Friday, August 8, 2008

SUBJECTS AND SYLLABUS

BIOTECHNOLOGY:


V-SEMESTER:-

Theory
1.Management and Entrepreneurship
2.Biokinetics & Bioreaction Engg.
3.Biosensors & Bioinstrumentation
4.Immunotechnology
5.Genetic Engg. & Applications
6.Bioinformatics

Practicals
1.Genetic Engg. & Immunotechnology Lab
2.Bioinformatics Lab

VI-SEMESTER:-

Theory
1.Bioprocess Control & Automation
2.Clinical Biotechnology
3.Enzyme Technology & Biotransformation
4.Genomics and Proteomics
5.Pharmaceutical Biotechnology
6.Elective
-Animal BT
-Plant BT
-Microbial BT
-Perl Programming
-Transport Phenomena
-Bioprocess Equipment Design & CAED

Practicals
7.Bioprocess Control & Automation Lab
8.Biokinetics & Enzyme Technology Lab

VII SEMESTER:-

Theory
1.Economics & Plant Design
2.Upstream Process Technology
3.Downstream Process Technology
4.Food Biotechnology
5.Elective
-Aqua Culture & Marine BT
-Dairy BT
-Forensic Science
-Data structures with C
-Bioreactor Design Lab
6.Elective
-Biochips & Micro arry Technology
-Biomaterials
-Health Diagnostics
-Fundamentals of OS & DBMS
-CAD & MATLAB

Practicals
7.Upstream Processing Lab
8.Downstream Processing Lab

VIII SEMESTER:-

Theory
1.Project Management & IPR
2.Bioethics & Bio safety
3.Elective
-Nano Bio-Technology
-Lab to Industrial Scaling
-Protein Engg & Insilico Drug Design
-Biomedical Instrumentation
-Biomolecular Engg.
4.Elective
-Environmental BT
-Metabolic Engg.
-Medical Informatics
-Tissue Engg.
-Facilitation, Validation & QC
5.Project Work
6.Seminar

Syllabus:


V SEMESTER


MANAGEMENT AND ENTREPRENEURSHIP
Sub Code : 06AL51 IA Marks : 25
Hours/Week : 04 Exam Hours : 03
Total Hours : 52 Exam Marks : 100
PART – A
UNIT -1. (7 Hours)
Management-Introduction- meaning nature & characteristic of management, scope &
functional areas of management. Management as a science, art or profession, management
and Administration, Role of management, levels of management, Development of
management thought – early management approaches – modern management and
approaches
UNIT -2 (6 Hours)
Planning-Nature, Importance and purpose of planning process, objectives, types of plans
(meaning only), decision – making, importance of planning, steps in planning and
planning premises, Hierarchy of plans
UNIT -3 (6 Hours)
Organizing and Staffing-Nature and purpose of organization, principles of organization,
Types of organization – Departmentation – committees – centralization v/s
decentralization of authority and responsibility, span of control- MBO and MBE (meaning
only), nature and importance of staffing, process of selection and recruitment (in brief)
UNIT -4 (7 Hours)
Directing & Controlling-Meaning and nature of directing, leadership styles, motivation
theories, communication- meaning and importance, co-ordination, meaning and
importance, techniques of co-ordination, Meaning and steps in controlling, essentials of a
sound control system, methods of establishing control (in brief)
PART – B
UNIT -5 (6 Hours)
Entrepreneur-Meaning of entrepreneur, evaluation of the concept, function of an
entrepreneur types of entrepreneur, evolution of entrepreneurship, development of
entrepreneurship, stages in entrepreneurial process, role of entrepreneurs in economic
development entrepreneurship in India, entrepreneurship - its barriers
UNIT -6 (7 Hours)
Small Scale Industry-Definition, characteristics, need and rationale, objectives, scope,
role of SSI in economic development, advantages of SSI, steps to start an SSI – Govt
policy towards SSI, different policies of SSI, Govt support for SSI during 5 year plans.
Impact of liberalization, privatization, globalization on SSI, effect of WTO/ GATT,
supporting agencies of Govt for SSI, meaning; nature of support, objectives, and functions,
types of help, ancillary industry and tiny industry (Definition only)
UNIT -7 (6 Hours)
Institutional Support-Different Schemes, TECKSOK, KIADB, KSSIDC, KSIMC, DIC
single window Agency SISI, NSIC, SIDBI, KSFC
UNIT -8 (7 Hours)
Preparation of Project-Meaning of Project; Project Identification Project Selection
Project Report, Need and significance of Report, Contents, Formulation Guidelines by
Planning Commission for Project report; Network Analysis; Errors of Project Report,
Project Appraisal, Identification of Business Opportunities. Market Feasibility Study,
Technical Feasibility study, Financial Feasibility Study & Social Feasibility study.
TEXT BOOKS:
1. “Principles of Management” , PC Tripati, P N Reddy,–Tata Mc Graw Hill, (Chapter
1,2,3,4,5,15,16,17)
2. “Dynamics of Entrepreneurial Development & Management” Vasant Desai Himalaya
Publishing House – (Chapter 1,2,4,8,9,10,13,15,16,17,18,19,20,21,22,42,46,47)
3. “Entrepreneurship Development – small Business Enterprises” Poornima M
Charanthmath Pearson Education – 2005 (2 & 4)
REFERENCE BOOKS:
1. “Management Fundamentals “, Robert Lusier,– Concepts, Application, Skill
Development” Thomson – (Chap 1,4,12)
2. “Entrepreneurship Development” S S Khanka S Chand & Co (Chapter
1,2,5,11,12,13,16,18,20)
3. “Management” Stephon Robbins Pearson Education/PHI 17th Edition 2003.
NOTE: Details of Institutional support can also be downloaded from the Internet.
Question paper pattern:
One full question to be set from each unit.
Totally five questions are to be answered choosing at least two from each part.

