GANDHI INSTITUTE OF TECHNOLOGY AND MANAGEMENT

(GITAM)
(Deemed to be University, Estd. u/s 3 of UGC Act 1956)
VISAKHAPATNAM HYDERABAD BENGALURU
Accredited by NAAC with A Grade

REGULATIONS & SYLLABUS

Of

Master of Technology
in

Biotechnology
(Drug Design and Development)
Programme Code: EPRBT201001
(W.e.f 2012-13 admitted batch)

Website: www.gitam.edu

M.Tech. Biotechnology
(Drug Design and Development)
REGULATIONS
Programme Code: EPRBT201001

(w.e.f. 2012-13 admitted batch)

1.0

ADMISSIONS
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:
Score obtained in GAT (PG), if conducted.
Performance in Qualifying Examination / Interview.
The actual weightage is 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)
(ii)
(iii)

3.2

A core programme imparting to the student specialization of

engineering branch concerned.
Separate remedial courses may be prescribed for engineering & science
students.
Carry out a technical project approved by the Department and submit a
report.

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
4.0

Project Dissertation has to be submitted by each student individually.

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 shall be

based on continuous evaluation and semester-end examination. The
marks for each component of assessment are as shown in the Table 1.

Table 1: Assessment Procedure

S.
No.

Component of
Assessment

Marks
Allotted

Type of
Assessment

Scheme of Examination/Evaluation
i)

40
1

Theory

ii)
60

Total

Practicals

Continuous
Evaluation

Semester-end
Examination

Sixty (60) marks for Semester-end examinations

100

100

Continuous
Evaluation

i)

Fifty (50) marks for regularity and performance, records

and oral presentations in the laboratory. Weightage for
each component shall be announced at the beginning of
the Semester.

ii)

Ten (10) marks for case studies.

iii)

Forty (40) marks for two tests of 20 marks each

(one at the mid-term and the other towards the end of the
Semester) conducted by the concerned lab Teacher.
Forty (40) marks for periodic evaluation on originality,
innovation, sincerity and progress of the work, assessed
by the Project Supervisor.
Thirty (30) marks for mid-term evaluation for defending
the Project, before a panel of examiners*.
Thirty (30) marks for final Report presentation and Vivavoce, by a panel of examiners*

i)

Project work
(Interim
evaluation III
semester )

Thirty (30) marks for mid Semester examinations. Three

mid examinations shall be conducted for
15 marks
each; performance in best two shall be taken into
consideration.
Ten (10) marks for Quizzes, Assignments and
Presentations.

100

Continuous
Evaluation

ii)
iii)
i)

50

Continuous
Evaluation

50

Semester-end
Examination

Fifty (50) marks for final Report presentation and

Viva-voce assessed by external examiners.

100

Continuous
Evaluation

Through five periodic Viva-voce exams for

20 marks each, conducted by a panel of examiners*.
The course content for Viva exams shall be announced at
the beginning of the Semester.

Project work
(Final evaluation
IV semester )

Comprehensive
Viva

Twenty (20) for periodic evaluation on originality,

innovation, sincerity and progress of the work, assessed
by the Project Supervisor.
ii) Fifteen (15) marks for mid-term evaluation for defending
the Project, before a panel of examiners*.
iii) Fifteen (15) marks for interim Report presentation and
Viva-voce.

*Panel of Examiners shall be appointed by the concerned Head of the Department.

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

10.0

11.0

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.

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.

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 2.

Table 2: Grades & Grade Points

11.2

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
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.

11.3

Marks for project work and for electives taught by different teachers, will
be examined, and scaling may be applied if necessary.

11.4

No credits will be awarded for remedial courses and free-electives. If the

student manages to secure more than 50% marks for any of the freeelectives, an S grade (satisfactory) will be awarded, otherwise a U grade
(unsatisfactory) will be awarded.

12.0 GRADE POINT AVERAGE

12.1

A Grade Point Average (GPA) for the semester will be calculated

according to the formula:
[Cx G]
GPA = ---------------C
Where
C = number of credits for the course,
G = grade points obtained by the student in the course.

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 3.

Table 3: 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.
e) Following is applicable to students admitted to M.Tech. (Biotechnology)
course without a B.Tech. (Biotechnology) degree:

Successfully completed additional remedial courses at B.Tech. Level

prescribed by BOS.
Additional remedial courses may be prescribed by the Board of Studies for
students who do not have a B.Tech. (Biotechnology) degree based on
examination of their syllabus.
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.

