PROSPECTUS (FACULTY OF SCIENCE) …sgbau.ac.in/Syllabus/pdf/Science/m.sc.-biotechnology-10.pdf · polynucleotide and polysaccharides – secondary and tertiary, structural features

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(SEMESTER PATTERN TW

O YEAR DEG

REE COURSE

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M. W

/2010

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-II EXA

M. S/2011

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. S/2012

2010

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o part of this prospectus can be reprinted or published without

specific permission of Sant G

adge BabaA

mravati U

niversity"

M.Sc.

Prospectus No. 20111214

Biotechnology

12

SAN

T GA

DG

E BA

BA

AM

RAVATI U

NIVER

SITYSPEC

IAL N

OTE FO

R IN

FOR

MATIO

N O

F THE STU

DEN

TS

(1)N

otwithstanding anything to the contrary, it is notified for general

information and guidance of all concerned that a person, w

ho haspassed the qualifying exam

ination and is eligible for admission only

to the corresponding next higher examination as an ex-student or an

external candidate, shall be examined in accordance w

ith the syllabusof such next higher exam

ination in force at the time of such

examination in such subjects papers or com

bination of papers inw

hich students from U

niversity Departm

ents or Colleges are to be

examined by the U

niversity.

(2)B

e it known to all the students desirous to take exam

ination/s forw

hich this prospectus has been prescribed should, if foundnecessary for any other inform

ation regarding examinations etc.,

refer the University O

rdinance Booklet the various conditions/

provisions pertaining to examination as prescribed in the follow

ingO

rdinances.

Ordinance N

o. 1:

Enrolment of Students.

Ordinance N

o. 2:

Adm

ission of Students

Ordinance N

o. 4:

National cadet corps

Ordinance N

o. 6:

Examinations in G

eneral (relevent extracts)

Ordinance N

o. 18/2001:

An O

rdinance to provide grace marks for

passing in a Head of passing and

Inprovement of D

ivision (Higher C

lass) andgetting D

istinction in the subject andcondonation of defficiency of m

arks in asubject in all the faculties prescribed by theStatute N

O.18, O

rdinance 2001.

Ordinance N

o. 9:

Conduct of Exam

inations (relevent extracts)

Ordinance N

o. 10:

Providing for Exemptions and Com

partments

Ordinance N

o. 19:

Adm

ission of Candidates to D

egrees.

Ordinance N

o. 109:

Recording of a change of nam

e of aU

niversity student in the records of theU

niversity.

Ordinance N

o. 6/2008:

For improvem

ent of Division/G

rade.

Ordinance N

o.19/2001:

An O

rdinance for Central A

ssessment

Programm

e, Scheme of Evaluation and

Moderation

of answ

erbooks and

preparation of results of the examinations,

conducted by the University, O

rdinance2001.

Dineshkum

ar JoshiR

egistrarSant G

adge Baba

Am

ravati University.

PATTERN

OF Q

UESTIO

N PA

PER O

N TH

E UN

IT SYSTEM

.

The pattern of question paper as per unit system w

ill be broadlybased on the follow

ing pattern

(1)Syllabus has been divided into units equal to the num

ber ofquestion to be answ

ered in the paper. On each unit there w

illbe a question either a long answ

er type or a short answer

type.

(2)N

umber of question w

ill be in accordance with the unit

prescribed in the syllabi for each paper i.e. there will be one

question on each unit.

(3)For every question long answ

er type or short answer type

there will be an alternative choice from

the same unit. H

owever,

there will be no internal choice in a question.

(4)D

ivision of marks betw

een long answer and short answ

er typequestion w

ill be in the ratio of 40 and 60

(5)Each short answ

er type question shall contain 4 to 8 short subquestion w

ith no internal choice.

6Syllabus Prescribed for M

.Sc. BiotechnologySEM

ESTER ITheory Paper BT- 101 : C

ELL BIOLO

GY

UNIT-I:

Origin of cells and unicellular evolution: O

rigin of basicbiological m

olecules; abiotic synthesis of organicm

onomers and polym

ers; concept of Oparin and H

aldane;experim

ent of Miller (1953); the first cell; evolution of

prokaryotes; origin of eukaryotic cells; evolution ofunicellular

eukaryotes; anaerobic

metabolism

,photosynthesis and aerobic m

etabolism. D

iversity of cellsize and shape.C

ell theory. Structure of Prokaryotic andEukaryotic cells - Isolation and grow

th of cells.M

icroscopic techniques: Visualization of cells and

subcellular components by light m

icroscopy, resolvingpow

ers of different microscopes, m

icroscopy of living cells,scanning and transm

ission microscopes, different fixation

and staining techniques for EM, freeze-etch and freeze-

fracture methods for EM

, image processing m

ethods inm

icroscopy..

Sub-cellular fractionation and criteria of functional integrity.UNIT-II

:Structural organization and function of intracellularorganelles: C

ell wall, nucleus, m

itochondria, Golgi bodies,

lysosomes, endoplasm

ic reticulum, peroxisom

es, plastids,vacuoles, chloroplast, structure &

function of cytoskeletonand its role in m

otility, Cell m

otility- cilia, flagella ofeukaryotes and prokaryotes.C

ell signaling: Horm

ones and their receptors, cell surfacereceptor, signaling through G

-protein coupled receptors,signal transduction pathw

ays, second messengers,

regulation of signaling pathways, bacterial and plant tw

o-com

ponent signaling systems, bacterial chem

otaxis andquorum

sensing.UNIT-III

:M

embrane structure and function: Structure of m

odelm

embrane, lipid bilayer and m

embrane protein diffusion,

osmosis, ion channels, active transport, ion pum

ps,m

echanism of sorting and regulation of intracellular

transport, electrical properties of mem

branes.C

ell division and cell cycle: Mitosis and m

eiosis, theirregulation, steps in cell cycle, and control of cell cycle.C

ellular comm

unication: Regulation of hem

atopoiesis,general principles of cell com

munication, cell adhesion and

roles of different adhesion molecules, gap junctions,

extracellular matrix, integrins, neurotransm

ission and itsregulation.

UNIT-IV:

Cancer: G

enetic rearrangements in progenitor cells,

oncogenes, tumor suppressor genes, cancer and the cell

cycle, virus-induced cancer, metastasis, interaction of

cancer cells with norm

al cells, apoptosis, therapeuticinterventions of uncontrolled cell grow

th.B

ioenergetics, glycolysis, oxidative phosphorylation,coupled reaction, group transfer, biological energytransducers.C

ellular energy transactions - role of mitochondria and

chloroplast.UNIT-V

:B

asic concepts of development: Potency, com

mitm

ent,specification, induction, com

petence, determination and

differentiation; morphogenetic gradients; cell fate and cell

lineages; stem cells; genom

ic equivalence and thecytoplasm

ic determinants; im

printing; mutants and

transgenics in analysis of development.

Gam

etogenesis, fertilization and early development:

Production of gametes, cell surface m

olecules in sperm-

egg recognition in animals; em

bryo sac development and

double fertilization in plants; zygote formation, cleavage,

blastula formation, em

bryonic fields, gastrulation andform

ation of germ layers in anim

als; embryogenesis,

establishment of sym

metry in plants; seed form

ation andgerm

ination.B

rief introduction to the Life Cycle and M

olecular Biology

of some im

portant pathogens of AID

S, Malaria, H

epatitis,Tuberculosis, Filaria, K

alazar.

Practicals (BT

– 105A)

1M

icroscopy: Bright field (Flagella staining), D

ark Field (Bacterial

Motility)

2Cell D

iversity (Shape, Size)3

Microtom

y techniques (Anim

al Tissue)4

Instrumental m

ethods for Cell B

iology.5

Sub-cellular fractionation by differential centrifugation/Density

Gradient C

entrifugation .6

Isolation and identification of subcellular organelles(M

itochondria, Chloroplast, N

ucleus and Lysosomes)

7H

istochemical techniques: (D

ifferential Staining, Barr B

odyD

emonstration, B

lood cell counting and AB

O blood grouping)

5

78

8M

itosis and Meiosis.

Recom

mended readings

1.M

olecular Biology of C

ell, By B

ruce Alberts 4

th Edition2.

Molecular C

ell Biology, Lodish (5

th Edition)3.

Reproduction in Eukaryotic cells, D

M Prescott, A

cademic press.

4.D

evelopmental B

iology, SF Gilbert, Sinauer A

ssociates Inc.5.

Cell in Developm

ent and Inheritance, EB Wilson, M

ac-Milan, N

ewYork.

6.The C

oiled Spring, Ethan Bier, C

old Spring Harbor Press.

7.Fertilization, FT Longo, C

hapman and H

all8.

