course structure integrated m.sc. in … integrated msc.pdf · integrated m.sc. in bioscience and...

1

COURSE STRUCTURE

INTEGRATED M.Sc. IN BIOSCIENCE AND BIOINFORMATICS

Detailed Syllabi:

Semester-I Course code Course name L T P CH CR BI 101 Biology-I 2 0 1 4 3

PI 101 Physics-I 2 0 1 4 3

CI 101 Chemistry-I 2 0 2 6 4

MI 101 Mathematics-I 2 1 0 3 3

CS 101 Basics in Computer Applications 2 0 1 4 3

EG 101 Communicative English 2 0 0 2 2

Semester-II Course code Course name L T P CH CR BI 102 Biology-II 2 0 1 4 3

PI 102 Physics-II 2 0 2 6 4

CI 102 Chemistry-II 2 0 1 4 3

MI 102 Mathematics-II 2 1 0 3 3 ES 102 Elementary Environmental Science 2 0 0 2 2 SC 102 Basic Sociology 2 0 0 2 2 NS 102 NSS 0 0 1 2 1

Semester-III Course code Course name L T P CH CR BI 201 Cell Biology 2 1 0 3 3

BI 203 Molecular Genetics 2 1 0 3 3

BI 205 Animal and Plant Physiology 2 1 0 3 3

BI 207 Bioscience Laboratory-I 0 0 3 6 3

MI 201 Introductory Statistics (Common Paper) 2 1 0 3 3

CI 201 Chemistry-III 2 1 0 3 3

CI 209 Chemistry Laboratory-II 0 0 2 4 2

Semester-IV

Course code Course name L T P CH CR

BI 202 Ecology and Environmental Biology 2 1 0 3 3

BI 204 Microbiology 2 1 0 3 3

BI 206 Basics in Bio-computing & IT 2 1 0 3 3

BI 208 Bioscience Laboratory IIA (Biology students) 0 0 3 6 3

BI 210

Bioscience Lab IIB

(For non-Bioscience Majors) 0 0 2 4 2

MI 204 Mathematical Methods & PDE 2 1 0 3 3

CI 202 Chemistry-IV 2 1 0 3 3

CI 210 Chemistry Laboratory-IV 0 0 2 4 2

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Semester –V


BI-301 Biochemistry 3 0 0 3 3

BI-303 Molecular Biology 3 0 0 3 3

BI-305 Cell and Tissue Culture 3 0 0 3 3

BI-307 Bioprogramming 3 0 0 3 3

BI-309 Developmental Biology 3 0 0 3 3

BI-311 Laboratory – V 0 0 4 8 4

Semester -VI


BI-302 Applied Bioscience 3 0 0 3 3

BI-304 Biophysics 3 0 0 3 3

BI-306 Computational Biology 3 0 0 3 3

BI-308 Biological Database Management System 3 0 0 3 3

BI-310 Applied Microbiology & Bioprocess

Engineering

3 0 0 3 3

BI-312 Laboratory – VI 0 0 4 8 4

Semester -VII


BI-401 Genomics and Proteomics 3 0 0 3 3

BI-403 Genetic Engineering 3 0 0 3 3

BI-405 Immunology 3 0 0 3 3

BI-407 Credit Seminar 3 0 0 3 3

BI-409 Laboratory - VII 0 0 4 8 4

Semester –VIII (Specialization) – any two from BI-402 to BI-408


BI-402 Animal Biotechnology 3 0 0 3 3

BI-404 Plant Biotechnology 3 0 0 3 3

BI-406 Nano Biotechnology 3 0 0 3 3

BI-408 Environmental Biotechnology 3 0 0 3 3

BI-410 Bioinformatics software and Algorithms 3 0 0 3 3

BI-412 Bioethics, Biosafety & Intellectual

Property Rights

3 0 0 3 3

BI-414 Structural Bioinformatics 3 0 0 3 3

BI-416 Laboratory - VIII 0 0 4 8 4

Semester – IX


BI-501 Project - I 0 0 16 32 16

Semester – X


BI-502 Project -II 0 0 16 32 16

Credit Load from 5th

- 10th Semesters = 19+19+16+19+16+16 =105

Credit Load from 1st - 4

th Semesters = 18+18+20+20 =76

Total Credit load = 76+105 = 181

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SYLLABUS

(INTEGRATED M.Sc. IN BIOSCIENCE AND BIOINFORMATICS)

Semester I

Biology – I (BI-101)

Diversity of Microbial, Plant and Animal World

Introduction, difference between living and non-living, unicellular, colonial and multicellular forms.

Chemical basis of life

Chemistry of the living state: micro and macro molecules (including trace elements) associated with

structure of the cells and their biological significance. Water: molecular structure, dipolar nature,

dissociation of water, concept of pH, Acid and base, buffers.

Basic Principles of Taxonomy

Concepts of species and hierarchical taxa, biological nomenclature, classical and quantititative methods of

taxonomy of plants, animals and microorganisms.

Microbial world

Characteristics with examples of archaebacteria, eubacteria, viruses, viroids and prions, eubacteria and

archaea, bacteria.

Plant Kingdom

A general description on lower and higher groups of plants; Specific studies on each of the following

groups of plants with description of a typical example from (i) Thallophyta, (ii) Bryophyta, (iii)

Pteridophyta, (iv) Gymnosperm, and (v) Angiosperm.

Animal Kingdom

Nonchrodates and chordates-definition, , classification with examples.

Structural organization

Organization of tissues, organs and organ systems.

Basic concept of organic evolution

Theories of evolution: Lamarckism; Darwinism and Neo-Darwinism. Evolution and diversity of bacteria,

archabacteria; plants (thallophytes to higher plants); animals (protozoans to mammals)

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Semester II

Biology – II (BI-102)

1. Anatomy and Physiology – Basic concepts

Anatomy of root, stem and leaf of monocotyledous and dicotyledous plants. Plant physiology: Absorption

and transpiration in plants, photosynthesis, nitrogen metabolism, plant growth regulators induction to the

site of synthesis and effects, introduction to physiology of flowering a) photoperiodism b) vernalisation.

Anatomy and physiology of Human: digestive system, vascular, respiratory, exceretory system.

2. Basics of cell and developmental biology

Cell structure and division, regulation of development of cell; fertilization and embryogenesis.

3. Fundamentals of genetics (5)

Mendelian laws of inheritance, chromosome theory of inheritance, gene interaction, crossing over, sex

determination in plants and animals, mutation: spontaneous and induced, mutagens: physical and

chemical.

4. Outlines of immunology (4)

Type of immunity: cell mediated immunity, description of various types of T-cells and their functions,

innate immunity (specific and non specific) acquired: active and passive immunity, humoral and cell

mediated immunity, immune system- lymphocytes. Immunoglobulins- structure and function. A brief

account of antigen-antibody reactions.

5. Elements of Biochemistry (4)

Basic structure and physiological functions of carbohydrates, protein, lipids and nucleic acids. Role of

minerals and vitamins in growth and development. Thermodynamics of biological system. Examples of

high energy biomolecules.

6. Conservation biology (4)

Level of biodiversity; global biodiversity and hot spots, tropical biodiversity, economics of biodiversity,

threatened and endangered species, conservation of forest and wild life, social forestry, deforestation and

consequences. Indian case studies on conservation/management strategy (project tiger, biosphere reserve)

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SECOND YEAR (SEMESTER –III)

BI 201: Cell Biology L2-T1-P0-CH3-CR3

1. The Cell - dimensions and classifications with reference to plant and animal cells.

2. Methods for studying cells - microscopy, fractionation of cells and cellular organelles, tracing

and imaging cellular molecules.

3. Internal organization of the cell - membrane structure, lipid bilayer and membrane protein, cytosol,

endoplasmic reticulum, golgi bodies, lysosome, peroxisome, ribosome, mitochondria and chloroplast,

4. Cell nucleus - nuclear membrane, structure and organization of chromosomes.

5. Cellular traffic - transport of macromolecules and particles, endocytosis and exocytosis, regulated and

constitutive secretion of macromolecules, protein sorting to different localization.

6. Cytoskeleton - nature of cytoskeleton, intermediate filaments- microtubules, actin filament, cillia and

centrioles.

7. The cell cycle- cell cycle, regulatory factors in cell cycle

8. Cell signaling- autocrine, paracrine, endocrine and synaptic signaling

9. Cell junction- cell-cell communications, adhesion, and the extracellular matrix.

10. Cancer-causes of cancer, proto-oncogenes, metastasis.

Textbooks:

1. Karp G., Cell and Molecular Biology: Concepts and Experiments, 3rd

Edition (John Wiley & Sons,

Inc., 2002).

2. Scott, M. P. et al, Molecular Cell Biology, 5th

Edition (W. H. Freeman, 2004).

3. Alberts, B. et al., Molecular Biology of the Cell, 4th

Edition(Garland Publishing, 2004).

4. Cooper, G. M. and Hausman, R. E., The Cell: a Molecular Approach, 5th

Edition (ASM Press and

Sinauer Associates, Inc., 2009).

5. Becker, W. M. et al., The World of Cell, 5th

Edition (Benjamin Cummings, 2002).

6

BI 203: Molecular Genetics

L2-T1-P0-CH3-CR3

1. Definition, scope and importance of Molecular Genetics.

2. Chemical nature of genetic materials; structure of DNA and RNA, DNA topology.

3. Genetics of bacteria and viruses, plasmids, double and single stranded DNA and RNA viruses,

λ bacterio-phage life cycle.

4. DNA replication - enzymes, mechanism and modes of replication of DNA, correction of errors.

5. Transcription - kinds of RNA, enzymes involved in transcription, gene structure and

organization, RNA template for DNA and RNA synthesis, RNA processing and co-and post

transcriptional modifications of RNA, antisense and ribozyme technology, RNA-mediated

inactivation of gene expression and anti- termination.

6. Translation – genetic code, ribosome, initiation, elongation and termination of polypeptide

chain, post translational processing, modifications and transport of protein, inhibitors of protein

synthesis.

7. Gene regulation in prokaryotes - activation, repression, attenuation and generalized controls; lac and

tra operons.

8. Mutations – molecular basis, mutant isolation, mutant frequency, mutagenesis, mutation rates in

prokaryotes and eukaryotes; point mutation; reversion and complementation analysis, suppressor

mutation, conditional lethal mutants, mutator strains.

9. Genetic control of developments in nematode, Drosophila and Arabidopsis; genetics of cell

cycle regulation and cancer; molecular evolution: selection versus mutation on nucleotide

composition and codon usage.

10. Molecular basis of genetic recombination and exchange – Holliday junction, gene targeting and

disruption, FLP/FRT, Cre/Lox, and RecA and other recombinations; enzymes in recombination;

transposable elements, their types and mechanism of transposition, Tn5 and Tn10, retrotransposons

and uses.

11. Gene transfer within species and beyond.

12. Human genetics: chromosomes and karyotype, chromosome abnormalities, inborn-errors in

metabolism, polygenic and multifactorial inheritance; genome organization and mapping of human

genome.

Textbooks

1. Lewin, B. Genes IX & X, (Jones and Barlett, 2008).

2. Tropp, B. E. , Molecular Biology: Genes to Proteins, (Jones and Barlett, 2008).

3. Das H.K. (Ed), Textbook of Biotechnology, (Wiley Dream Teach India Pvt. Ltd., 2007).

4. Satyanarayana , U., Biotechnology, (Books and Allied (P) Ltd., 2007).

5. Hartl, D. L. and Jones, E. W., Genetics: Analysis of Genes and Genomes, 6th

edition (Jones and Barlett,

2005).

6. Watson, J. D. et al., Molecular Biology of the Gene, 5th

edition (Pearson Education, 2004).

7. Tamarin, R. H., Principles of Genetics, (Tata Mcgraw Hill, 2002)

8. Weaver , R. F., Molecular Biology, (WCB McGraw-Hill, 1999 ).

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BI 205: Animal and Plant Physiology

L2-T1-P0-CH3-CR3

1. Introduction to physiology, homeostasis.

2. Transport mechanism in plant: Osmosis, Active transport, carrier mediated transport, Xylem

transport, Phloem Transport, Short Distance Intracellular transport.

3. Photosynthesis - Photophosphorylation , C3, C4 and CAM pathways, photorespiration.

4. Photomorphogenesis - Phytochrome, cryptochrome and their role in photomorphogenesis.

5. Plant Hormones and their physiological roles - Auxin, Gibberellins, Cytokinins, Ethylene,

Abscissic Acid, salicylic acid and Jasmonic acid.

6. Blood: function and composition, RBC – morphology, composition, and functions,

erythropoiesis, Hemoglobin; leukocyte; plasma proteins, blood groups

7. Respiratory system and digestive system: elemental and anatomical consideration, composition

function and mechanism of gastric secretion,pancreatic juice, bile; digestive adsorptive function of

small intestine, ventilation, Oxygen dissociation curve, myoglobin, high altitude sickness.

8. Cardiovascular system: Gross anatomy of heart, mechanical and electrical properties of heart muscles,

measurement and regulation of blood pressure.

9. Endocrinology: classification of hormones, mechanisms and action of protein and steroid

hormones, estimation of hormone level in blood, hormone degradation, local hormone –

histamine, prostatglandines and bradykinin.

10. Reproductive system: male reproductive system – functional anatomy and spermatogenesis;

female reproductive system – ovarian cycle, menstrual cycle.

11. Muscular system: functional anatomy and properties of skeletal and smooth muscle, mechanism of

contraction, neuromuscular junction.

12. Nervous system: elementary neuroanatomy, spinal cord neurons, synapse, action potential and

propagation.

13. Thermoregulation – importance and mechanism of thermoregulation, fever

Textbooks 1. Slater, A., Scott, N. and Fowler, M., Plant Biotechnology: The Genetic Manipulation of Plants,

(Oxford University Press, 2003).

2. Taiz, L. and Zeiger, E., Plant Physiology, 4th

edition (Sinauer Associates, 2006).

3. Lambers, H. and Chapin , F. S., Plant Physiological Ecology (Springer, 2000).

4. Guyton, C. and Hall, E., Text book of Medical Physiology , 10th

edition (W.B. Saunders Company,

2001).

5. Hill, R.W., Wyse, G. A. and Anderson, M., Animal Physiology, 2nd

edition (Cambridge

University Press, 2008).

6. Sherwood, Klendorf and Yancy, Animal Physiology: From Genes to Organisms

(Thomson Brooks/Cole Publishers, 2005).

7. Moyes, C.D. and Schutte, P. M., Principles of Animal Physiology, 2nd

edition, (Peerson

Benjamin Cummings, 2007).

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BI 207: Bio-Science Laboratory-I

L0-T0-P3-CH6-CR3

1. Quantitative estimation of protein by Folin-Lowry method and Biuret method

2. Quantitative estimation of carbohydrates by anthrone method

3. Isolation of DNA from microorganisms, plant and animal tissues.

4. Identification of stages from permanent slides showing Mitosis and Meiosis.

5. Separation of different cellular components.

6. Separation of proteins by polyacrylamide gel-electrophoresis electrophoresis

7. Study of microbial growth

8. Isolation of pure culture and Gram staining.

Reference books

1. Plummer, D. T., An Introduction to Practical Biochemistry, 3rd

Edition (Tata McGraw-

Hill, 1988).

2. Cappucciino, J. G. and Sherman, N., Microbiology Laboratory Manual, 5th

Edition

(Bejamin-Cummins, 1998).

3. Sambrook, J., Fristsch, E.F. and Maniatis, T., Molecular Cloning: A Laboratory Manual

–I &II, 2nd

Edition (Cold Spring Harbor Laboratory Press, 1989) .

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SECOND YEAR (SEMESTER –IV)

BI 202: Ecology and Environmental Biology (Common Paper) L2-T1-P0-CH3-CR3

1. Environment and the Concept Ecology: Environmental factors; Abiotic factors- light, temperature,

soil, water, air. Biotic factors- Autotrophs, phagotrophs and saprotrophs. Concept of Ecology. (2 lectures)

2. Ecosystem: Ecosystem concept, interaction and inter-relationship between biotic and abiotic factors

the cybernetic nature and the stability of the ecosystem. Structure and function; energy flow and mineral

cycling (CNP); primary production and secondary production; some major Indian ecosystems: terrestrial

(forest, grassland) and aquatic (fresh water, marine, eustarine). (6 lectures)

3. Habitat and niche: Concept of habitat and niche; niche width and overlap; fundamental and realized

niche; resource partitioning; character displacement. (2 lectures)

4. Population ecology: Characteristics of a population; density, natality, mortality, population growth

curves age distribution, population regulation; life history strategies (r and K selection); concept of

metapopulation – demes and dispersal, interdemic extinctions, age structured populations. (3 lectures)

5. Species interactions: Types of interactions, interspecific competition, herbivory, carnivory,

pollination, symbiosis. (2 lectures)

6. Community ecology: Nature of communities; community structure and attributes; levels of species

diversity and its measurement; edges and ecotones. (4 lectures)

7. Ecological succession: Types; mechanisms; changes involved in succession; concept of climax. (3

lectures)

8. Biogeography: Major terrestrial biomes; theory of island biogeography; biogeographical zones of

India. (2 lectures)

9. Environmental monitoring: Monitoring techniques and methodology, pH, Dissolved Oxygen (DO);

Chemical oxygen demand (COD); Biological Oxygen Demand (BOD). (4 lectures)

10. Conservation biology and Management: Principles of conservation, major protected areas and case

studies. Conservation of biological diversity and management. Nature of Environmental Policies; Rio

Conference (UNCED)(1992). (5 lectures)

Textbooks/References: 1. Odum, E. , Brewer, R., and Barrett, G. W., Fundamentals of Ecology , 5th Edition (Thomson

Brooks/Cole, 2004).

2. Kormondy, E. J., Concepts of Ecology, (Prentice-Hall, Englewood Cliffs, N. J, 1969).

3. Golley, F. B., A History of the Ecosystem Concept in Ecology: More Than the Sum of the

Parts, (Yale University Press, 1996).

4. Wainwright, M., An Introduction to Environmental Biotechnolog, (Kluwer Academic

Publishers, 1999).

