition, the
students shall undertake project on research/industrial problems relevant to industrial
biotechnology.

The in
-
plant training of 4
-
6 weeks shall be undertaken by stu
dents at
various industries/institutes/R&D centres, etc. after completion of theory and practical
examinations of semester II
, which will be evaluated
during the
semesters III and IV.





Each theory paper shall have
5

hours teaching and 3 practical hours
per week.
Each theory paper shall be of 100 marks, of which 80 marks shall be allocated to the
theory paper set by external examiner. The internal assessment in each paper shall have
20 marks. There shall be a seminar and assignment of 5 marks each and two

tests of 10
marks
each. Only best of these two tests
shall be
considered.
The seminars will be
allotted to all the students from the respective syllabi of theory papers in such a way that
each student could be assessed by the teacher of the

concerned
subj
ect.
The awards of
internal assessment shall be dispatched by the Head of the department before the
commencement of semester examinations.


The subjects
and distribution of marks shall be as under:

SEMESTER III

Theory Papers

Paper IX: Enzymology and Enzym
e Technology



100 marks

Paper X: Microbial and Food Technology




100 marks

Paper X
I
: Environmental Biotechnology




100 marks

Paper X
II
: IPR
s
, TQM, Biosafety & Commercial Biotechnology

100 marks

Practical Papers

Practical Paper V

Pertaining to Theory Pap
er IX & X


100 marks

Practical Paper VI

Pertaining to Theory Paper XI & XII


100 marks



SEMESTER I
V

Theory Papers

Paper XIII: Bioinformatics and Computational Biology



100 marks

Paper XIV: Tissue and Cell Culture Technology




100 marks

Practical Papers

Practical Paper VII: Pertaining to Theory Paper XIII & XIV


100 marks


Total marks for M.Sc.
-
II shall be as under:

SEMESTER III

Theory Papers

(4)








400 marks

Practical Papers (2)








200 marks









Total


600 marks

SEMESTER I
V

Theory Papers

(2)








200 marks

Practical Papers (1)








100 marks

Industrial Visits, In
-
plant Training Seminars and Project Work


Satisfactory/

Unsatisfactory

(Fail)

Total


3
00 marks

Grand
Total (Semester III & Semester IV)

900 marks



Evaluation and viva
-
voce of pr
oject work will be conducted by one examiner. In
-
plant training seminar and industrial visits shall be evaluated by a board of three teachers
and communicated by Head of department before commencement of final exam
ination
s.









SEMESTER
-
III


PAPER IX
:
ENZYMOLOGY
AND

ENZYME TECHNOLOGY

M
aximum

M
arks:
80






Lectures to be delivered
: 60

Time
A
llowed: 3 Hours


INSTRUCTIONS FOR THE PAPER
-
SETT
ER


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 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.

Enzymes
:
S
tructure, evolution and its basis.

2.

Enzyme action:
S
pecificity,

molecular aspects of enzyme action, and examples
from different classes of enzyme.

3.

Regulation of enzymic action:
A
ctivation of enzymes, covalent modification,

allosteric interaction, multienzyme complexes.

.

SECTION
-

B

4.

Industrial production of en
zymes:
S
ources of enzymes, criteria for the selection of

source for enzyme production, methods of large scale production
-
solid substrate

fermentation and submerged fermentation, factors affecting enzyme production,

amylases, cellulases, pectinases, lacta
ses, in
vertases, lipases, proteases
.

5.

Immobilization of biocatalysts:
D
efinition, objectives and advantages of
immobilization; techniques of immobilization, matrices

-

types, advantages and
limitations.

6.

Kinetic characterization:
I
mmobilized enzymes

-

compa
rative account of
immobilized biocatalysts, concept of co
-
immobilization.


SECTION
-
C

7.

Biochemical applications:
R
ole of soluble and immobilized enzymes in the
synthesis and production of amino acids and chiral compounds; use of enzymes as
detergents.

8.

Pharma
ceuticals:
R
ole of soluble and immobilized enzymes in production of
antibiotics, steroids, and other important intermediates of biotechnological
industry; role of soluble and immobilized enzymes in diagnosis and treatment of
diseases; enzyme therapy.