BIOKINETICS & BIOREACTION ENGINEERING
Sub. Code :06BT-52 I.A Marks: 25
Hours/week: 04 Exam Hrs: 03
Total Hours: 52 Exam Marks: 100
PART A
UNIT 1. INTRODUCTION
Law of mass action and rate equation, definitions and examples of
elementary and non-elementary reactions, theories of reaction rate
and temperature dependency, analysis of experimental reactor data:
evaluation of rate equation, integral and differential analysis for
constant volume system. Conceptual numericals.
08 Hours
UNIT 2. BIOCHEMICAL EQUILIBRIA
Equilibrium in chemically reactive systems (single and multiple reactions),
evaluation of reaction equilibrium constant, concentration/conversion data,
effect of temperature on equilibrium – derivation of G vs. T relation,
application of above concepts to biochemical systems. Conceptual numericals.
04 Hours
UNIT 3. BIOREACTORS
Design equations for homogeneous system: batch, stirred tank and
tubular flow reactor, size comparison of reactor systems, combination
reactor systems. Optimization of output and yield problems, Qualitative
design for consecutive, parallel and mixed reactions and recycle. Factors
affecting choice of reactors: optimum yield, conversion, selectivity and
reactivity. Conceptual numericals. 08 Hours
UNIT 4. NON-IDEAL BIOREACTORS
Non-ideal reactors, residence time distribution studies, pulse and step input
response of reactors, RTD’s for CSTR and PFR, calculations of conversions
for First order reactions, tanks in series and dispersion models. Conceptual
numericals.
06 Hours
PART B
UNIT 5. ENZYME KINETICS
Enzyme active site, types of enzyme specificities, enzyme kinetics, initialvelocity
studies, formation of ES complex, derivation of Michaelis-Menton equation,
definition of Km and Vmax, Lineweaver-Burk and Eadie-Hofsteeplots. Units of
enzyme activity, Enzyme inhibition: competitive, uncompetitive andnon-competitive;
Regulations – allosteric and feed back regulation.Conceptual numericals.
10 Hour
UNIT 6. KINETICS OF MICROBIAL GROWTH AND PRODUCT FORMATION
Phases of cell growth in batch cultures; simple unstructured kinetic models formicrobial
growth - Monod model; Growth of FilamentousOrganisms.
Growth associated (primary) and non-growth associated (secondary) product formation
kinetics; Leudeking-Piret models; substrate and product inhibition oncell growth and
product formation; Conceptual numericals.
05 Hours
UNIT 7. METABOLIC STOICHIOMETRY AND ENERGETICS
Stoichiometry of cell Growth and Product Formation- elemental balances, degrees of
reduction of substrate and biomass; available-electron balances; yield coefficients of
biomass and product formation; maintenance coefficients. Energetic analysis of
microbial growth and product formation - oxygen consumption and heat evolution
in aerobic cultures; thermodynamic efficiency of growth.Conceptual numericals.
05 Hours
UNIT 8. MEDIA DESIGN AND STERILIZATION
Medium requirements for fermentation processes- Carbon, nitrogen, minerals, vitamins
and other complex nutrients; oxygen requirements; Medium formulation for optimal
growth and product formation - examples of simple and complex media; Thermal death
kinetics of microorganisms;Batchandcontinuous
heat – Sterilizationof Liquid media; Filter sterilization of liquid media
07 Hours
TEXT BOOKS
Chemical Reaction Engineering by Levenspiel O., John Wiley, 3rd Edition, 2006.
Elements of Chemical Reaction Engineering by Fogler, H.S., Prentice Hall, 1986.
Bioprocess Engineering by Shuler and Kargi Prentice Hall, 1992.
Enzyme Kinetics and Mechanism by Paul F Cook & W W Cleland, Garland Science, 2007
REFERENCE BOOKS
Bioprocess Engineering by Aiba, Humprey & Millis, Academic Press.
Biochemical Engineering, James Lee, 1992.
Biochemical Engineering Fundamentals by Bailey and Ollis, McGraw Hill (2nd Ed.) 1986.
Bioprocess Engineering Principles by Pauline M. Doran, 1995. London.
Principles of Biochemistry by Leninger A.L., II Edition, 1993.
Enzyme Kinetics by Plowman, McGraw Hill, 1972.
Chemical Engineering Kinetics by Smith J.M., McGraw Hill, 3rd Edition, New
Delhi,1981.
Wolf R. Vieth, Bioprocess Engineering – Kinetics, Mass Transport, Reactors and Gene
Expression. A Wiley – Interscience Publication, 1992.
Chemical Reactor Analysis and Design by Forment G F and Bischoff K B., John Wiley,
1979.
Biocatalytic Membrane Reactor by Drioli, Taylor & Francis, 2005
QUESTION PAPER PATTERN
For every 6-7 Hours of teaching One Question to be Set. Eight questions to be set
(four from each part) out of which five full questions (considering at least two from
each part) to be answered.