Molecular B

iology of Steroid and Nuclear H

ormone R

eceptors, LPFreedm

an, Birkhuser.9.

Molecular B

iology of the Cell B

y Gerrald K

arp 3rd Edition.

10.The C

ell By C

ooper11.

The cell cycle: Principele of controls By M

organ12.

Biochem

istry of Cell signaling B

y Helm

reich

Theory Paper BT- 102 : Macrom

olecules and Enzymology

Unit-I:

Acids, B

ases, pH, pK

, buffers, weak bonds, covalent bonds

Laws of therm

odynamics, entropy, G

ibbs energy, free energychanges and redox potentials, phosphate potentialM

itochondrial respiratory chain: Organization of carrier,

proton gradient, iron sulphur proteins and cytochromes.

Reversed electron transfer, respiratory controls and

oxidative phosphorylation, uncouplers and inhibitors ofenergy transferATP: Synthetase com

plex, microsom

al electron transport,partial reduction of oxygen, superoxides

Unit-II:

Proteins and Am

ino Acids

Am

ino acids: Classification, properties, peptide bond

Anabolism

and catabolism of A

mino A

cidsProteins: C

lassification and functionStructure (prim

ary, secondary, tertiary and quaternary),stabilizing bonds, R

amchandran Plot, principle of am

inoacid sequencing.

Unit-III:

Enzymes as Biocatalysts

International classification of enzymes

Enzyme K

inetics (negative and positive co-operativity);

Methods for m

easuring kinetic and rate constants of enzyme

reactions and their magnitudes, Inhibitors.Isozym

esEnzym

e turnover: methods of its m

easurements and

significanceA

llosteric enzymes, sigm

oidal kinetics and theirphysiological significance. Sym

metric and sequential m

odesfor action of allosteric enzym

esCo-enzym

es and cofactors: Water soluble vitam

ins and theirco-enzym

es, metalloenzym

esG

eneral mechanism

s of enzyme regulation: Feed back

inhibition and feed forward stim

ulation, enzyme repression,

induction and degradation, control of enzyme activity by

products and substrates; Ribozym

es and abzymes

Unit-IV:

Carbohydrates and Lipids

Carbohydrates: C

lassification, mono-, oligo-, and poly-

saccharides, physical and chemical properties, sugar acids

and amino sugars ;G

lycolysis and TCA

cycle;G

lycogen breakdown and synthesis; G

luconeogenesis;Interconversion of hexoses and pentoses;ATP cycle andcell bioenergeticsLipids: Classification (sim

ple, compound and derived lipids),

Structure, function and industrial significance, Oxidation

of lipids; Biosynthesis of fatty acids; Triglycerides;

Phospholipids; Glyco and Lipoproteins, Sterols, Circulating

lipids with relevance to pathological changes

Unit- V

:Sequencing of proteins and nucleic acidsProtein-protein and protein-ligand interactions, physical andchem

ical methods for study, C

onformational properties of

polynucleotide and polysaccharides – secondary andtertiary, structural features and their analysis – Theoreticaland experim

ental; protein folding – biophysical and cellularaspects.

Practicals (BT- 105B

)1.

Titration of amino acids.

2.Colorim

etric determination of pK

.3.

Reactions of am

ino acids, sugars and lipids.4.

Isolation, purity determination and quantiation of cholesterol, D

NA

and RN

A.

5.Q

uantitation of Proteins and Sugars.6.

Analysis of oils-iodine num

ber, saponification value, acid number.

910

7.U

V, Visible, Fluorescence and IR spectroscopy, Absorption spectra.

8.Separation techniques- C

entrifugation, Chrom

atography (Gel

permeation, Ion exchange, TLC

etc.) and electrophoresis.9.

Electrophoresis of Proteins - native and under denaturingconditions

10.Electrophoresis of D

NA

- linear, circular and super coiled.11.

Determ

ination of Tm of nucleic acid

12Enzym

e: purification and kinetic analysis.13

Imm

obilization of Enzymes

14H

ydrodynamic properties - m

easurement and applications.

15D

etermination of Tm

of nucleic acid.

Recom

mended readings

1.Lehninger’s Principles of B

iochemistry (5

th edition) by Nelson D

Land Cox M

M, CBS Publications, 2008.

2.B

iochemistry by Stryer L. (5

th edition) W.H

. Freeman &

Co., N

ewYork, U

SA, 1

3.Fundam

entals of Enzymology (3

rd edition) by Price NC and Stevens

L. Oxford U

niversity Press, NY, U

SA, 2000.

4.Principles of protein structure by Shulz and Schirm

er, SpringerVerlag, 1979 .

5.Fundam

entals of Enzymology by R

oyer. 19896.

Harper’s Biochem

istry. (27th Edition) Ed. M

urray RK, G

ranner DK

,M

ayes PA and R

odwell V

W. A

ppleton and Lange, Stamford,

Connecticut. McG

raw H

ill Companies, 2006

7.Textbook of B

iochemstry w

ith Clinical C

orrelations. (6th Edition)

Ed. Thomas M

. Devlin.W

iley-Liss Publishers. 20058.

Genes IX

. by Lewin B

. Pearson Education International, NJ, U

SA,

2008.9.

Fundamentals of Biochem

istry. (2nd Edition) Ed Voet D

and Voet JG.A

nd Pratt CW

. John Wiley &

Sons, Inc., 2006

Theory Paper BT- 103: Microbes: Physiology and G

eneticsUNIT I

:Prokaryotic D

iversityBacteria: Purple and green bacteria; Cyanobacteria; A

ceticacid bacteria; Spirilla; Spirochaetes; Pseudom

onads; Lacticand propionic acid bacteria; M

ycobacteria; Rickettsias,

Chlam

ydias and Mycoplasm

s.A

rchaea: Archaea as earliest Life form

s; Halophiles;

Methanogens; H

yperthermophilic archaea; Therm

oplasma.

Eukarya: Algae, Fungi, Slim

e molds and Protozoa.

Viruses: B

acterial, Plant, Anim

al and Tumor viruses;

Discovery, classification and structure of viruses and

importance

UNIT II:

Methods in M

icrobiologyIsolation of Pure culture techniques; Theory and practiceof sterilization; Principles of m

icrobial nutrition;C

onstruction of culture media; Enrichm

ent culturetechniques

for isolation

of chem

oautotrophs,chem

oheterotrophs and photosynthetic microorganism

s,C

ulture collection and maintenance of cultures.

Microbial Evolution, System

atics and Taxonomy

Evolution of earth and earliest life forms; Prim

itiveorganism

s and their metabolic strategies and m

olecularcoding; N

ew approaches to bacterial taxonom

yclassification including ribotypeing; R

ibosomal R

NA

sequencing; Characteristics of primary dom

ains; Taxonomy,

Nom

enclature and Bergey’s M

anual.UNIT III

:O

verview of Basic M

etabolism &

Microbial N

utritionM

etabolic Diversity am

ong Microorganism

sPhotosynthesis in m

icroorganisms; R

ole of Chlorophylls,

carotenoids and

phycobilins; C

alvin cycle;

Chem

olithotrophy; Hydrogen - iron - nitrite - oxidizing

bacteria; Nitrate and sulfate reduction; M

ethanogenesisand acetogenesis: Ferm

entations - diversity, syntrophy,UNIT IV

:D

earmatophytosis, A

spergillosis, Blastom

ycosis,C

ryptococcosis, burden of opportunistic fungal infectionsin im

munocom

promised hosts w

ith special reference tosecondary infections in A

IDS and C

ancer patients,know

ledge about MD

RC

hemotherapy/A

ntibioticsA

ntimicrobial agents; Sulfa drugs; A

ntibiotics: Pencillinsand C

ephalosporins; Broad- spectrum

antibiotics;A

ntibiotics from prokaryotes; A

ntifungal antibiotics; Mode

of action; Resistance to antibiotics.

UNIT V:

Bacterial Genetic System

Transform

ation, C

onjugation, T

ransduction,R

ecombination, Plasm

ids and Transposons. Bacterial

genetics map w

ith reference to E coli.V

iruses and Their Genetic System

Phage I and its life cycle; RN

A phages; R

NA

viruses;

1112

Retroviruses.

Genetic System

s of Yeast and Neurospora

Extra-Chromosom

al Inheritance

Practical (BT- 106A)

1)Preparation of liquid and solid m

edia for growth of m

icroorganisms.

2)Isolation and m

aintenance of organisms by plating, streaking and

serial dilution methods. Slants and stab cultures. Storage of

microorganism

s.3)

.Isolation of pure cultures from soil, w

ater, air and human beings.

