M. Tech Biotechnology

M.
Tech Biotechnology (Drug Design & Development)

Overview: The PG-Programme has been structured to impart information oriented development
and design of drugs. This, in addition to their broad-based UG - Programme would enable them
to meet the requirements of Bio and Pharma based industries. The curriculum is designed
to enable students to master the fundamentals of design and development of novel drugs, so that
they can adapt easily to rapid technological changes. During the 3
rd
semester the students
carryout a mini project under the guidance of the faculty and submit a report. In the fourth
semester students carryout a project work in a reputed industry / research organization and the
report on the completed project is submitted at the end of 4
th
semester.

Duration: The duration of M. Tech programme is of four semesters spread over two years. Four
semesters includes classroom instruction, laboratory work and project work.
GITAM UNIVERSITY
(Declared as Deemed to be University U/S 3 of UGC Act, 1956)

REGULATIONS & SYLLABUS
OF
M.Tech. (Biotechnology)
(w.e.f 2010-11 admitted batch)

Gandhi Nagar Campus, Rushikonda
VISAKHAPATNAM 530 045
Website: www.gitam.edu

REGULATIONS
(w.e.f. 2010-11 admitted batch)
1.0 ADMISSIONS
1.1 Admissions into M.Tech (Biotechnology) programme of GITAM University are governed by
GITAM University admission regulations.
2.0 ELIGIBILTY CRITERIA

2.1 A pass in B E / B Tech or equivalent in Biotechnology or B Pharm or equivalent or B Tech in
Chemical Engg. / M Sc in Chemistry with Basic Biology/ M.Sc. Biotechnology or M Sc in any
Biological Science with Mathematics.
2.2 Admissions into M.Tech will be based on the following:

(i) Score obtained in GAT (PG), if conducted.
(ii) Performance in Qualifying Examination / Interview.
The actual weightage to be given to the above items will be decided by the authorities before the
commencement of the academic year. Candidates with good GATE/GRE score shall be exempted
from appearing for GAT (PG).
[
3.0 STRUCTURE OF THE M.Tech. PROGRAMME

3.1 The Programme of instruction consists of:
(i) A core programme imparting to the student specialization of engineering branch concerned.
(ii) Separate elective courses may be prescribed for engineering & science students.
(iii) Carry out a technical project approved by the Department and submit a report.
3.2 Each academic year consists of two semesters. Every branch of the M.Tech programme has a
curriculum and course content (syllabi) for the subjects recommended by the Board of Studies
concerned and approved by Academic Council.
3.3 Project Dissertation has to be submitted by each student individually.
4.0 CREDIT BASED SYSTEM

4.1 The course content of individual subjects - theory as well as practicals is expressed in terms of a
specified number of credits. The number of credits assigned to a subject depends on the number of
contact hours (lectures & tutorials) per week.
4.2 In general, credits are assigned to the subjects based on the following contact hours per week per
semester.
One credit for each Lecture hour.
One credit for two hours of Practicals.
Two credits for three (or more) hours of Practicals.
4.3 The curriculum of M.Tech programme is designed to have a total of 70 -85 credits for the award
of M.Tech degree. A student is deemed to have successfully completed a particular semesters
programme of study when he / she earns all the credits of that semester i.e., he / she has no F
grade in any subject of that semester.
5.0 MEDIUM OF INSTRUCTION

The medium of instruction (including examinations and project reports) shall be English.
6.0 REGISTRATION
Every student has to register himself/herself for each semester individually at the time specified by the
College / University.
7.0 CONTINUOUS ASSESSMENT AND EXAMINATIONS
7.1 The assessment of the students performance in each course will be based on continuous internal
evaluation and semester-end examination. The marks for each of the component of assessment are
fixed as shown in the Table 2.:
Table 2: Assessment Procedure
S.No. Component of
assessment
Marks allotted Type of
Assessment
Scheme of Examination

1

Theory

Total

40

Continuous
evaluation
(i) Two mid semester examinations
shall be conducted for 10 marks each.
(ii) Two quizzes shall be conducted
for 5 marks each.
(iii) 5 marks are allotted for
assignments.
(iv) 5 marks are allotted for
attendance
60 Semester-end
examination
The semester-end examination in
theory subjects will be for a maximum
of 60 marks.
100

2

Practicals

100

Continuous
evaluation
(i) 40 marks are allotted for record
work and regular performance of the
student in the lab.
(ii) One examination for a maximum
of 20 marks shall be conducted by the
teacher handling the lab course at the
middle of the semester
(iii) One examination for a maximum
of 40 marks shall be conducted at the
end of the semester (as scheduled by
the Head of the Department
concerned).

3

Project work

100

Project evaluation
(i) 50 marks are allotted for
continuous evaluation of the project
work throughout the semester by the
guide.
(ii) 50 marks are allotted for the
presentation of the project work &
viva-voce at the end of the semester.*
* Head of the Department concerned shall appoint two examiners for conduct of the examination.
8.0 REAPPEARANCE
8.1 A Student who has secured F Grade in any theory course / Practicals of any semester shall have
to reappear for the semester end examination of that course / Practicals along with his / her juniors.

8.2 A student who has secured F Grade in Project work shall have to improve his report and
reappear for viva voce Examination of project work at the time of special examination to be
conducted in the summer vacation after the last academic year.
9.0 SPECIAL EXAMINATION
9.1 A student who has completed the stipulated period of study for the degree programme concerned
and still having failure grade (F) in not more than 5 courses ( Theory / Practicals), may be
permitted to appear for the special examination, which shall be conducted in the summer vacation
at the end of the last academic year.
9.2 A student having F Grade in more than 5 courses (Theory/practicals) shall not be permitted to
appear for the special examination.
10.0 ATTENDANCE REQUIREMENTS
10.1 A student whose attendance is less than 75% in all the courses put together in any semester will
not be permitted to attend the end - semester examination and he/she will not be allowed to
register for subsequent semester of study. He /She has to repeat the semester along with his / her
juniors.
10.2 However, the Vice Chancellor on the recommendation of the Principal / Director of the
University college / Institute may condone the shortage of attendance to the students whose
attendance is between 66% and 74% on genuine medical grounds and on payment of prescribed
fee.
11.0 GRADING SYSTEM