5. Alexander, M., Biodegradation and Bioremediation, 2nd Edition (Academic Press, 1999).

6. Rittman B. and McCarty, P.L., Environmental Biotechnology: Principles and Applications,

2nd Edition (McGraw-Hill, 2000).

10

BI 204: Microbiology

L2-T1-P0-CH3-CR3

1. Brief history and development of microbiology: Introduction to study of Microbiology, conflict over

spontaneous generation, role of microorganisms in disease, development of Koch’s molecular

postulate.

2. Microbial diversity: taxonomy, classification system- phenetic, phylogenetic, numerical, morphological

and biochemical characteristics; nucleic acid base composition (G+C %), nucleic acid hybridization,

nucleic acid sequencing; phylogeny-molecular chronometer, phylogenic tree, significance of rRNA

and rDNA as indicators of phylogeny

3. Prokaryotic microorganisms: bacterial cell wall, cell membrane, glycocalyx, appendages; cytoplasmic

structure and inclusions bodies, sporulation and spore, diversity in bacterial structure actinomycetes,

rickettsias, mycoplasma); archaea- ultrastructure.

4. Eukaryotic microorganisms: eukaryotic cells protozoan, algae, yeast and fungi.

5. Viruses: basic structure, classification, double stranded and single stranded DNA and RNA viruses,

replication of DNA and RNA viruses; viroids and prions; bacteriphages with suitable examples.

6. Microbial growth and control: culture media, microbial growth curve, measurement of microbial

growth, influence of environmental factors on growth like temperature, pH, osmotic pressure and

oxygen; quorum sensing, quorum quenching, control of microorganisms by physical and chemical

agents.

7. Microbial Nutrition and Metabolism: common nutrient requirements, introduction to nutritional types

in microorganisms, uptake of nutrient by the cell, energetic of biosynthetic reactions; photosynthesis

(oxygenic an anaoxygenic), synthesis of sugar and polysaccharides, assimilation of inorganic

phosphorous, sulphur and nitrogen; peptidoglycan synthesis, pseudo peptidoglycan, patterns of cell

wall formation.

8. Genetic exchange in bacteria: transformation, conjugation and transduction, horizontal gene transfer,

synthetic biology.

9. Microbial diseases and their control-: host-pathogen relationship, mechanisms of virulence, immune

evasion, virulence factors, pathogenesis in plants and animals.

10. Antimicrobial chemotherapy – general characteristics of antimicrobial drugs, mechanism of action of

antimicrobial agents, drug resistance.

Textbooks 1. Willey, J., Sherwood, L. and Woolverton C., Microbiology, 7th edition (McGraw-Hill Science,

2008).

2. Pelczar, M.J., Chan, E.C.S. and Kreig, N.R., Microbiology, (Mc. Graw Hill., 1993).

3. Brock, T.D., Smith, D.W. and Madigam, M.T., Biology of Microorganisms, 4th

Edition

(Prentice Hall International, 1993).

4. Tortora, G.J., Fernke, B.R. and Case, C.L., Microbiology – An Introduction, 9th

Edition

(Benjamin Cummings, 2009).

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BI-206: Basics in Bio-computing and Information Technology

L2-T1-P0-CH3-CR3

1. Basic Concepts: Basic computer organization, Processor and memory, secondary storage devices,

Input-Output devices, Computer software, planning the computer program, Computer languages,

Operating system: MS DOS, Unix (some basic commands), Data communication and computer network

2. Programming Basics: Elements of programming in C: Variables, Constants, Keywords, Input/output,

Control Statements, Functions, Structures (Basic Ideas with illustrations only)

3. Internet Technology: Internet and world wide web, Client- server organization, FTP, HTTP, Telnet,

Browsers: Netscape and Internet explorer, Searching the web, Search engines, Intelligent use of a search

engine, html, Scripting, Basic ideas of CGI and perl (only the working principles).

4. Word Processing and Documentation: Basic word processing in Microsoft word, Power Point and

Excel, Preparing and processing text documents, MS-Acess.

5. Bioinformatics and Information Technology: What is Bioinformatics, Use of information technology

for studying Biosciences, Emerging areas in Bioinformatics, Future prospects of Bioinformatics.

6. Bioinformatics Basics: Introduction to Genomics, Proteomics, Human Genome Project, Biological

Software, Public Database, Gene Bank, Using Public Database.

Text Books

1. Rastogi, B.C., Bioinformatics, Concept, Skills & Applications, 2nd

Edition (CBS Publications, 2009).

2. Sinha, P.K., Computer Fundamentals, (BPB Publications, 2002).

Reference Books

1. Kanitkar Y., Programming in C, (BPB Publications, 2008).

2. Mount, D. W., Bioinformatics, Sequence & Genome Analysis, 2nd

Edition (CBS, 2005).

12

BI 208: Bio-Science Laboratory-IIA

L0-T0-P3-CH6-CR3

1. Use of differential and selective media for bacterial culture

2. Spore and capsule staining and biochemical activities of microorganism

3. Purification of protein by chromatographic techniques

4. Assay of enzymatic activity of amylase/protease/cellulose

5. Plasmid isolation and quantification

6. Gel electrophoresis and DNA restriction mapping

7. Sampling techniques; waste water analysis for physiochemical characteristics such as pH

conductivity, TDS, DO, BOD, COD.

8. Windows and Linux installation, user interface, File management, Data Security, Users

management. Using Linux and Windows commands.

9. Sequence Alignment Software: Searching for sequence databases; Protein databases,

PDB, BLAST, FASTA, CLUSTALW.

Reference books

1. Plummer, D. T., An Introduction to Practical Biochemistry, 3rd

Edition (Tata McGraw-

Hill, 1988).


Edition


3. Sambrook, J., Fristsch, E.F. and Maniatis, T., Molecular Cloning: A Laboratory Manual

–I &II, 2nd

Edition (Cold Spring Harbor Laboratory Press, 1989) .

4. Savitch, W., Problem Solving and Programming, (Pearson, 2003).

5. Baxevanis, A.D. and Ouellette, B. F. F., Bioinformatics: A Practical Guide to the Analysis

of Genes and Proteins, (John Wiley and Sons (ASIA) Pvt. Ltd., 2002).

BI 210: Bio-Science Laboratory-IIB (For Non-Bioscience Majors)

L0-T0-P2-CH4-CR2

1. Use of differential and selective media for bacterial culture

2. Sampling techniques; waste water analysis for physiochemical characteristics such as pH

conductivity, TDS, DO, BOD, COD.

3. Windows and Linux installation, user interface, File management, Data Security, Users

management. Using Linux and Windows commands.

4. Sequence Alignment Software: Searching for sequence databases; Protein databases,

PDB, BLAST, FASTA, CLUSTALW.

Reference books


Edition


2. Savitch, W., Problem Solving and Programming, (Pearson, 2003).

3. Baxevanis, A.D. and Ouellette, B. F. F., Bioinformatics: A Practical Guide to the Analysis

of Genes and Proteins, (John Wiley and Sons (ASIA) Pvt. Ltd., 2002).

13

Semester-V

BI-301 Biochemistry

L3–T0–P 0-CH 3-CR 3

1. Metabolism: basic concept and function of metabolism, metabolic pathways, cellular regulation

of metabolic pathways.

2. Enzyme: enzyme nomenclature, unique features of enzyme

3. Enzyme catalysis: unique features of enzyme catalysis, concept of enzyme –substrate complex,

thermodynamic principles – effect of catalyst on activation energy, enzyme kinetics, enzyme

regulation,

4. Isolation and purification of enzymes: Methods of enzyme isolation and purification,

introduction to enzyme immobilization.

5. Carbohydrate metabolism: glycolysis and citric acid cycles, glyoxalate cycle, gluconeogenesis,

pentose phosphate pathway and glycogen metabolism.

6. Biological oxidation: oxidoreductases, redox potential, electron transport chain, oxidative

phosphorylation and mechanism of ATP synthesis.

7. Lipid metabolism: metabolism of fatty acids, ketone bodies – formation and utilization,

biosynthesis of sphingomylins, phosphoglycerides and cholesterol.

8. Protein metabolism: pathways of amino acid metabolism, transamination, transdeamination and

deamination,

9. Degradative pathways: the urea cycle, biosynthesis of amino acids and nitrogen balance.

10. Nucleic acid metabolism: synthesis and degradation of nucleotides; metabolism of purines and

pyrimidines.

Text books

1. Stryer, L. Biochemistry ( Freeman Company, 2002).

2. Voet D and Voet J.G.,. Fundamentals of Biochemistry (John Wiley and Sons, 2004)

3. Nelson, D.L and Cox M M Lehninger Principles of Biochemistry (Freeman. 2009)

Reference books

1. Zubey, G.L. Parson., W W and Vance, D.E., Principles of Biochemistry (Brown Publishers 1995) .

2. Devlin, T.M., Text book of Biochemistry (John. Wiley and Sons. 2002)

3. Goodwin, T. W and Mercer E.I., Introduction to Plant Biochemistry (CBS Publishers and

distributors 1998).

14

BI-303 Molecular Biology

L 3–T 0–P 0-CH 3-CR 3

1. Detail structural organisation of DNA

2. Detail structural organisation of RNA 3. DNA replication - Enzymes in DNA replication, mechanism of DNA replication, different modes

of replication.

4. Transcription - Different types of RNA, enzymes involved in transcription, gene structure and

sequence organisation, RNA as a template for DNA and RNA synthesis,

5. RNA processing: co- and post transcriptional modification of RNA, catalytic RNA (ribozymes)

6. Translation - Ribosomes, genetic code, polypeptide chain (initiation, elongation and termination)

7. Post -translational modification: post translational processing, modification and transport of

protein.

8. Regulation of gene expression in prokaryotes - Activation, repression, attenuation and

generalised controls.

9. Regulation of gene expression in eukaryotes - DNA- protein interaction, DNA- drug interaction,

10. Mutagenesis - Types of mutations, molecular basis of mutations, DNA repair.

Text books

1. Benjamin, L. Gene IX (Jones and Barlett Publishers, 2007)

2. Watson, et al Molecular Biology of the Gene (Benjamin Cummings Publishing Company Inc,

2007)

3. Alberts, B. Molecular Biology of the Cell (Garland Publishing, 2007)

Reference books

1. Allison, L.A. Fundamental Molecular Biology (Blackwell Publishers, 2007)

2. John Wilson, J. & Hunt, T. Molecular Biology of the Cell, Fifth Edition: The Problems Book

(Garland Publishing, 2007)

3. Tropp, B. E. Molecular Biology: Genes To Proteins (Jones & Bartlett Publishers, 2007)

15

BI-305 Cell and Tissue Culture

L 3–T 0–P 0-CH 3-CR 3

1. Introduction to animal and plant tissue culture: historical background, advantages and limitations

of tissue culture, major differences in in vitro culture and types of tissue culture and the terminology,

finite/infinite cell lines, immortalization of cells, genetic transitions in primary culture, monolayer

cultures, immobilized cultures and suspension cultures.

2. Requirements and techniques of plant tissue culture: media compositions, growth hormones and

other organic compounds; gelling agents, culture environment, behavior of cells in culture conditions:

division and growth pattern.

3. Requirements and techniques of animal cell culture: Aseptic techniques, cell type, choice of

materials - substrates-culture vessel/ treated surfaces, Development of media, physiochemical

properties, complete media, serum, chemically defined basal and minimal essential media, serum and

protein free media;

4. Behaviour of animal cells in culture: cell adhesion, cell proliferation, differentiation, energy

metabolism. Initiation of culture, evolution of cell lines, development of continuous cell line and stem

cells

5. Characterization, cell separation and maintenance of animal cell lines: Cryopreservation, physical

methods of cell separation, antibody based techniques, magnetic sorting, cell counting and cell

proliferation. Common cell culture contaminants.

6. Animal cell culture applications and products: Cell products - antibodies and immuno-regulators,

recombinant products, viral vaccines, cell and tissue therapy.

7. Micro-propagation: Techniques; multiplication by axillary buds and apical shoot; meristem, shoot

tip and bud cultures; factors affecting micro-propagation; organogenesis- direct and indirect; somatic

embryogenesis; elimination of viruses and other pathogen in plants. Somaclonal variation and

production of disease free plants.

8. Haploid production: Androgenesis; anther and pollen culture; factors affecting androgenesis;

gynogenesis - ovary and ovule cultures; embryo culture and rescue.

9. Protoplast culture and somatic hybridization: Isolation, regeneration of protoplast; culture media

and methods; cell wall formation, division and growth. Fusion of protoplasts and their culture;

selection of hybrid cells and generation of hybrid plants and their characterization; symmetric and

asymmetric hybrids; cybrids; applications and limitations of somatic hybridizations.

10. Hardening, acclimatization and cultivation of tissue culture-derived plants: Exposure of tissue

culture-derived plants to normal environment and their gradual acclimatization. Cultivation of the

acclimatized plants in pots and filed.

Text books

1. Freshney R. I., Culture of Animal Cells, (5th Edition, Wiley-Liss, 2005).

2. Neumann K. H., Kumar A. , Imani J. Plant Cell and Tissue Culture - A Tool in

Biotechnology: Basics and Application (Principles and Practice), (Springer; 1st edition

2009)

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

Reference books 1. John R.W. Masters, Animal Cell Culture: Practical Approach, (3

rd Edition, Oxford, 2000).

2. Clynes, M., Animal Cell Culture Techniques, 1st Edition, Springer, 1998.

3. Dixon R A. Plant Cell Culture, IRL Press, Oxford – Washingto DC, 1987

16

BI-307 Bio-programing

L 3–T 0–P 0-CH 3-CR 3

1. Bioprogramming in C++: Introduction to C++ , Decision and Loops, Array, Functions, Pointer,

Structure, ,Object Oriented Approach, Inheritance, Polymorphism, Virtual Functions.

2. Bio-perl,: Introduction to Perl, Bio-perl

3. Bio-java : Object Orientation and Introduction to JAVA, Bio-java

4. Bio-Markup Languages

i. HTML Introduction to HTMLDocument Structure Element, HTML Element and advanced

HTML , Style Sheet

ii. XML: Introduction to XML, Linking with XMLUnderstanding and creating XML document

Creating XML Document Type Definition (DTDs)XML Character, Notations and Entities

iii. CML : Introduction to CML, Applications of CML

iv. BSML : Introduction to BSML, Importance of BSML

Reference books

1. Kanetkar. Y. P. Let us C++ (BPB Publications, 2003)

2. Tisdall, J. D.. Mastering Perl for bioinformatics (O'Reilly Media, Inc., 2003)

3. Bal, H., Hujol, J. . Java for bioinformatics and biomedical applications.

4. Baxevanis, D. A. , Francis B. F. O. . Bioinformatics: a practical guide to the analysis of genes

and proteins (John Wiley and Sons, 2001)

17

BI-309 Developmental Biology

L 3–T 0–P 0-CH 3-CR 3

1. Developmental genetics: Developmental events and genetics, Genes in early development, ,

Pattern formation genes; Maternal gene effects, Homeotic genes; Signaling and adhesion

molecules, Zygotic gene effects;

2. Differential gene expression: control of gene expression and cell signaling.

3. Early embryonic development : Gametogenesis, Fertilization ,Cleavage I, Cleavage II ,

Gastrulation I , Gastrulation II

4. Cellular Movements and Pattern Formation: Laying of body axis planes; Differentiation of

germ layers; Cellular polarity;

5. Embryogenesis in plant: Embryogenesis and early pattern formation in plants , cell lineages and

developmental control genes in a model plant

6. Embryogenesis in animals: Embryogenesis and early pattern formation in animal , cell lineages

and developmental control genes in C. elegans/ Drosophila.

7. Patterning of body plan: Axis formation in amphibians / C.elegans/ mouse Anterior/posterior

patterning in amphibians/ C.elegans/ mouse, Anterior/posterior patterning in Drosophila

(maternal effect genes), Anterior/posterior patterning in Drosophila (segmentation genes), Hox

genes and dorsal ventral patterning,

8. Differentiation of Specialized Cells: Stem cell differentiation cell fate determination, cell

adhesion and migration and Morphogenesis; Blood cell formation; Fibroblasts and their

differentiation; Cellular basis of immunity; Differentiation of cancerous cells and role of proto-

oncogenes; Phasechanges in Salmonella; Mating cell types in yeast; Heterocyst differentiation

inAnabaena; Sex determination in Drosophila.

9. Plant Meristem Organization: Organization of Shoot Apical Meristem (SAM); Organization of

Root Apical Meristem(RAM);

10. Plant Meristem Differentiation: Pollen germination and pollen tube guidance; Phloem

differentiation; Self-incompatibility and its genetic control; Embryo and endosperm development;

Heterosis and apomixes.

Text books

1. Scott, F. G ., Susan, R. S. Developmental Biology (Sinauer Associates,9th

edition 2010)

2. Lewis, W. Principles of Development, (Oxford University Press, 4th

edition2010)

Reference books 1. Lewin, B. Gene IX (Jones and Barlett Publishers, 2007).

2. Watson et al., Molecular Biology of the gene (Pearson Prentice Hall. USA, 5th

edition

2003).

3. B. M. Turner, Chromatin & Gene regulation (Wiley- Blackwell, 2002).

18

BI-311 Laboratory-V

L 0–T 0–P 4-CH 8-CR 4

1. Estimation of blood cholesterol and glucose

2. Determination of activity, specific activity and kinetics (Km and Vmax values) of enzyme

(cellulose/protease/amylase) catalyzed reaction.

3. Assessment of purity of protein by SDS-PAGE

4. Isolation of DNA and RNA from microorganism, plant and animal cell

5. Restriction digestion of DNA and agarose gel-electrophoresis

6. Meristem culture and micropropagation

7. Callus, suspension and single cell culture

8. Primary culture techniques

9. Isolation of lymphocytes and cultivation

10. Suspension culture techniques and cryopreservation

11. Study of plant and animal embryo development

Practical books

1. David T. Plummer. An Introduction To Practical Biochemistry (Mcgraw-hill 1987)

2. J. Sambrook, E.F. Fritsch, T. Maniatis. Molecular Cloning: A Laboratory Manual (Volume 1, 2,

3) (Cold Spring Harbor laboratory Press 1989)

3. Roberta H. Smith. Plant Tissue Culture, Second Edition: Techniques and Experiments (Academic

Press)

Reference books 1. Scott, F. G ., Susan, R. S. Developmental Biology (Sinauer Associates,9

th edition 2010)

19

Semester-VI

BI -302 Applied Bioscience

L 3–T 0–P 0-CH 3-CR 3

1. Ethnobotany: Definition and Scope

2. Economic Zoology: definition, scope and commercial aspects of sericulture, apiculture,

pisciculture, dairy, mushroom culture and poultry.