4)G

rowth; G

rowth curve; M

easurement of bacterial population by

turbidometry and serial dilution m

ethods. Effect of temperature,

pH and carbon and nitrogen sources on grow

th.5)

Microscopic exam

ination of bacteria, yeast and molds and study

of organisms by G

ram stain, A

cid fast stain and staining for spores.6)

Study of mutations by A

mes test.

7)A

ssay of antibiotics and demonstration of antibiotic resistance.

8)A

nalysis of water for potability and determ

ination of MPN

.9)

Bacterial transform

ation.10)

Biochem

ical characterization of selected microbes.

11) Transduction

12)O

ne step growth curve of coliphage.

13) Isolation of Plasm

ids.14)

CO

2 fixation by photosynthetic microbes.

Recom

mended readings

1.G

eneral Microbiology, Stainer, R.Y., Ingraham

, J.L., Wheelis, M

.L.and Painter, P.R

. The MacM

illan Press Ltd.2.

BrOck Biology of M

icroogranisms, M

adigan, M.T., M

artinko, J.M.

and Parker, J. Prentice-Hall.

3.M

icrobiology, Peiczar, M.J. Jr., C

han, E.C.S. and K

reig, N.R

., TataM

cGraw

Hill.

4.M

icrobial Genetics, M

aloy, S.R., C

ronan, J.E. Jr. and Freitelder, D.

Jones, Bartlett Publishers.

5.M

icrobiology - a Laboratory Manual, C

appuccino, J.G. andSherm

an, N. A

ddison Wesley.

6.M

icrobiological Applications, (A

Laboratory Manual in G

eneralM

icrobiology) Benson, H

.J. WC

B: W

m C

. Brow

n Publishers.

Theory Paper BT- 104 : Biology of The Imm

une SystemU

nit I:

Basic Imm

unology :Introduction & overview

of the imm

unesystem

, Phylogeny of Imm

une System- Types of im

munity

- innate, acquired, active and passive,Clonal nature of

imm

une response.Organization and structure of lym

phoidorgans, N

ature and Biology of antigens and super antigens,

Antibody-structure and function A

ntigen - antibodyInteractions .

Unit II

:C

ells of the Imm

une system: H

ematopoiesis and

differentiation, lymphocytes trafficking, T- lym

phocytes-cells, B

- lymphocytes-cells, M

acrophages [Dendritic cells,

Natural killer cell and lym

phokine activated killer cells,Eosinophiles, N

eutrophiles and Mast C

ells.( antigenpresenting cells, cell m

ediated subset of T-cells, helper andsuppressor cells, cell m

ediated and humoral im

munity,

antibody dependent cell mediated cytotoxicity, N

Kcells)R

egulation of imm

une response: Antigen processing

and presentation, generation of humoral and C

ell mediated

imm

une response( Cell m

ediated cytotoxicity, lysis andm

acrophage mediated cytotoxicity),B

CR

and TC

R,A

ctivation of B and T lym

phocytes, Cytokines and their

role in imm

une response-T-cell regulationUnit III

:A

dvanced imm

unology: Major histo-com

patibility complex

(MH

C): C

ellular and molecular aspects: - types, structure

and function, MH

C restriction, C

omplem

ent System,

Generation of diversity and Im

munological tolerance.

Unit IV

:H

yper-sensitivity : Nature and types of H

ypersensitivereactions Types, autoim

munity, Transplantation: tissue and

organ grafting and rejection mechanism

, Imm

unity toinfectious agents (Intracellular parasites, helm

inthes andviruses

Unit V

:Tum

or Imm

unology : Cancer and the imm

une system, A

IDS

and others imm

unodeficiencies. Hybridom

a Technology andm

onoclonal antibodies. Concept of ideotypes and anti-

ideotypes, Synthetic vaccines, Role of im

munodiagnostic

in Biotechnology.

Practical (BT- 106B)1.

Blood film

preparation and identification of cells2.

Lymphoid organs and their m

icroscopic organization.3.

Imm

unization and collection of serum.

4.D

ouble diffusion: To perform precipitation reactions in gel by

Ouchterlony Technique given an antigen and antibody (double

1314

Imm

unodiffusion)5.

To perform precipitation tests (a) ring test (b) slide test in solution

given an antigen and antibody6.

Radial Imm

unodiffusion.: To perform single radial Im

munodiffusion

(Mancini’s Technique) using an antigen and antibody.

7.To perform

imm

unoelectrophoresis given an antigen and antibody.8.

To perform counter electrophoresis given an antigen and antibody

9.To perform

rapid Agglutination Test for detection of R

A factor in

serum.

10.Purification of IgG

from serum

.11.

Separation of mononuclear cells by Ficoll-H

ypque.12.

Western B

lotting13.

To perform ELISA

.(Using Teaching K

it)14.

Imm

unodiagnostic (Dem

onstration using comm

ercial kits.)

Recom

mended readings

1.K

uby- Imm

unology -,4th edition,R

A G

oldsby,Thom

as J,K

indt,Barbara,A.O

sbarne.(Freeman).

2.Im

munology-A

short course,4th edition,-Eli B

eniamini,R

ichardsCoico,G

eoffry Sushine,(Wiley-Liss)

3.Fundam

entals of Imm

unology,William

Paul4.

Essentials of Imm

unology (6th Edition)- Ivan Roitt

5.C

ellular aaand Molecular Im

munology - A

bul K. A

bbas , Andrew

H. Lichtm

an and Jordan S6.

Imm

unology: An Introduction - Ian R

. Tizard7.

A H

andbook of Practical Imm

unology - G.P. Talwar.

Syllabus for SEMESTER

IITheory Paper BT - 201: M

olecular BiologyU

nit I:

Introduction to molecular biology, basic concept of

molecular biology and genetics. D

NA

Replication :

Prokaryotic and eukaryotic replication. Models of

replication, theta mode of replication, rolling circle m

odel ofreplication, B

i directional replication, replication of linearD

NA

, unidirectional replication. Functions of variousproteins involved in prokaryotic replication of D

NA

andeukaryotic replication. Properties of various replicationenzym

es. Replication of telom

eres and enzymes involved

in telomere replication. Repair of D

NA and Various enzym

esinvolved in repair of D

NA

.R

ecombination of D

NA

: Recom

bination of viral DN

A in

genome, various m

odels of recombination.

Unit II

:Transcription:Prokaryotic and eukaryotic transcription.Various R

NA

polymerases and their properties. R

ole ofsigm

a sub factor in initiation of transcription. Variousdom

ains of sub units of RN

A polym

erase. Structure andregulation of prokaryotic and eukaryotic genes. Initiationand elongation transcription factors. Various m

echanismof term

ination of transcriptions. Transcriptional and posttranscriptional gene silencing.M

odification of RN

A : 5‘ cap form

ation, 3‘ end processing,addition of polyA

tail, enzyme involved in polyadenylation

and function of poly A tail. Splicing of R

NA

, classes ofintrons, exon ligation, editing, N

uclear transport of RN

A,

and stability of RN

A.

Unit III:

Translation: Organization of prokaryotic and eukaryotic

translation machinery. Structure of prokaryotic and

eukaryotic ribosomoes and their com

ponents. ShineD

algarno sequence, Ribosom

al protein synthesis.R

egulation of protein synthesis, co and post translationalprotein m

odification. Non ribosom

al protein synthesis.Protein localization:Synthesis of secretary and m

embrane protein. M

echanismof secretion of extracellular enzym

es, Mechanism

oflocalization of proteins in nucleus, chloroplast,m

itochondria, peroxisomes and receptor m

ediatedendocytosis.

Unit IV

:O

ncogenes and tumor suppressor genes

Viral and cellular oncogenes, tumor suppressor genes from

1516

humans, structure, function, and m

echanism of action of

RB

and p53 tumor suppressor proteins.

Antisense and ribozym

e technology: Molecular m

echanismof

antisense m

olecules, inhibition

of splicing,

polyadenylation and translation, disruption of RN

Astructure and capping, Biochem

istry of robozyme, stratigies

for designing ribozyme, A

pplicaton of antisense andribozym

e technologies. Short Nuclear R

NA

and theirapplication.

Unit V

:M

olecular mapping of genom

e:G

enetic and physical maps, physical m

apping and map

based cloning, choice of mapping population, sim

plesequence repeat loci, Southern and fluorescence in situhybridization for genom

e analysis, Chrom

osome

microdissection and m

icro cloning.M

olecular markers in genom

e analysis.Prelim

inary concept of RFLP, R

APD

, AFLP. M

olecularm

arkers linked to disease resistant genes, application ofR

FLP in forensic, disease progonosis, genetic counseling,pedigree, varietals etc., A

nimal trafficking and poaching,

Germ

plasm m

aintenance, taxonomy and B

io diversity.G

enome size, G

enome m

apping by conjugation, organellegenom

e with concept of D

NA

barcoding, and cloning inorganelle genom

e. Genetic defects due to m

utations inorganelle genom

e.