BIOINSTRUMENTATION & BIOSENSORS
Sub. Code : 06BT-53 I.A Marks :25
Hours/week : 04 Exam Hrs. : 03
Total Hours : 52 Exam Marks : 100
PART A
UNIT 1. INTRODUCTION
Electrical quantities and units; functional elements of an instrumentation system;
static and dynamic characteristics; principles of analog and digital meters; CRO, energy
meters, time and frequency meters; multimeters.Transducers: Classification, resistive
strain gages, RTD, LVDT, Peizoelectric transducers, electromagnetic transducers,
optical transducers, transducersfor biomedical applications. Conceptual numericals.
06 Hours
UNIT 2. BIOMEDICAL INSTRUMENTATION
The terminology of medical instrumentation, a review of medical and
physiological signals, Principles of EEG, ECG and EMG, PC based
Instrumentation, Microcontroller based Instrumentation, Case study on
advanced instrumentation design in Cardiac Mapping. Conceptual numericals.
08 Hours
UNIT 3.CARDIAC AND VASCULAR SYSTEM
Overview of cardiovascular system, Types of blood pressure sensors,
Lumped parameter modeling of a catheter-sensor system, Heart sounds
Cardiac catheterization, Indirect measurement of blood pressure, Measuring
blood flow rate, Measuring blood volume, Pacemakers, Defibrillators,
Cardiac-assist devices, Replacement heart valves – related instrumentation
of equipments involved and sensors. Conceptual numericals.
06 Hours
UNIT 4.RESPIRATORY SYSTEM
Modeling the respiratory system, Measuring gas flow rate, Measuring
lung volume, Tests of respiratory mechanics, Measuring gas concentration,
Tests of gas transport, Ventilators, Anesthesia machines, Heart-Lung
machine – related instrumentation of equipments involved and sensors. Conceptual
numericals.
06 Hours
PART B
UNIT 5.ANALYTICAL INSTRUMENTS
pH meters, Radiometric Devices, Fluorescence Spectrophotometers,
Chromatology (chromatographic techniques – GC & HPLC), Electrophoresis,and Lab
on a chip - related instrumentation, Validation, Commissioning and Maintenance of
all the above equipments. Conceptual numerical.
06 Hours
UNIT 6. ASSAY TECHNOLOGIES AND DETECTION METHODS
Introduction; Bioassay Design and Implementation; Radiometric Assays;
Scintillation Proximity Assays; Fluorescence methodology to cover all
types of fluorescence measurements and instrumentation; Reporter gene
Assay applications; Bio-analytical Applications. Conceptual numericals.
06 Hours
UNIT 7. AUTOMATION AND ROBOTICS
Introduction to Automation, types, LERT classification system, components of a robot,
softwares used in robotics, Barcode technology, objectives, decoding, symbologies
used, barcode reader (pen-type, laser type, CCDcamera and camera based readers).
Conceptual numericals
04 Hours
UNIT 8. BIOSENSORS
Introduction to Biosensors: Concepts and applications. Biosensors for
personal diabetes management. Microfabricated Sensors and the
Commercial Development of Biosensors. Electrochemical sensors, Chemica
fibrosensors, Ion-selective FETs, Noninvasive blood-gas monitoring,Blood-glucose
sensors. Noninvasive Biosensors in Clinical Analysis. Applications of Biosensorbased
instruments to the bioprocess industry. Application of Biosensors to
environmental samples. Introduction to Biochips and their application to genomics.
BIAcore - an optical Biosensor. Conceptual numericals.
10 Hours
TEXT BOOKS
Bioinstrumentation and Biosensors by Donald L Wise, Marcel Dekker Inc. 1991
BIOSENSORS by COOPER JM (2004). Oxford Publications.
Hand book of Biomedical Instrumentation – R. S. Khandpur, 2nd Edition, TMH, 2003.
Biosensors and their applications by Yang Victor C & Ngo That T. 2000.
Biosensors – An introduction by Eggins Brain R. 1997.
Advances in Laboratory Automation-Robotics by J.R. Strimaitis and J.N. Little,
Zymark
Corporation, MA 1991.
REFERENCE BOOKS
Automation technologies for genome characterization, John Wiley & Sons, Inc. 1997.
Transducers and Instrumentation by Murthy D V S. Prentice Hall, 1995
High Throughput Screening, Edited by John. P. Devlin. Published by Marcel Dekker.
(1998)
Commercial Biosensors by Graham Ramsay, John Wiley & Son, INC. (1998)
Introduction to bioanalytical sensors by Alice J Cunningham Newyrok, John Wiley, 1988.
Applied biosensors by Doland L Wise (1989).
Encyclopedia of Medical devices and Instrumentation – J G Webster – John Wiley 1999
Introduction to Biomedical equipment technology – J J Carr, J M Brown, Prentice Hall.
1998.
Introduction to Biomedical Engineering by J Enderle, S Blanchard & J Bronzino, Elsevier,
2005.
QUESTION PAPER PATTERN
For every 6-7 Hours of teaching One Question to be Set. Eight questions
to be set (four from each part) out of which five full questions
(considering at least two from each part) to be answered.