9.

Analy
tical applications:
T
heory and applications of various enzyme electrodes
e.g. enzyme sensors, enzyme membranes, biochips/bio
-
semiconductors.

10.

Applications in f
ood

industry:
S
oluble and immobilized enzymes

-

food
production and processing, amylases, pectinas
es, proteases, lipases,
glucoisomerases, naringinase.


SECTION
-
D

11.

Enzyme engineering
:

I
n

vitro

approaches to improve functional efficiency.

12.

Recombinant enzymes:
O
verproduction and applications.

13.

Enzymes in organic solvents:
M
odes of using enzymes, fundamenta
ls and new
properties.


RECOM
M
ENDED READING

1.

Funda
mentals of Enzymology: The cell and
Molecular Biology
of
Catalytic
Proteins

by N
.
C
.

Price and L
.

Stevens: Oxford University, 2000.

2.

Enzymolgoy
L
ab Fax
., edited by P.C. Engel, Academic Press, 2003.

3.

Enzyme S
tructure and Function
, 2nd edition by A, Fersht, W.H. Freeman and
Co., NY, 1999.

4.

Enzymes, Biomass, Food and Feed (Biotechnology 2E,

Vol.

9) Ed. Rehm, Reed,

A.

Phuler, Wiley
-
VCH, Berlin, 2001.

5.

Enzyme Kinetics: Principles and Methods

by Hans Bisswang
er and Leonie
Bubenheim, April 2002.

6.

Industrial Enzymology: The
A
pplication of Enzymes in Industry

edited by T.

Godfrey and S. May. McMillan publishers, 2001.

7.

Enzyme Technolog
y

by M.F. Chaplin and C. Bucke, Cmabrigde University Press,

NY, 1990.

8

E
nzymes in Food Processing
, 2nd Edition, Edited by G
.
A
.
Tucker and L
.
F
.
J
.
Woods.

10.

Manual of Industrial Microbiology and Biotechnology
,

2nd edition, edited by
A.L.

Demain and

N.A. Soloman, American Society for Microbiology
Washington,

2003.

11.


A
Textbook of Industrial Microbiology
,

2nd edition (Biotechnology) by W.Cruger
and A.Cruger,

Sinauer Associates, Sunderland,US, 2004.

12.

Enzymatic
R
eactions in
Organic Media
,

Ed
.

Munishwar N
.

Gupta 2000.

Birkhauser
Verlag publication.

13

Supramolecular

Enzyme Organization Quaternary Structure and Beyond

by Peter

Friedrick, Pregamon Press, Oxford, 1994
.

P
APER

X
:
MICROBIAL AND FOOD TECHNOLOGY

Maximum Marks: 80






Lectures to be delivered: 60

Time Allowed: 3 Hours


INSTRUCTIONS FOR THE PAPER
-
SETTER


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 ca
lculators is allowed.

SECTION


A

1.

Microbial transformation: T
ypes of trans
f
ormation, applications in bi
otechnology
and food technology, steroid transformation
s
.

2.

Pharmaceutical pr
oducts: F
ermentative production of antibiotics,

penicillins,

cephalosporins, e
rythromycin
s, vancomycins and streptomycin
.

3.

Vaccines
: F
ermentative production of vaccines

&

recombinant vaccines
;

edible
vaccines
.

SECTION


B

4.

Production

of f
ood additives and ingredients: F
ermentative production of amino
acids

-

L
-
glutamic acid and L
-
aspa
rtic acid.

5.

Production

of vitamins:
T
hiamin (B
-
1), riboflavin (B
-
2), vitamin (B
-
12).

6.

M
icrobial polysac
c
harides:
F
ermentative production of xa
nthan gums, dextra
ns,
cyclodextrins

and pullulan
.

SECTION


C

7.

F
ermented foods
:
P
roduction technology of cheese

and b
read; brief account of
Indian fermented foods

(
Idli, Vada, Dosa, Papad, Jalebi, Bhatura, Warries,
Marchu, Gundruk
)
.

8.