Practical (BT- 205A)

1.Isolation of genom

ic DN

A2.

Southern blotting3.

RFLP analysis

4.Isolation of R

NA

5.Isolation of polyA

+ RN

A6.

Northern blotting

7.Preparation of probes

8.In vitro transcription

9.In vitro translation

10.M

etabolic labeling of proteins and imm

unoprecipitation.R

ecomm

ended readings1.

Molecular Cloning.- a Laboratory M

anual, J. Sambrook, E.F Fritsch

and T. Maniatis, C

old Spring Harbor Laboratory Press, N

ew York,

2000

2.Introduction to Practical M

olecular Biology, P.D. D

abre, John Wiley

& Sons Ltd., N

ew York, 1988

3.M

olecular Biology LabFax, TA

. Brow

n (Ed.), Bios Scientific

Publishers Ltd., Oxford, 1991

4.M

olecular Biology of the G

ene (4th Edition), J.D. W

atson, N.H

.H

opkins, J.W. Roberts, J.A

. Steitz and A.M

. Weiner, The Benjam

in/Cum

mings Publ. Co., Inc., California, 1987.

5.M

olecular Ceii B

iology (2nd Edition) J. Darnell, H

. Lodish and D.

Baltimore, Scientific A

merican Books, Inc., U

SA, 1994

6.M

olecular Biology of the C

ell (2nd Edition) B. A

lberts, D. B

ray, J.Lew

is,M. R

aff, K. R

oberts, and J. D. W

atson. Garland publishing,

Inc., New

York, 19947.

Gene V

I (6th Edition) Benjam

in Lewin, O

xford University Press,

U.K

., 19988.

Molecular B

iology and Biotechnology. A

comprehensive desk

reference, R.A. M

eyers (Ed.) VCH

Publishers, Inc., New

York, 19959.

Genom

es, TS. Brown

Theory Paper BT - 202 : Bioprocess Engineering and TechnologyUnit-I

:M

icrobial Strain: Screening and Improvem

entIndustrial m

icrobial strain: Isolation by enrichment culture;

Preservation of industrial strains: Methods, Q

uality controlof preserved stock cultures; Strain im

provement: Prim

aryand secondary screening; M

utagenesis: Selection ofm

utants synthesizing improved levels of prim

ary andsecondary m

etabolites; Genetic engineering for strain

improvem

ent: General schem

e, methods, hom

ologous andheterologous gene expressions (suitable exam

ples).Unit-II

:M

icrobial Grow

th and Grow

th Media

Grow

th kinetics: Batch and continuous culture (m

ultistageand feed back system

s), Fed batch culture; Industrialferm

entation media: Ingredients, sources and role of carbon,

nitrogen, minerals, grow

th factors, buffers, precursors,antifoam

agents; Medium

optimization: N

eed andsignificance, Plackett-B

urman design; M

edia Sterilizationand Inoculation; C

omparative account of batch and

continuous sterilization, Factors affecting sterilization;B

atch sterilization: Del factor, D

and Z value, Methods,

Scale-up of batch sterilization; Continuous sterilization:

Design and M

ethods; Filter sterilization of air, media,

exhaust air; Developm

ent of inocula: Criteria for transfer,

Cascade system

, Inocula for yeast, bacterial, mycelial

processes

1718

Unit-III:

Bioreactor StudiesD

esign of fermenter, Types of bioreactors (stirred tank,

packed bed, bubble column, air-lift, M

TB, plug flow reactor,

rotating biological contactors (RB

C), photobioreactors;

Mass transfer in bioreactor (oxygen and heat transfer)

Measurem

ent and control of bioprocess parameters: pH

,tem

perature, aeration, agitation and foam; A

utomation for

monitoring and control: O

nline-Offline sensors, C

ontrolsystem

s (Two position, proportional, integral and

derivative); Use of com

puters: data logging, data analysisand process control (tw

o layer neural network); Process

scale-up: Factors involved, Scale-up window

for aerationand agitation, steps involved.

Unit-IV:

Dow

nstream Processing

Strategy for recovery; Harvesting of B

iomass and Product:

Precipitation, Cell aggregation and flocculation, Filtration,

Centrifugation; C

ell Disintegration: Physical-m

echanicaland chem

ical methods; Liquid-liquid extraction: Solvents

used, two-phase aqueous extraction, supercritical fluid

extraction; Chrom

atography and mem

brane processes,pervaporation

Unit-V

:Solid State Ferm

entationsIntroduction, G

eneral characteristics; Com

parison between

solid state cultivation (SSC) and subm

erged liquid culture(SLC); Factors affecting solid state ferm

entations: Moisture

and water activity, tem

perature and heat exchange, pH, m

asstransfer, substrate concentration and availability;Econom

ical applications of solid state fermentations

Practical (BT

– 205B)

1.Isolation of industrially im

portant microorganism

s for microbial

processes.2.

Determ

ination of thermal death point (TD

P) and thermal death

time (TD

T) of microorganism

for design of a sterilizer.3.

(a)D

etermination of grow

th curve of a supplied microorganism

and also determine substrate degradative profile.

(b)Com

pute specific growth rate (m

), growth yield (Y

x/s) fromexperim

ent.4.

Simulate the m

icrobial growth in batch, fed batch and continuous

culture using fermisym

.5.

Determ

ine the mixing tim

e for CSTR.6.

Com

parative studies of ethanol production using different

substrates.7.

Microbial production of citric acid using Aspergillus niger.

8.M

icrobial production of antibiotics.9.

Production and estimation of A

lkaline protease / amylase.

10.Im

mobilization of enzym

es – Inveratase/ Protease/ Am

ylase.11.

Whole cell im

mobilization (Yeast) for production of G

lucose syprup.

Recom

mended readings:

1.Principles of Ferm

entation Technology by Stanbury PF, Whitaker

A and H

all SJ. Aditya B

ooks (P) Ltd., New

Delhi, 1998.

2.Process B

iotechnology: Fundamentals (2

nd Edition) by

Mukhopadhyay SN

, Viva B

ooks Pvt Ltd., New

Delhi, 2004.

3.B

iotechnology: Hand B

ook by Board N

. Asia Pacific B

usinessPress Inc., N

ew D

elhi, 2005.4.

Solid Substrate Cultivation edited by D

oelle HW

, Mitchell D

A andRolz CE. Elsevier A

pplied Science, London, 1992.5.

Introduction to Biochemical Engineering by Rao D

G. Tata McG

raw-

Hill Pub Co Ltd., N

ew D

elhi, 2005.6.

Microbial Technology: Ferm

entation Technology (2nd Edition) Vol.

I & II, by Peppler H

J and Perlman D

. Academ

ic Press, NY, U

SA,

2004.7.

Biochem

ical Reactors by A

tkinson B. Pion Ltd, London. 1974

8.B

ioprocess Technology: Fundamentals and A

pplications, KTH

,Stockholm

. 2000.9.

Bioprocess Engineering-K

inetics, Mass Transport, R

eactors andG

ene Expression by Vieth W

F. John Wiley &

Sons, Inc.1994.

Theory Paper BT - 203 : Plant BiotechnologyU

nit I:

Conventional plant breeding –Introduction to plant

breeding, objectives of plant breeding;G

enetic variabilityand its role in plant breeding, C

enters of Origin of crop

plants, Methods of reproduction and breeding, B

reedingm

ethods in self pollinated, cross pollinated and vegetativelypropagated plants; H

eterosis and inbreeding depression,genetic basis of inbreeding depression, G

enetic,physiological and biochem

ical basis of heterosis;Exploitation of hybrid vigour, production of hybrids,com

posite and synthetics; Population improvem

entUnit-II

:Introduction to cell and tissue culture as a technique toproduce novel plants and hybrids; Tissue culture m

edia (com

position and preparation )

1920

Initiation and maintanace of callus and suspention culture,

single cell clones.O

rganogenesis, somatic em

bryo genesis, transfer andestablishm

ent of cut whole plant in soil

Shoot tip culture ; rapid clonal propagation and productionof virus free plants; Em

bryo culture and embryo rescue;

Protoplast isolation, culture and fusion selection of hybridcells and regeneration of hybrid plants, sym

etric andasym

etric hybrids, cybrids; Anther, pollen and ovary culture

for production of haploids plants and homozygous line;

Cryopreservation , slow grow

th and DN

A banking for germ

plasm conservation; G

reen house and green home

technologyU

nit- III:

Plant transformation technology

Basis of tum

our formation , hairy root, features of Ti and R

iplasm

id,M

echanisms of D

NA

transfer , role of virulence genes,use of Ti and R

i plasmid as vector, binary vector; U

se of35S and other prom

otors, genetic markers, use of reporter

genes, reporter genes with introns, use of scaffold

attachment regions; M

ethods of nuclear transformation,

viral vectors and their application , multiple gene transfer;

Vectors-less or direct D

NA

transfer and particlebom

bardment, eletroporation, m

icroinjection.Unit-IV

:A

pplication of plant Transformation for productivity and

performance:

Herbicides resistance, phosphoinothricin, glyphosate,

sufonyl urea, atrazine;Insect resistance , B

t genes, Non-B

t like protease inhibitors,alpha am

ylase inhibitors; Virus resistance, coat protein

mediated , nucleocapsid genes, diseases resistance ;

Nem

atode resistance, abiotic stress, post harvest losses,long shelf life of fruits and flow

ers; Male sterile lines, bar

and barness systems, C

hloroplast transformation,

Unit-V

:M

etabolic engineering and industrial products:Plant secondary m

etabolites, control mechanism

s andm

anipulation of phenylpropanoid pathway, shikim

atepathw

ay, Alkaloid industrial enzym

es, purification strategies,B

iodegradable plastics.

Practicals (BT

– 206A)

1)Preparation of m

edia

2)Surface sterilization

3)Isolation of explant, induction of callus, establishm

ent andm

aintenance of callus4)

Organogenesis and plant regeneration through clonal propagation.

5)Em

bryogenesis in cultured cell from different explants.

6)M

icropropagation of banana, citrus Papaya, Sugarcane etc.7)

Cell suspension culture from

different tissues.8)

Embryo culture and em

bryo rescue of different plant species9)

Effect of various growth harm

ones on cell divisions and cellproliferation

10)Isolation, purification and culture of protoplast

11)A

nther culture pollen culture and production of haploids12)

Artificial seed preparation

13)C

ytological examination of regenerated plants

14)Agrobacterium

culture and selection of transformants.

15)Selection of salt tolerance, am

ino acids analogous resistancethrough cell cultures.

16)H

ardening of tissue culture raised plants.

Recom

mended readings

1)A

mritrao, P.V.D

.A. Evans, W

.P.Sharp and Bajaj Y.P.S. (1990)

Handbook of Plant Cell Culture volum

es I-V, McG

raw H

ill PublishingCo.,N

ew York.

2)B

hojwani S.S. A

nd Rajdan M

.K. (1983). Plant Tissue C

ulture :Theory and practice.

3)Reinert J.and Bajaj Y.P.S. (1977). A

pplied and Fundamental A

spectsof Plant Cell, Tissue and O

rgan Culture, By Springer - Verlag, Berlin.4)

Grierson, D

. and Coyey S.N

. (1984) Molecular B

iology Bllakie

Publishers, New

York.5)

Allard R

.W.Principle of Plant B

reeding.6)

Gupta P.K

. (1995) Elements of Biotechnology, Rastogi and Com

pany7)

Choudhary, Elem

entary Principle of Plant Breeding.

8)B

hojwani S.S. (1991). Plant tissue culture : A

pplication andlim

itations, Elsevier, Am

sterdam.

9)C

hopra, Plant Biotechnology.

10)D

ixon R.A. and G

onzales, IRL Press, Plant Cell culture : A PracticalA

pproach.11)

Debergth P.C. and Zim

merm

an (1990) : Micro propogaton : K

luwer,

Academ

ic Publication, Dordrecht.

2122

12)C

.J.Lever : Genom

e organization and Expression in plants, Plenumpress.

13)S.D

.Kung and R

.Wu (1993) Transgenic Plant Vol.1 &

2, Academ

icpress, San D

iego.14)

Robert B.Goldbergh (1983) : Plant M

olecular Biology, Allan R.Liss,

Inc.New

York.15)

K.Lindsey and M

.G.K.Jones (1990) : Plant B

iotechnology inA

gricultural, Prentice Hall, N

ew Jersey.

BT

– 204Elective Paper

As given in Schem

e of examination (in A

ppendix-B)

BT – 206BPractical based on Elective Paper

SYLLA

BUS FO

RSEM

ESTER IIITheory Paper BT – 301 : A

nimal C

ell Science and TechnologyUnit-I

:A

nimal Cell

Structure and organization of animal cell; Term

inologies incell culture: O

rgan, cell, histotypic, organotypic, primary

culture and cell line; Primary and established cell line

cultures; Biology and characterization of the cultured cells;

Principle, Merits and D

emerits of A

nimal cell/tissue culture

Unit-II:

Equipments and M

edia for Cell C

ulture; Infrastructure forcell culture:Equipm

ents, culture vessel and materials; M

edia forculturing cells and tissues; natural and defined m

edia;Preparation of various tissue culture m

edia ; Chem

ical,physical and m

etabolic functions of media constituents;

Sterilization of culture media, equipm

ents and apparatusUnit-III

:Techniques of C

ell Culture; M

easurement of viability and

cytotoxicityM

easurement of grow

th parameters; B

asic techniques ofm

amm

alian cell culture in vitro; disaggregation of tissueand prim

ary culture, maintenance of cell culture, cell

separation; Cell synchronization; Scaling-up of anim

al cellculture;C

ell transformation; Invitro culture of oocytes/

embryos; C

ell/embryo cryopreservation

Measurem

ent of cell death, apoptosis; Cell cloning and

microm

anipulation; Risks and safety in the anim

al cellculture

Unit-IV:

Applications of Cell Culture; Cell hybridization: hybridom

aand m

onoclonal antibody production; Stem cell cultures,

embryonic stem

cells and their applicationsSom

atic cell genetics; Organ and histotypic cultures; Three

dimensional culture and tissue engineering

Unit-V

:Em

bryo Technology:C

onventional methods of anim

al improvem

ent : selectivebreeding and cross-breeding; Em

bryo biotechniques foraugum

entation of reproductive efficiency and fasterm

ultiplication of superior germplasm

; Super ovulation andO

estrus synchronization; Embryo collection, evaluation and

transfer; Invitro maturation of oocytes; Invitro fertilisation

and embryo culture; E

mbryo preservation, m

icrom

anipulation and cloning; Somatic cell cloning and em

bryosexing

Practical (BT

– 304)1.

Preparation of tissue culture medium

and mem

brane filtration.2.

Preparation of single cell suspension from spleen and thym

us.3.

Cell counting and cell viability.

4.M

acrophage monolayer from

PEC and m

easurement of phagocytic

activity.5.

Trypsinization of monolayer and subculturing.

6.C

ryopreservation and thawing.

7.M

easurement of doubling tim

e.8.

Role of serum

in cell culture.9.

Preparation of metaphage chrom

osomes from

cultured cells.10.

Isolation of DN

A and dem

onstration of apoptosis of DN

Aladdering,

11.M

TT assay for cell viability and growth.

12.Cell fusion w

ith PEG.

Recom

mended readings

1.C

ulture of animal cells (3

rd Edition) by Freshney R.I. W

iley-Liss.2.

Genes IX

by Lewin. Pearson Education International, N

J, USA

,2008.

3.A

nimal C

ell Culture – Practical A

pproach Edited by John RW.

Masters, O

xford.4.

Cell G

rowth and D

ivision: A Practical A

pproach edited by Basega

R, IRL Press.5.

Anim

al Cell Culture Techniques edited by Martin Clynes, Springer.

6.M

ethods in Cell Biology Vol.57, Anim

al Cell Culture Methods edited

by Mather JP and B

arnes D, A

cademic Press.

2324

7.B

iotechnology by Satyanarayana U. B

ooks and Allied (P) Ltd.,

Kolkata, India, 2005.

8.Cell and M

olecular Biology (8th edition) by de Robertis ED

P and deR

obertis EMF (Jr). Lippincott W

illiams &

Wilkins, Philadelphia,

2001.Theory Paper BT - 302 : Genetic Engineering

UNIT I:

Scope of genetic engineering.M

ilestones of inventions in Genetic Engineering; D

NA

chemical synthesis, separation by eletropherosis, various

types of agarose used in electropherisis and PAG

E,D

enaturating agents used in gel electropherosis, cloning,control of expression of cloned genes, cloning and patentingof life form

s. Guidelines on experim

entation in geneticengineering. G

uidelines of bio- safety according to WH

O(G

eneva Convention) and D

BT India.

Molecular tools: Polym

erase enzymes, N

ucleic acidm

odifying enzymes, nucleic acid ligases, proteases, types

of restriction enzymes and their sub types and application,

various types of DN

A and R

NA

markers and m

ethods ofcalculation of m

olecular weight of nucleic acids.