IMMUNOTECHNOLOGY
Sub. Code: 06BT-54 I.A Marks: 25
Hours/week: 04 Exam Hrs.: 03
Total Hours: 52 Exam Marks: 100
PART A
UNIT 1.THE IMMUNE SYSTEM
Introduction, cells and organs of the immune system, Primary and secondary Lymphoid
organs, antigens, antibodies and their structure, types of immune responses; anatomy
of immune response. Classification of immune system - innate and adaptive immunity.
06 Hours
UNIT 2. HUMORAL-IMMUNITY
B-lymphocytes and their activation; structure and function of
immunoglobulins;immunoglobulin classes and subclasses, idiotypes and anti-idiotypic
antibodies, genetic control of antibody production, production of monoclonal and
polyclonal antibodies.
08 Hours
UNIT 3. CELL-MEDIATED IMMUNITY
Thymus derived lymphocytes (T cells) - their ontogeny and types, MHC Complex,
antigen presenting cells (APC), mechanisms of T cell activation, macrophages,
dendritic cells, langerhans cells, mechanism of phagocytosis, Antigen processing and
presentation.
06 Hours
UNIT 4. IMMUNE REGULATION AND TOLERANCE
Complement activation and types and their biological functions,
cytokines and their role in immune response, immunotolerance,
Hypersensitivity its types and treatment.
06 Hours
PART B
UNIT 5. IMMUNOLOGICAL DISORDER
Autoimmune disorders and types, pathogenic mechanisms, treatment,
experimental models of auto immune disease, primary and secondary
immunodeficiency disorders, mechanism of AIDS, rheumatoid arthritis
and allergies.
06 Hours
UNIT 6. TRANSPLANTATION IMMUNOLOGY
Immunological basis of graft, types of transplantation, mechanism of
graft rejection, role of HLA in graft rejection, tissue typing,
immunosuppression and immunosuppressive drugs, tumor specific antigens.
06 Hours
UNIT 7. MOLECULAR IMMUNOLOGY
Vaccines and their types, production of recombinant-DNA vaccines.
Catalytic antibodies, application of PCR technology to produce antibodies,
immunotherapy with genetically engineered antibodies. Brief mention about stem cells
and applications to immunology.
06 Hours
UNIT 8. IMMUNODIAGNOSIS
Antigen antibody interaction – Precipitation reactions, Agglutination reactions
, Blood typing, A, B, ABO & Rh, principles and applications of ELISA, Radio
Immuno Assay (RIA), western blot analysis, immuno-electrophoresis,
Immunofluorescence, chemiluminescence assay.
08 Hours
TEXT BOOKS
Immunology – an Introduction by Tizard, Thomson 2004.
Immunology by J Kubey, WH Freeman. 2003.
Immunology & Immunotechnology by Ashim K Chakravarthy, Oxford University Press,
2006.
Immundiagnostics by S C Rastogi, New Age International. 1996.
REFERENCE BOOKS
Essential Immunology by Roitt I. Blackwell Scientific Publications, Oxford, 1991.
Molecular Immunology By Benjamini E. 2002.
Immunology A short course by Benjamini E. and Leskowitz S. Wiley Liss, NY, 1991.
The Immune System by Peter Parham, Garland Science, 2005
Understanding Immunology by Peter Wood, Pearson Education, II edition, 2006
QUESTION PAPER PATTERN
For every 6-7 Hours of teaching One Question to be Set. Eight questions
to be set (four from each part) out of which five full question
(considering at least two from each part) to be answered.