3. Probiotics and antibiotics: definition, advantages and disadvantages of probiotics,

mechanism of action, commercial aspects of probiotics and antibiotics manufacturing

4. Bio-fertilisers and weedicides: their uses and advantages, commercial production of bio-

fertilizers and –weedicides.

5. Bio-energy: Production of biogas, biomass energy, bio-diesel, bio-ethanol, biohydrogen

6. Genetically modified crops and plant tissue culture: definition, technique and biological,

social and environmental impact of genetically modified crops,

7. Tissue culture and its its commercial prospects: tissue culture of commercially important

plants, including hardening, fertilizer, pest and diseases management.

8. Vaccines and Immunotherapy: Basics of vaccinology, challenges of developing a vaccine,

types of vaccine, vaccine trials and evaluation of vaccine efficacy.

9. Cytokines and its uses: Use of cytokines and antibodies as drugs, as immunopotentiators and

immunosuppressive agents, drug targeting, antibodies and cytokines in cancer therapy.

10. Industrial enzymes: production, recovery, stability and formulation of bacterial and fungal

enzymes-amylase, protease, cellulase, penicillin acylase, glucose isomerase; Immobilised

Enzyme

Text books

1. Shukla, G. S. and Upadhyay, V. B. Economic Zoology (Rastogi Publication, 4th Edition, 2008)

2. Suman, B C & Sharma, V. P. Mushroom Cultivation in India (Eastern Book Corporation, Delhi,

2007)

3. Moingeon, P. Vaccines: Frontiers In Design And Development (Taylor & Francis Group Jan

2005 )

Reference books

1. O, Peter. Manual on mushroom cultivation: techniques, species and opportunities for the

commercial application in developing countries (Tool Publications, Amsterdam,1991)

2. Fuller, R. Probiotics in human medicine Gut 1991;32:439-442 .

3. K, Samir. Tumor Immunology And Cancer Vaccines (Kluwer Academic Publishers Jan2005).

4. Radbruch, A., Volk,H-d., Asadullah, K. Immunotherapy In 2020: Visions And Trends For

Targeting Inflammatory Disease (Springer-verlag Sep 2007)

20

BI-304 Biophysics

L 3–T 0–P 0-CH 3-CR 3

1. Introduction and scope of Biophysics.

2. Thermodynamics in living system: Laws of thermodynamics, free energy, solution

thermodynamics and chemical potential, thermodynamics in bioenergetics, energetic of biopolymer

conformation.

3. Centrifugation techniques: Principles of different centrifugation, ultracentrifugation, rotor designs

and uses: application of analytical centrifugation (molecular weight determination) and density

gradient centrifugation.

4. Chromatographic techniques: General principles of chromatography, adsorption chromatography,

column, affinity, TLC, partition, ion exchange, gel filtration chromatography;

5. Principles and applications of: RP-HPLC, GLC, HPLC, FPLC etc.

6. Electrophoretic techniques: Principles and application of gel electrophoresis, SDS PAGE,

isoelectric focusing, pulse field electrophoresis etc.

7. Microscopic techniques: Principles and application of electron microscopy, optical, phase contrast

and fluorescent microscopy.

8. Spectroscopic techniques: Principles and application of spectroscopy, colorimetry, fluorometry,

turbidometry and flame photometry: UV, IR, Raman spectroscopy, ESR, NMR, MS spectroscopy,

circular dichroism (CD) spectroscopy, optical rotator dichroism (ORD), X-ray diffraction

9. Manometric techniques : Principle and applications, Hernnberg techniques, oxygraph.

10. Radioisotope technique: Principles of radioisotopes and radiations.

Text books

1. Wilson K. and Walker J., Principles and Techniques of Biochemistry and Molecular

Biology (6th

Edition, Cambridge University Press, 2008).

2. Freifielder D., Physical Biochemistry, (2nd

Edition, W.H. Freeman and Co., New York 1982).

3. Ghosal S. and Srivastav A.K., Fundamentals of Bioanalytical Techniques and

instrumentation, (PHI Learning Private Limited, New Delhi, 2009).

Reference Books 1. Aruldas G., Molecular Structure and Spectroscopy, (2

nd Edition, Prentice-Hall, New Delhi, 2007).

21

BI-306 Computational Biology

L 3–T 0–P 0-CH 3-CR 3

1. Data search and Pair-wise Alignments: Dynamic Programming BLAST, FASTA.

2. Algorithms: for Multiple sequence alignments (CLUSTALW)

3. Substitution Patterns: Jukes Cantor Model, Kimura’s model etc.Phylo-genetic Analysis:

Distance based methods and character based methods and soft-wares.

4. Statistical approaches to Gene Prediction.

5. Structural prediction of biomolecules (Protein/nucleic acid)

6. Methods for comparison of 3D structure of proteins. (Swiss-PdbViewer- A program to

display, analyse and superimpose protein 3D structures, MOLMOL - a molecular graphics

program for display, analysis, and manipulation of three-dimensional structures of biological

macromolecules, TopMatch-web – For protein structure comparison)

7. Molecular interactions: protein-protein, protein-DNA, protein-carbohydrate, DNA small

molecules etc.

8. Docking of molecules: Drug designing.

9. Computational methods: Calculation of conformational energy for biomolecules. Molecular

Mechanics, Monte Carlo, Molecular dynamics and quantum mechanics,

10. Molecular modeling.

Text books

1. Brown, T. A. Genomes II (2nd

Edition, Wiley – Liss2002).

2. Primrose. Principles of Genome Analysis and Genomics (3rd

Edition,

Blackwell2003).

3. Baxevanis A. D Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins,

(Wiley-Interscience.2001)

Reference books

1. Krane, D. E,. Raymen, M. L. Fundamental Concepts of Bioinformatics (2002 Benjamin

Cummings)

2. Mount, D. W. Bioinformatics: Sequence and genome Analysis (CHSL Press. 2001).

3. Bourne P. E. and Weissig, H. Structural Bioinformatics (2003, WILEY).

4. Ghosh Z. and Mallick B. Bioinformatics Principles and Applications, (Oxford

4. University Press, 2010)

22

BI-308 Biological Databases Management System

L 3–T 0–P 0-CH 3-CR 3

1. Database Concepts:

o Introduction

o History of Databases

o Database Management Systems

o Types of Databases

o Codd Rule

o Data Normalization

2. Introduction to SQL

o Structured Query Language

o Constraints

o Types of SQL Commands

o Data Correlation

o Introduction to Index

o Types of Index

3. Biological Databases

o Introduction

o Biological Databases and its importance

o Biological databases and their functioning

o Types of Biological Databases

Microbiological Databases

Virological Databases

Organism Databases

Primary Sequence Databases

Carbohydrate Databases

RNA databases

Biodiversity

Sequence Database (Nucleotide and Protein Sequence DB)

Structural Databases

Gen bank sequence database, submitting sequences to database: NCBI, EMBL, PDB etc.

Textbooks

1. Elmasr, R. and Navathe S. B. Fundamentals of Database Systems (4th

Edition , Pearson

Education).

2. Korth, H. F., Sudarshan S. Database System Concepts, Abraham Silberschatz,, (McGraw-Hill

Publication)

Reference books

1. Bosu O. and Kaur S. T. Bioinformatics Databases, Tools and Algorithms, l, (Oxford University

Press)

2. Gautham, N Bioinformatics Databases and Algorithms, (Narosa Publication, Delhi)

23

BI-310 Applied Microbiology and Bioprocess Engineering

L 3–T 0–P 0-CH 3-CR 3

1. Introduction: Bioprocess Development an Interdisciplinary Challenge

2. Engineering calculation fundamentals: Physical variables, Dimensions and Units, Measurement

conversion, Stoichiometry of microbial growth and chemical reaction and product formation.

3. Chemical kinetics Reaction rate, Zero order kinetics First order kinetics,

4. Microbial growth kinetics: microbial growth in Batch culture, phases of the growth cycle,

equations describing, exponential growth, Effect of nutrient concentration on growth, Monod

equation, Growth in continuous culture, mathematical relationship of growth in chemostats,

Determination of growth constants and growth yield, Turbidostate and Fed batch culture

5. Energy and Material balance: Thermodynamics preliminaries: System and process, steady state

and equilibrium, Law of conservation of mass, Procedure for material balance calculation,

6. Basic energy concepts: Intensive and extensive, properties, Enthalpy, General energy balance

equation, Enthalpy calculation procedure

7. Mass transfer: Diffusion theory, Analogy between mass heat and momentum transfer, Role of

diffusion in bioprocessing, Film theory, Convective mass transfer: liquid solid mass transfer, liquid

liquid mass transfer, Gas liquid mass transfer

8. Unit operations and Reactor Engineering: Filtration, Centrifugation, Cell disruption, Adsorption,

Chromatography, Bioreactor configuration, Practical consideration, Reaction time for batch,

continuous and plug flow reactor.

9. Fermentation Technology: Introduction to fermentation technology: definition of fermentation,

aerobic and anaerobic, submerged and solid state fermentation;

10. Different Fermentation processes: ranges of fermentation processes with special reference to

microbial biomass, enzymes, metabolites and transformation processes.

Text Books

1. Shuler, M. L. and Kargi, F.L. Bioprocess Engineering: Basic Concepts (2nd

Edition, Prentice

1. Hall, 2002)

2. Doran, P. Bioprocess Engineering Principles (Academic Press, 1995)

3. Stanbury P. F. et al., Principals of Fermentation Technology (2nd

Edition, Aditya Books Pvt.Ltd.

1997)

Reference Books

1. Waites,M., Morgan, N. et al. Industrial Microbiology: An Introduction (Blackwell Science Ltd.,

2001).

2. Singhania et al. Recent Advances in Solid-State Fermentation, Biochem. Eng. J. 13, 13-18(2009).

24

BI-312 Laboratory-VI

L 0–T 0–P 4-CH 8-CR 4

1. Production of microbial enzymes in solid-state and submerged fermentations

2. Screening and isolation of industrially enzyme producing microorganisms

3. Determination of molecular weight of protein using electrophoresis and chromatographic

techniques.

4. Database search

5. Different databases of genome sequences

6. Analysis of DNA, RNA and Protein sequences: composition and structure

7. Study of mutational bias in genomes

8. Codon usage analysis: CodonW usage

9. RASMOL, MOLMOL, Chimera, Hyperchem and other MM/ MD software, Clustal V and W

Oligo, MolScript, TreeView, AlScript, Genetic Analysis Software Package, Phylip

Practical book


2. Frederick M. Ausubel, Roger Brent, Robert E. Kingston, David D. Moore, J. G. Seidman, John A.

Smith, Kevin Struhl. Short Protocols in Molecular Biology, (Wiley John & Sons Inc)

Reference




Edition,

Blackwell2003).


(Wiley-Interscience.2001) book.

25

Semester-VII

BI 401 Genomics and Proteomics

L 3–T 0–P 0-CH 3-CR 3

1. Genomes of Prokaryotes: introduction to genomes of prokaryotes

2. Genomes of Eukaryotes: introduction to genomes of eukaryotes and metagenomes.

3. Nucleic acid sequencing: Chemical and enzymatic method of DNA sequencing, Automated DNA

sequencing

4. Chemical synthesis of oligonucleotide

5. Genome sequencing and genome annotation: Expressed Sequence Tags (EST). Single

nucleotide polymorphism (SNPs), Short Tandem Repeats (STR), Simple Sequence Length

Polymorphism, (SSLP), Short Interspersed Nuclear Elements (SINEs) and Long Interspersed

Nuclear Elements (LINES). DNA chips

6. Comparative analysis of genomes: orthologous and paralogous genes, hypothetical and

conserved hypothetical genes, genomic islands, altered codon usage region.

7. Proteomics and Proteome: Introduction to proteomics and proteome, protein analysis (including

concentration, amino acid composition and N-terminal sequencing analysis)

8. Tools of proteomics: 2D electrophoresis, LC/MS-MS, MALDI-TOF/TOF, Microarray, SPR

9. Metabolomics: Metabolome, analysis of metabolites using various chromatography techniques.

Text books

1. Primrose B. and Twyman, R. Principles of Genome Analysis and Genomics (3rd

Edition,

Blackwell2003).

2. Liebler D. C. Introduction to Proteomics (Humana Press. 2004)

Reference book

1. Simpson, R. J. Proteins and Proteomics: A laboratory Manual (2002)

2. William F. Wu, Peter B. Kaufman, Michael J. Welsh, Helen H. Zhang. Methods in Gene

Biotechnology (CRC. Press)

26

BI-403 Genetic Engineering

L 3–T 0–P 0-CH 3-CR 3

1. Introduction to Genetic Engineering: definition, history, scope

2. Molecular techniques: hybridization techniques: Southern, Northern, Colony hybridization,

DNA-Protein interaction-electromobility shift assay, Gene silencing techniques, siRNA

technology, Yeast two hybrid system

3. Molecular Genetic tools: Restriction enzymes, T4 DNA ligase, DNA ligation (cohesive and blunt

end), modification of DNA ends (terminal transferases, linkers and adaptors), T4 kinase, alakaline

phosphatase, klenow fragment, DNase I, single strand specific nucleases, RNase H.

4. PCR and its application: Primer design, DNA polymerase, Types of PCR, Diagnostic application

of PCR, RT-PCR and differential gene expression.

5. Cloning vector: Plasmids, Bacteriophages, Expression vectors (His-Tag, GST-Tag, MBP-Tag),

Animal virus derived vectors.

6. Recombinant protein expression in E. coli,

7. Recombinant protein expression in yeast

8. Recombinant protein expression in insect cell line.

9. Transgenic animals: methods of producing transgenic animals (microinjection, retrovirus and

embryonic stem cells), expression of foreign DNA in transgenic mice, gene knock-outs in

transgenic mice.

10. Gene library: Genomic DNA and cDNA library, Screening of library (complementation and

nucleic acid hybridization); immunological recognition, confirmation of clone identity,

Text books


Edition,

Blackwell2003).

2. John R. Analysis of Genes and Genomes (Wiley and Sons. 2004),

3. Miesfeld, R. L. Applied Molecular Genetics (John Wiley Sons1999).

Reference books

1. Greene and Rao, Recombinant DNA: Principles and Methodologies (Marcel and Dekker. 1998)

2. Winnacker, E.-L. From Genes to Clones (VCH Publisher. 1987),

27

BI- 405 Immunology

L 3–T 0–P 0-CH 3-CR 3

1. Introduction: innate and acquired immune response, cells of immune system, solublemediators of

immunity, antigens, inflammation, vaccination, immunopathology, neurobiology, immunology

and evolution of immune system.

2. Cells, tissues and organs of the immune system: haematopoeisis, cells of innate and adaptive

immune system, organs of the immune system.

3. Antigen: antigenicity vs immunogenicity, factors that influence immunogenicty, B and T cell

epitopes, haptens and adjuvants.

4. Immunoglobulins: basic structure, sequencing studies, Ig fold and domains, classes and

subclasses of Ig, biological activities of Igs, B cell receptor, antigenic determinants on Ig,

monoclonal antibodies, Ig diversity -multigene organization of Ig genes, variable region gene

rearrangements, mechanism of variable region DNA rearrangements, generation of antibody

diversity and class switching, expression of Ig genes and regulation of Ig gene transcription,

affinity maturation and somatic hypermutation, antibody engineering.

5. MHC: general organisation and inheritance of the MHC, MHC molecules and genes, cellular

distribution of MHC genes molecules, MHC and immune responsiveness and genetic

susceptibility to diseases, self-MHC restriction of T cells.

6. Antigen processing and presentation: antigen- presenting cells, antigen processing and

presentation, endogenous antigens (cytosolic and endocytic pathway), co-stimulatory molecules,

presentation of non-peptide antigens.

7. T cell and B cell maturation and activation: thymic selection of T-cell repertoire, T helper cell

activation, T-Cell differentiation, peripheral gd T cells, B - cell maturation, B-cell activation &

proliferation, humoral response, germinal centers and antigen induced B-cell differentiation.

8. Cytokines and cytokine receptors: properties of cytokines, cytokine receptors, cytokine

antagonists, cytokine secretion by Th1 and Th2 subsets and signal transduction.

9. Complement: complement components, complement activation, regulation of complement

system, biological consequences of complement activation, complement deficiencies.

10. Cell mediated effector mechanisms: effector T cells, cytotoxic T cells, NK cells, ADCC, and

hypersensitivity.

Textbooks

1. Delves, P., Martin, S., Burton, D., Roitt, I. Roitt's Essential Immunology (Wiley-Blackwell, 11th

Edition,)

2. Janeway, C. Immunobiology (Garland Science, 6th edition)

Reference books

1. David, M. Advanced Immunology (Mosby, 1996)

2. Sompayrac, L. M. How the Immune System Works (Wiley-Blackwell, 3th edition,)

28

BI- 409 Laboratory VII

L 0–T 0–P 4 CH 8-CR 4

1. Analysis of proteins by SDS-PAGE and 2-D gel-electrophoresis.

2. Analytical softwares related to proteomics and genomics

3. Preparation of competent cell and transformation

4. Amplification of gene and restriction digestion

5. Isolation of plasmid and restriction digestion

6. Ligation of gene to vector and transformation to competent cells

7. Expression and isolation recombinant protein

8. Blood film preparation and identification of cells.

9. Harvesting of cells from lymphoid organs ( spleen) and peritoneal cavity.

10. Agglutination and precipitation

11. Immunoelectrophoresis

12. Western blot and ELISA

Practical book


2. Frederick M. Ausubel, Roger Brent, Robert E. Kingston, David D. Moore, J. G. Seidman, John

A. Smith, Kevin Struhl. Short Protocols in Molecular Biology, (Wiley John & Sons Inc)

3. J. Sambrook, E.F. Fritsch, T. Maniatis. Molecular Cloning: A Laboratory Manual (Volume 1,

2, 3) (Cold Spring Harbor laboratory Press 1989)

Reference




Edition,

Blackwell2003).