UNIT II:

Gene cloning vectors: Plasm

ids: general cloning vector,fusion plasm

ids, plasmids w

ith bacteriophage promoters,

shuttle vectors, phagmids, phages: ? as cloning vector, ?

insertion vectors,?? replacement vectors, Vectors derived

from A

grobacterium T1 plasm

id, Ca MV, A

nimal viral vectors

- SV-40, Vaccinia/Bacculo and retro viral cosmids, A

rtificialchrom

osomes: yA

Cs, m

ega yAC

s. BA

C vector; M

ethodsof detection of recom

binant; Nucleic acid purification:

Different chem

icals used in isolation and purification ofnucleic acids, Y

ield analysis: A260/280 .

Nucleic acid am

plification and its application: History and

Method of nucleic acid am

plification, Nucleic acid

amplification: D

NA am

plification, RAPD

, AFLP, asym

metric

PCR, RT PCR, 5‘RACE, 3‘ RA

CE, invert PCR, Syber green,hybridization probe am

plification, hydrolysis probeam

plification (Taq man), Scorpion prim

ers; Basic biochemical

requirement of therm

al cycler: Solutions, enzymes, buffer,

primers, designing of prim

ers, necessary conditions requiredfor designing prim

ers, use of fluorescent dyes andquenchers in prim

ers used for real time PC

R, annealing

temperature, calculation of Tm

of primers and optim

izationof PC

R conditions; Instrum

entation of thermal cycler:

Instrumentation of general therm

al cycler, gradient cyclerand R

eal time cycler; A

pplications of nucleic acidam

plifications in different fields.UNIT III

:N

ucleic acid sequencing; Sequencing of nucleic acids byM

axum &

Gillbert m

ethod and Sangers method.

Requirem

ent of manual sequencing m

ethod and automated

sequencing methods. D

ye primer chem

istry and dyeterm

inator chemistry. Various types of gels used for

sequencing methods. Pyrohosphatase, analysis of gels.

Radio active and non radioactive m

ethod of sequencing.Instrum

entation of sequencings, Applied biosystem

, Licor,and B

eckmann sequencing system

. Bi directional

sequencing method.

Restriction m

apping: construction of restriction map,

analysis of restriction fragments and its application; cD

NA

synthesis: mR

NA

enrichment, digestion using restriction

enzymes or m

echanical shearing, size fractionation,selection of appropriate vector, preparation of genom

iclibrary, use of linkers and adapters, m

ethod of screening oflibrary and chrom

osome w

alking and chromosom

e jumping

strategies. STS tagging.A

lternative strategies of gene cloning: Two and three

hybrid system, cloning differentially expressed genes;

Nucleic acid m

icro array: Construction of D

NA

chip, use offluorescent dyes, detection of m

icroarray and application;D

NA

Profiling: History, D

NA

profiling based on RFLP

method and N

A am

plification method.

UNIT IV:

Gene regulation:D

NA

transfection: Northern blot, Southern

Blotting, D

ot blots, colony hybridization different types oflabels used in N

orthern and Southern blotting methods.

Various methods of detection in analysis of blots;S1

mapping,

RN

ase protection

assay, R

eporterassay;Expression strategy for heterogeneous genes: Vectorengineering, and codon optim

ization, host engineering, invitro transcription and translation, expression in bacteria,Yeast, insects, m

amm

alian cells, plants and phage display.UNIT V

:Site directed m

utagenesis: Oligonucleotide directed

mutagenesis,

Mutagenesis

with

degenerateoligonucleotides, region specific m

utagenesis, linkerscanning

mutagenesis,

linker scanning

usingoligonucleotide directed m

utagenesis;Processing ofrecom

binant proteins, purification of recombinant proteins,

purification of fusion proteins, In vitro refolding and

2526

chaterization of rProteins and methods adopted for

stabilizations of rProteins;T D

NA

- T –D

NA

andTransposon tagging, identification and isolation of genesthrough transpososn tagging; Transgeneic and geneknockout technologies; Targeted gene replacem

ent andchrom

osome engineering; G

ene therapy; Vector engineering,Strategies for gene delivery, gene replacem

ent/augum

entation, gene correction, gene editing, generegulation and siliencing; Ethical values associated w

ithgene therapy , G

MO

, diagnosis; Molecular m

arkers in cropim

provement and inherited hum

an disorders.R

ecombinant D

NA

products/applications: Insulin, hepatitisB

antigen vaccine, growth horm

ones. Molecular farm

ingPracticals (B

T – 304)

1.B

acterial culture and antibiotic selection media. Preparation of

competent cells.

2.Isolation of plasm

id DN

A.

3.Isolation of Lam

bda phage DN

A.

4.Q

uantitation of nucleic acids.5.

Agarose gel electrophoresis and restriction m

apping of DN

A.

6.C

onstruction of restriction map of plasm

id DN

A7.

Cloning in plasm

id/phagemid vectors.

8.Preparation of helper phage and its titration

9.Preparation of single stranded D

NA

template.

10.D

NA

sequencing.11.

Gene expression in E coli and analysis of gene product

12.PCR

Recom

mended readings

1.M

olecular Cloning: a Laboratory Manual, J. Sam

brook, E.F. Fritschand T. M

aniatis, Cold Sprin H

arbor Laboratory Press, New

York,2000

2.D

NA

Cloning: a Practical Approach, D

.M. G

lover and B.D. H

ames,

IRL Press, Oxford, 1995

3.M

olecular and Cellular M

ethods in Biology and M

edicine, P.B.

Kaufm

an, W. W

u, D. K

im and L.J: Cseke, CRC Press, Florida, 1995

4.M

ethods in Enzymology Vol. 152, G

uide to Molecular C

loningTechniques, S.L. B

erger and A.R

. Kim

mel, A

cademic Press, Inc.

San Diego, 1998

5.M

ethods in Enzymology Vol 185, G

ene Expression Technology,

D.V. G

oeddel, Academ

ic Press, Inc., San Diego, 1990

6.D

NA

Science. A First C

ourse in Recom

binant Technology, D.A

.M

ickloss and G.A. Freyer, C

old Spring Harbor Laboratory Press,

New

YorK, 1990

7M

olecular Biotechnology (2"d Edn.), S.S. Prim

rose, Blackw

ellScientific Publishers, O

xford, 19948.

Milestones in B

iotechnology. Classic papers on G

eneticEngineering, J.A

. Davies and W

.S. Reznikoff, B

utterworth-

Heinem

ann, Boston, 1992

9.R

oute Maps in G

ene Technology, M.R

. Walker and R

. Rapley,

Blackwell Science Ltd., O

xford, 199710.

Genetic Engineering. A

n Introduction to gene analysis andexploitation in eukaryotes, S.M

. Kingsm

an and A.J. K

ingsman,

Blackwell Scientific Publications, O

xford, 199811.

Molecular B

iotechnology - Glick.

12R

ecombinanat D

NA

and Biotechnology: G

uide to teachers byH

elen Kreuzer

13.A

cademia to biotechnology B

y Jeffery M G

imble

14.B

iotechnology and safety assessment by Jhon A

Thomas

15.M

ethods in biotechnology by Michel Schw

eizer16.

Bioethics an introduction for the B

ioscience By M

epham.

Theory Paper BT- 303 : Biostatistics and Bioinformatics

UNIT-I:

Introduction to BiostatisticsSam

pling techniques.;Data collection, tabular and graphical

representation of Data; M

ean, mode, m

edian, range,variance, standard deviation and standard Error; Test ofsignificance: Z-test, T-test and C

hi square test; ProbabilityD

istribution: Binom

ial Pioson and Norm

al distribution;C

orrelation and linear regression, Analysis of variance,

AN

OVA

; One-w

ay and two-w

ay classificationUnit-II

:M

ajor Bioinformatics R

esourcesN

CB

I, EBI, ExPA

Sy The knowledge of various databases

Open access bibliographic resources and literature

Sequence and Structure; Databases: K

nowledge of the

following databases w

ith respect to: organization of data,contents and form

ats of database entries, retrieval of datausing text- based search tools; sources of data (e.g.sequencing projects, individual scientists, patent officesetc.), m

ethod for deposition of data to databases.N

ucleic acid sequence databases: GenBank, EM

BL, DD

BJ;

2728

Protein sequence databases: SWISS-PR

OT, TrEM

BL,

PIR_PSD

; Genom

e Databases at N

CB

I, EBI, TIG

R,

SAN

GER; Viral G

enomes; A

rcheal and Bacterial Genom

es;Eukaryotic genom

es with special reference to m

odelorganism

s (Yeast, Drosophila, C

. elegans, Rat, M

ouse)H

uman, plants such as A

rabidopsis thaliana, Rice, etc.