GENETIC ENGINEERING & APPLICATIONS
Sub. Code: 06BT-55 I.A Marks: 25
Hours/week: 04 Exam Hrs : 03
Total Hours: 52 Exam Marks: 100
PART A
UNIT 1. INTRODUCTION
Role of genes within cells, genetic code, genetic elements that
control gene expression, method of creating recombinant DNA
molecules, vectors in recombinant DNA technology, biology and salient
features of vectors, types of vectors – plasmids, cosmids, phages and viruses.
06 Hours
UNIT 2. ENZYMES IN GENETIC ENGINEERING
Introduction. Restriction Endonculeases - Exo & exdo nucleases,
classification, mode of action. Enzymes in modification - Polynucleotide
phosphorylase, DNase, Methylases, phosphatases, polynucleotide Kinase,Ligases,
RNase and their mechansim of action.
06 Hours
UNIT 3. NUCLEIC ACID HYBRIDIZATION AND AMPLIFICATION
Methods of nucleic acid detection, polymerase chain reaction (PCR)
and its applications, variations in PCR and applications, methods of nucleic acid
hybridization, probe and target sequences, Southern and Northern hybridization
techniques, nucleic acid mutagenesis in vivo and in vitro.
08 Hours
UNIT 4. CONSTRUCTION OF DNA LIBRARIES
Isolation and purification of nucleic acids, quantification,
storage, Isolation of plasmids, Construction of genomic and
cDNA libraries, screening and preservation.
06 Hours
PART B
UNIT 5. GENE TRANSFER TECHNIQUES
Gene transfer techniques in plants, animals and microbes –
Transformation,electroporation, microprojectile system, liposome mediated transfer,
genegun etc. Agrobacterium-mediated gene transfer in plants – Ti plasmid:structure and
functions, Ti plasmid based vectors - advantages.
Chloroplast transformation.
08 Hours
UNIT 6. TRANSGENIC SCIENCE AND GENETIC IMPROVEMENT
Transgenic science in plant improvement, biopharming – plants as bioreactors,transgenic
crops for increased yield, resistance to biotic and abiotic stresses. Techniques of gene
mapping in plants. Marker-assisted selection and breeding for improvement. Transgenic
science for animal improvement, biopharming - animals as bioreactors for
recombinant proteins, Gene mapping in farm animals. Marker-assisted selection and
genetic improvement of livestock.
08 Hours
UNIT 7. OTHER APPLICATIONS
Microbial biotechnology - Genetic manipulation, engineering microbes for the
production of antibiotics, enzymes, Insulin, growth hormones, monoclonal antibodies,
clearing oil spills.
06 Hours
UNIT 8. GENE THERAPY
Introduction. Methods of Gene therapy. Gene targeting and silencing. Gene
therapy in the treatment of cancer, SCID, muscular dystrophy, respiratory
disease (emphysema) etc., Challenges in gene therapy. Future of gene therapy.
04 Hours
TEXT BOOKS
Introduction to Genetic Engineering by Nicholl. Cambridge Low Price Edition, 2006.
Principles of gene manipulation - An introduction to genetic engineering, Old R.W.,
Primrose
S.B., Blackwell Scientific Publications, 1993.
From Genetics to Gene Therapy – the molecular pathology of human disease by
David S
Latchman, BIOS scientific publishers, 1994.
Genes VIII by Benjamin Lewis. Oxford University & Cell Press, 2007.
DNA Science by David A Micklos, Greg A Freyer and Dvaid A Crotty, I K International,
2003.
REFERENCE BOOKS
Molecular Biotechnology: Prnciples and Practices by Channarayappa, 2006, University
Press.
Genetic Engineering Vol. 1-4 (Williamson Edition)
Recombinant DNA by Watson et al., 1983.
Vectors by Rodriguer and Denhardt, 1987.
Current protocols in molecular biology, Greena Publishing Associates, NY, 1988.
Berger S.L. Kimmel A.R. Methods in enzymology, Vol.152, Academic Press, 1987.
Molecular cloning Volumes I, II and III. Sambrook J et al (2000). Cold Spring Harbor lab
Press.
QUESTION PAPER PATTERN
For every 6-7 Hours of teaching One Question to be Set. Eight
questions to be set (four from each part) out of which five full
questions(considering at least two from each part) to be answered.