Fermented

dairy
products
and sugar

syrups
:
P
roduction of cultured

dairy milk,
cultured cream, yo
g
h
urt; Sugar syrups
-

cane syrup, invert syr
up, high fructose
syrup, maltose syrup.

9.

Immobilized whole cell technology in food industry
:
Brief account in wine, beer
& dairy

industry.


SECTION


D

10.

Food

preservation:
P
hysical (dehydration, freeze
-
drying, heat, irradiation) and
chemical (antibiotics, or
ganic acids, nitrates and nitrites, sulphites and sulphur
dioxide
)

methods.

11.

Food

regulations:
Brief account on PFA, FPO, FAO, FDA, AGMARK, HACCP,
CODEX ALIMENTARIUS
.

12.

Waste

utilization:
T
echnology for the utilization of waste from

dairy,

fruit a
nd
vegetable

processing industries
.


RECOMMENDED READING

1.

Prescott and Dunn’s
Industrial Microbiology

by B. Reed McMillan Publishers
Ltd., Connecticut, 1982.

2.

Principles of
Fermentation Technology

by P.
F. Stan
bury, A
.

Whitaker and Hall,
Pergamon Press, NY, 1984.

3.

Compreh
ensive Biotechnology

by
M.
Moo Young (Vol. 3 and 4), Pergamon
Press, NY, 1985.

4.

Fundamentals of Biotechnology

by P. Praive, B. Fraust, W. Sitting and D. A.
Sukatesh WCH Weinheim, 1987.

5.

Biotechnology, Principles and Applications

by J. Higgins, D.J. Bestand
,
J
. Jones,
Blackwell Scientific Publications, London, 1985.

6.

Biotechnology

by R.
H. Rehm and G. Reed (Vol
.

4, 5, 6 and 7a), Verlag Press,
NY, 1982 and 1987.

7.

Essays
i
n Applied Microbiology

by J. R. Norris and M. H. Richmong: John Wiley
and Sons, NY, 1981.

8.

Yeas
t Biotechnology

by D.
R. Berry, I. Russel and G.G. Stewart: Allen and Unwin,
Boston, 1987.

9.

Microbial Biotechnology, Fundamentals of Applied Microbiology

by A.N.
Glazerand, H. Nikaido, W.
H. Freeman and Co., NY, 1995.

10.

Biotechnology: Food Fermentation Technolo
gy

by V.
K. Joshi and A. Pandey,
Educational Publishers and Distributers, New Delhi, 1997.


P
APER

XI
:
ENVIRONMENTAL
BIO
TECHNOLOGY


Maximum Marks: 80






Lectures to be delivered: 60

Time Allowed: 3 Hours


INSTRUCTIONS FOR THE PAPER
-
SETTER


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 s
yllabus 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 to environment
: N
ature of pollutants, biochemical and physiological
effects of pollutants on plants, animals and microbes, biomarkers

and
bioindicators
.

2.

Environmental applications of biotechnology:
Treatment of
municipal
waste
for
removal of
low molecular weight organic compounds

and metal ions
, microbial
enhanced oil recovery, bioremediation, biological deodorization
, solid municipal
waste management
.

3.

Principles o
f Treatment: L
aboratory and equipment, design for containme
nt of
biohazards, stoichiometry and kinetics

of treatment of biohazardous compounds,
Monod’s equation
.


SECTION


B

4.

Heavy metal contamination: Biochemistry and applications of
biohydrometallurgy and biomineralization processes, microbe
-
metal interactions,
metal speciation.

5.

Aerobic tr
eatment technologies: A
ctivated sludge (AS), Completely mixed
conventional activated sludge (CCAS), contact stabilizer (CSAS), step aeration
(SAAS), completely mixed (CMAS), extended aeration (EAAS), pure oxygen or
high purity o
xygen (POAS), tapered aeration (TAAS) systems.

6.

Aerated lagoons: A
erobic and facultative tricking filters and rotating biological
contactors, sludge characterization, aerobic land based tr
eatment systems, land
farming,

composting and vermicomposting.


SECTI
ON


C

7.