29

BI-402 Animal Biotechnology

L 3–T 0–P 0-CH 3-CR 3

1. Introduction: review of animal cell culture technology.

2. Cell line authentication: cell line authentication by species verification and testing for

intraspecies cross- contamination and microbial contamination, cell line banking

3. Three dimensional culturing: multicellular tumor spheroids, MCTS monocultures and MCTS

cocultures, experimental tissue modelling, embryoid bodies, organ and embryo cultures

4. Tissue engineering: principles, regeneration vs tissue engineering, biomaterial scaffolds-

characterstics , and design,

5. Cells in tissue engineering: cell types, cell seeding of implantable materials, cellular – fate

processes, tissue engineered skin and other implants, application of tissue engineering.

6. Stem cells: concept of stem cells, niche and its role on differentiation of stem cells,

molecularbiology of cell differentiation and application of stem cells.

7. Haematopoietic and Epithelial Stem cells- niche characterstics, differentiation of HSC and ESC,

regulation of differentiation

8. Transfection and transformation of cells: why choose animals to produce proteins, gene

manipulation, introduction to the recombinant DNA, the host system, oncogenes and cell

transformation

9. Applied aspects: production of transgenic animal from manipulated cells, use of transgenic

animals, nuclear transfer technology and its applications, gene therapy. production of human

and animal viral vaccines and pharmaceutical proteins

10. Ethical consideration: of animal biotechnology.

Textbooks:

1. Lee, K. Tissue Engineering II: Basics Of Tissue Engineering And Tissue Applications (Springer,

Berlin, 2006)

2. Freshney, R. I. Culture Of Animal Cells: A Manual Of Basic Technique And Specialized

Applications (Wiley-Blackwell, 2010)

3. Kiessling, A.A. & Anderson, S.C. Human Embryonic Stem Cells (Jones & Bartlett Publishers,

2006)

Reference Books:

1. Vunjak-novakovic, G. & Freshney, R. I. Culture Of Cells For Tissue Engineering (Wiley India

Pvt. Ltd., 2010)

30

BI-404 Plant Biotechnology L 3–T 0–P 0-CH 3-CR 3

1. Plant genome: nuclear, chloroplast and mitochondrial genomes; their size, structure and

organization; gene structure and expression; complementary traits and cytoplasmic male sterility.

2. Plant tissue and cell culture: equipment used, media composition, maintenance of aseptic

condition, light-temperature-humidity requirement, cells-tissues-organs used and culture

techniques.

3. Plant genetic engineering and their prerequisites: cloning vectors; detection and selection of

cloned genes.

4. Transgenic plants: problems, strategies, techniques of transferring genes; cloning of plastid and

mitochondrial genes.

5. Nif genes Rhizobium and Anabaena based Nif genes and their mode of expression

6. Agrobacterium-mediated genetic transformation of plants – tumour induction, Ti and Ri

plasmids, T-DNA transfer, plasmid vecotrs, oncogenic and non-oncogenic Ti Plasmids, vir genes

and plant host range, transformation enhancer and chromosomal background of Agrobacterium.

Problems associated with Agrobacterium-mediated transformation – host range limitation,

regeneration problem, T-DNA organization and gene expression

7. Direct gene transfer into plants: electroporation of gene(s) in to single cell protoplasts, micro-

injection, liposome-mediated gene delivery, and microprojectile gene bomberdment

8. Gene tagging and Expression: gene tagging and application and cDNA library construction

Analysis and expression of cloned genes in plants, insertion elements, transposons, maize-yeast

(Ty)-copi elements, maize mitochondrial elements and nuclear genomic components

9. Plant virus vectors: RNA viruses, caulimovirus and geminivirus; viroids.

10. Molecular characterization of plants – Restriction Fragment Length Polymorphisim (RFLP),

Polymerase Chain Reaction (PCR) Random Amplified Polymorphic DNA (R APD), Amplified

Fragment Length Polymorphism (AFLP) and map-based cloning.

Textbooks 1. Adrian, S. Plant Biotechnology: The Genetic Manipulation Of Plants (Oxford University Press,

2008)

2. Razdan, M.K. Introduction to Plant Tissue Culture (Oxford & Ibh Publishing Co. Pvt. Ltd, 2006)

3. Agrios G.N. Plant Pathology (Elsevier, 2008)

Reference Books 1. Philip M. Gilmartin, P.M. & Bowler, C. Molecular Plant Biology (Vol. 1) (Oxford University

Press, USA, 2002)

1. Philip M. Gilmartin, P.M. & Bowler, C. Molecular Plant Biology (Vol. 2) (Oxford University

Press, USA, 2002)

31

BI-406 Nanobiotechnology

L 3–T 0–P 0-CH 3-CR 3

1. Introduction to Nano-Biotechnology; Nanotechnology definition and concepts. Nano materials,

nano composites and their properties. Quantum dots and its application

2. Cellular Nanostructures; Nanopores; Biomolecular motors; Criteria for suitability of

nanostructures for biological applications, Carbon nanotube and DNA nano tubes

3. Basic characterization techniques; Electron microscopy; Atomic force microscopy; Photon

correlation Spectroscopy

4. Colloidal nanostructures: structure, function and applications.

5. Fullerene: structure, function and applications.

6. Nanovesicles : structure, function and applications.

7. Nanocapsules: structure, function and applications.

8. Nanowires: structure, function and applications.

9. Drug Delivery: Nanostructures for drug delivery, concepts, targeting, routes of delivery and its

advantages.

10. Applications of Nanostructures: diagnostics/ bioassys/ biosensing/imaging

Text Books

1. Labhasetwar, V. D. Biomedical Applications of Nanotechnology (Wiley-interscience, 2007)

2. Cao, G. Nanostructures and Nanomaterials: Synthesis, Properties & Applications (World

Scientific Publishing Company, 2004)

3. Vollath, D. Nanomaterials: An Introduction To Synthesis, Properties And Applications (Wiley-vch

Verlag Gmbh, 2008)

Reference Books

1. Niemeyer, C. M. & Mirkin, C. A. Nanobiotechnology II: Concepts, Applications and

Perspectives (Wiley-vch Verlag Gmbh, 2007)

2. Shoseyov, O. & Levy, I. NanoBioTechnology: BioInspired Devices and Materials of the Future

(Humana Press, USA, 2008)

3. Vo-Dinh, T. Nanotechnology in Biology and Medicine: Methods, Devices, and Applications (I. K

International Pvt. Ltd., 2007)

32

BI-408 Environmental Biotechnology

L 3–T 0–P 0-CH 3-CR 3

1. Concept of environmental pollution: Origin of pollution; Classification and nature of Environmental

Pollutants; Major sources;

2. Impacts of Environmental Pollution: local, regional and global impact of environmental pollution,

an overview of environmental biotechnology

3. Solid waste management of municipal and biomedical waste: Concept of solid waste, basic aspects

of solid waste management; Aerobic and anaerobic treatments of solid wastes;

4. Composting; Vermiculture; Comparison of aerobic and anaerobic methods;

5. Hazadarous materials and their treatment: Treatment of hazardous wastes; Hazards caused by

biomedical wastes; Treatment strategies for biomedical wastes.

6. Bioremediation: Bioremediation; In situ and Ex situ bioremediation; Constrains and priorities of

bioremediation; Use of microbes (bacteria and fungi) and plants in biodegradation and

Biotransformation, use of biosurfactant and bioemulsifiers on bioremediation,

7. Biosorption - Biotechnology and heavy metal pollution;

8. Oil field microbiology: Microbial enhanced oil recovery; Biotechnology and oil spills; Hydrocarbon

degradation.

9. Environmental impacts on agriculture: Biodegradation of agricultural chemicals; Biological

nitrogen fixation; Phosphate solubilization; Biofertilizers; Ecology and IPM.

10. Biopesticide: Definition and concept of biopesticid, overview of biopesticides regulations, microbial

biopesticides for integrated crop management, baculoviurs as biopesticide

Text books

1. Foster C.F., John Ware D.A., Environmental Biotechnology (Ellis Horwood Ltd.,

1987).

2. Rittman, B.E. and McCarty, P.L. Environmental Biotechnology: Principles and

Application (McGraw Hill, 2001)

3. Vallero D. A. Environmental Biotechnology: A Biosystems Approach (Elsevier Inc,

2010).

Reference books/ articles

1. Braverman, M. P., Baron, J. J., Kunkel, D. L An Overview and Future Trends of US

Biopesticide Regulations Outlooks on Pest Management 21, 132-134 (2010)

2. Szewczyk, B. et al. Baculoviruses — re-emerging biopesticides, Biotechnolgy

Advances, 24, 143-160 (2006)

3. Alexender M. Biodegradation & Bioremediation (Academic Press, 1999).

33

BI-410 Bioinformatics Software and Algorithms

L 3–T 0–P 0-CH 3-CR 3

1. Algorithms : Simple Algorithms, Analyzing Algorithms, Asymptotic Notation

2. Design Methods: General Consideration, Algorithm Design Paradigms and Representative

Problems: Divide and Conquer (Binary search, Merge Sort), Dynamic Programming (Chained

Matrix Multiplication), Longest common subsequence, Branch and Bound (0/1 Knapsack Problem).

3. String Matching Problem, Boyer-Moore Algorithm, Approximate String matching

4. Intractable Problems: Basic Concepts

5. Flow Chart : Logic of programming, Introduction to Complexity , Structure of Flowchart with

Biological applications: Various Searching , Sorting & Classification techniques.

6. Bioinformatics Softwares and their applications: i. Sequence analysis and alignment - Clustal V, Clustal W, Phylip , Genetic Analysis Software

Package 9. and TreeView, DNASTAR

ii. Structure Visualisation- Rasmol, MolScript, AlScript, Swiss PDB viewer .

iii. Molecular modeling and designing :-Tripos, Chemoffice.

iv. Molecular biology softwares:- Oligos

v. Clementine Bioinformatics ([email protected]).

Text Books

1. Basu, S.K., Design Methods and Analysis of Algorithms (Prentice Hall of India (Pvt)

Ltd, New Delhi. 2005).

34

BI-412 Bioethics, Biosafety & Intellectual Property Rights

L3–T0–P0-CH3-CR3

1. Moral and ethical issues in Biotechnology. 2. Biosafety: Introduction; Historical Backround; Introduction to Biological Safety Cabinets;

Primary Containment for Biohazards; Biosafety Levels; Biosafety Levels of Specific

Microorganisms; Recommended Biosafety Levels for Infectious Agents and Infected Animals;

3. Biosafety guidelines - Government of India; Definition of GMOs & LMOs; Roles of Institutional

Biosafety Committee, RCGM, GEAC etc. for GMO applications in food and agriculture;

Environmental release of GMOs;

4. Risk Analysis: Risk Assessment; Risk management and communication;

5. Regulations: Overview of National Regulations and relevant International Agreements including

Cartegana Protocol.

6. Intellectual Property: Types of IP: Patents, Trademarks, Copyright & Related Rights, Industrial

Design, Traditional Knowledge, Geographical Indications, Protection of GMOs IP as a factor in

R&D; IPs of relevance to Biotechnology and few Case Studies

7. Agreements and Treaties: History of GATT & TRIPS Agreement; Madrid Agreement; Hague

Agreement; WIPO Treaties; Budapest Treaty; PCT; Indian Patent Act 1970 & recent amendments

8. Basics of Patents and Concept of Prior Art: Introduction to Patents; Types of patent

applications: Ordinary, PCT, Conventional, Divisional and Patent of Addition; Specifications:

Provisional and complete; Forms and fees Invention in context of “prior art”;

9. Patent databases: Searching International Databases; Country-wise patent searches (USPTO,

esp@cenet(EPO), PATENT Scope(WIPO), IPO, etc.)

10. Patent filing procedures: National & PCT filing procedure; Time frame and cost; Status of the

patent applications filed; Precautions while patenting –Financial assistance for patenting -

introduction to existing schemes Patent licensing and agreement Patent infringement- meaning,

scope, litigation, case studies

Text books

1. BAREACT, Indian Patent Act 1970 Acts & Rules, (Universal Law Publishing Co. Pvt.

1. Ltd., 2007).

2. Kankanala C., Genetic Patent Law & Strategy, (1st Edition, Manupatra Information

3. Solution Pvt. Ltd., 2007).

Important Links:

1. http://www.w3.org/IPR/

2. http://www.wipo.int/portal/index.html.en

3. http://www.ipr.co.uk/IP_conventions/patent_cooperation_treaty.html

4. www.patentoffice.nic.in

5. www.iprlawindia.org/ - 31k - Cached - Similar page

6. http://www.cbd.int/biosafety/background.shtml

35

BI-414 Structural Bioinformatics

L 3–T 0–P 0-CH 3-CR 3

1. Introduction to Macromolecular Structure;

a. Proteins: Primary Structure, Secondary Structure, Tertiary Structure, Quaternary Structure

b. Nucleic Acids: DNA – A, B, Z forms, RNA

c. Viewing Tools: Rasmol, DeepView, GRASP

d. Graphics Tools: Molscript, Raster3D

2. Introduction to Force Fields and Modeling: Introduction to Force Fields, Building small

molecules, Building small peptides/nucleic acids, Energy Minimization

3. Molecular Dynamics: Basic Theory, Introduction to the AMBER & GROMACS software

packages, Applications of Molecular Dynamics in Protein folding, Protein unfolding, Stability of

drug/receptor complexes, NMR structure refinement.

4. Homology Modeling: Sequence Alignment (Multiple Sequence Alignments, BLAST, FASTA,

PAM, GCG, SeqLab (Unix GUI), SeqWeb, Databases), Homology Model Programs (SwissProt

(submission to a web resource), InsightII Homology, Look, Model Refinement)

5. Docking: Simulated Annealing, Genetic Algorithms, Other Methods like TABU, DOCK (spheres

vs grids), FTDOCK (Docking small/medium sized polypeptides to proteins), FRED

6. Scoring Methods: Simple Interaction Energies, GB/SA scoring (implicitsolvation), CScore

(consensus scoring algorithms)

7. Structure-Based Drug Design Strategies: Simple Structure Activity Relationships, Drug

Action and interactions with receptors

Textbooks 1. Polanski A. Bioinformatics, (Springer, 2007).

2. Mount D. Bioinformatics Sequence and Genome Analysis, (2nd

Edition, Cold Spring

1. Harbor Laboratory Press, New York, 2004)

2. Chorghade M.S. Drug Discovery and Development, Vol: 1, (Wiley Interscience, New Jersey,

2006)

Reference Books

1. Bransdan B.H., Quantum Mechanics, 2nd

Edition, Pearson Education, Delhi, (2007)

2. Voet, D., Fundamentals of Biochemistry, (2nd

John Wiley and sons, 2006)

36

BI-416 Laboratory VIII

L 0–T 0–P 4-CH 8-CR 4

Animal Biotechnology

1. Preparation of reagents and media for cell culture.

2. Primary culture technique

3. Determination of cell viability by dye exclusion and MTT method

4. Cultivation of continuous cell lines.

Plant Biotechnology

1. Plasmid DNA multiplication, isolation and purification.

2. Gene identification-tagging, isolation and cloning.

3. Mobilization of plasmid vector into Agrobacterium through E coli.

4. Transfer of gene into plant system through co-cultivation.

5. Assessment of plant transformation with foreign gene.

Environmental Biotechnology

1. Screening and isolation of crude oil degrading microbes

2. Screening and isolation of heavy metal resistant microbes

3. Isolation and characterization of waste degrading microbes

Bioinformatics

1. Advanced Visualization Software and 3D representations.

2. Coordinate generations and inter-conversions.

3. Secondary Structure Prediction

4. Fold Recognition, ab initio (Rosetta Server)

5. Homology based comparative protein modeling.

6. Energy minimizations.

7. Validation of models.

a. WHATIF

b. PROSA

c. PROCHECK

d. VERIFY 3D

8. Protein Structure Alignment.

9. Modeller

10. Geno-3D

11. Discovery Studio Server.

Semester-IX

BI-501 Project-I L 0–T 0–P 16-CH 32-CR 16

Semester-X

BI-502 Project-II L 0–T 0–P 16-CH 32-CR 16

--End-of-the-Intgd. M.Sc. in BIOSCIENCE AND BIOINFORMATICS —

37

DETAILED SYLLABUS

INTEGRATED M.Sc. in Chemistry


CI 201: Chemistry-III (For Non-Chemistry Majors) L2-T1-P0-CH3-CR3

Inorganic:

Transition Elements (d-block elements)

Defination and electronic configuration of atoms, General characteristics of transition elements,

Comparison of elements of first transition series(3d-series) with those of second(4d-series) and third(5d-

series) series.

Basic concepts of co-ordination chemistry:

Classification of ligands, Chelation, Coordination number and stereochemistry of complexes,

Nomenclature of co-ordination compounds, Detection and structure determination of complexes,

polynuclear or bridge complexes, Inner metallic complexes, Werners Coordination theory, Sidgwick’s

electronic interpretation of coordination, Effective atomic number-EAN concept.

Organic:

38

To be prepared by the Dept. of Chemistry.

Physical:

Second law of thermodynamics: Maxwel relations, entropy, variation of entropy with temperature and

pressure.

Third law of thermodynamics: residual entropy, spectroscopic entropy. Tautons law

Free energy functions: Gibbs and Helmholtz free energy, variation of free energy with temperature and

pressure criteria of spontaneity, Gibbs-Helmholtz equation.

Gaseous state: Real gases and ideal gases, Boyle temperature, critical temperature, equation of state for

real gases, compression factor, the law of corresponding state, Second virial coefficient. Fugacity,

fugacity and equilibrium constant for real gases.

Textbooks

1. Huheey, J. E., Keiter, E. A., Keiter, R. L. and Medhi, O. K., Inorganic Chemistry: Principles of

Structure and Reactivity, 4th

Edition (Pearson Education, 2006).

2. Atkins, P., Overton, T., Rourke, J., Weller, M. and Armstrong, F., Inorganic Chemistry, (Oxford

University Press, 2006).