BIOINFORMATICS
Sub. Code: 06BT-56 I.A Marks: 25
Hours/week: 04 Exam Hrs. : 03
Total Hours: 52 Exam Marks: 100
PART A
UNIT 1. DATABASES & TOOLS
Introduction to Bioinformatics, Need for informatics tools and
exercises, Significance of databases towards informatics projects.
The nucleotide and protein sequence Databases: GenBank, DDBJ,EMBL, PIR,
Primary and Secondary Databases; Format of databases,Gene bank flat file. Protein
Data Bank (PDB) flat file; FASTAFormat, PIR Format; Structure file formats,
PDBSUM, PDBLite,MMDB, SCOP, Pfam; Database of structure viewers.
Specializeddatabases: NCBI, Pubmed,OMIM,Medical databases,KEGG, EST
databases;Overview of other popular tools for bioinformatics exercises.
06 Hours
UNIT 2. SEQUENCE ALIGNMENT AND DATABASE SEARCHES
Introduction, The evolutionary basis of sequence alignment, the Modular Nature of
proteins, Optional Alignment Methods, Substitution scores, substitution matrices,PAM,
BLOSUM, Gap penalties, Statistical significance of Alignments, Database similarity
searching, FASTA, BLAST, Low-Complexity Regions, Repetitive Elements. Practical
Aspect of Multiple Sequence Alignment, Progressive Alignment Methods,
CLUSTALW,
Motifs and Patterns, PROSITE, 3DPSSM. Hidden Markov Models (HMMs),
andThreading methods. Conceptual numericals.
08 Hours
UNIT 3. PHYLOGENETIC ANALYSIS
Introduction to Phylogenetic analysis, rooted and unrooted trees,
Elements of phylogenetic Models, Phylogenetic Data Analysis:
Alignment, Substitution Model Building, Tree Building, and Tree Evaluation,
Building the Data Model (Alignment), Determining the Substitution Model, Tree -
Building Methods, Searching for Trees, Rooting Trees, Evaluating Trees and Data,
Phylogenetic softwares (CLUSTALW, PHYLIP etc), Conceptual numericals.
06 Hours
UNIT 4. PREDICTIVE METHODS
Predictive Methods using Nucleotide sequences: Framework, Masking
repetitiveDNA, Database searches, Codon Bias Detection, Detecting Functional Sites
in the DNA (promoters, transcription factor binding sites, translation initiation sites),
Integrated Gene Parsing, finding RNA Genes, Web based tools (GENSCAN, GRAIL,
GENEFINDER). Predictive Methods using Protein sequences: Protein Identity based on
composition, Physical properties Based on sequence, secondary structure and folding
classes, specialized structures or features, tertiary structure. Related web based
software (JPRED, PROSEC, NNPREDICT, SOPMA)
06 Hours
PART B
UNIT 5. PLASMID MAPPING AND PRIMER DESIGN
Restriction mapping, Utilities, DNA strider, MacVector and OMIGA, gene
construction KIT, Vector NTI, Web based tools (MAP, REBASE); Primer design – need
for tools,Primer design programs and software (PRIME3).Conceptual numericals.
04 Hours
UNIT 6. GENOME BIOINFORMATICS
Sequencing methods (qualitative), Bioinformatics tools and automation in
Genome Sequencing, analysis of Raw genome sequence data, Utility of
EST database in sequencing,Bioinformatics in detection of Polymorphisms,
SNPs and their relevance, Bioinformatics tools in microarray data analysis, tools for
comparative genomics.
04 Hours
UNIT 7. MOLECULAR VISUALIZATION
Generation or Retrieval, Structure Visualization, Conformation
Generation. Graphical representation of molecular structures: small molecules (low
molecular weight – peptides, nucleotides, disaccharides, simple drugs molecules) and
macromolecules (high molecular weight molecules - proteins, DNA, RNA,
membranes). Usages of visualization software available in public domain like VMD,
Rasmol, Pymol, SpdbViewer, Chime, Cn3D.Rotameric Structures of Proteins
(Conformational Flexibility), Canonical DNAForms (DNA Sequence Effects).
Systematic methods of exploring
conformational space.
06 Hours
UNIT 8. INSILICO MODELING & DRUG DESIGN
Scope and applications of insilico modeling in modern biology. Comparative
modeling, Constructing an initial model, refining the model, manipulating the model,
molecule superposition and structural alignment, concept of energy minimization,
different types of interactions and formulation of force fields. Basic MD algorithm,
its limitations, treatment of long range forces. Molecular modeling in drug
discovery, deriving bioactive conformations, molecular docking, quantitative structureactivity
relationship (QSAR), deriving the Pharmacophoric Pattern, Receptor Mapping,
Estimating Biological Activities, Ligand - ReceptorInteractions: Docking, Calculation of
Molecular Properties, Energy Calculations(no derivation). Conceptual numericals.
12 Hours
TEXT BOOKS
BIOINFORMATICS by Andreas D Baxevanis. Wiley Interscience, 1998.
BIOINFORMATICS: by David W Mount, cold spring harbor, 2001.
Introduction to Bioinformatics by Arthur Lesk, Oxford, 2006.
BIOINFORMATICS: Stuart M Brown, NYU Medical Center, NY USA. 2000.
Fundamental Concepts of Bioinformatics by D E Krane & M L Raymer, Pearson, 2006.
REFERENCE BOOKS
Computational methods for macromolecular sequence analysis: R F Doolittle. Academic
Press, 1996.
Computational methods in Molecular Biology. S.L.Salzberg, D B Searls, S Kasif, Elsevier,
1998.
BIOINFORMATICS –METHODS AND APPLICATIONS:GENOMICS,PROTEOMICS
AND DRUG
DISCOVERY BY S C RASTOGI, N MENDIRATTA & P RASTOGI, PHI, 2006.
The molecular modeling perspective in drug design by N Claude Cohen, 1996, Academic
Press
Analytical Tools for DNA, Genes & Genomes: by Arseni Markoff, New Age, 2007.
INTRODUCTION TO BIOINFORMATICS by ANNA TRAMONTANO (2007)
TAYLOR & FRANCIS.
BIOINFORMATICS by DES HIGGINS & WILLIE TAYLOR (2005) OXFORD.
QUESTION PAPER PATTERN
For every 6-7 Hours of teaching One Question to be Set. Eight questions to be
set(four from each part) out of which five full questions (considering at least two
from each part) to be answered.