Treatment of liqui
d and solid waste: A
naerobic technologies: anaerobic
decomposition, anaerobic filter reactor, anaerobic contact reactor, fluidized bed
reactor, up
-
flow anaerobic sludge blanket (UASB), anaerobic baffled reactor,
mechanism of anaero
bic fermentation, biodegradation of organic compounds,
factors affecting process operation.

8.

Bio
-
energy: B
io
fuel cells, fuel alcohol production, hydrogen gas production,
biogas technology raw materials, biochemistry, microbiology, biogas plant,
factors affe
cting biogas production and its status in India.

9.

Treatment of waste air:
B
iological technologies of waste air treatment
.


SECTION


D

10.

Biosensors: D
efinition, advantages and disadvantages of biosensor,
immobilization strategies for the construction of biose
nsors, types of transducers,
development of b
iosensors for heavy metal ions, BOD biosensor
.

11.

Construction of biosensors and kits for pathogens, insecticides and pesticides
,
Immuno biosensors

12.

Protein engineering and construction of generic biosensors. Modifi
cation at DNA
level, modification of polypeptide chain

(i)

Zinc finger, carbonic anhydras
e, CAM, CAMBP

(ii)

Engineered antibodies and i
on channels

Modifications that increase the activity, modification that alter the surface
properties, modification that alter spec
ificity, coenzyme attachment, new enzyme
activities


RECOMMENDED READING

1.

Environmetal Issues
by Shuchi Mathur, 2006.

2.

Verms and Vermitechnology
by Arvind Kumar, 2005

3.

Advanced Environmental Biotechnology
b
y Aggrawal S.K., 2005.

4.

Text Book of Environmetal Biotechnology
by Mohapatra Pradipta, 2006

5.

Methods in Environmetal Analysis, Water, Soil and Air,
2
nd

edition, P.K. Gupta,
2007.

6.

Waste Water Treatment by Immobilized Cells
by Tyagi and Vembu, 1990.

7.

A Text Boo
k
of
Biotechnology

by R.C. Dubey
,

S. Chand &
C
ompany Ltd.
,

New
Delhi
,
2002.

8.

Environmental Science and Biotechnology,
Murugesan A.G., 2006.

9.

Environmental Biotechnology
by Fuleker M.H., 2005.

10.

Environmental Biotechnology
by Thakur Indu Shekhar, 2006.

11.

Ecotechn
ology for Pollution Control and Environmental Management
by Trivedi
and Kumar, 1998.

12.

Microbiual Bioremediation
by Rajendran P., 2006.

13.

Environmental Studies and Ethics
by Suresh Gouri.

14.

Biofertilizers and Organic Farming,
NIIR Board of Technology.


15.

Modern Te
chniques of Agroprocessing and Agricultural Waste Products

by NIIR
Board of Technology.

16.

Environmental Management
by Kulkarni and Ramachandra, 2006.

17.

Biotechnology in Environmental Management
by Pathade G.R. and Goel P.K.,
2004.

18.

Indu
s
trial
Water Pollution
Co
ntrol
, W. Wesley Elbenfields
-
jr. Mc graw Hill
I
nternational Editions
,
1998.

19.

Biotechnology
-
Applications to
Environmental Protection
,
First Edition 1993,
Published by Mo Mera Pandey, for Himalaya Publishing House.

20.

Advances in Industrial
Waste Water Treatment

edited by P.
K. Goel,
Technoscience
P
ublications, First Editions, 1999.

21.

Commercial Biotechnology

by

Elsevier Science publishers
,

B.V.

Amsterden, The
Newdesk, 1984.

22.

Environmental Engineering

by
Peavy S.
Howard
a
nd Donald R. Rowe and
George Technologies, Mc
Graw Hill International Edition (198
5
).

23.

Protein Immobilization: Fundamentals and
A
pplications

edited by Richard F.
Taylor, 1991.

24.

Basic Environmental Science

by G.
S.P. Iyer, Educational Publisher
s and
Distributo
rs, New Delhi, 1997.

25.

Comprehensive Biotechnolo
gy

by M. Moo
-
Young (Vol. 4),

Pergamon Press, New
York, 1985.