11.1 Based on the student performance during a given semester, a final letter grade will be awarded
at the end of the semester in each course. The letter grades and the corresponding grade points are
as given in Table 3.
Table 3: Grades & Grade Points

11.2 A student who earns a minimum of 5 grade points (C grade) in a course is declared to have
successfully completed the course, and is deemed to have earned the credits assigned to that
course. However, a minimum of 24 marks is to be secured at the semester end examination of
theory courses in order to pass in the theory course
12.0 GRADE POINT AVERAGE
12.1 A Grade Point Average (GPA) for the semester will be calculated according to the formula:
[ C x G ]
GPA =----------------
C
Where
C =number of credits for the course,
G =grade points obtained by the student in the course.
Grade Grade points Absolute Marks
O 10 90 and above
A+ 9 80 89
A 8 70 79
B+ 7 60 69
B 6 50 59
C 5 40 49
F Failed, 0 Less than 40
12.2 Semester Grade Point Average (SGPA) is awarded to those candidates who pass in all the subjects
of the semester.
12.3 To arrive at Cumulative Grade Point Average (CGPA), a similar formula is used considering the
students performance in all the courses taken in all the semesters completed up to the particular
point of time.
12.4 The requirement of CGPA for a student to be declared to have passed on successful completion of
the M.Tech programme and for the declaration of the class is as shown in Table 4.

Table 4: CGPA required for award of Degree

Distinction 8.0*
First Class 7.0
Second Class 6.0
Pass 5.0

* In addition to the required CGPA of 8.0, the student must have necessarily passed all the courses of every
semester in first attempt.
13.0 ELIGIBILITY FOR AWARD OF THE M.Tech DEGREE
13.1 Duration of the programme:
A student is ordinarily expected to complete the M Tech. programme in four semesters of two
years. However a student may complete the programme in not more than four years including
study period.
13.2 However the above regulation may be relaxed by the Vice Chancellor in individual cases for
cogent and sufficient reasons.

13.3 Project dissertation shall be submitted on or before the last day of the course. However, it can be
extended up to a period of 6 months maximum, with the written permission of the Head of the
Department concerned.
13.4 A student shall be eligible for award of the M.Tech degree if he / she fulfils all the following
conditions.
a) Registered and successfully completed all the courses and projects.
b) Successfully acquired the minimum required credits as specified in the curriculum
corresponding to the branch of his/her study within the stipulated time.
c) Has no dues to the Institute, hostels, Libraries, NCC / NSS etc, and
d) No disciplinary action is pending against him / her.
13.5 The degree shall be awarded after approval by the Academic Council.

RULES
1. With regard to the conduct of the end-semester examination in any of the practical courses of the
programme, the Head of the Department concerned shall appoint one examiner from the department not
connected with the conduct of regular laboratory work, in addition to the teacher who handled the
laboratory work during the semester.
2. In respect of all theory examinations, the paper setting shall be done by an external paper setter having a
minimum of three years of teaching experience. The panel of paper setters for each course is to be prepared
by the Board of Studies of the department concerned and approved by the Academic Council. The paper
setters are to be appointed by the Vice Chancellor on the basis of recommendation of Director of
Evaluation / Controller of Examinations.
3. The theory papers of end-semester examination will be evaluated by two examiners. The examiners may
be internal or external. The average of the two evaluations shall be considered for the award of grade in
that course.
4. If the difference of marks awarded by the two examiners of theory course exceeds 12 marks, the paper will
have to be referred to third examiner for evaluation. The average of the two nearest evaluations of the three
shall be considered for the award of the grade in that course.
5. Panel of examiners of evaluation for each course is to be prepared by the Board of Studies of the
department concerned and approved by the Academic Council.
6. The examiner for evaluation should possess post graduate qualification and a minimum of three years
teaching experience.
7. The appointment of examiners for evaluation of theory papers will be done by the Vice Chancellor on the
basis of recommendation of Director of Evaluation / Controller of Examinations from a panel of examiners
approved by the Academic Council.
8. Project work shall be evaluated by two examiners at the semester end examination. One examiner shall be
internal and the other be external. The Vice Chancellor can permit appointment of second examiner to be
internal when an external examiner is not available.
9. The attendance marks (maximum 5) shall be allotted as follows:

Percentage of Attendance Marks
76% to 80% 1
81% to 85% 2
86% to 90% 3
91% to 95% 4
96% to 100% 5
SYLLABUS
M.Tech. (Biotechnology) Programme Course Code: EPRBT200901
M.Tech Biotechnology I Semester
Note: Students from biological sciences will have to qualify themselves in additional examinations in mathematics
at undergraduate level at the end of 1
st
semester (after admission) of M.Tech.
Course Code Name of the Course Instruction hours Maximum marks
Cred
its
L T P Total C S Total
Semester 1
EPRBT 101 Molecular physiology, pathology and
pharmacology
3 - - 3 40 60 100 3
EPRBT 102 Pharmacokinetics 3 - - 3 40 60 100 3
EPRBT 103 Advanced genetics and statistics 3 - - 3 40 60 100 3
Electives:
EPRBT 121
EPRBT 122
Molecular biology and genetic engineering
Introduction to biochemical engineering
3 - - 3 40 60 100 3

EPRBT 104
Fermentation and cell culture
3 - - 3 40 60 100 3
EPRBT 111 Pharmacology and genetic engineering lab - - 6 6 100 -- 100 2
EPRBT 112 Fermentation and cell culture lab - - 6 6 100 -- 100 2
EPRBT 113 Seminar - 3 - 3 100 -- 100 2
Total 30 21