GENETIC ENGINEERING & IMMUNOTECHNOLOGY
LABORATORY
Sub. Code: 06BTL-57 I.A Marks: 25
Hours/week: 03 Exam Hrs. : 03
Exam Marks : 50
1. Preparation of DNA for PCR applications- Isolation, purity & quantification
2. Introduction to PCR – working of PCR equipment, programming, preparation of
reagents
and buffers
3. Primer designing using softwares
4. Gene/ DNA amplification by random/ specific primers
5. Southern hybridization
6. Gene Transformation
7. Agglutination Technique: Blood group identification
8. Bacterial Agglutination Technique-Widal test (Tube / slide agglutination)
9. Ouchterlony Double Diffusion (ODD) and Radial Immunodiffusion (RID)
10. ELISA
11. Countercurrent immunoelectrophoresis (CCIEP)
12. Immunoelectrophoresis (IEP)
13. Rocket immunoelectrophoresis (RIEP)
14. Western blot
15. Separation of lymphocytes from peripheral blood.
TEXT/REFERENCE BOOKS
Principles of gene manipulation - An introduction to genetic engineering, Old R.W.,
Primrose
S.B., Blackwell Scientific Publications, 1993.
Genetic Engineering Vol. 1-4 (Williamson Edition)
Immunology & Immunotechnology by Ashim K Chakravarthy, Oxford University Press,
2006.11
Immunodiagnostics by S C Rastogi, New Age International.
Genes VIII by Benjamin Lewis. Oxford University & Cell Press
Current protocols in molecular biology, Greena Publishing Associates, NY, 1988.
Berger S.L. Kimmel A.R. Methods in enzymology, Vol.152, Academic Press, 1987.
DNA Science by David A Micklos, Greg A Freyer and David A Crotty, I K International,
2003.
Molecular cloning Volumes I, II and III. Sambrook J et al (2000). Cold Spring Harbor lab
Press.
Introduction to Genetic engineering by Sandhya Nair