P
APER

XII
:
IPRs, TQM, BIOSAFETY AND

COMMERCIAL
BIOTECHNOL
OGY

Maximum Marks: 80






Lectures to be delivered: 60

Time Allowed: 3 Hours


INSTRUCTIONS FOR THE PAPER
-
SETTER


The question paper w
ill 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.

Intellectual property rights
: Intellectual property, types and related Indian
legislations; Intenational conventions: TRIPs

Agreement
, PCT, Paris convention,
Budapest treaty, UPOV; preparation and preservation of invention records


2.

Patents:
P
atentable subject matter; patentability criteria;
prior
a
rt;

types of patent
applications, patent
s
pecification;

patent claims

3.

P
atenting systems: India, USA and Europe;
p
atent infringement;
patentability of
biological processes and products in India, pate
ntability of food technology
processes and products in India; trade secret protection.


SECTION


B

4.

Perceptions to food
technology:

Social aspects of food technology, status of food
technology in India and Punjab.

5.

Development and assistance:
U
niversity
-
i
ndustry relationships in food
technology, Government programmes in development of microbial and food
technology; role of international
organizations

in the development of microbial
and food technology programme.

6.

Biosafety:

Introduction;
b
iohazards;
r
ecomme
nded
b
iosafety
l
evels for
i
nfectious
a
gents,
b
iosafety guidelines,
i
nstitutional
biosafety committee, cartegana protocol.


SECTION


C

7.

Total quality managem
ent
:
I
ntroduction, concept, role and its importance;
contributions of management thinkers in quality

management, introduction to six
-
sigma
.

8.

Core concepts of TQM: Quality of profit, cost and economic of quality,
competitive bench marking.

9.

Tools and techniques of TQM:
T
echniques for
analyzing

quality process,
statistical process control, problem solving t
ools
.

SECTION


D

10.

International Organization for Standardization (ISO)
:

About the
organization, its
functioning
,
membership and

relevance of certificati
on; m
ethod of procuring
certification
.

11.

QMS
: M
ember an
d requirements of ISO 9000:2008: B
r
ief about the va
rious
revisions; i
ntroduction to GMP,
v
arious GMPs, its relevance and application; a
brief of ICH guidelines about quality of biotechnologically produced products

12.

EMS
-
ISO 14000:2004: M
embers and requirements.

RECOMMENDED READING

1.

Bare Act, Indian Patent Act

1970 Acts & Rules
, Universal Law Pubs. Ltd., 2007
.

2.

Genetic Patent Law & Strategy
, Kankanala C., 1st Edition, Manupatra
Information Solution Pvt. Ltd., 2007
.

3.

Law of
Intellectual Property

by Myneni, S.R., Asia Law House, Hyderabad,

2001.


4.

Intellectual Prope
rty Law
by Davis, Jennifer, Butterworth’s, London 2001.


5.

Intellectual
P
roperty:
Patents, Trade Marks
and
Allied Rights

by Cornish

W.R.,
Universal Law P
ublishing
, Delhi 2001
.

6.

Intellectual Property Rights on Biotechnology

by Singh, KC (2004
) BCIL, New
Delhi
.


7.

Total Quality in Research and Development

by G.C. Mclauyjlin.

8.

Guide to Total Quality Management

by Ralph
E
arly.

9.

Total Quality Management

by Feighan Baum.

10.

Total Quality
M
anagement

by Duncan.

11.

Total Quality in Information Systems and Technology

by J. Woodal
i.

12.

Guide to Quality Management Systems for the Food Industry

by R Early,
Blackie
Academic,

N
Y,

1995.


PRACTICAL PAPER V

Pertaining to:

Theory paper
IX
: Enzymology and Enzyme Technology

Theory paper X: Microbial and Food Technology


Max. Marks: 100






Practical Time: 60 hours

Time: 4 hours


1.

Standardization and optimization of immobilization techniques for enzymes and
cells.

2.

Comparative kinetic characterization of soluble/free and immobilized
enzymes/cells.

3.

Production of enzymes at laboratory scale

-

α
-
amylase,
inulinase, aspartase
,
pectinase etc.

4.

Demonstration of activities
of
soluble and immobilized enzymes

-

invertase,
α
-
amylase,
inulinase, aspartase
, pectinases and naringinase.

5.