Repositories for high throughput genom

ic sequences: EST,STS G

SS, etc.PDB, N

DB, CCSD

;Derived D

atabases for bio-m

olecular sequencesUnit-III

:Sequence A

nalysisVarious file form

ats for bio-molecular sequences: genbank,

fasta, gcg, msf, nbrfpir etc. B

asic concepts of sequencesim

ilarity, identity and homology, definitions of

homologues,orthologues, paralogues.

Scoring matrices: basic concept of a scoring m

atrix,M

atrices for nucleic acid and proteins sequences, PAM

and BLO

SUM

series, principles based on which these

matrices are derived. D

ifferences between distance &

similarity m

atrix,Sequence-based D

atabase Searches: what are sequence-

based database searches, BLA

ST and FASTA

algorithms,

Various versions of basic BLA

ST and FASTA

, Use of these

methods for sequence analysis including the on-line use of

the tools and interpretation of results.Pairw

ise sequence alignments: basic concepts of sequence

alignment, N

eedleman &

Wuncsh, Sm

ith & W

aterman

algorithms for pairw

ise alignments, use of pairw

isealignm

ents for analysis of Nucleic acid and protein

sequences and interpretation of resultsM

ultiple sequence alignments (M

SA): the need for M

SA,

basic concepts of various approaches for MSA

(e,g.progressive, hierarchical etc.). A

lgorithm of C

LUSTA

LWand Pileup and their application for sequence analysis(including interpretation of results), concept of dendogram

sand its interpretation.

Unit-IV:

Taxonomy and phylogeny

Basic concepts in system

atics, taxonomy and phylogeny;

molecular evolution; nature of data used in Taxonom

y andPhylogeny, D

efinition and description of phylogenetic treesand various types of trees,Sequence patterns and profiles: B

asic concept anddefinition of sequence patterns, m

otifs and profiles, various

types of pattern representations viz. consensus, regularexpression (prosite-type) and profiles; profile-baseddatabase searches using PSI-B

LA

ST, analysis andinterpretation of profile-based searches.Protein and nucleic acid sequences properties: e.g.Proteom

ics tools at the ExPASy server and G

CG

utilitiesand EM

BOSS

Com

parative genomics: B

asic concepts and applications:Full G

enome alignm

ents: basic concepts, the need forgenom

e alignments

Unit- V

:Prediction of protein structureSecondary structure: B

asic principles on which the

prediction methods of first, second and third generation

are based; algorithms of C

hou Fasman, G

OR

methods;

Predicting the secondary structures using these methods

and analysis; concepts in measuring the accuracy of

predictions (Q3, Segm

ent overlap, Mathew

’s correlationcoefficient etc.)Tertiary Structure: Theoretical basis of the m

ethods forstructure prediction (sequence sim

ilarity / identity of targetprotein w

ith proteins of known structure, fundam

entalprinciples of protein folding etc.) and choice of appropriateprediction approach; basic principles and protocol ofH

omology M

odeling; Databases of m

odels; Basic principlesfor fold recognition, 1D

profiles and threading approaches,basic principles of abinitio structure prediction and thebroad approaches (w

hat are the hierarchical andenum

erative approaches,their general outline),Protein structure com

parison and classification: classes,folds; the concepts in 3D

structure comparison, purpose

of structure comparison, algorithm

s such as FSSP, VAST

and DA

LI

Practical (BT

– 304)1.

Com

puter oriented statistical techniques.2.

Preparations of charts / graphs using computers.

3.D

ata Retrieval System

: Entrez and SRS.

4.Paiw

ise sequence Alignm

ent methods: D

ynamic Program

ming and

Dot PlotA

nalysis5.

Multiple sequence alignm

ent using ClustalW

/ ClustalX

6.Phylogenetic analysis of protein and D

NA

sequences by Phylipand M

EGA

2930

7.A

nalysis of multiple aligned sequences for their physico – chem

icalproperties using G

eneDoc.

8.Search for active site / probase/ blocks in given sequence usingon line / off line softw

ares.9.

Determ

ination of secondary structure of amino acid sequence using

SOPM

/ GO

R/ C

hou Fasman other softw

ares.10.

Visualization of m

olecular structure of protein / Nucleic acid

molecule using R

asmol / C

n311.

Tertiary Structure prediction methods.

12.Full G

enome A

lignment.

Recom

mended readings

1.Baxevanis A

., Ouellette F.B.F. (Eds.) Bioinform

atics: a practical guideto the analysis of genes and proteins John W

iley and Sons, New

York2.

Bishop M

.J., Raw

lings C.J. (Eds.) D

NA

and protein sequenceanalysis. A

Practical approach IRL Press, O

xford Lesk A.M

. (Ed.)C

omputational m

olecular biology. Sources and methods for

sequence analysis. Oxford U

niversity Press, Oxford

3.Structural Bioinform

atics, Philip E. Bourne, Helge W

eissig (Editors),John W

iley & Sons

4.Protein Structure Prediction: B

ioinfomatic A

pproach, I.F. Tsigelny,International U

niversity Line5.

Introduction to Protein Architecture: The Structural B

iology ofProteins, A

rthur M. Lesk, 2001, O

xford University Press

6.Protein Structure Prediction: M

ethods and Protocols, David M

.W

ebster (Editor), 2000, Hum

ana Press7.

Introduction to Protein Structure, Carl-Ivar B

randen, John Tooze,G

arland Publishing8.

Handbook of Com

parative Genom

ics: Principles and Methodology,

Cecilia Saccone, Graziano Pesole, 2003, W

iley-Liss9.

Sequence - Evolution - Function: Com

putational Approaches in

Com

parative Genom

ics, Eugene V. Koonin, M

ichael Y. Galperin,

2002, Kluw

er Academ

ic Publishers10.

Genom

e Analysis: A

Laboratory Manual, 4 volum

es, Bruce B

irren,et al. (Editors), C

old Spring Harbor Laboratory Press

11.Bioinform

atics: Sequence and Genom

e Analysis by D

avid W. M

ount12.

Bioinform

atics : Sequence, Structure, and Databanks : A

PracticalA

pproach (Practical Approach Series by D

es Higgins (Editor), W

illieTaylor (Editor)

13.Introduction to B

ioinformatics by Teresa K

. Attw

ood, David J.

Parry-Smith

14.B

ioinformatics : A

Practical Guide to the A

nalysis of Genes and

Proteins, 2nd edition by Andreas B

axevanis (Editor), B.F.Francis

Ouellette (Editor)

SYLLA

BUS FO

RSEM

ESTER IVTheory Paper BT- 401 : Environm

ental BiotechnologyUNIT I

:Environm

ent: Basic Concept

Environment pollution: Types of pollution, M

easurement

of pollution, Microbial quality of A

ir, Aerosol, H

ospital site,Sew

age treatment site, Industrial process and solid w

astedum

ping site, Carcinogenic chem

icals and odour in air,M

ethods of control through Biotechnology, G

reen beltdevelopm

ent; Water: D

ifferent sources of water and their

quality, Nitrate Fluorides, H

eavy metal in w

ater, Methods

of its removal M

icrobial corrosion and its control methods

UNIT II:

Waste and its generation: C

ollection methods of sew

ageand industrial w

aste and its characterization; Waste w

atertreatm

ent: Physical, chemical and biological, Principles of

biological waste treatm

ent process; Aerobic process:

Activated sludge, O

xidation ditch, Trickling filter, Biotowers,

Rotating disc, O

xidation pond, Extended aeration methods

Anaerobic Process: A

naerobic digestion, Anaerobic filters,

Up-flow

anaerobic sludge blanket (UA

SB), Biomethanation

process; Treatment schem

e of Dairy, D

istillery, Tannery,Sugar, Fertilizers, R

efinery, Chem

ical and Antibiotic w

aste.M

easurement of w

ater pollution. Waste m

icrobiology ofaerobic and anaerobic treatm

ent processes. Recycle and

Reuse of w

aste water.