BIOINFORMATICS LABORATORY
Sub. Code: 06BTL-58 I.A Marks: 25
Hours/week: 03 Exam Hrs.: 03
Exam Marks: 50
1. Bibliographic search from PUBMED, SCIRUS, MEDMINER
2. Sequence retrieval from Nucleic acid and Protein databases.
3. Sequence (FASTA and BLAST) searches – Retrieval of homologs, paralogs,
orthologs, and xenologs
4. Pair wise comparison of sequences – Analysis of parameters affecting alignment.
5. Multiple alignments of sequences and pattern determination using PROSITE
6. Evolutionary studies / Phylogenetic analysis – Analysis of parameters affecting trees.
7. Identification of functional sites in Genes / Genomes.
8. Secondary structure prediction of proteins and comparison with PDB.
9. Restriction mapping: Analysis of maps for suitable molecular biology experiment.
10. Primer Design: Factors affecting primer design.
11. PDB structure retrieval and visualization: Analysis of homologous structures.
12. Comparative Modeling of homologous sequences and validation of modeled
structures.
13. Determination of ligand-protein interactions using SPDBV/ LIGPLOT
14. Superposition of structures – Calculation of RMSD.
15. Docking studies – Analysis of substrate / ligand binding using homologous structures.
16. Derivation of pharmacophore patterns for sigma selective ligands.
TEXT/REFERENCE BOOKS
BIOINFORMATICS by Andreas D Boxevanis. Wiley Interscience, 1998.
BIOINFORMATICS by David W Mount, cold spring harbor, 2001.
BIOINFORMATICS: A biologists guide to biocomputing and the internet. Stuart M
Brown,
NYU Medical Center, NY USA. 2000.
Analytical Tools for DNA, Genes & Genomes: by Arseni Markoff, New Age, 2007.
DISCOVERING GENOMICS, PROTEOMICS & BIOINFORMATICS BY A M
CAMPBELL & L J HEYER,
PEARSON EDUCATION, 2007
Fundamental Concepts of Bioinformatics by D E Krane & M L Raymer, Pearson, 2006.
Computational methods in Molecular Biology. S.L.Salzberg, D B Searls, S Kasif, Elsevier,
1998.
BIOINFORMATICS –METHODS AND APPLICATIONS:
GENOMICS,PROTEOMICS AND DRUG
DISCOVERY BY S C RASTOGI, N MENDIRATTA & P RASTOGI, PHI, 2006
Introduction to Bioinformatics by Arthur Lesk, Oxford, 2006

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