Semester 2
EPRBT 201 Pharmacoinformatics 3 - - 3 40 60 100 3
EPRBT 202 Proteomics and genomics for target
identification
3 - - 3 40 60 100 3
EPRBT 203
Screening and target validation
3 - - 3 40 60 100 3
EPRBT 204 Biological programming 3 - - 3 40 60 100 3
EPRBT 205 Regulatory issues in drug design and
development
3 - - 3 40 60 100 3
EPRBT 211 Pharmacoinformatics lab - - 6 6 100 -- 100 2
EPRBT 212 Biological Programming Lab - - 6 6 100 -- 100 2
EPRBT 213 Seminar - 3 - 3 100 -- 100 2
Total 30 21

Semester 3
EPRBT 301 Molecular modeling and lead optimization 3 - - 3 40 60 100 3
EPRBT 302 Modeling and simulation of drug
manufacturing process
3 - - 3 40 60 100 3
EPRBT 311 Molecular modeling lab - - 6 6 100 -- 100 2
EPRBT 312 Modeling and simulation lab - - 6 6 100 -- 100 2
EPRBT 313
Project
- - - 15 50 50 100 10
Total 33

20

Semester 4
EPRBT 411 Project - - - 35 50 50 100 20
Total 35

20

Grand Total 82


MOLECULAR PHYSIOLOGY, PATHOLOGY AND PHARMACOLOGY

Code : EPRBT 101
Credits : 3 No. of hours: 4 per week

Unit-I: Physiology of the central, peripheral and autonomous nervous system. The blood-brain barrier.
Common diseases, drugs, targets and modes of action for nervous system.
Unit-II: Physiology of the musculoskeletal and gastroenteric systems. Common diseases, drugs, targets
and modes of action for drugs of musculoskeletal and gastroenteric systems.
Unit-III: Physiology of the cardiovascular and respiratory system. Common diseases, drugs, targets and
modes of action for drugs of cardiovascular and respiratory systems. Infectious diseases: Bacterial-
Tuberculosis, Parasitic Malaria, Antibiotic Drugs and their targets.
Unit-IV: Physiology of endocrine system, excretory systems. Common diseases, drugs, targets and
modes of action for drugs of endocrine and excretory systems.
Unit V: Physiology of the immune system: Organs and cells of immune system, antigen and antibody
structures, immune response, autoimmune disorders. Common diseases, drugs, targets and modes of
action for drugs of immune system. Infectious diseases: Viral HIV, Viral Drugs and their targets.
Textbooks:

1) Textbook of physiology by Guyton
2) Human Physiology by Wikibooks contributors
3) Pharmacology by Satoshkar and Bandarkar

Reference books:

1) Brody's Human pharmacology: Molecular to clinical by K.P.Minneman (2004)
2) Neuropharmacology by Cooper, Bloomand Roth.
3) Reviews of Medical Physiology by W.F.Ganong
4) Pharmacology by Rang and Dale.
5) Medical microbiology. 24
th
Edition (J awetz, Melnick and Adelberg's Medical
Microbiology) by Geo. F. Brooks. (2007)


PHARMACOKINETICS

Course Code : EPRBT 102
Credits : 3 Hours: 3 per week

Unit-I:
Requirements of a drug: binding, delivery (absorption, distribution), stability (metabolization,
elimination), toxicity, synthesizability and formulation.
Unit-II:
Transport of drugs across biological membranes. Factors affecting drug absorption. Role of intestinal
transporters in drug absorption. Bioequivalence. Absorption kinetics. Estimation of pharmacokinetic
parameters. Prediction of plasma levels. Wagner-nelson calculation and bioavailability.
Unit -III:
Drug Metabolism: Clearance. Half life. Oxidative and reductive metabolism. Conjugative metabolism.
Metabolism mediated drug-drug interactions. Factors effecting drug metabolism. Models to study drug
metabolism. Dose effect relationships. Protocols for assessment of bioactivation potential of drug
candidates. Reaction phenotyping. Inhibition of Cytochrome P450.
Unit-IV:
Potency, efficacy, therapeutic index, margin of safety, dose optimization. Drug transporters in drug
disposition, interaction and resistance. Renal and hepatic clearance. Assessment of bioavailability.
Unit-V:
Drug reactions: Adverse drug reactions and drug interactions. Toxic reactions, allergic reactions,
idiosyncracy. Acute poisoning and its treatment. Toxicokinetic studies. Brief introduction to
experimental methods for study of drug toxicity, stability, effectiveness of delivery and binding.
Textbooks:
1) Clinical Pharmacokinetics: Concepts and Applications, M.Rowland and T.N. Tozer, 3rd edition, Lea
and Febiger, Philadelphia, 1995.
2) Basic Clinical Pharmacokinetics, Michael Winter, 4th edition, Lippincott, Williams&Wilkins,
Philadelphia, 2004.
3) Applied Biopharmaceutics and Pharmacokinetics, L. Shargel and A.B.C. Yu, 5th edition, Appleton
and Lange, Norwalk, CT, 2005.
4) Drug metabolism in drug design and development. Zhang, Zhu and Humphreys. (2007) Wiley-
Interscience.
5) Introduction to drug metabolism. Gibson and P. Skett. 3
rd
Ed. (2001). Nelson Thornes.

ADVANCED GENETICS AND STATISTICS
Code : EPRBT 103

Unit-I: Genetic polymorphism. Genetic variability in drug metabolizing enzymes, drug transporters and
drug receptors. Immunogenetic polymorphisms. Methods for genotyping.
Case study: Host genetics and tuberculosis susceptibility.
Unit-II: Monogenic traits: Mendelian pedigree patterns. Linkage analysis, Pedigree analysis. Hardy-
Weinberg Law. Allele frequency estimation for two alleles and three alleles at a locus. Linkage
disequilibriumand Association mapping.
Unit-III: Multifactorial inheritance. Heritability. Twin studies in pharmacogenetics. Interval mapping.
Polygenic models. Haplotyping.
Unit-IV: Introduction to Univariate (normal, poisson and extreme value distributions) and multivariate
distributions. ANOVA, Regression analysis. Linear discriminant analysis. Principle components
analysis. Partial least squares. Principle components regression. Support vector machines (No
Numericals for this unit).
Unit-V: Markov chains. Hidden markov models. Viterbi algorithm, Parametric estimation for HMM's
(Baum-Welch and Viterbi training). EM algorithm. (Numerical problems only for Markov chains).
Recommended books:
1) W.Weber. (2008). Pharmacogenetics. Oxford University Press.
2) Biological sequence analysis, Durbin, Eddy, Krogh and Mitchison (1998) Cambridge University
Press.
3) Strachan and Read. (2004) Human Molecular Genetics 3, Garland Press.