3. Atkins, P. W., Physical Chemistry, 7th

Edition (Oxford University Press, 2006).

4. Silby, R.J. and Alberty, R.A., Physical Chemistry, 3rd

Edition (Wiley, 2000).

5. Berry, R. S., Rice, S. A. and Ross, J., Physical Chemistry, 2nd

Edition (Oxford University

Press, 2000).

6. Mcquarrie, D. A. and Simon, J. D., Physical Chemistry, 1st Edition (Viva, 2008).

7. Moore, W. J., Physical Chemistry, 5th

Edition , (Orient Longman, 1990).

8. Castellan, G.W., Physical Chemistry, 4th

Edition , (McGraw Hill 1999).

CI 203: Physical Chemistry-I L2-T1-P0-CH3-CR3

Second law of thermodynamics: Maxwel relations, entropy, variation of entropy with temperature and

pressure.

Third law of thermodynamics: residual entropy, spectroscopic entropy. Tautons law

Free energy functions: Gibbs and Helmholtz free energy, variation of free energy with temperature and

pressure criteria of spontaneity, Gibbs-Helmholtz equation.

System of variable compositions:Partial Molar quantity, chemical potential, Gibbs-Duhem equation,

thermodynamic functions of mixing, excess thermodynamic functions.

Statistical mechanics: Probability and probability distribution function, most probable distribution,

complexions, combinatory rules, distribution of non-distinguishable particle, Maxwell-Boltzmann, Bose

Einstein and Fermi-Dirac distribution formula, Stirling approximation, concept of partition function,

equipartition theorem.

Gaseous state : Kinetic theory and its limitations, kinetic gas equation, Distribution of molecular speed,

most probable, root mean square and average velocity .Real gases and ideal gases, Boyle temperature,

39

critical temperature, equation of state for real gases, compression factor, the law of corresponding state,

Second virial coefficient.

Fugacity, fugacity and equilibrium constant for real gases.

Textbooks



2. Silby, R. J. and Alberty, R.A., Physical Chemistry, 3rd


Reference books

1. Berry, R. S., Rice, S. A. and Ross, J., Physical Chemistry, 2nd

Edition (Oxford University

Press, 2000).

2. Mcquarrie, D. A. and Simon, J. D., Physical Chemistry, 1st Edition (Viva, 2008).


Edition , (Orient Longman, 1990).

4. Engel, T. and Reid, P., Physical Chemistry, (Pearson Education, 2006).


Edition (McGraw Hill, 1999).

6. Alberty, R.A., Physical Chemistry, 7th


7. Levine, I., Physical Chemistry, 5th

Edition (Tata McGraw Hill,.2007).

8. Barrow, G.M., Physical Chemistry, 5th


CI 205: Organic Chemistry-I L2-T1-P0-CH3-CR3


CI 207: Inorganic Chemistry-I L2-T1-P0-CH3-CR3

Hydrogen bonding, Metallic bonding, band theory

Classification of hard and soft acids and bases, HSAB principle and its applications.

Oxidation and Reduction: Oxidation numbers, redox potential, half-cell reaction, Nernst equation,

Electrochemical series, Latimer and Frost diagrams.

Statistical methods of analysis: Types of errors, accuracy, precision, significant numbers, standard and

mean deviations, f-test and t-test.

Nuclear chemistry: Nuclear stability, isotopes, isobars and isotones, laws of radioactivity, artificial

radioactivity, nuclear fission and fusion, radiocarbon dating.

Textbooks

1. Huheey, J. E., Keiter, E. A., Keiter, R. L. and Medhi, O. K., Inorganic Chemistry:

Principles of Structure and Reactivity, 4th

Edition (Pearson Education, 2006).

2. Atkins, P., Overton, T., Rourke, J., Weller, M. and Armstrong, F., Inorganic Chemistry,

(Oxford University Press, 2006).

3. Mendham, J., Denney, R.C., Barnes, J. D. and Thomas, M.J.K., Vogel’s Quantitative

Chemical Analysis, 6th Edition (Pearson Education, 1999).

4..Arnikar, H.J., Essentials of Nuclear Chemistry, 4th

Edition (New Age International, 2008)

CI 209: Chemistry Laboratory-I L0-T0-P3-CH6-CR3

40

Physical: 1. Thermochemistry expts.( heat of hydration) 2. Electrochemistry( redox potential), 3. chemical

kinetics(methyl acetate hydrolysis), 4. conductometric/potentiometric ( ostwald dilution law etc), 5. UV-

VIS spectrophotometric e.g., determination of dissociation constant of ferricthyocyanate complex.

Inorganic:

Qualitative Analysis of Inorganic Mixtures, Volumetric estimation of iron and copper, Determination of

water of crystallization in a molecule of hydrated Mohrs salt.

CI 211: Chemistry Laboratory-II (For Non-Chemistry Majors) L0-T0-P2-CH4-CR2

Inorganic: Qualitative Analysis of Inorganic Mixtures, analysis, Estimation of total hardness of water.

Organic: To be Prepared by the Dept. of Chemistry.

Physical: 1. Thermochemistry expts.( heat of hydration) 2. Electrochemistry( redox potential), 3. chemical

kinetics(methyl acetate hydrolysis), 4. conductometric/potentiometric ( ostwald dilution law etc), 5. UV-

VIS spectrophotometric e.g, detn of dissociation constant of ferricthyocyanate complex.


CI 202: Chemistry-IV (For Non-Chemistry Majors) L2-T1-P0-CH3-CR3

Inorganic:

Nature of Metal –Ligand Bonding in Complexes

Crystal Field Theory (CFT): Important features of crystal field theory, Crystal field splitting of d-orbitals

in octahedral, square planar and tetrahedral complexes.CFSE, factors affecting the magnitude of∆, strong

and weak field ligands and spectrochemical series. Colour of transition metal complexes. Distortion of

octahedral complexes and Jahn Teller Theorem. Cause of distortion with few examples. Ligand field

theory.

Bioinorganic and Environmental chemistry:

Porphyrins and related complexes (Hemoglobins, Myoglobins and cytochromes), nitrogen fixation,

inorganic complexes in medicine (cisplatin, auranofin, vanadium complexes).

Toxicity of metals (mercury, lead, arsenic, cadmium), non metals (sulfur, nitrogen oxides, photochemical

smog), radioactive waste, catalytic converters.

Organic: To be Prepared by the Dept. of Chemistry.

Physical:

41

Electrochemistry : Types of electrodes, types of cells, EMF, electrochemical series, application of EMF

measurement( calculation of ∆G, ∆H and ∆S), Nernst equation, potentiometric titration, batteries, fuel

cell, corrosion and its prevention. Electrical double layer, polarization and overvoltage.

Macromolecules : Classification of polymers, number average and weight average molar masses of

polymers, techniques for determination of molar masses of polymers, electrically conducting polymers

and their applications.

Colloids and nano-particles : Definition of colloids and crystalloids, classification of colloids,

preparation and purification techniques of colloidal dispersion, Tyndal effect, Brownian movement,

electrophoresis, electro-osmosis, protective colloids, gold number, zeta potential, lyophilic, lyophobic ,

ampiphilic colloids, gels, emusifiers, stabilization by emulsification, micelles, critical micelles

concentration(CMC).

Nano particles- definition, techniques for preparation and characteristic properties, application of nano-

particles, nanotechnology and its relevance.

Text Books.

1. Meissler, G. L., Tarr, D. A., Inorganic Chemistry, 3rd

Edition (Prentice Hall, 2003).

2. Cotton, F. A. and Wilkinson, G., Advanced Inorganic Chemistry, 5th Edition (John Wiley,

1988).



Reference books 1. Kapoor, A. and Goswami, P., Introduction to Nanophysics and Nanotechnology, (Narosa,

2010).

2. Levine, I., Physical Chemistry, 5th

Edition (Tata McGraw Hill,.2007).


Edition (Orient Longmann, 1990).



CI 204: Physical Chemistry-II L2-T1-P0-CH3-CR3

Electrochemistry : Types of electrodes, types of cells, EMF, electrochemical series, application of EMF

measurement( calculation of ∆G, ∆H and ∆S), Nernst equation, potentiometric titration, batteries, fuel

cell, corrosion and its prevention. Electrical double layer, polarization and overvoltage.

Chemical kinetics: Steady state approximation, kinetics of complex reactions( opposing 1st order,

consecutive, parallel, chain, and photochemical reactions). Lindemann theory of unimolecular reaction,

fast reactions and oscillatory reactions.

Catalysis: Classification, characteristic of catalytic reaction, homogeneous and heterogeneous catalysis,

acid base catalysis, autocatalysis, inhibitor, enzyme catalysis, Michaelis-Menten equation, lineweaver -

burk plot.

Adsorption : Difference between absorption and adsorption, physical and chemical adsorption, factors

influencing adsorption, adsorption isotherms ( Langmuir, Freundlich and BET), application of adsorption

isotherms for surface area measurement, application of adsorption.

Macromolecules : Classification of polymers, number average and weight average molar masses of

polymers, techniques for determination of molar masses of polymers, electrically conducting polymers

and their applications.

42

Colloids and nano-particles : Definition of colloids and crystalloids, classification of colloids,

preparation and purification techniques of colloidal dispersion, Tyndal effect, Brownian movement,

electrophoresis, electro-osmosis, protective colloids, gold number, zeta potential, lyophilic, lyophobic ,

ampiphilic colloids, gels, emusifiers, stabilization by emulsification, micelles, critical micelles

concentration(CMC).

Nano particles- definition, techniques for preparation and characteristic properties, application of nano-

particles, nanotechnology and its relevance.

Textbooks



Reference books

1. Kapoor, A. and Goswami, P., Introduction to Nanophysics and Nanotechnology, (Narosa,

2010).

2. Adamson, A. W.and Gast, A.P., Physical Chemistry of Surfaces, (John Wiley and Sons, 1997).

3. Laidler, K. J. , Chemical Kinetics, 3rd

Edition (Harper and Row, 1987).

4. Connors, K. A., Chemical Kinetics: A Study of Reaction Rates in Solution, (VCH Publications,

1990).

5. Bockris, J.O.M. and Reddy, A.K.N., Modern Electrochemistry, (Springer, 2006).


Edition (Orient Longmann, 1990).



CI 206: Organic Chemistry-II L2-T1-P0-CH3-CR3


CI 208: Inorganic Chemistry-II L2-T1-P0-CH3-CR3

Chemistry of Group 13 Elements: The elements and their properties; Chemistry of Boron; Borides; Boron hydrides( Preparation, structure,

bonding, reactions and properties); Wade’s rule, Boron halides, Boron-Nitrogen chemistry; Boron-

Oxygen chemistry.

Chemistry of Group 14 Elements: The elements and their properties; Allotropy of Carbon: Diamond, Graphite, and Fullerenes;

Intercalation); Carbides; Carbon halides and oxides; Compounds with C-N and C-S bonds; Silane

reagents, Synthesis, properties and modifications on polysilanes. Condensation vs catenation, Silicides,

Silicone Polymers; Oxygen compounds of silicon.

Chemistry of Group 15 Elements: The elements and their properties; Nitrides; Hydrides of Nitrogen; Oxides of Nitrogen; Oxo acids and

anions of Nitrogen; Activation of Nitrogen; Reaction of coordinated NO; Phosphides; Phosphorous

halides and oxides; Oxoacids of phosphorous and their salts.

43

Textbooks

1. Greenwood, N. N. and Earnshaw, A., Chemistry of the Elements, Pergamon Press, 1984).

2. Cotton, F. A. and Wilkinson, G., Advanced Inorganic Chemistry, 5th

Edition (John Wiley, 1988).

CI 210: Chemistry Laboratory-III L0-T0-P3-CH6-CR3

Physical:

Electrochemistry expts., Michelis -Menten kinetics, adsorption, Mol wt of polymer, CMC, zwiter ion,

Gold number.

Inorganic:

Inorganic preparations, complexometric titration, Gravimetric estimation of copper and Nickel.

CI 212: Chemistry Laboratory-IV (For Non-Chemistry Majors) L0-T0-P2-CH4-CR2

Inorganic: Paper chromatographic separation of Ag(I),Hg(II) and Pb(II) ions, Inorganic Preparations.

Organic: To be prepared by the Dept. of Chemistry.

Physical: Electrochemistry expts., Michelis -Menten kinetics, adsorption, Mol wt of polymer, CMC,

zwiter ion, Gold number.

44

DETAILED SYLLABUS

INTEGRATED M.Sc. in Mathematics


MI 201: Introductory Statistics (Common Paper) L2-T1-P0-CH3-CR3

Collection of data, methods of collections of primary data, presentation and classification of data, Discrete

and continuous variables, Frequency distributions, Graphical representation, cumulative frequency

distribution and ogives.

Measure and location of dispersion, the arithmetic mean of group data, properties of arithmetic mean,

median and mode; other measures of location: quartiles, deciles and percentiles.

Variance and standard deviation of ungrouped and grouped data, properties of standard deviation.

Moments of higher order, relation between rm and ′

rm , skewness and Kurtosis.

Elements of probability theory, classical definition of probability, axiomatic approach to probability,

probability of a simple event, probability of composite event, addition rule, multiplication rule:

conditional probability.

Correlation and regression: scatter diagram, coefficients of correlation, linear regression, fitting of

regression line, the method of least squares, explained and unexplained variation, coefficient of variation,

correlation and regression for grouped data.

Textbooks:

1. Medhi, J., Statistical Methods: An introductory Text, (New Age International (P)

Ltd,, 2000).

2. Feller, W., An Introduction to Probability Theory and Its Applications, Vol. I,

( Wiley, 2005).

3. Uspensky, J.V., Introduction to Mathematical Probability, (McGraw Hill, 2005).

MI 203: Linear Spaces and Complex Numbers L2-T1-P0-CH3-CR3

Algebra of matrices, symmetric, skew symmetric, Hermitian and skew hermitian matrices, rank of a

matrix, elementary transformations, reduction to echelon and normal form; System of linear equations,

existence and uniqueness of solutions, rank of matrix.

Definitions and examples of vector spaces, elementary properties of nR and nC as vector spaces,

subspaces, operations on subspaces; linear dependence and independence of vectors, basis and dimension

of vector spaces; linear mappings and their algebraic properties; eigen values and eigen vectors,

characteristic equation, statement of Cayley-Hamilton theorem and its use in finding the inverse of a

matrix.

Complex numbers, geometrical representation, modulus and argument of complex numbers; exponential

and trigonometric functions of a complex variable; theorems on limit and continuity of a function of

complex variable, differentiability, analytic function, Cauchy-Riemann equations, Harmonic functions,

derivatives of elementary functions; Contour integration, Cauchy’s integral theorem, Cauchy’s integral

formula.

45

Text books

1. Churchill R. V., Brown, J. W., Complex Variables and Applications, (McGraw-Hill International

Edition, 2006).

2. Datta, K. B., Matrix and Linear Algebra, (Prentice Hall of India, 2000).

3. Lang, S., Linear Algebra, (Springer-Verlag, 2006).

Reference books:

1. Hoffman K. and Kunze, R., Linear Algebra, 2nd

Edition (Prentice Hall, 2008).

2. Spiegel, M. R., Theory and Problems of Complex Variables, Schum’s Outline Series (McGraw-

Hill, 2000).

MI 205: Algebra L2-T1-P0-CH3-CR3

Relations, Equivalence relations, Mapping, and binary operations, Groups, subgroups, cosets, Lagrange’s

theorem, Subgroup generated by a set, cyclic groups, permutation groups, normal subgroups, quotient

groups.

Polynomials, Euclid’s Algorithm greatest common divisor, unique factorization of polynomials over a

field F of numbers (statement only), Fundamental theorem of Algebra (statement only), roots and their

multiplicity, Irreducible polynomials over Q, R, C. Relationship between roots and the coefficients,

Fundamental theorem of symmetric polynomial (without proof) Evaluation of symmetric functions of

roots. Rational roots of polynomials with integral coefficients.

Descartes rule of sign, Strum’s theorem (statement only) Solution of cubic equation, Cardon’s method

and solution of bi-quadratic equation.

Textbooks 1. J. A. Gallian, Contemporary Abstract Algebra, Narosa, 1995.

2. S Barnard, J M child, Higher Algebra, Macmillan, 2001.

3. S. K. Mapa, Higher Algebra, Asoke Prakashan, Calcutta, 2006.

Reference books

1. Herstein, I. N., Topics in Algebra, 2nd

Edition (Wiley Eastern Limited, 1998).

2. Fraleigh, J. B., A First Course in Abstract Algebra, (Narosa, 1995).

3. Barbeau, E. J., Polynomials, (Springer 2003).

4. Prasad, C., A Text Book of Algebra and Theory of Equations, (Pothishala Private Ltd., 2006).

MI 207: Co-ordinate Geometry L2-T1-P0-CH3-CR3

Transformation of co-ordinate axes. Pair of straight lines. General equation of second degree and the

conditions for representing a pair of straight lines, a parabola, an ellipse, a hyperbola and a circle, the

equation of tangent, condition of tangency of line, pole and polar, centre of a conic, equation of a pair of

tangents. Reduction to standard forms, central conics, Equation of the axes and length of the axes. Polar

equation of a conic, tangent and normal, properties. Parabola, parametric co-ordinates, tangent and

normal. Ellipse and its conjugate diameters with properties. Hyperbola and its asymptotes. Circle and its

parametric form, Orthogonal circle, condition of orthogonality of circles.

Plane, straight line and shortest distance. change of axes, shift of origin, rotation of axes, Sphere, Cone

and Cylinder. Central Conicoids, Ellipsoid, Hyperboloid of one and two sheets. Generating lines,

Diametral planes, tangent lines, plane section of conicoids, director sphere, polar plane, section with a

given centre, enveloping cone and cylinder. Confocal conicoids. Reduction of second degree equations.

Text books:

46

1. Jain, P. K. and Ahmed, K., Textbook of Analytical Geometry of Two Dimensions, (New Age

Publications, 2006).

2. Jain, P. K. and Ahmde, K., Textbook of Analytical Geometry of Three Dimensions, 2nd

Edition

(New Age Publication, 2006).