Fabrication of enzyme sensors and demonstrations of their functions.

6.

En
zymatic preparation of high fructose syrup and maltose syrup.

7.

Utilization of industrial waste for fermented products.

8.

Preparation of Indian fermented foods.

9.

Microbial production of polysaccharides.

10.

Preparation of fermented dairy products.

11.

Preservation of f
ood by physical/chemical methods.


PRACTICAL PAPER VI

Pertaining to:

Theory paper XI: Environmental
Bio
technology

Theory paper XII
:
IPR
s
,

TQ
M
, Biosafety
and Commercial

Biotechnology



Max. Marks: 100






Practical Time: 60 hours

Time: 4 hours


1.

Isolati
on of phage from sewage.

2.

Separation of pesticides by HPLC method.

3.

Determination of heavy metal ions in industrial effluents by Atomic absorption
spectrophotometer and spectrophotometric methods.

4.

Characterization of industrial effluents for pH, TS, TDS, TSS
, alkalinity and
hardness parameters.

5.

Evaluation of population potential of waste materials as Biochemical Oxygen
Demand (BOD).

6.

Determination of chemical oxygen demand (COD) in various effluents.

7.

Development of biosensor (enzyme based/ microbe based) for m
onitoring heavy
metal ion/pesticides in the environment.

8.

Testing of xenobiotic degradative abilities of microorganisms.

9.

Demonstration of methane production from industrial effluents using batch and
anaerobic baffled reactors.

10.

Biogas production monitoring b
y gas chromatography.

11.

Bioremediation of heavy metal laden (Ni
+2
) industrial effluent by immobilized
cyanobacteria through packed bed reactor.

12.

Bioresin for treatment of chromium
-
laden effluents.

13.

To demonstrate the development of a small
-
scale vermicompostin
g bin for
commercialization.

14.

Use
of MS
-
Office software to sketch a company profile
.

15.

Overview of present status of food industries in Punjab
.

16.

Overview of present status of food industries in India
.

17.

Overview
of patent

databases
.

18.

Patent search excercises on U
S patents and EPO patents
.


19.

An over view of ISO 9000 family of Quality Management Standards
.

20.

A brief about ISO 9000 certified Indian companies
.

21.

An overview of ISO 14000 family of Environment Management Standards
.

22.

A brief about ISO 14000 certified Indian co
mpanies
.

23.

A brief about ISO 22000 certified Indian companies
.

24.

To identify the TQM related problems in an organization and to give a possible
solution.

25.

To study the essential elements of TQM.

SEMESTER
-
IV


PAPER XIII: BIOINFORMATICS AND COMPUTATIONAL BIOLOGY

Maximum Marks: 80






Lectures to be delivered: 60

Time Allowed: 3 Hours


INSTRUCTIONS FOR THE PAPER
-
SETTER


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 o
f 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 ques
tion 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.

Fundamentals of computers: Definition of computers, computer organization,
memory, number systems, input and o
utput devices. Types of computers, network
computers, working wit
h mainframe, personal computers, ftp, http, web, internet
and intranet, web browsing.

2.

Operating system: Wind
ows and Linux.


3.

Programming language C: C
haracter set, identifiers and keywords
,

da
ta types,
operator and expression control statements, switch break, continue statements,
function arrays, pointers.


S
ECTION
-
B

4.

I
ntroduction to b
ioinformatics: W
hat is bioinformatics,
use of computer for
biological research, o
verview of web servers and soft
ware: NCBI, EBI,
Expasy,
PDRB
.


5.

Overview of databases flat file formats: Classification of biological databases,
primary nucleic acid and protein sequence databases: INSDC, EMBL, GenBank,
DDBJ, UNIPROT knowledge base, SWISS
-
PROT and TrEMBL, PIR
-
PSD, PDB;
s
econdary nucleic acid and protein databases: Unigene, Ribosomal Database
Project, REBASE,
ENZYME
, PRINTS, SCOP, CATH; Composite databases:
OWL, Biosilico.

6.

Search e
ngines:
R
ole in biological research, PubMed, ENTREZ, SRS

and
eTBLAST.


SECTION
-
C

7.