Reference Books:
4) Ewens and Grant (2001) Statistical methods in bioinformatics: an introduction. Springer verlag.
5) D.A.P.Evans. (1994) Genetic factors in drug therapy: Clinical and molecular pharmacogenetics.
Cambridge University Press.

6) I.P.Hall and M.Pirmohamed. (2006). Pharmacogenetics. Informa healthcare.
7) K.Lange. Mathematical and statistical methods for genetic analysis. 2
nd
Ed. (2003) Springer.
8) Genetics. Hartl and J ones, J ones and Bartlett publishers (2005)
9) Introduction to quantitative genetics, Falconer and Mckay 4
th
Edition.
Reference for case study 1) Current science. Vol.86 #1 (2004)

MOLECULAR BIOLOGY AND GENETIC ENGINEERING
ELECTIVE
Unit-I:
Genome organization in prokaryotes and eukaryotes. Review of Replication. Epigenetic methods of
inheritance. Plasmids. Group I introns. Group II introns. LINEs and SINEs. Vectors for bacteria, yeast
and animal cells.
Case study: Homologous recombination in mycobacteria.
Unit-II:
Review of transcription and translation. Regulatory mechanisms. Posttranscriptional regulatory
mechanisms. SnRNPs. Spliceosome structure and function. Posttranslational regulatory mechanisms.
MicroRNAs. RNAi.
Case study: Transcriptional regulation in mycobacteria.
Unit-III:
Major signal transduction pathways and regulation of the Cell cycle. Transport mechanisms. Regulatory
mechanisms of metabolic and signal transduction pathways: feedback and feedforward controls.
Case study: Signal transduction systems of mycobacteria.
Unit-IV:
Methods: DNA sequencing by Sanger's method. High throughput DNA sequencing methods. Protein
sequencing by Edman degradation and by Mass spectrometry. Oligonucleotide synthesis. Solution phase
and solid phase peptide synthesis.
Unit-V:
Review of transformation, transduction and conjugation in bacteria. Restriction and ligation. Construction
and screening of libraries. Site-specific, casette mutagenesis and transposon based mutagenesis.
Introduction to PCR and microarray technology. Construction and screening of a subtractive cDNA
library.
Recommended books:
1. H.D. Watson, T.Baker, S.P.Bell, A.Gann, M.Levine, R.Losick. Molecular Biology of the gene.6
th
Ed.
(2007) Benjamin Cummings.
2. Alberts et al. Molecular biology of the cell. 4
th
Ed. (2002) Garland publishers.
3. Molecular cell biology. Lodish et al. 5
th
Ed. (2003) W.H.Freeman.
Reference:
4. Primrose and Twyman. Principles of gene manipulation and genomics. 7
th
Ed. (2006) Blackwell
publishers.
5. B.Lewin. Genes-IX. 9
th
Ed. (2007). J ones and Bartelett publishers.
6. B.K.Nunnaly. Analytical techniques in DNA sequencing. (2005). CRC Press.
7. Current Science. Vol.86#1. (2004)

INTRODUCTION TO BIOCHEMICAL ENGINEERING (Elective)

Code : EPRBT 122
Credits: 3 No. of hours: 3 per week

UNIT I : Fluid Mechanics : Properties of Fluids, Types of Fluids, Laminar and Turbulent Flow,
Basic equations of fluid flow: Conservation of mass, conservation of energy, Boundary Layer,
Hagen-Poiseuille equation, Flow through porous media, Fluidization.
(Chapter-4: Introduction to Chemical Engineering by S.K.Ghosal & S.K.Sanyal

UNIT-II: Conduction: Fouriers Law of Heat Conduction, Conduction through a composite plane
wall. Conduction through resistances in parallel. Convection: Definitions of Natural convection
and forced convection, individual heat transfer coefficients, correlations for calculation of heat
transfer coefficients, Heat Transfer with phase change, overall heat transfer coefficient, LMTD.
Radiation: Black body Radiation, Radiation from the sun. Heat Transfer Equipment: Double
Pipe Heat Exchanger. Shell and Tube Heat Exchanger, Extended Surface Heat Exchanger.
(Chapter-5: Introduction to Chemical Engineering by S.K.Ghosal & S.K.Sanyal)
(Note: Problems may come from conduction through a composite plane wall only)

UNIT-III: Diffusion: Ficks Law, Diffusivity of fluids, Steady State diffusion of fluids. Inter phase
Mass Transfer: Mass Transfer coefficient, relation between mass transfer coefficients, overall
mass transfer coefficient. Absorption: Choice of solvent for absorption, material balance for
counter current absorption process, HETP. Distillation: Concept of VLE, relative volatility,
concept of simple, flash, steam, fractional distillation, calculation of number of theoretical stages
by Mc-Cabe-Thiele method, plate efficiency. Liquid-Liquid Extraction: Liquid-Liquid
Equilibria, distribution coefficient, choice of solvent for extraction, material balance for single
stage extraction operation.
(Chapter-6: Introduction to Chemical Engineering by S.K.Ghosal & S.K.Sanyal)
(Note: Distillation problems may be given on Mc-Cabe- Thiele method only).

UNIT-IV: Chemical Reaction Engineering & Bioreactor Design: Kinetics of Homogeneous
reactions, single and multiple reactions. Elementary & Non elementary reactions; molecularity
and order of reactions; representation of reactions; testing kinetic models. Temperature-
dependent term of a rate equation (Chapter-2 of O.Levernspiel, 3e). Interpretation of Batch
Reactor Data: Constant Volume Batch Reactor; Integral Method of Analysis; Differential
variable Volume Batch Reactor (Chapter -3, O.Levernspiel, 3e). Simple problems based on the
three chapters. Single Ideal Reactors: Performance equations for batch reactors, Fed Batch
reactors, MFR and PFR (Chapter 5, O.Levernspiel, 3e).Basic Concept of Non-ideal Flow and
RTD.