3. Das, B., Analytical Geometry and Vector Analysis, (Orient Book Company, 1995).

Reference books:

1. Khan, R.M., Analytical Geometry & Vector Analysis, (New Central Book Agency Pvt. Ltd.,

2004).

2. Askwith, E. H., A Course of Pure Geometry, Michigan Historical Reprint Series,

(University of Michigan Library, 2005).

3. Askwith, E. H. and Askwith, E., A Course Of Pure Geometry, (Hard Press, 2007).

4. Spain, B., Analytical Conics, (Dover, 2007).

5. McCrea, W. H., Analytical Geometry of Three Dimensions, (Dover, 2006).

MI 209: Statics and Dynamics L2-T1-P0-CH3-CR3

Parallel forces, Couples, Reduction of coplanar forces. Analytical conditions of equilibrium of coplanar

forces.

Centre of gravity of a plane area, arc and sector of a curve. C. G. of solids and surface of revolution.

Friction, laws of friction, limiting friction, equilibrium of a particle in rough inclined plane.

Principle of virtual work in two dimensions. Stable and unstable equilibrium.

Velocities and acceleration along radial and transverse directions, along tangential and normal directions.

Rectilinear motion with variable acceleration. Motion under inverse square law and other laws of force.

Simple harmonic motion. Motion in resisting medium. Motion of particles of varying mass. Motion of a

projectile.

Central orbit and Kepler’s laws of planetary motion.

Moments and products of inertia. Parallel axes theorem, theorem of six constants. Principal axes.

Textbooks:

1. Whittaker, E.T. and McCrea, W. A Treatise on the Analytical Dynamics of Particles and Rigid

Bodies: with an Introduction to the Problem of Three Bodies, (Cambridge University Press,

1988).

2. Chorlton, F. Textbook of Dynamics, 2nd

edition (Horwood, 1983).

3. Loney, S. L., Elements of Statics & Dynamics, Part I, (Maxford Books, 2003).

4. Rao, S. Engineering Mechanics - Statics and Dynamics, (Pearson Education, 2008).

5. Meriam, J.I., Engineering Mechanics Statics, 5th

Edition, (John Wiley & Sons, 2002).

Reference books:

1. Spiegel, M. R., Schaum's Outline of Theory and Problems of Theoretical Mechanics: with an

Introduction to Lagrange's Equations and Hamiltonian Theory, (McGraw-Hill, 2007).

2. Ramsey, A. T., Dynamics, 2nd

Edition, (The University Press, 2007).

3. Loney, S. L., An Elementary Treatise on the Dynamics of a Particle and of Rigid Bodies,

(Read Books, 2007).


MI 202: Probability and Mathematical Statistics L2-T1-P0-CH3-CR3

47

Discrete sample space, Bayes’ formula, Discrete random variable, expected value of a random variable,

standard probability distribution: Bernoulli, Binomial, Hypergeometric, Geometric, Poisson and Normal

distribution.

Elements of Sampling theory: sampling with and without replacement, sampling distribution of the

sample mean, sampling distribution of proportion, standard error.

Text books:

1. Medhi, J., Statistical Methods: An introductory Text, (New Age International (P)

Ltd,, 2000).

2. Feller, W., An Introduction to Probability Theory and Its Applications, Vol. I,

( Wiley, 2005).

3. Uspensky, J.V., Introduction to Mathematical Probability, (McGraw Hill, 2005).

MI 204 Mathematical Methods and Partial Differential Equations (Common Paper)

L2-T1-P0-CH3-CR3

Partial differential equations: What are partial differential equations (PDEs), and where do they come

from? Flows, vibrations and diffusions. Solutions of first order PDEs: Charpits method, Jacobi method.

Second-order linear equations and their classification. Initial and boundary conditions, with an informal

description of well-posed problems. D'Alembert's solution of the wave equation. Duhamel's principle for

one dimensional wave equation.

Separation of variables: application of the method to simple problems in Cartesian coordinates for one

dimensional wave and heat equations.

Calculus of variation: Variational problems with fixed boundaries-Euler’s equation for functionals

containing first order derivative and one independent variable. Extremals. Functionals dependent on

higher order derivatives. Functionals dependent on more than one independent variable. Variational

problems in parametric form. Invariance of Euler’s equation under co-ordinate transformation.

Variational problems with Moving boundaries-Functionals dependent on one and two functions. One

sided vatiations. Sufficient conditions for an extremum - Jacobi and Legendre conditions.

Special Functions: Series solution of differential equations. Power series method. Bessel and Legendre

equations. Bessel and Legendre functions and their properties. Convergence. Recurrence and generating

functions.

Text books

1. Rao, K. S., Introduction to Partial Differential Equations, 2nd

Edition (Prentice Hall of

India, 2007).

2. Gupta, A. S., Calculus of Variation with Applications, (Prentice Hall of India, 1997).

3. Gelfand, I. M. and Fomin, S. V., Calculus of Variation, (Dover Publications, 2000).

Reference book

1. Andrews, G.E., Askey, R. A. and Roy, R.., Special Functions, (Cambridge University

Press, 1999).

MI 206: Integral Equations and Transforms L2-T1-P0-CH3-CR3

Linear integral equations of the first and second kind of Fredholm and Volterra type: Definitions of

integral equations and their classification. Eigen values and Eigen functions. Integral equations of second

48

kind with separable kernels. Reduction to a system of algebraic equations. Method of successive

approximations. Iterative scheme for integral equations of the second kind.

Integral Transform Methods: Fourier Series, Generalized Fourier series, Fourier Cosine series, Fourier

Sine series, Fourier integrals. Fourier transform, Laplace transform.

Inverse Transform: Inverse Laplace and Fourier Transform, Solution of differential equation by Laplace

and Fourier transform methods.

Elementary idea of Improper Integrals, their convergence, Beta and Gamma functions, their properties.

Integral as a function of parameter (excluding improper integrals). Continuity and derivability of an

integral as a function of a parameter.

Tensor: Transformation of coordinates, summation convention, kronecker delta. Definition of tensors,

covariant, contravarient and mixed tensor, symmetric and antisymmetric tensors, outer and inner product

of tensors, contraction, quotient law.

Text books:

1. Poularikas, D., The Transforms and Applications –Handbook, (CRC Press, 1996).

2. Mikhlin, S. G., Linear Integral Equations, (Hindustan Book Agency, 1990).

3. Spain, B., Tensor Calculus, (Radha Publishing House, 2000).

Reference book:

1. Kanwal, R. P., Linear Integral Equation. Theory and Techniques, (Academic Press, 1991).

MI 208: Linear Algebra L2-T1-P0-CH3-CR3

Review of vector spaces, linear maps, matrix representation of linear maps, Eigen vectors and Eigen

values of linear maps, characteristic equation, and statement of Cayley-Hamilton theorem.

Linear functional and the double dual; annihilating polynomial, minimal polynomial, triangulation and

diagonalization; direct sum decomposition, invariant direct sums, the Primary Decomposition theorem;

rational and Jordan forms.

Inner product spaces: inner product; Gram-Schmidt orthogonalization process; linear functional and

adjoint; self adjoint, normal and unitary operators; orthogonal projections; spectral theorem for normal

operators on a finite dimensional vector space.

Bilinear forms: bilinear, positive and quadratic forms.

Text books

1. Strang, G. Linear Algebra and Its Applications, 4th

Edition, (Cengage, 2006).

2. Halmos P. R., Finite Dimensional Vector Spaces, (Springer-Verlag, 1987).

3. Hoffman, K. and Kunze, R., Linear Algebra, 2nd

Edition, (Prentice Hall, 2008).

4. Halmos, P. R., Linear Algebra Problem Book, (The Mathematical Association of America

(MAA), USA, 1995).

Reference books

1. Williams, G., Linear Algebra with Applications, (Jones and Burlet Publishers, 2001).

49

2. Lang, S., Linear Algebra, (Springer-Verlag, Indian Reprint, 2008).

MI 210: Set Theory and Mathematical Logic L2-T1-P0-CH3-CR3

Sets; relations, functions and orderings; natural numbers; finite, countable and uncountable sets; cardinal

numbers and ordinal numbers; the axiom of choice; arithmetic of cardinal numbers; the continuum

hypothesis; sets of real numbers: completeness and Archimedean property;

Introduction to mathematical logic and proof, propositional logic, predicate calculus, mathematical

systems.

Text books

1. Hrbacek K.and Jech, T., Introduction to Set Theory, 3rd

Edition, (CRC Press, 1999).

2. Kelly, J. J., The Essence of Logic, (Prentice Hall of India, 1997).

3. Vaught, R. L., Set Theory: An introduction, 2nd

Edition (Birkauser, 1995.

4. Eccles, P. J., An Introduction to Mathematical Reasoning, (Cambridge University Press,

2004).

5. Mendelson, E., Introduction to Mathematical Logic, 4th

Edition (Chapman & Hall, 1997).

Reference books

1. Hamilton, A. G., Logic for Mathematicians, 2nd

Edition (Cambridge University Press), 1988.

2. Halmos, P. R., Naïve Set Theory, Undergraduate Text in Mathematics, (Springer, 2000).

50

Semester-V

BI-301 Biochemistry L3–T0–P 0-CH 3-CR 3

11. Metabolism: basic concept and function of metabolism, metabolic pathways, cellular regulation

of metabolic pathways.

12. Enzyme: enzyme nomenclature, unique features of enzyme

13. Enzyme catalysis: unique features of enzyme catalysis, concept of enzyme –substrate complex,

thermodynamic principles – effect of catalyst on activation energy, enzyme kinetics, enzyme

regulation,

14. Isolation and purification of enzymes: Methods of enzyme isolation and purification,

introduction to enzyme immobilization.

15. Carbohydrate metabolism: glycolysis and citric acid cycles, glyoxalate cycle, gluconeogenesis,

pentose phosphate pathway and glycogen metabolism.

16. Biological oxidation: oxidoreductases, redox potential, electron transport chain, oxidative

phosphorylation and mechanism of ATP synthesis.

17. Lipid metabolism: metabolism of fatty acids, ketone bodies – formation and utilization,

biosynthesis of sphingomylins, phosphoglycerides and cholesterol.

18. Protein metabolism: pathways of amino acid metabolism, transamination, transdeamination and

deamination,

19. Degradative pathways: the urea cycle, biosynthesis of amino acids and nitrogen balance.

20. Nucleic acid metabolism: synthesis and degradation of nucleotides; metabolism of purines and

pyrimidines.

Text books

4. Stryer, L. Biochemistry ( Freeman Company, 2002).

5. Voet D and Voet J.G.,. Fundamentals of Biochemistry (John Wiley and Sons, 2004)

6. Nelson, D.L and Cox M M Lehninger Principles of Biochemistry (Freeman. 2009)

Reference books

4. Zubey, G.L. Parson., W W and Vance, D.E., Principles of Biochemistry (Brown Publishers 1995) .

5. Devlin, T.M., Text book of Biochemistry (John. Wiley and Sons. 2002)

6. Goodwin, T. W and Mercer E.I., Introduction to Plant Biochemistry (CBS Publishers and

distributors 1998).

51

BI-303 Molecular Biology L 3–T 0–P 0-CH 3-CR 3

11. Detail structural organisation of DNA

12. Detail structural organisation of RNA 13. DNA replication - Enzymes in DNA replication, mechanism of DNA replication, different modes

of replication.

14. Transcription - Different types of RNA, enzymes involved in transcription, gene structure and

sequence organisation, RNA as a template for DNA and RNA synthesis,

15. RNA processing: co- and post transcriptional modification of RNA, catalytic RNA (ribozymes)

16. Translation - Ribosomes, genetic code, polypeptide chain (initiation, elongation and termination)

17. Post -translational modification: post translational processing, modification and transport of

protein.

18. Regulation of gene expression in prokaryotes - Activation, repression, attenuation and

generalised controls.

19. Regulation of gene expression in eukaryotes - DNA- protein interaction, DNA- drug interaction,

20. Mutagenesis - Types of mutations, molecular basis of mutations, DNA repair.

Text books

4. Benjamin, L. Gene IX (Jones and Barlett Publishers, 2007)

5. Watson, et al Molecular Biology of the Gene (Benjamin Cummings Publishing Company Inc,

2007)

6. Alberts, B. Molecular Biology of the Cell (Garland Publishing, 2007)

Reference books

4. Allison, L.A. Fundamental Molecular Biology (Blackwell Publishers, 2007)

5. John Wilson, J. & Hunt, T. Molecular Biology of the Cell, Fifth Edition: The Problems Book

(Garland Publishing, 2007)

6. Tropp, B. E. Molecular Biology: Genes To Proteins (Jones & Bartlett Publishers, 2007)

52

BI-305 Cell and Tissue Culture L 3–T 0–P 0-CH 3-CR 3

11. Introduction to animal and plant tissue culture: historical background, advantages and limitations

of tissue culture, major differences in in vitro culture and types of tissue culture and the terminology,

finite/infinite cell lines, immortalization of cells, genetic transitions in primary culture, monolayer

cultures, immobilized cultures and suspension cultures.

12. Requirements and techniques of plant tissue culture: media compositions, growth hormones and

other organic compounds; gelling agents, culture environment, behavior of cells in culture conditions:

division and growth pattern.

13. Requirements and techniques of animal cell culture: Aseptic techniques, cell type, choice of

materials - substrates-culture vessel/ treated surfaces, Development of media, physiochemical

properties, complete media, serum, chemically defined basal and minimal essential media, serum and

protein free media;

14. Behaviour of animal cells in culture: cell adhesion, cell proliferation, differentiation, energy

metabolism. Initiation of culture, evolution of cell lines, development of continuous cell line and stem

cells

15. Characterization, cell separation and maintenance of animal cell lines: Cryopreservation, physical

methods of cell separation, antibody based techniques, magnetic sorting, cell counting and cell

proliferation. Common cell culture contaminants.

16. Animal cell culture applications and products: Cell products - antibodies and immuno-regulators,

recombinant products, viral vaccines, cell and tissue therapy.

17. Micro-propagation: Techniques; multiplication by axillary buds and apical shoot; meristem, shoot

tip and bud cultures; factors affecting micro-propagation; organogenesis- direct and indirect; somatic

embryogenesis; elimination of viruses and other pathogen in plants. Somaclonal variation and

production of disease free plants.

18. Haploid production: Androgenesis; anther and pollen culture; factors affecting androgenesis;

gynogenesis - ovary and ovule cultures; embryo culture and rescue.

19. Protoplast culture and somatic hybridization: Isolation, regeneration of protoplast; culture media

and methods; cell wall formation, division and growth. Fusion of protoplasts and their culture;

selection of hybrid cells and generation of hybrid plants and their characterization; symmetric and

asymmetric hybrids; cybrids; applications and limitations of somatic hybridizations.

20. Hardening, acclimatization and cultivation of tissue culture-derived plants: Exposure of tissue

culture-derived plants to normal environment and their gradual acclimatization. Cultivation of the

acclimatized plants in pots and filed.

Text books

1. Freshney R. I., Culture of Animal Cells, (5th Edition, Wiley-Liss, 2005).

2. Neumann K. H., Kumar A. , Imani J. Plant Cell and Tissue Culture - A Tool in

Biotechnology: Basics and Application (Principles and Practice), (Springer; 1st edition

2009)

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

Reference books 1. John R.W. Masters, Animal Cell Culture: Practical Approach, (3

rd Edition, Oxford, 2000).

2. Clynes, M., Animal Cell Culture Techniques, 1st Edition, Springer, 1998.

3. Dixon R A. Plant Cell Culture, IRL Press, Oxford – Washingto DC, 1987

BI-307 Bio-programing L 3–T 0–P 0-CH 3-CR 3

53

5. Bioprogramming in C++: Introduction to C++ , Decision and Loops, Array, Functions, Pointer,

Structure, ,Object Oriented Approach, Inheritance, Polymorphism, Virtual Functions.

6. Bio-perl,: Introduction to Perl, Bio-perl

7. Bio-java : Object Orientation and Introduction to JAVA, Bio-java

8. Bio-Markup Languages

v. HTML Introduction to HTMLDocument Structure Element, HTML Element and advanced

HTML , Style Sheet

vi. XML: Introduction to XML, Linking with XMLUnderstanding and creating XML document

Creating XML Document Type Definition (DTDs)XML Character, Notations and Entities

vii. CML : Introduction to CML, Applications of CML

viii. BSML : Introduction to BSML, Importance of BSML

Reference books

5. Kanetkar. Y. P. Let us C++ (BPB Publications, 2003)

6. Tisdall, J. D.. Mastering Perl for bioinformatics (O'Reilly Media, Inc., 2003)

7. Bal, H., Hujol, J. . Java for bioinformatics and biomedical applications.

8. Baxevanis, D. A. , Francis B. F. O. . Bioinformatics: a practical guide to the analysis of genes

and proteins (John Wiley and Sons, 2001)

54

BI-309 Developmental Biology L 3–T 0–P 0-CH 3-CR 3

11. Developmental genetics: Developmental events and genetics, Genes in early development, ,

Pattern formation genes; Maternal gene effects, Homeotic genes; Signaling and adhesion

molecules, Zygotic gene effects;

12. Differential gene expression: control of gene expression and cell signaling.

13. Early embryonic development : Gametogenesis, Fertilization ,Cleavage I, Cleavage II ,

Gastrulation I , Gastrulation II

14. Cellular Movements and Pattern Formation: Laying of body axis planes; Differentiation of

germ layers; Cellular polarity;

15. Embryogenesis in plant: Embryogenesis and early pattern formation in plants , cell lineages and

developmental control genes in a model plant

16. Embryogenesis in animals: Embryogenesis and early pattern formation in animal , cell lineages

and developmental control genes in C. elegans/ Drosophila.

17. Patterning of body plan: Axis formation in amphibians / C.elegans/ mouse Anterior/posterior

patterning in amphibians/ C.elegans/ mouse, Anterior/posterior patterning in Drosophila

(maternal effect genes), Anterior/posterior patterning in Drosophila (segmentation genes), Hox

genes and dorsal ventral patterning,

18. Differentiation of Specialized Cells: Stem cell differentiation cell fate determination, cell

adhesion and migration and Morphogenesis; Blood cell formation; Fibroblasts and their

differentiation; Cellular basis of immunity; Differentiation of cancerous cells and role of proto-

oncogenes; Phasechanges in Salmonella; Mating cell types in yeast; Heterocyst differentiation

inAnabaena; Sex determination in Drosophila.