Computation
b
iology: Analysis of
n
ucleic acid and protein sequences,

homology
analysis, ePCR, ORF finder, restriction pattern analysis, gene prediction;
analysis
of protein sequences: homology analysis, prediction of 2D and 3D structures;

sequence comparison algorith
m, sequence scoring schemes, BLOSUM

62
, PAM
250.

8.

Sequence and
g
enome 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

for generating EST and full length inserts, EST
clustering and assembly, statistical analysis of EST and EST data, microarray.


SECTION
-
D

10.

Functional
p
roteomics: Protein family and domain databases (PROSITE, Pfam,
SMART), algorithms for multiple sequence
alignment (CLUSTAL x and
CLUSTAL w) and comparison with sequence datab
a
ses. Biological motifs
(PSSMs, HMMs), finding protein
-
coding regions.

11.

Prediction of macromolecular structure (protein secondary and tertiary structures)
and properties, software for dis
playing macromolecular structures (ProtParam,
PREDATOR).

12.

Protein modeling software: RASMOL, MOLMOL, INSIGHT, EMBOSS and
their applications
.



RECOM
MENDED READING
S

1

Introduction to Bioinformatics

By A
.
M
.

Lesk, Oxford University Press, USA,
2005

2.

Bioinformati
cs Basics:
A
pplication in
Biological Science
and
M
edicine

by
Hoonuill

Rashidi and L
.
K
.

Buehler, CRC Press
,

2005.

3.

Proteins and Proteomics:
A Lab Manual

by R.
J
. S
impson, Cold Spring Harbor,
US
,

2003.

4.

Bioinformatics: Genes,
P
roteins and Computers

by C.
A
.

Oren
go and J
.
M
.

Thornton, Taylor and Francis, US
,

2003.

5.

Bioinformatics Computing

b
y Bryan Bergeron, Pearson Education, US
,

2002.

6.

Bi
oinformatics: Sequence and Genes

Analysis

by Mount, D.
A
.,
2001.

7.

Bioinformatics:
M
ethods and Protocols
by Baxevanis, A.
D.
,
2001.

8.

I
ntroduction to
P
rotein Architecture: The
Structural Biology
of
P
roteins

by A.
M
.

Lesk, Oxford University Press, UK, 2000.

9.

Bioinformatics: A
Practical Guide
to Analysis of
G
enes and
P
roteins

2
nd

ed.

10.

Let us C

by Y.
K
anitkar, BPB Publications.

11.

Computer Fundam
entals

by P.
K. Sinha
.


PAPER
XIV
:
TISSUE AND CELL CULTURE TECHNOLOGY

Maximum Marks: 80






Lectures to be delivered: 60

Time Allowed: 3 Hours


INSTRUCTIONS FOR THE PAPER
-
SETTER


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.


INSTRUCTION
S 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.

Plant tissue culture
:
H
istory of plant c
ell culture, culture media
-
composition,
preparation and development, cellular totipotency, cryopreservation.

2.

Callus and cell culture: Isolation of cells, growth of single isolated cells.

3.

Suspension culture: R
egeneration and maintenance of callus, org
anogenesis and
embryogenesis.

SECTION
-
B

4.

Organ culture: M
eristem culture, embryo culture and embryo rescue, anther
culture, virus free plant production and haploid plant production, production of
synthetic seed, micropropagation.

5.

Protoplast culture an
d fusion:
I
solation of protoplasts, culture and regeneration;
fusion of protoplasts, selection of fusion products of protoplasts; cybrids.

6.

Somaclonal variation, instability and somaclonal variations, plant transformation
-
Agrobacterium

mediated and parti
cle gun mediated, secondary plant metabolites
and application of plant biotechnology in crop improvement.

SECTION
-
C

7.

Animal cell culture
: H
istory, culture media
-
composition, preparation and
development, cell isolation, establishment and evaluation of cel
l culture, culturing
of specialized cells, cryopreservation of animal cells.

8.

Animal cell lines
:
E
stablishment, properties and use of cell lines, cultures of
tumor cells.

9.