UNIT-V: Material and Energy balances Stoichiometry. Batch and continuous sterilization of
media substrate utilization and product formation kinetics- Microbial kinetics, Bioreactor and
its accessories, types of bioreactors in brief Oxygen transfer in microbial systems, oxygen
demand, K
La
measurement Power requirement Monitoring of Bioprocess variables Product
Recovery Isolation, Purification, Crystallization and Drying One Case Study, Simple
problems based on the above.
Scope: As given in the book Introduction to Chemical Engineering by S.K.Ghosal &
S.K.Sanyal, Tata Mc Graw Hill Publishing House, New Delhi.

Text Books:
1. Introduction to Chemical Engineering by S.K.Ghosal & S.K.Sanyal, Tata Mc Graw Hill
Publishing House, New Delhi.
2. Chemical Reaction Engineering by Octave Levenspiel., 3
rd
edition. John Wiley. 1999

FERMENTATION AND CELL CULTURE


Unit-I:
Production of antibiotics using microbes. Production of penicillin and semisynthetic analogs of penicillin.
Production of streptomycin, insulin, human growth hormone. Use of humanized yeast for glycosylation.
Unit-II:
Pharmaceutical production using plant cell culture.
Unit-III:
Animal cell culture and its uses. The insect cell-baculovirus system. Production of haematopoeitic growth
factors, cytokines and interferons.
Unit-IV:
Transformed human cell lines and their applications. Embryonic Stemcells and adult stemcells and their
therapeutic applications.
Unit-V:
Metabolic engineering: Flux control analysis, Flux control coefficients, summation theorem, elasticity
coefficient, connectivity theorem. Scale up of fermentation processes: engineering and regulatory issues.
Textbooks:

1) Glazer and Nikaido. Microbial biotechnology: Fundamentals of Applied Microbiology. 2
nd
Ed. (2007)
2) S. Ozturk and Wei-shou Hu. Ed. Cell culture technology for pharmaceutical and cell-based therapies
(Biotechnology and Bioprocessing series). (2005) CRC.
3) M.El-Mansi, C.F.Bryce, A.L.Demain and A.R.Allman. Fermentation microbiology and
biotechnology. Taylor and Francis.

Reference:
4) V.A.Vinci and S.R.Parekh. Ed. Handbook of industrial cell culture: Mammalian, microbial and plant
cells. (2002). Humana Press.
5) Stephanopoulos. Metabolic engineering. (1998) Academic Press.

PHARMACOLOGY AND GENETIC ENGINEERING LABORATORY


Minimumof 10 experiments fromthe following:
Determination of clotting time and effect of anticoagulant on coagulation time.
Recording of systemic arterial blood pressure and effect of posture on blood pressure.
Determination of lung volumes and capacities.
Recording of 12 lead ECG.
Study of simple muscle twitch (SMT).
Study of fatigue in skeletal muscle.
MTT assay for cell viability
Scatchard plots.
Plasmid isolation and Restriction.
Ligation.
Transformation of E.coli.
Construction and screening of a cDNA library.
DNA sequencing.
Molecular weight determination by electrospray Mass spectrometry.
Peptide mapping of proteins.
Edman sequencing of polypeptide.
Polypeptide sequencing using Mass spectrometry.
PCR.
DNA arrays for gene expression.
Note: If equipment for conducting experiments is not available, data obtained fromdatabases or
simulation may be used.

Textbook:
Molecular cloning. Vol.I, II and III. Sambrook, Fritsch and Maniatis.

FERMENTATION AND CELL CULTURE LABORATORY


Production and isolation of penicillin.
Production and isolation of streptomycin.
Plant cell culture for production of medicinal compounds e.g. Quinine or vincristine and vinblastine.
Maintenance of human cell lines.
Production, isolation and characterization of monoclonal antibodies.

M.Tech Biotechnology 1
st
Semester
SEMINAR


nd
Semester

PHARMACOINFORMATICS

Code : EPRBT201

Unit-I: Edit distance. Similarity score matrices (PAM, BLOSUM).
Pairwise sequence alignment using dynamic programming Needleman-Wunsch algorithm for
global alignment, Smith-waterman algorithm for local alignment. Repeat matches. Pairwise
alignment with affine gap penalty functions. Linear space algorithms. Blast and Psi-blast.

Unit-II: Multiple sequence alignment: multidimensional dynamic programming, profile
alignment.
Hidden markov models: pairwise sequence alignment, profile HMMs for sequence families,
multiple sequence alignment by profile HMM tranining.
Prediction of RNA secondary structure: Nussinov folding algorithm, energy minimization and
Zuker folding algorithm, covariance models.

Unit-III: Molecular phylogenetics: introduction to binary trees. Phylogenetic tree construction
using weighted parsimony and neighbor-joining. Combined multiple sequence alignment and
phylogeny Sankoff and Cedergren method. Sequence graphs. Probabilistic models of
evolution Jukes cantor model and Kimura model. Using the likelihood for inference.

Unit-IV: Chemoinformatics: Pharmacology databases, structure databases, Molecular
descriptors. Molecular similarity. 2D substructure searching. 3D database searching.
Pharmacophore keys. SQL: Data definition, data manipulation and control statements.

Unit-V: Gene prediction frequentist approaches, model based approaches and similarity based
approaches. Genome assembly and annotation. Fragment assembly. Mapping, Interval graphs.
Comparative genomics: Genome alignment and Genome rearrangements. Sorting by reversals.
The breakpoint graph. Interleaving graphs and hurdles. Duality theorem for genomic distance.