19. Plant Meristem Organization: Organization of Shoot Apical Meristem (SAM); Organization of

Root Apical Meristem(RAM);

20. Plant Meristem Differentiation: Pollen germination and pollen tube guidance; Phloem

differentiation; Self-incompatibility and its genetic control; Embryo and endosperm development;

Heterosis and apomixes.

Text books

3. Scott, F. G ., Susan, R. S. Developmental Biology (Sinauer Associates,9th

edition 2010)

4. Lewis, W. Principles of Development, (Oxford University Press, 4th

edition2010)

Reference books 4. Lewin, B. Gene IX (Jones and Barlett Publishers, 2007).

5. Watson et al., Molecular Biology of the gene (Pearson Prentice Hall. USA, 5th

edition

2003).

6. B. M. Turner, Chromatin & Gene regulation (Wiley- Blackwell, 2002).

55

BI-311 Laboratory-V L 0–T 0–P 4-CH 8-CR 4

12. Estimation of blood cholesterol and glucose

13. Determination of activity, specific activity and kinetics (Km and Vmax values) of enzyme

(cellulose/protease/amylase) catalyzed reaction.

14. Assessment of purity of protein by SDS-PAGE

15. Isolation of DNA and RNA from microorganism, plant and animal cell

16. Restriction digestion of DNA and agarose gel-electrophoresis

17. Meristem culture and micropropagation

18. Callus, suspension and single cell culture

19. Primary culture techniques

20. Isolation of lymphocytes and cultivation

21. Suspension culture techniques and cryopreservation

22. Study of plant and animal embryo development

Practical books


5. J. Sambrook, E.F. Fritsch, T. Maniatis. Molecular Cloning: A Laboratory Manual (Volume 1, 2,

3) (Cold Spring Harbor laboratory Press 1989)

6. Roberta H. Smith. Plant Tissue Culture, Second Edition: Techniques and Experiments (Academic

Press)

Reference books 2. Scott, F. G ., Susan, R. S. Developmental Biology (Sinauer Associates,9

th edition 2010)

56

Semester-VI

BI -302 Applied Bioscience L 3–T 0–P 0-CH 3-CR 3

11. Ethnobotany: Definition and Scope

12. Economic Zoology: definition, scope and commercial aspects of sericulture, apiculture,

pisciculture, dairy, mushroom culture and poultry.

13. Probiotics and antibiotics: definition, advantages and disadvantages of probiotics,

mechanism of action, commercial aspects of probiotics and antibiotics manufacturing

14. Bio-fertilisers and weedicides: their uses and advantages, commercial production of bio-

fertilizers and –weedicides.

15. Bio-energy: Production of biogas, biomass energy, bio-diesel, bio-ethanol, biohydrogen

16. Genetically modified crops and plant tissue culture: definition, technique and biological,

social and environmental impact of genetically modified crops,

17. Tissue culture and its its commercial prospects: tissue culture of commercially important

plants, including hardening, fertilizer, pest and diseases management.

18. Vaccines and Immunotherapy: Basics of vaccinology, challenges of developing a vaccine,

types of vaccine, vaccine trials and evaluation of vaccine efficacy.

19. Cytokines and its uses: Use of cytokines and antibodies as drugs, as immunopotentiators and

immunosuppressive agents, drug targeting, antibodies and cytokines in cancer therapy.

20. Industrial enzymes: production, recovery, stability and formulation of bacterial and fungal

enzymes-amylase, protease, cellulase, penicillin acylase, glucose isomerase; Immobilised

Enzyme

Text books

4. Shukla, G. S. and Upadhyay, V. B. Economic Zoology (Rastogi Publication, 4th Edition, 2008)

5. Suman, B C & Sharma, V. P. Mushroom Cultivation in India (Eastern Book Corporation, Delhi,

2007)

6. Moingeon, P. Vaccines: Frontiers In Design And Development (Taylor & Francis Group Jan

2005 )

Reference books

5. O, Peter. Manual on mushroom cultivation: techniques, species and opportunities for the

commercial application in developing countries (Tool Publications, Amsterdam,1991)

6. Fuller, R. Probiotics in human medicine Gut 1991;32:439-442 .

7. K, Samir. Tumor Immunology And Cancer Vaccines (Kluwer Academic Publishers Jan2005).

8. Radbruch, A., Volk,H-d., Asadullah, K. Immunotherapy In 2020: Visions And Trends For

Targeting Inflammatory Disease (Springer-verlag Sep 2007)

57

BI-304 Biophysics L 3–T 0–P 0-CH 3-CR 3

11. Introduction and scope of Biophysics.

12. Thermodynamics in living system: Laws of thermodynamics, free energy, solution

thermodynamics and chemical potential, thermodynamics in bioenergetics, energetic of biopolymer

conformation.

13. Centrifugation techniques: Principles of different centrifugation, ultracentrifugation, rotor designs

and uses: application of analytical centrifugation (molecular weight determination) and density

gradient centrifugation.

14. Chromatographic techniques: General principles of chromatography, adsorption chromatography,

column, affinity, TLC, partition, ion exchange, gel filtration chromatography;

15. Principles and applications of: RP-HPLC, GLC, HPLC, FPLC etc.

16. Electrophoretic techniques: Principles and application of gel electrophoresis, SDS PAGE,

isoelectric focusing, pulse field electrophoresis etc.

17. Microscopic techniques: Principles and application of electron microscopy, optical, phase contrast

and fluorescent microscopy.

18. Spectroscopic techniques: Principles and application of spectroscopy, colorimetry, fluorometry,

turbidometry and flame photometry: UV, IR, Raman spectroscopy, ESR, NMR, MS spectroscopy,

circular dichroism (CD) spectroscopy, optical rotator dichroism (ORD), X-ray diffraction

19. Manometric techniques : Principle and applications, Hernnberg techniques, oxygraph.

20. Radioisotope technique: Principles of radioisotopes and radiations.

Text books

4. Wilson K. and Walker J., Principles and Techniques of Biochemistry and Molecular

Biology (6th

Edition, Cambridge University Press, 2008).

5. Freifielder D., Physical Biochemistry, (2nd

Edition, W.H. Freeman and Co., New York 1982).

6. Ghosal S. and Srivastav A.K., Fundamentals of Bioanalytical Techniques and

instrumentation, (PHI Learning Private Limited, New Delhi, 2009).

Reference Books 2. Aruldas G., Molecular Structure and Spectroscopy, (2

nd Edition, Prentice-Hall, New Delhi, 2007).

58

BI-306 Computational Biology L 3–T 0–P 0-CH 3-CR 3

11. Data search and Pair-wise Alignments: Dynamic Programming BLAST, FASTA.

12. Algorithms: for Multiple sequence alignments (CLUSTALW)

13. Substitution Patterns: Jukes Cantor Model, Kimura’s model etc.Phylo-genetic Analysis:

Distance based methods and character based methods and soft-wares.

14. Statistical approaches to Gene Prediction.

15. Structural prediction of biomolecules (Protein/nucleic acid)

16. Methods for comparison of 3D structure of proteins. (Swiss-PdbViewer- A program to

display, analyse and superimpose protein 3D structures, MOLMOL - a molecular graphics

program for display, analysis, and manipulation of three-dimensional structures of biological

macromolecules, TopMatch-web – For protein structure comparison)

17. Molecular interactions: protein-protein, protein-DNA, protein-carbohydrate, DNA small

molecules etc.

18. Docking of molecules: Drug designing.

19. Computational methods: Calculation of conformational energy for biomolecules. Molecular

Mechanics, Monte Carlo, Molecular dynamics and quantum mechanics,

20. Molecular modeling.

Text books




Edition,

Blackwell2003).


(Wiley-Interscience.2001)

Reference books

5. Krane, D. E,. Raymen, M. L. Fundamental Concepts of Bioinformatics (2002 Benjamin

Cummings)

6. Mount, D. W. Bioinformatics: Sequence and genome Analysis (CHSL Press. 2001).

7. Bourne P. E. and Weissig, H. Structural Bioinformatics (2003, WILEY).

8. Ghosh Z. and Mallick B. Bioinformatics Principles and Applications, (Oxford

8. University Press, 2010)

59

BI-308 Biological Databases Management System L 3–T 0–P 0-CH 3-CR 3

1. Database Concepts:

o Introduction

o History of Databases

o Database Management Systems

o Types of Databases

o Codd Rule

o Data Normalization

2. Introduction to SQL

o Structured Query Language

o Constraints

o Types of SQL Commands

o Data Correlation

o Introduction to Index

o Types of Index

3. Biological Databases

o Introduction

o Biological Databases and its importance

o Biological databases and their functioning

o Types of Biological Databases

Microbiological Databases

Virological Databases

Organism Databases

Primary Sequence Databases

Carbohydrate Databases

RNA databases

Biodiversity

Sequence Database (Nucleotide and Protein Sequence DB)

Structural Databases

Gen bank sequence database, submitting sequences to database: NCBI, EMBL, PDB etc.

Textbooks

1. Elmasr, R. and Navathe S. B. Fundamentals of Database Systems (4th

Edition , Pearson

Education).

2. Korth, H. F., Sudarshan S. Database System Concepts, Abraham Silberschatz,, (McGraw-Hill

Publication)

Reference books

3. Bosu O. and Kaur S. T. Bioinformatics Databases, Tools and Algorithms, l, (Oxford University

Press)

4. Gautham, N Bioinformatics Databases and Algorithms, (Narosa Publication, Delhi)

60

BI-310 Applied Microbiology and Bioprocess Engineering L 3–T 0–P 0-CH 3-CR 3

11. Introduction: Bioprocess Development an Interdisciplinary Challenge

12. Engineering calculation fundamentals: Physical variables, Dimensions and Units, Measurement

conversion, Stoichiometry of microbial growth and chemical reaction and product formation.

13. Chemical kinetics Reaction rate, Zero order kinetics First order kinetics,

14. Microbial growth kinetics: microbial growth in Batch culture, phases of the growth cycle,

equations describing, exponential growth, Effect of nutrient concentration on growth, Monod

equation, Growth in continuous culture, mathematical relationship of growth in chemostats,

Determination of growth constants and growth yield, Turbidostate and Fed batch culture

15. Energy and Material balance: Thermodynamics preliminaries: System and process, steady state

and equilibrium, Law of conservation of mass, Procedure for material balance calculation,

16. Basic energy concepts: Intensive and extensive, properties, Enthalpy, General energy balance

equation, Enthalpy calculation procedure

17. Mass transfer: Diffusion theory, Analogy between mass heat and momentum transfer, Role of

diffusion in bioprocessing, Film theory, Convective mass transfer: liquid solid mass transfer, liquid

liquid mass transfer, Gas liquid mass transfer

18. Unit operations and Reactor Engineering: Filtration, Centrifugation, Cell disruption, Adsorption,

Chromatography, Bioreactor configuration, Practical consideration, Reaction time for batch,

continuous and plug flow reactor.

19. Fermentation Technology: Introduction to fermentation technology: definition of fermentation,

aerobic and anaerobic, submerged and solid state fermentation;

20. Different Fermentation processes: ranges of fermentation processes with special reference to

microbial biomass, enzymes, metabolites and transformation processes.

Text Books

2. Shuler, M. L. and Kargi, F.L. Bioprocess Engineering: Basic Concepts (2nd

Edition, Prentice

4. Hall, 2002)

5. Doran, P. Bioprocess Engineering Principles (Academic Press, 1995)

6. Stanbury P. F. et al., Principals of Fermentation Technology (2nd

Edition, Aditya Books Pvt.Ltd.

1997)

Reference Books

3. Waites,M., Morgan, N. et al. Industrial Microbiology: An Introduction (Blackwell Science Ltd.,

2001).

4. Singhania et al. Recent Advances in Solid-State Fermentation, Biochem. Eng. J. 13, 13-18(2009).

61

BI-312 Laboratory-VI L 0–T 0–P 4-CH 8-CR 4

10. Production of microbial enzymes in solid-state and submerged fermentations

11. Screening and isolation of industrially enzyme producing microorganisms

12. Determination of molecular weight of protein using electrophoresis and chromatographic

techniques.

13. Database search

14. Different databases of genome sequences

15. Analysis of DNA, RNA and Protein sequences: composition and structure

16. Study of mutational bias in genomes

17. Codon usage analysis: CodonW usage

18. RASMOL, MOLMOL, Chimera, Hyperchem and other MM/ MD software, Clustal V and W

Oligo, MolScript, TreeView, AlScript, Genetic Analysis Software Package, Phylip

Practical book


4. Frederick M. Ausubel, Roger Brent, Robert E. Kingston, David D. Moore, J. G. Seidman, John A.

Smith, Kevin Struhl. Short Protocols in Molecular Biology, (Wiley John & Sons Inc)

Reference




Edition,

Blackwell2003).


(Wiley-Interscience.2001) book.

62

7. Semester-VII

BI 401 Genomics and Proteomics L 3–T 0–P 0-CH 3-CR 3

10. Genomes of Prokaryotes: introduction to genomes of prokaryotes

11. Genomes of Eukaryotes: introduction to genomes of eukaryotes and metagenomes.

12. Nucleic acid sequencing: Chemical and enzymatic method of DNA sequencing, Automated DNA

sequencing

13. Chemical synthesis of oligonucleotide

14. Genome sequencing and genome annotation: Expressed Sequence Tags (EST). Single

nucleotide polymorphism (SNPs), Short Tandem Repeats (STR), Simple Sequence Length

Polymorphism, (SSLP), Short Interspersed Nuclear Elements (SINEs) and Long Interspersed

Nuclear Elements (LINES). DNA chips

15. Comparative analysis of genomes: orthologous and paralogous genes, hypothetical and

conserved hypothetical genes, genomic islands, altered codon usage region.

16. Proteomics and Proteome: Introduction to proteomics and proteome, protein analysis (including

concentration, amino acid composition and N-terminal sequencing analysis)

17. Tools of proteomics: 2D electrophoresis, LC/MS-MS, MALDI-TOF/TOF, Microarray, SPR

18. Metabolomics: Metabolome, analysis of metabolites using various chromatography techniques.

Text books


Edition,

Blackwell2003).

2. Liebler D. C. Introduction to Proteomics (Humana Press. 2004)

Reference book

3. Simpson, R. J. Proteins and Proteomics: A laboratory Manual (2002)

4. William F. Wu, Peter B. Kaufman, Michael J. Welsh, Helen H. Zhang. Methods in Gene

Biotechnology (CRC. Press)

63

BI-403 Genetic Engineering L 3–T 0–P 0-CH 3-CR 3

11. Introduction to Genetic Engineering: definition, history, scope

12. Molecular techniques: hybridization techniques: Southern, Northern, Colony hybridization,

DNA-Protein interaction-electromobility shift assay, Gene silencing techniques, siRNA

technology, Yeast two hybrid system

13. Molecular Genetic tools: Restriction enzymes, T4 DNA ligase, DNA ligation (cohesive and blunt

end), modification of DNA ends (terminal transferases, linkers and adaptors), T4 kinase, alakaline

phosphatase, klenow fragment, DNase I, single strand specific nucleases, RNase H.

14. PCR and its application: Primer design, DNA polymerase, Types of PCR, Diagnostic application

of PCR, RT-PCR and differential gene expression.

15. Cloning vector: Plasmids, Bacteriophages, Expression vectors (His-Tag, GST-Tag, MBP-Tag),

Animal virus derived vectors.

16. Recombinant protein expression in E. coli,

17. Recombinant protein expression in yeast

18. Recombinant protein expression in insect cell line.

19. Transgenic animals: methods of producing transgenic animals (microinjection, retrovirus and

embryonic stem cells), expression of foreign DNA in transgenic mice, gene knock-outs in

transgenic mice.

20. Gene library: Genomic DNA and cDNA library, Screening of library (complementation and

nucleic acid hybridization); immunological recognition, confirmation of clone identity,

Text books


Edition,

Blackwell2003).

2. John R. Analysis of Genes and Genomes (Wiley and Sons. 2004),

3. Miesfeld, R. L. Applied Molecular Genetics (John Wiley Sons1999).

Reference books

1. Greene and Rao, Recombinant DNA: Principles and Methodologies (Marcel and Dekker. 1998)

2. Winnacker, E.-L. From Genes to Clones (VCH Publisher. 1987),

64

BI- 405 Immunology L 3–T 0–P 0-CH 3-CR 3

11. Introduction: innate and acquired immune response, cells of immune system, solublemediators of

immunity, antigens, inflammation, vaccination, immunopathology, neurobiology, immunology

and evolution of immune system.

12. Cells, tissues and organs of the immune system: haematopoeisis, cells of innate and adaptive

immune system, organs of the immune system.

13. Antigen: antigenicity vs immunogenicity, factors that influence immunogenicty, B and T cell

epitopes, haptens and adjuvants.

14. Immunoglobulins: basic structure, sequencing studies, Ig fold and domains, classes and

subclasses of Ig, biological activities of Igs, B cell receptor, antigenic determinants on Ig,

monoclonal antibodies, Ig diversity -multigene organization of Ig genes, variable region gene

rearrangements, mechanism of variable region DNA rearrangements, generation of antibody

diversity and class switching, expression of Ig genes and regulation of Ig gene transcription,

affinity maturation and somatic hypermutation, antibody engineering.

15. MHC: general organisation and inheritance of the MHC, MHC molecules and genes, cellular

distribution of MHC genes molecules, MHC and immune responsiveness and genetic

susceptibility to diseases, self-MHC restriction of T cells.

16. Antigen processing and presentation: antigen- presenting cells, antigen processing and

presentation, endogenous antigens (cytosolic and endocytic pathway), co-stimulatory molecules,

presentation of non-peptide antigens.

17. T cell and B cell maturation and activation: thymic selection of T-cell repertoire, T helper cell

activation, T-Cell differentiation, peripheral gd T cells, B - cell maturation, B-cell activation &

proliferation, humoral response, germinal centers and antigen induced B-cell differentiation.