UNIT III:

Xenobitics in environm

ental. Oil pollution and its m

ethodsof control, B

iodegradation of Hydrocarbons, Substituted

hydrocarbons, Surfactant, Pesticides, Lignin, Tannin,Synthetic dyes, B

ioremediation of contam

inated soil andw

aste land, Mine spoil dum

ps, Biopesticides and integrated

paste managem

ent, Bioaccum

ulation and their types.U

nit IV:

Solid waste: Industrial and dom

estic, characterization ofsolid w

aste and managem

ent (composting, Verm

iculture andA

naerobic processes)H

azardous Waste: D

efinition, collection, characterizationand treatm

ent process (Hospital w

aste, Sludges fromchem

ical industries containing toxic waste); O

zone

3132

depletion, UV-6 green house effect, A

cid rain, Global

warm

ing their impacts and B

iotechnological approachesfor m

anagement

UNIT V:

Bioleaching, B

iofertilizer, Eutrophication, Sustainableagriculture and environm

ent (AM

F, ECM

, PGPR

s, PSB),

with special reference to agriculture; B

iosafety, Biological

warfare, C

arcinogenicity, Health risk and Environm

entaltoxicity, B

iodiversity and its methods of conservation,

Bioluminescence.

Practicals (BT- 404)1.

Detection of coliform

s for determination of the purity of potable

water.

2.D

etermination of total dissolved solids of w

ater3.

Determ

ination of dissolved oxygen concentration of water sam

ple4.

Determ

ination of biological oxygen demand (500) of n sew

agesam

ple5.

Determ

ination of chemical oxygen dem

and (CO

D) of sew

agesam

ple.6.

Determ

ine the efficiency of removal of air pollutant using fibrous

air filter.7.

Isolation of xenobiont degrading bacteria by selective enrichment

technique8.

Test for the degradation of a aromatic hydrocarbons by bacteria

9.Survey of degradative plasrnids in m

icrobes growing in polluted

environment

10.Effect of Sulphur dioxide on crop plants

11.Estim

ation of heavy metals in w

ater/soil by Atom

ic absorptionspectrophotom

etry,12.

Estimation of nitrate in drinking w

ater.13.

Role of m

icroorganisms in elevation of heavy m

etal induced stressI plants.

Recom

mended readings

1.C

hatterji, 2004 Introduction to Environmental B

iotechnology,Prentice-H

all of India.2.

Sincero and Sincero, 2004 Environmental Engineering : A

Design

Approach, Prentice-H

all of India.3.

Abbasi and A

bbasi, 2004 Renew

able Energy sources and theirEnvironm

ental Impacts. Prentice-H

all of India.

4.G

ilbert Masters. 2004. Introduction to Environm

ental Engineeringand Science, Second addition, Prentice-H

all of India.5.

Marshall Laird, 1990. Safety of M

icrobial Insecticides, InternationalB

ooks.6.

Kum

ar and Arw

ind 2004, Environmental B

iotechnology, Daya

Publishing.Theory Paper BT- 402 : Industrial Biotechnology

Unit I

:Ferm

entation products:D

airy products: Milk processing - C

heese - principles ofcheese m

aking. Cheddar C

heese, Swiss C

heese, Surfaceripened C

heeses; Mold ripened C

heeses. Cottage and

Indian Channa cheese. G

eneral principles of manufacture

of Yogurt, acidophilus milk, K

efir, Koum

iss Fermented foods:

Soy sauce, Miso, ,Sufu, N

atto, Idli, fermented fish products,

Sauer Krant, pickles, ferm

entation of Olives, ferm

entedsausages; Production of distilled beverage alcohol, w

ine,brandy and beer.

Unit II

:Biopesticide and biofertilizersB

iopesticides: Biological control, plant biopesticides or

botanical pest control (BPC

), Recent interest in Bt-

biopesticides, Nuclear polyhydrosis virus (N

PV),

Baculoviruses, T

richoderma and T

richogramm

a asbiopesticides, G

enetically engineered bacteria asbiopesticide, Im

pact of biopesticides in sustainableagriculture.B

iofertilizers: Principles and objectives of Biofertilizers

and Integrated Nutrient M

anagement (IN

M), N

eed forintegrated nutrient m

anagement, C

omponents of integrated

nutrient managem

ent: Chemical fertilizers, organic fertilizers,

legumes as a green m

anures, vermicom

post for sugarcane,organic Farm

ing and organic Food.Unit III

:Bioprospecting:Introduction: B

iodiversity prospecting; Biochem

icalresources from

plants and fungi, natural products: the roleof natural products in drug discovery, natural products asm

odern drugs; Prospecting for New

Com

pounds fromPlants particularly from

Melghat forest: D

iscovery of novelcom

pounds, Screening of traditional knowledge-based

herbal drugs, Preparation of crude compounds, Isolation

of pure compounds, bio-assay guided isolation, high

throughput screening of extracts.Bioprospecting from

microbes (A

ctinomycetes, Bacteria,

fungi) with special reference to m

arine actinomycetes,

endophytes and metagenom

ics by products.A

nticancer, antiviral, antibacterial, antifungal, antidiabeticsfrom

microbial origin.

Unit IV

:Industrially im

portant productsIndustrial production of alcohol, A

cetone, Citric acid,

Gluconic acid, A

cetic acid, lactic acid; Production ofpolysaccharides, Penicillin, X

anthan; Industrial enzymes

(proteases, pectinases, cellulases and lipases)U

nit V:

Bionanotechnology and industrial applicationsIntroduction to bionanotechnology and overview

ofnanoscale m

aterials; effect of length scale on properties;challenges and opportunities associated w

ith biology onthe N

anoscale; top-down and bottom

-up approach,m

ethods of nanoparticle synthesis, its characterization andanalysis of nanoparticles by different techniques such asU

V-Visible spectroscopy, NM

R, SEM, TEM

, X-RD

, FTIR.Synthesis of N

anoparticles by Biological system

,Extracellular biosynthesis w

ith a case study of silver andgold nanoparticles, Intracellular biosynthesis case bybacteria.A

pplications of bionanotechnology in various fields.

Practicals (BT- 404)1.

Lab scale production of alcohol and acetic acid.2.

Production of amylase/ pectinase and cellulase.

3.Preparation and form

ulation of microbial biopesticide (bacteria,

fungi and viruses)4.

Screening of microbes for enzym

e/metabolites production.

5.Production of m

etal nanoparticles using microbes.

6.Estim

ation of lignocellulose degradation.7.

In vitro evaluation of medicinal plants against pathogenic m

icrobes.8.

Effect of mycorrhizal fungi on grow

th promotion of plants.

9.Production of m

icrobial fertilizers (Rhizobium

, Azotobacter and

AM

F).

Recom

mended readings

1.M

odern Food Micro-B

iology by J.M.Jay, (1986), Van N

ostrandR

einhold company, N

ew York.

2.C

omprehensive B

iotechnology Vol. 1- 4 : M.Y. Young (Eds.),

Pergamon Press.

3.B

iotechnology : A Text B

ook of Industrial Microbiology : T.D

.B

rock, Smaeur A

ssociates, 1990.4.

Industrial Microbiology : L.E. C

asida, Willey Eastern Ltd., 1989.

5.Industrial M

icrobiology : Prescott & D

unn, CB

S Publishers,1987.

6.B

ioprocess Technology- fundamentals and applications, S O

Enfors & L H

agstrom (1992), R

IT, Stockholm.

7.B

iotechnology, Economic &

Social Aspects : E.J. D

asilva, CR

atledge & A

Sasson, Cam

bridge Univ. Press, C

ambridge.

8.B

iotechnology - a hand book of industrial microbiology : W

.C

rueger and A. C

rueger.9.

Microbial B

iotechnology : A. N

. Glazer and H

. Nikaids.

BT – 403 Elective papersA

s given in Scheme of exam

inaton as per Appendix-D

BT- 404 Practical based on Elective Paper

BT- 405 Project

*****

3334

IND

EXM

.Sc.Part-I & Part-II Exam

ination in Biotechnology(Prospectus N

o.20111214)

Sr.No.

PaperTitle of the Paper

Page Nos.

Code/Practical

1.-

Special Note

12.

-O

rdinance No. 4 of 2008

33.

-D

irection No. 26 of 2010 &

27 of 20106

SEMESTER I - TH

EORY

4.B

T- 101C

ell Biology

55.

BT- 102

Macrom

olecules and Enzymology

76.

BT- 103

Microbes: Physiology and G

enetics9

7.B

T- 104B

iology of the Imm

une system12

SEMESTER II - TH

EORY

8.B

T - 201M

olecular Biology

149.

BT - 202

Bioprocess Engineering &

Technology16

10.B

T - 203Plant B

iotechnology18

11.B

T - 204Elective Paper (C

hoice based)-

SEMESTER III - TH

EORY

12.B

T – 301A

nimal C

ell Science & Technology

2113.

BT – 302

Genetic Engineering

23

14.B

T – 303B

iostatistics and Bioinform

atics26

SEMESTER IV - TH

EORY

15B

T – 401E

nvironmental B

iotechnology30

16.B

T – 402Industrial B

iotechnology (Special)32

17.B

T – 403Elective Paper (C

hoice based)-