Recommended books:

1) Biological sequence analysis. Durbin, Eddy, Krogh and Mitchison. (Cambridge University
Press). (For Units I,II and III)
2) Computational Molecular Biology: An algorithmic approach Pavel, A.Pevzner. (PHI) (for
Unit V)

Reference books:

3) Molecular modeling, Principles and applications, Andrew R. Leach, 2
nd
Ed.(2007) Prentice
Hall (Unit IV)
4) Bioinformatics, D.Mount (Unit V)
5) Database Management systems: C.J.Date (Unit IV)
A practical guide to the analysis of gene and proteins. Baxevanis. 3
rd
Ed. (2005) Wiley, (Unit IV
and Unit V)
nd
Semester
PROTEOMICS AND GENOMICS FOR TARGET IDENTIFICATION
Code : EPRBT 202
Unit-I: Protein expression profiles. Brief description of methods for generating protein expression
profiles: 2D gel-electrophoresis, 2D LCMS and 2D Mass-spectrometry. Analysis of data from2DGE
experiments.
Analysis of data fromMass spectrometry: Peptide sequencing using mass spectrometry -spectrum graphs.
MS for protein identification via database search. Spectral convolution. Spectral alignment.
Unit-II: Protein function: Use of sequence patterns, motifs and profiles. Pattern representation methods:
consensus, regular expressions, profiles.
Protein protein interactions: Methods (phage display, yeast two-hybrid technique, protein arrays) and
Tools for analysis of protein-protein interaction.
Unit-III: Gene and Genome sequencing strategies. DNA sequencing overlap, layout and consensus.
Functional genomics. Differential display of alterations in gene expression. Serial analysis of gene
expression. Identification of clinically relevant biomarkers using Metabonomics.
Unit-IV: Marker genes and polymorphismat the genomic level. DNA Microarrays for detecting SNPs.
Algorithmic approaches to clustering gene expression data. Components of phenotypic variance.
Unit-V: Modeling of metabolic pathways. Modeling of signal transduction pathways and Gene networks.
Algorithms for inference of gene regulatory networks.

Recommended books:

1. Charles R. Cantor, Cassandra L.Smith (1999) Genomics: the science and technology behind the
human genome project. J ohn wiley and sons (asia) pvt. ltd. Singapore.
2. Kohane, IS., Kho, A and Butte, A.J . 2002. Microarrays for an integrative genomics. Barnes and
Nobles, MIT press.
3. T.A.Brown. Genomes. 2
nd
edition. Bios scientific. 2002.
4. S.R.Pennington and M.J .Dunn. Proteomics. Viva books. New delhi, 2002.
5. Villas-Boas. Neilsen. Smedgard. Hansen, Roessner-Tunali. Metabolome analysis an
introduction.
6. Hiroaki kitano. Foundations of sytem sbiology. Mit press. (2001)
7. Bioinformatics. D.Mount.
8. Functional genomics. A practical approach. S.P.Hunt and R.Livesey. (IK Publishers). 2004.
9. Primrose and Twyman. Principles of gene manipulation and genomics. 7
th
Ed.(2006) Blackwell
publishers.

nd
Semester
SCREENING AND TARGET VALIDATION
Code : EPRBT 203
Unit-I: Experimental methods for binding studies: ELISA. SPR. Use of linear and non-linear
Scatchard plots for studies of ligand-receptor binding. The Hill plot.

Unit-II: NMR. Chemical shifts, chemical exchange and relaxation. Use of NMR for structure
determination of small molecules application of chemical shift, J -coupling and relative areas.
The Nuclear Overhauser effect. 2D and 3D NMR spectroscopy principles. Structure
determination of macromolecules and complexes. Determination of binding sites for weakly
interacting ligands. Screening by NMR. Principles of MRI.

Unit-III: X-ray crystallography for target and lead characterization. . Small molecule structure
determination using direct methods. Phase determination of large molecules using MIR, MAD
and molecular replacement. The Laue method.
Introduction to metabolic profiling. Experimental methods for Metabolic flux analysis.

Unit-IV: Combinatorial chemistry: Principles of combinatorial synthesis. Design of
combinatorial libraries. Measures of diversity of a combinatorial library. Characterization of
combinatorial libraries. High throughput screening. High throughput screening for lead
discovery. Tools for high throughput screening. Assay technologies.

Unit V: Uses of comparative genomics; Gene expression profiling for target validation. Gene
knockouts, Gene traps and gene knockdown in mice for target validation. Animal models for
important therapeutic areas.

Textbooks:
1) Biophysical Chemistry , Cantor and Schimmel (Unit-I and Unit-III)
2) R.Mannhold, H.Kubinyi, G.Folkers. High-throughput screening in drug discovery in
Methods and Principles in Medicinal Chemistry (2006). Wiley-VCH (Unit IV)
3) O.Zerbe, R.Mannhold, H.Kubinyi and G.Folkers. BioNMR in drug research. Methods and
principles in medicinal chemistry. Vol. 16. (2006). Wiley-VCH. (Unit II)

Reference:

4) B.W.Metcalf and S.Dillon. Target validation in drug discovery.(2006) Academic Press.
5) Burgers Medicinal Chemistry, 6
th
Edition, Vol.I and II (Unit-I, II, III,IV)
6) Villas-Boas. Neilsen. Smedgard. Hansen, Roessner-Tunali. Metabolome analysis an
introduction (Unit III)
7) I. Pelczer. NMR in Ligand screening: Theory, methods and applications. (2006). Oxford
University Press.
8) N. Beckmann. In vivo MR techniques in drug discovery and development. (2006). Informa
healthcare.
9) Primrose and Twyman. Principles of gene manipulation and genomics. 7
th
Ed.(2006)
Blackwell publishers. (Unit V)
10) Model Organisms in Drug Discovery by Pamela M.Carroll and Kevin Fitzgerald (2003)
(Unit V)
11) D.Leon and S.Markel. Insilico strategies in drug target identification and validation.(2006).
Drug discoveries series. CRC.
nd
Semester
BIOLOGICAL PROGRAMMING: BIOPERL, JAVA AND BIOJAVA
Code : EPRBT 204

Unit-I: Perl : Variables, operators and functions. Regular expressions. Pattern matching. Data
structures. Arrays. Modules. Example programmes : Program to find restriction sites, Program to
convert genbank format file to Fasta format.