18. Cytokines and cytokine receptors: properties of cytokines, cytokine receptors, cytokine

antagonists, cytokine secretion by Th1 and Th2 subsets and signal transduction.

19. Complement: complement components, complement activation, regulation of complement

system, biological consequences of complement activation, complement deficiencies.

20. Cell mediated effector mechanisms: effector T cells, cytotoxic T cells, NK cells, ADCC, and

hypersensitivity.

Textbooks

3. Delves, P., Martin, S., Burton, D., Roitt, I. Roitt's Essential Immunology (Wiley-Blackwell, 11th

Edition,)

4. Janeway, C. Immunobiology (Garland Science, 6th edition)

Reference books

3. David, M. Advanced Immunology (Mosby, 1996)

4. Sompayrac, L. M. How the Immune System Works (Wiley-Blackwell, 3th edition,)

65

BI- 409 Laboratory VII L 0–T 0–P 4 CH 8-CR 4

13. Analysis of proteins by SDS-PAGE and 2-D gel-electrophoresis.

14. Analytical softwares related to proteomics and genomics

15. Preparation of competent cell and transformation

16. Amplification of gene and restriction digestion

17. Isolation of plasmid and restriction digestion

18. Ligation of gene to vector and transformation to competent cells

19. Expression and isolation recombinant protein

20. Blood film preparation and identification of cells.

21. Harvesting of cells from lymphoid organs ( spleen) and peritoneal cavity.

22. Agglutination and precipitation

23. Immunoelectrophoresis

24. Western blot and ELISA

Practical book


5. Frederick M. Ausubel, Roger Brent, Robert E. Kingston, David D. Moore, J. G. Seidman, John

A. Smith, Kevin Struhl. Short Protocols in Molecular Biology, (Wiley John & Sons Inc)

6. J. Sambrook, E.F. Fritsch, T. Maniatis. Molecular Cloning: A Laboratory Manual (Volume 1,

2, 3) (Cold Spring Harbor laboratory Press 1989)

Reference




Edition,

Blackwell2003).

66

BI-402 Animal Biotechnology L 3–T 0–P 0-CH 3-CR 3

11. Introduction: review of animal cell culture technology.

12. Cell line authentication: cell line authentication by species verification and testing for

intraspecies cross- contamination and microbial contamination, cell line banking

13. Three dimensional culturing: multicellular tumor spheroids, MCTS monocultures and MCTS

cocultures, experimental tissue modelling, embryoid bodies, organ and embryo cultures

14. Tissue engineering: principles, regeneration vs tissue engineering, biomaterial scaffolds-

characterstics , and design,

15. Cells in tissue engineering: cell types, cell seeding of implantable materials, cellular – fate

processes, tissue engineered skin and other implants, application of tissue engineering.

16. Stem cells: concept of stem cells, niche and its role on differentiation of stem cells,

molecularbiology of cell differentiation and application of stem cells.

17. Haematopoietic and Epithelial Stem cells- niche characterstics, differentiation of HSC and ESC,

regulation of differentiation

18. Transfection and transformation of cells: why choose animals to produce proteins, gene

manipulation, introduction to the recombinant DNA, the host system, oncogenes and cell

transformation

19. Applied aspects: production of transgenic animal from manipulated cells, use of transgenic

animals, nuclear transfer technology and its applications, gene therapy. production of human

and animal viral vaccines and pharmaceutical proteins

20. Ethical consideration: of animal biotechnology.

Textbooks:

4. Lee, K. Tissue Engineering II: Basics Of Tissue Engineering And Tissue Applications (Springer,

Berlin, 2006)

5. Freshney, R. I. Culture Of Animal Cells: A Manual Of Basic Technique And Specialized

Applications (Wiley-Blackwell, 2010)

6. Kiessling, A.A. & Anderson, S.C. Human Embryonic Stem Cells (Jones & Bartlett Publishers,

2006)

Reference Books:

2. Vunjak-novakovic, G. & Freshney, R. I. Culture Of Cells For Tissue Engineering (Wiley India

Pvt. Ltd., 2010)

67

BI-404 Plant Biotechnology L 3–T 0–P 0-CH 3-CR 3

11. Plant genome: nuclear, chloroplast and mitochondrial genomes; their size, structure and

organization; gene structure and expression; complementary traits and cytoplasmic male sterility.

12. Plant tissue and cell culture: equipment used, media composition, maintenance of aseptic

condition, light-temperature-humidity requirement, cells-tissues-organs used and culture

techniques.

13. Plant genetic engineering and their prerequisites: cloning vectors; detection and selection of

cloned genes.

14. Transgenic plants: problems, strategies, techniques of transferring genes; cloning of plastid and

mitochondrial genes.

15. Nif genes Rhizobium and Anabaena based Nif genes and their mode of expression

16. Agrobacterium-mediated genetic transformation of plants – tumour induction, Ti and Ri

plasmids, T-DNA transfer, plasmid vecotrs, oncogenic and non-oncogenic Ti Plasmids, vir genes

and plant host range, transformation enhancer and chromosomal background of Agrobacterium.

Problems associated with Agrobacterium-mediated transformation – host range limitation,

regeneration problem, T-DNA organization and gene expression

17. Direct gene transfer into plants: electroporation of gene(s) in to single cell protoplasts, micro-

injection, liposome-mediated gene delivery, and microprojectile gene bomberdment

18. Gene tagging and Expression: gene tagging and application and cDNA library construction

Analysis and expression of cloned genes in plants, insertion elements, transposons, maize-yeast

(Ty)-copi elements, maize mitochondrial elements and nuclear genomic components

19. Plant virus vectors: RNA viruses, caulimovirus and geminivirus; viroids.

20. Molecular characterization of plants – Restriction Fragment Length Polymorphisim (RFLP),

Polymerase Chain Reaction (PCR) Random Amplified Polymorphic DNA (R APD), Amplified

Fragment Length Polymorphism (AFLP) and map-based cloning.

Textbooks 1. Adrian, S. Plant Biotechnology: The Genetic Manipulation Of Plants (Oxford University Press,

2008)

2. Razdan, M.K. Introduction to Plant Tissue Culture (Oxford & Ibh Publishing Co. Pvt. Ltd, 2006)

3. Agrios G.N. Plant Pathology (Elsevier, 2008)

Reference Books 1. Philip M. Gilmartin, P.M. & Bowler, C. Molecular Plant Biology (Vol. 1) (Oxford University

Press, USA, 2002)

2. Philip M. Gilmartin, P.M. & Bowler, C. Molecular Plant Biology (Vol. 2) (Oxford University

Press, USA, 2002)

68

BI-406 Nanobiotechnology L 3–T 0–P 0-CH 3-CR 3

11. Introduction to Nano-Biotechnology; Nanotechnology definition and concepts. Nano materials,

nano composites and their properties. Quantum dots and its application

12. Cellular Nanostructures; Nanopores; Biomolecular motors; Criteria for suitability of

nanostructures for biological applications, Carbon nanotube and DNA nano tubes

13. Basic characterization techniques; Electron microscopy; Atomic force microscopy; Photon

correlation Spectroscopy

14. Colloidal nanostructures: structure, function and applications.

15. Fullerene: structure, function and applications.

16. Nanovesicles : structure, function and applications.

17. Nanocapsules: structure, function and applications.

18. Nanowires: structure, function and applications.

19. Drug Delivery: Nanostructures for drug delivery, concepts, targeting, routes of delivery and its

advantages.

20. Applications of Nanostructures: diagnostics/ bioassys/ biosensing/imaging

Text Books

4. Labhasetwar, V. D. Biomedical Applications of Nanotechnology (Wiley-interscience, 2007)

5. Cao, G. Nanostructures and Nanomaterials: Synthesis, Properties & Applications (World

Scientific Publishing Company, 2004)

6. Vollath, D. Nanomaterials: An Introduction To Synthesis, Properties And Applications (Wiley-vch

Verlag Gmbh, 2008)

Reference Books

4. Niemeyer, C. M. & Mirkin, C. A. Nanobiotechnology II: Concepts, Applications and

Perspectives (Wiley-vch Verlag Gmbh, 2007)

5. Shoseyov, O. & Levy, I. NanoBioTechnology: BioInspired Devices and Materials of the Future

(Humana Press, USA, 2008)

6. Vo-Dinh, T. Nanotechnology in Biology and Medicine: Methods, Devices, and Applications (I. K

International Pvt. Ltd., 2007)

69

BI-408 Environmental Biotechnology L 3–T 0–P 0-CH 3-CR 3

1. Concept of environmental pollution: Origin of pollution; Classification and nature of Environmental

Pollutants; Major sources;

2. Impacts of Environmental Pollution: local, regional and global impact of environmental pollution,

an overview of environmental biotechnology

3. Solid waste management of municipal and biomedical waste: Concept of solid waste, basic aspects

of solid waste management; Aerobic and anaerobic treatments of solid wastes;

4. Composting; Vermiculture; Comparison of aerobic and anaerobic methods;

5. Hazadarous materials and their treatment: Treatment of hazardous wastes; Hazards caused by

biomedical wastes; Treatment strategies for biomedical wastes.

6. Bioremediation: Bioremediation; In situ and Ex situ bioremediation; Constrains and priorities of

bioremediation; Use of microbes (bacteria and fungi) and plants in biodegradation and

Biotransformation, use of biosurfactant and bioemulsifiers on bioremediation,

7. Biosorption - Biotechnology and heavy metal pollution;

8. Oil field microbiology: Microbial enhanced oil recovery; Biotechnology and oil spills; Hydrocarbon

degradation.

9. Environmental impacts on agriculture: Biodegradation of agricultural chemicals; Biological

nitrogen fixation; Phosphate solubilization; Biofertilizers; Ecology and IPM.

10. Biopesticide: Definition and concept of biopesticid, overview of biopesticides regulations, microbial

biopesticides for integrated crop management, baculoviurs as biopesticide

Text books

1. Foster C.F., John Ware D.A., Environmental Biotechnology (Ellis Horwood Ltd.,

1987).

2. Rittman, B.E. and McCarty, P.L. Environmental Biotechnology: Principles and

Application (McGraw Hill, 2001)

3. Vallero D. A. Environmental Biotechnology: A Biosystems Approach (Elsevier Inc,

2010).

Reference books/ articles

1. Braverman, M. P., Baron, J. J., Kunkel, D. L An Overview and Future Trends of US

Biopesticide Regulations Outlooks on Pest Management 21, 132-134 (2010)

2. Szewczyk, B. et al. Baculoviruses — re-emerging biopesticides, Biotechnolgy

Advances, 24, 143-160 (2006)

3. Alexender M. Biodegradation & Bioremediation (Academic Press, 1999).

70

BI-410 Bioinformatics Software and Algorithms L 3–T 0–P 0-CH 3-CR 3

7. Algorithms : Simple Algorithms, Analyzing Algorithms, Asymptotic Notation

8. Design Methods: General Consideration, Algorithm Design Paradigms and Representative

Problems: Divide and Conquer (Binary search, Merge Sort), Dynamic Programming (Chained

Matrix Multiplication), Longest common subsequence, Branch and Bound (0/1 Knapsack Problem).

9. String Matching Problem, Boyer-Moore Algorithm, Approximate String matching

10. Intractable Problems: Basic Concepts

11. Flow Chart : Logic of programming, Introduction to Complexity , Structure of Flowchart with

Biological applications: Various Searching , Sorting & Classification techniques.

12. Bioinformatics Softwares and their applications: vi. Sequence analysis and alignment - Clustal V, Clustal W, Phylip , Genetic Analysis Software

Package 9. and TreeView, DNASTAR

vii. Structure Visualisation- Rasmol, MolScript, AlScript, Swiss PDB viewer .

viii. Molecular modeling and designing :-Tripos, Chemoffice.

ix. Molecular biology softwares:- Oligos

x. Clementine Bioinformatics ([email protected]).

Text Books

1. Basu, S.K., Design Methods and Analysis of Algorithms (Prentice Hall of India (Pvt)

Ltd, New Delhi. 2005).

71

BI-412 Bioethics, Biosafety & Intellectual Property Rights L3–T0–P0-CH3-CR3

11. Moral and ethical issues in Biotechnology. 12. Biosafety: Introduction; Historical Backround; Introduction to Biological Safety Cabinets;

Primary Containment for Biohazards; Biosafety Levels; Biosafety Levels of Specific

Microorganisms; Recommended Biosafety Levels for Infectious Agents and Infected Animals;

13. Biosafety guidelines - Government of India; Definition of GMOs & LMOs; Roles of Institutional

Biosafety Committee, RCGM, GEAC etc. for GMO applications in food and agriculture;

Environmental release of GMOs;

14. Risk Analysis: Risk Assessment; Risk management and communication;

15. Regulations: Overview of National Regulations and relevant International Agreements including

Cartegana Protocol.

16. Intellectual Property: Types of IP: Patents, Trademarks, Copyright & Related Rights, Industrial

Design, Traditional Knowledge, Geographical Indications, Protection of GMOs IP as a factor in

R&D; IPs of relevance to Biotechnology and few Case Studies

17. Agreements and Treaties: History of GATT & TRIPS Agreement; Madrid Agreement; Hague

Agreement; WIPO Treaties; Budapest Treaty; PCT; Indian Patent Act 1970 & recent amendments

18. Basics of Patents and Concept of Prior Art: Introduction to Patents; Types of patent

applications: Ordinary, PCT, Conventional, Divisional and Patent of Addition; Specifications:

Provisional and complete; Forms and fees Invention in context of “prior art”;

19. Patent databases: Searching International Databases; Country-wise patent searches (USPTO,

esp@cenet(EPO), PATENT Scope(WIPO), IPO, etc.)

20. Patent filing procedures: National & PCT filing procedure; Time frame and cost; Status of the

patent applications filed; Precautions while patenting –Financial assistance for patenting -

introduction to existing schemes Patent licensing and agreement Patent infringement- meaning,

scope, litigation, case studies

Text books

2. BAREACT, Indian Patent Act 1970 Acts & Rules, (Universal Law Publishing Co. Pvt.

4. Ltd., 2007).

5. Kankanala C., Genetic Patent Law & Strategy, (1st Edition, Manupatra Information

6. Solution Pvt. Ltd., 2007).

Important Links:

7. http://www.w3.org/IPR/

8. http://www.wipo.int/portal/index.html.en

9. http://www.ipr.co.uk/IP_conventions/patent_cooperation_treaty.html

10. www.patentoffice.nic.in

11. www.iprlawindia.org/ - 31k - Cached - Similar page

12. http://www.cbd.int/biosafety/background.shtml

72

BI-414 Structural Bioinformatics L 3–T 0–P 0-CH 3-CR 3

8. Introduction to Macromolecular Structure;

e. Proteins: Primary Structure, Secondary Structure, Tertiary Structure, Quaternary Structure

f. Nucleic Acids: DNA – A, B, Z forms, RNA

g. Viewing Tools: Rasmol, DeepView, GRASP

h. Graphics Tools: Molscript, Raster3D

9. Introduction to Force Fields and Modeling: Introduction to Force Fields, Building small

molecules, Building small peptides/nucleic acids, Energy Minimization

10. Molecular Dynamics: Basic Theory, Introduction to the AMBER & GROMACS software

packages, Applications of Molecular Dynamics in Protein folding, Protein unfolding, Stability of

drug/receptor complexes, NMR structure refinement.

11. Homology Modeling: Sequence Alignment (Multiple Sequence Alignments, BLAST, FASTA,

PAM, GCG, SeqLab (Unix GUI), SeqWeb, Databases), Homology Model Programs (SwissProt

(submission to a web resource), InsightII Homology, Look, Model Refinement)

12. Docking: Simulated Annealing, Genetic Algorithms, Other Methods like TABU, DOCK (spheres

vs grids), FTDOCK (Docking small/medium sized polypeptides to proteins), FRED

13. Scoring Methods: Simple Interaction Energies, GB/SA scoring (implicitsolvation), CScore

(consensus scoring algorithms)

14. Structure-Based Drug Design Strategies: Simple Structure Activity Relationships, Drug

Action and interactions with receptors

Textbooks 3. Polanski A. Bioinformatics, (Springer, 2007).

4. Mount D. Bioinformatics Sequence and Genome Analysis, (2nd

Edition, Cold Spring

3. Harbor Laboratory Press, New York, 2004)

4. Chorghade M.S. Drug Discovery and Development, Vol: 1, (Wiley Interscience, New Jersey,

2006)

Reference Books

3. Bransdan B.H., Quantum Mechanics, 2nd

Edition, Pearson Education, Delhi, (2007)

4. Voet, D., Fundamentals of Biochemistry, (2nd

John Wiley and sons, 2006)

73

BI-416 Laboratory VIII L 0–T 0–P 4-CH 8-CR 4

Animal Biotechnology

5. Preparation of reagents and media for cell culture.

6. Primary culture technique

7. Determination of cell viability by dye exclusion and MTT method

8. Cultivation of continuous cell lines.

Plant Biotechnology

6. Plasmid DNA multiplication, isolation and purification.

7. Gene identification-tagging, isolation and cloning.

8. Mobilization of plasmid vector into Agrobacterium through E coli.

9. Transfer of gene into plant system through co-cultivation.

10. Assessment of plant transformation with foreign gene.

Environmental Biotechnology

4. Screening and isolation of crude oil degrading microbes

5. Screening and isolation of heavy metal resistant microbes

6. Isolation and characterization of waste degrading microbes

Bioinformatics

12. Advanced Visualization Software and 3D representations.

13. Coordinate generations and inter-conversions.

14. Secondary Structure Prediction

15. Fold Recognition, ab initio (Rosetta Server)

16. Homology based comparative protein modeling.

17. Energy minimizations.

18. Validation of models.

a. WHATIF

b. PROSA

c. PROCHECK

d. VERIFY 3D

19. Protein Structure Alignment.

20. Modeller

21. Geno-3D

22. Discovery Studio Server.

Semester-IX

BI-501 Project-I L 0–T 0–P 16-CH 32-CR 16

Semester-X

BI-502 Project-II L 0–T 0–P 16-CH 32-CR 16

--End-of-the-Intgd. M.Sc. in BIOSCIENCE AND BIOINFORMATICS —

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