Culture and scale up
:
M
onolayer culture
-
surface requirements, gas phase
requirem
ents, capillary culture units, micro
-
carrier culture techniques for
laboratory and scale up of cultures, suspension culture scale up.

SECTION
-
D

10.

Somatic cell fusion
:
M
ethods of somatic cell fusion, selection, properties of cell
hybrids and their applica
tions.

11.

Ani
mal cloning and embryo transfer
:
S
uperovulation,
in vitro

fertilization,
embryo transfer technology in animals; concepts and techniques of cloning; stem
cell culture and its applications.

12.

Industrial applications of animal cell culture.

RE
COMMENDED READINGS

1.

Plant
T
issue Culture and Molecular Biology
, P.S. Srivastava, N.R. Book
Distributors, New Delhi, 1998.

2.

Genetic Transformation in Plants
, R. Walden,
Open University Press,
Buchingham, 1988.

3.

Animal Cell Culture Technology
, M. Buttl
er,

Open University Press,
Buching
h
am, 1987.

4.

Animal Cell Culture
, R.I. Greclmey,

A.R. Liss Inc., New York, 1989.

5.

Plant Cell Culture
, H.A. Collins, NR Book Distributors, New Delhi, 1998.

6.

Plant Tissue Culture
-
Theory and
Practice
, S.S. Bhojwani

and
M.K. Razdan,
Prentice Else
vier, London, 1983.

7.

Plant Tissue
Culture Methods
-

Applications in Agriculture
, J. Reinart and Y.P.S.
Bajaj
,

Springer
-

Verlag, Berlin, 1989.

8.

Plant Cell, Tissue and Organ Culture
, J. Reinart and Y.P.S. Bajaj
,

Narosa
Publicat
ion House, New Delhi, 1989.

9.

Plant Cell Culture
, A. Stafford and G. Warren
,

Open University Press,
Buchingham, 1990.

10.

Principles of Plant Biotechnology
, H. Maitell, J. Mathew and R.A. Mackee,
Blackwell Scientific Publishers, Oxford, 1985.

11.

Plant Ce
ll Culture Technology
, M.M. Yoeman
,

Blackwell Scientific Publication,
Oxford, 1986.

12.

Plant Cell and
Tissue Culture A Laboratory Man
ual
, J. Reinart and M.M.
Yoeman
,

Narosa Publishing House, New Delhi, 1982.


Practical Paper VII

Pertain
ing

to:

Theory pap
er XIII:

Bioinformatics and Computational Biology

Theory paper

XIV: Tissue and
Cell Culture Technology


Max. Marks
:
100







Practical time
: 60 Hours

Time: 4 hours


1.

Lymphocyte and monolayer culture technique, viability testing and subculturing.

2.

Anim
al cell quantitation.

3.

Growth curve of mammal
ian cell li
ne in culture and
determination of cell
doub
l
ing time.

4.

Orientation to a tissue culture facility.

5.

Preparation of medium
.

6.

Callus initiation using an explant
.

7.

Ca
llus subculturing from an estab
lished callu
s
.

8.

Micropropagation of provided plant material.

9.

Introduction to hardening and biological hardening.

10.

Accession of molecular databases ENTREZ, SRS.

11.

Flat file format of GENBANK and EMBL.

12.

Describe databases that can be used to access text information about hum
an
diseases.

13.

Compare the use of Entrez and ExPasy to retrieve information about a protein
sequence.

14.

Perform pairwise alignments of the proteins using PAM 30, P
AM

70 and PAM
250 matrices.

15.

Use of windows and Linux for protein softwares.

16.

Compare sequence info
rmation from BLAST, PSI
-
BLAST, PHI
-
BLAST
, etc.

17.

Microarray/chip analysis: Normalization of gene expression data.

18.

Creation of molecules and calculation of energy minimization, torsion angles,
band distance, bond angle, Ram
a
chandran plot.

19.

Prediction of
s
econd
ary structure.

20.

Perform m
olecular modeling of given protein structure (3D) database using
various softwares.

21.

Molecular docking: Download protein sequences and perform docking of a
substrate /inhibitor.

22.

Glucocorticoid receptors/
zinc fingers binding to DNA
.

23.

Identifying the ORF using EMBOSS.