Unit-II: Bioperl : Bio::SeqIO class. Features and location classes. Alignment analysis with
blast and genscan. Database classes. Connecting to Databases. Example programmes : Translate
given DNA sequence to predict possible polypeptides using BIOPERL, Program to convert
genbank format file to Fasta format using BIOPERL.

Unit-III: Java: Objects and Classes. Classes declaration, Use of Math function, Java Structure,
Constants, Variables and Data Types, Decision making and Branching, Classes, Objects and
Methods.

Unit-IV: Applet Programming, Java applets. Graphics. Fonts. color. animation. Graphics
programming, Managing Input/Output files in Java.

Unit-V: BioJava: Alphabets and symbols, Basic sequence manipulation, Translation,
Proteomics, Sequence I/O, Annotations, Locations and features, Protein alignments, Genetic
algorithms, Protein structure. Example Programmes: Write a Biojava program to get all the
Alphabets, DNA symbols and Protein symbols, How do I make a Cross Product Alphabet ?
Explain with a Biojava program.

Recommended books:

1. James D. Tisdall (2001) Beginning Perl for Bioinformatics. Oreilly and Associates
2. Cynthia Gibas and Per Jambeck (2000) developing bioinformatics computer skills.
Oreilly and Associates.
3. Rex A Dwyer. Genomic perl. Cambridge University Press.
4. Programming Perl by Larry Wall, Tom Christianson, Jon Orwant. Oreilly.
5. Programming with Java A premier by Balaguruswamy, Tata Mc Graw Hill, New Delhi.
6. Java for Bioinformatics and Biomedical appliations. H.Bal & J.Hujal(2006) Springer.

nd
Semester
REGULATORY ISSUES IN DRUG DESIGN AND DEVELOPMENT

Unit I: Quality control: GMP. Purity determination as per ICH guidelines.
Unit II: Intellectual Property: Concepts and Fundamentals
Mechanisms for protection of Intellectual Property- patents, copyright, trademark; factors affecting choice
of IP protection; penalties for violation, Role of IP in Pharma Industry.
Trade related aspects of Intellectual Property Rights: Intellectual Property and International Trade:
Concepts behind WTO (World Trade Organization),WIPO (World Intellectual Property Organization)
GATT (General Agreement on Tariff and Trade), TRIPs (Trade Related Intellectual Property Rights),
TRIMS (Trade Related Investment Measures) and GATS (General Agreement on Trade in Services);
Protection of plant and animal genetic resources; biological materials; gene patenting. Case studies and
examples.
Unit III:
Nuts and Bolts of patenting, copyright and trademark protection: Criteria for patentability, types of
patents; Indian Patent Act, 1970. Filing of a patent application: Precautions before patenting-
disclosure/non-disclosure, publication-article/thesis; Prior art search- published patents, internet search,
patent sites, specialized services- search requests, costs; Patent Application- Forms and guidelines, fee
structure, time frames, jurisdiction aspects. Types of patent applications- provisional, non-provisional,
PCT and convention patent applications; International Patenting- Requirements, procedures and costs;
Publication of Patents; Patent Annuity; rights and responsibilities of a patentee. Patent infringement.
Case studies: Drug related patents and infringements.
Unit-IV:
Patenting by research students, lecturers and scientists- University/organizational rules. Thesis,
Research Paper Publication, credit sharing by workers, financial incentives; Useful information
sources for patents related information.
Significance of copyright protection for researchers; Indian Copyright Law and digital
technologies- Berne convention, WIPO copyright treaty (WCT), WIPO performance and
Phonograms Treaty (WPPT); Protection for computer databases, multimedia works; Trademarks
legislation and registration system. Meaning of trademark, criteria for eligibility. Trade secrets-
scope, modalities and protection.

Unit V:
Technology Development/Transfer/Commercialization related aspects: Drug related
technology development. Toxicological studies, Bioequivalence (BU), Clinical Trials-Phase
1,Phase II and Phase III. Approved Bodies and Agencies. Scale-up, semi-commercialization and
commercialization.
Managing technology transfer (TOT). Compulsory Licensing, access to medicine issues; DOHA
declaration, POST WTO Product Patent Regime from 2005.
Drug Registration and Licensing Issues. Drug Master file submissions, SOPS; Funding sources for
commercialization of Technology: Preparation of a project report, financial appraisal. Business models.
Case Study : Antiretroviral drugs.
Textbooks:
1) The Generic Challenge: Understanding Patents, FDA and pharmaceutical life-cycle management by
M.A.Voet
2) Biotechnology and Pharmaceutial Patents: Law and Practice by Marc S. Gross, S. Peter Ludwig,
Robert C., Jr. Sullivan

nd
Semester

PHARMACOINFORMATICS LABORATORY

Code : EPRBT 211

Use any available software for the following experiments:
Sequence alignment using Needleman-Wunsch method.
Sequence alignment using Smith-Waterman method.
Effect of scoring matrices and gap penalties on sequence alignment.
Multiple sequence alignment.
Use of HMM profiles.
Phylogenetic tree construction using parsimony.
Phylogenetic tree construction using UPGMA.
Phylogenetic tree construction using neighbor joining.
Displaying phylogenetic information
RNA secondary structure prediction.
Microarray data analysis.
Use of SQL: Database design for biological data. Data manipulation. Queries, views and forms.
Databases:
Primary and Secondary Sequence and Structure databases: Organization of data, contents and formats of
database entries for major databases. Retrieval of data using text-based search tools.
Metabolic pathways and Signal transduction pathways databases.
Bioinformatics resources at the species level.
Introduction to databases for proteomics.
Pharmacology databases.
Servers:
Use of servers for literature search, sequence search, multiple sequence alignment, motif finding, gene
prediction, genomic analysis, secondary structure prediction.

nd
Semester
BIOLOGICAL PROGRAMMING LABORATORY
Code : EPRBT 212
Use Perl/Bioperl:
1. To convert sequence information between different formats.
2. To predict possible translations for a polynucleotide sequence.
3. For sequence alignment and
4. To create and access a local database.

Use Python/Biopython to display molecular structure.
Use of BioJ ava. To create web-interface.
Write a programto implement:
Dynamic programming for sequence alignment Needleman-Wunsch algorithm
Dynamic programming for sequence alignment Smith-Waterman algorithm.
Phylogenetic tree construction using parsimony
Phylogenetic tree construction using neighbor joining.
Displaying phylogenetic information
Gene prediction.
Fragment assembly.

nd
Semester
SEMINAR


rd
semester
MOLECULAR MODELING AND LEAD OPTIMIZATION


Unit-I:
Quantum chemistry for Modeling of small molecules: Variation method and Time independent
Perturbation theory. Ab initio methods for molecules: Hartree-Fock SCF method. Introduction to UHF,
electron correlation, CI and density functional theory.
Introduction to semi-empirical methods: Huckel molecular orbital theory. Pariser-Parr-Pople method.
CNDO, AM1 and PM3.
Unit-II:
Force fields for molecular modeling. Free energy calculations. Potentials of mean force. Molecular
surface area and solvent accessible surface area. Solvation models explicit water models, continuum
models. Structure functions studies of the G-protein coupled receptors with emphasis on adrenergic
receptor.
Unit-III:
Conformational analysis: Geometry optimization using steepest descent and conjugate gradients.
Distance geometry. Monte-carlo simulation. Molecular dynamics and simulated annealing.
Prediction of transmembrane segments in membrane proteins.
Protein 3D structure prediction: Comparative modeling. Threading and Fold prediction. Methods based
on minimization of energy.
Unit-IV:
Ligand based drug design: SAR, QSAR and 3D-QSAR. Partial least squares and Molecular field
analysis (COMFA). 3D-pharmacophores. Deriving 3D pharmacophores (Constrained systematic search,
Ensemble distance geometry, Ensemble molecular dynamics, genetic algorithms, clique detection,
maximumlikelihood).
Unit-V:
Receptor based drug design: Computational methods for identification of plausible binding sites.
Molecular Docking (rigid body and flexible docking). Receptor based de novo ligand design.

Recommended books:
1) Molecular modelling. Principles and applications. - Andrew R. Leach. 2
nd
Ed. (2007). Prentice Hall.
2) Structural Bioinformatics. Ed. P.E. Bourne and H.Weissig. (2003). Wiley-liss.
3) Molecular quantummechanics. P. Atkins and R. Friedman. 4
th
Ed. (2005). Oxford University Press.
4) Poul Krogsgaard-Larsen et al. (2002) Textbook of drug design and discovery. Taylor and Francis
publishers.

rd
semester
MODELING AND SIMULATION OF DRUG MANUFACTURING PROCESSES


Unit-I:
Mathematical modeling. Compartmental models. Models with memory. Models with time delay.
Parameter estimation. Model validation. Modelling of dynamical systems. Stability of dynamical
systems. Simulation.
Unit-II:
Modeling of Unit processes used in bulk drug manufacture: Introduction.
Unit-III:
Tablet manufacture: Machine theory, design and process troubleshooting of tablet compression. Modeling
and simulation of granulation scale-up. Modeling and simulation of coating. Packaging techniques
modeling and simulation..
Unit-IV:
Pilot plant design. Fermenter design calculations. Pilot plant operation (simulations).
Downstream processing calculations. Environmental assessment and Economic assessment.

Unit-V:
Scale-up of solid dosage forms. Plant design calculations for the Penicillin production system.
Introduction to Good manufacturing practices (GMP).

Textbooks:

1. Leon Lachman et al Theory and practice of industrial pharmacy. 3
rd
edition. Lea and
Febiger, 1986.
2. Encyclopedia of Pharmaceutical Technology. 3
rd
edition. (2006). Informa Healthcare.
3. Good manufacturing practices for pharmaceuticals. 6
th
edition.(Drugs and pharmaceutical
sciences. (2006). Informa Healthcare.

rd
Semester
MOLECULAR MODELING LABORATORY


Generating 3D representations from2D descriptions of small molecules.
Use of molecular mechanics for geometry optimization of a small molecule.
Evaluate energy of a small molecule using CNDO/MINDO/MNDO/AM1/PM3
Evaluate energy of a small molecule using ab initio QM with 631G basis set.
Calculate solvent accessible surface area.
Polypeptide conformational analysis using monte-carlo and molecular dynamics methods.
Secondary structure prediction. Servers: PHD, PSIPRED
Prediction of transmembrane helices.
Comparative modeling of a small protein.
Docking of a polypeptide ligand into a protein.
QSAR.
3D-QSAR.
CoMFA.
SXRs for ADMET.

rd
Semester
MODELING AND SIMULATION LABORATORY


Modelling of dynamical systems. Parameter estimation. Simulation. Stability of dynamical systems.
Modeling of metabolic pathways. Comparison of metabolic pathways.
Modeling of signal transduction pathways and networks.
Whole cell simulations.
Representation of signal transduction pathways using Systems biology markup language.
Ease of formulation.

Modeling and simulation of bioprocesses:
Biotransformation of drugs, microsomal and non-microsomal mechanisms.
Factors influencing enzyme induction and inhibition.

Modeling and simulation of unit operations used in bulk drug manufacture.

rd
Semester
PROJECT


th
Semester
PROJECT


Pedagogy:

The teaching-learning method for UG and PG programmes includes (a) Lecturing: Conventional
(b) Interactive session Discussion teaching and (c) Audio-visual methods. In-class student
collaboration within the classroom increases students critical thinking skills and has positive
effects on student achievement, persistency and attitudes. Teacher-student interactive sessions
improves the conceptual ideas which promote augmentative innovativeness in students.

Evaluation:

The assessment of the students performance in each course will be based on continuous internal
evaluation through mid semester examinations, quizzes, assignments & attendance (40%) and
semester end examinations (60%) with high level of transparency.

Student feedback:

Evaluation of the teachers by students is also carried out at the end of each semester. The data
obtained are analyzed and the teachers scoring lower levels are advised to adopt remedial
measures.

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