M.Tech. (Biotechnology) - Scheme of Instruction

Course Code

EPRBT 101
EPRBT 102
EPRBT 103
EPRBT 104
EPRBT 121
EPRBT 122
EPRBT 123
EPRBT 124
EPRBT 125
EPRBT 126
EPRBT 127
EPRBT 111
EPRBT 112
EPRBT 113

EPRBT 201
EPRBT 202
EPRBT 203
EPRBT 204
EPRBT 221
EPRBT 222
EPRBT 223
EPRBT 211
EPRBT 212
EPRBT 213

EPRBT 301
EPRBT 302
EPRBT 311
EPRBT 312
EPRBT 313
EPRBT 314

EPRBT 411

Name of the Course

Semester 1
Regulatory issues in drug design and
development
Physiology and Pharmacology
Advanced genetics and genetic engineering
Fermentation and cell culture
Remedial courses:
Molecular biology and genetic engineering*
Introduction to biochemical engineering*
Applicable mathematics*
Research Methodology *
Protein Chemistry*
Free Elective
Nanobiotechnology
Bioelectronics
Pharmacology and genetic engineering lab
Fermentation and cell culture lab
Seminar
Total
Semester 2
Pharmacoinformatics
Proteomics and genomics for target
identification
Screening and target validation
Biological programming
Elective
Advanced Instrumental methods of analysis
Molecular Diagnostics
Tissue engineering
Pharmacoinformatics lab
Biological Programming Lab
Seminar
Total
Semester 3
Molecular modeling and lead optimization
Modeling and simulation of drug
manufacturing process
Molecular modeling lab
Modeling and simulation lab
Project
Industrial Training Report
Total

Instruction hours

Maximum marks

Credit
s

Total

Cont

Sem

Total

40

60

100

3
3
3

3
3
3

40
40
40
40

60
60
60
60

100
100
100
100

3
3
3
-

3
6
6
3
3
3

3
6
6
3
3
3

100

--

100

6
6
-

6
6
3
30

100
100
100

----

100
100
100

2
2
3
19

3
3

3
3

40
40

60
60

100
100

3
3

3
3
3

3
3
3

40
40
40

60
60
60

100
100
100

3
3
3

6
6
-

6
6
3
30

100
100
100

----

100
100
100

2
2
3
22

3
3

3
3

40
40

60
60

100
100

3
3

6
6
-

6
6
15

100
100
100
100

-----

100
100
100
100

2
2
10
2
22

50

50

100

20
20

33

Semester 4
Project
Total

Grand Total

35
35

83

M.Tech. Biotechnology I SEMESTER

REGULATORY ISSUES IN DRUG DESIGN AND DEVELOPMENT
Course Code
Credits : 3

: EPRBT 101
Hours: 3 per week

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 ApplicationForms 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
scientistsUniversity/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),
9

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.
Text books:
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

10

M.Tech. Biotechnology I SEMESTER

PHYSIOLOGY AND PHARMACOLOGY
Code : EPRBT 102

Credits : 3

No. of hours: 3 per week

UNIT-I
Pharmacokinetics: Mechanisms, factors affecting and kinetics of
Absorption, Distribution, Metabolism (hepatic clearance) and elimination
(renal clearance) of drugs. Binding, Potency, efficacy, therapeutic index,
margin of safety, dose optimization. Formulation of therapeutics (small
molecule and biologicals). Toxicity. Concept of Adverse drug reactions and
drug interactions. Drug transporters in drug disposition, interaction and
resistance.
UNIT-II
Computational Approaches in Phamacokinetics :Bioequivalence and
bioavailability studies. Estimation of pharmacokinetic parameters. WagnerNelson calculation of bioavailability and Assessment of bioavailability,
Physiology-Based Pharmacokinetic (PBPK) Modelling.
UNIT-III
Physiology, common diseases, drugs, targets and modes of action of drugs of
the nervous system. Physiology, common diseases, drugs, targets and modes
of action of drugs of the musculoskeletal systems. Physiology, common
diseases, drugs, targets and modes of action of drugs of the endocrine,
gastroenteric and excretory systems.
UNIT-IV
Physiology, common diseases, drugs, targets and modes of action of drugs of
the cardiovascular and respiratory system. Physiology, common diseases,
drugs, targets and modes of action of drugs of the immune system.
UNIT-V
Molecular basis of cancer. Tumor pathology, classification and treatment of
cancers. Targets and modes of action of major anti-cancer drugs. Drugs and
targets for the infectious diseases: Tuberculosis and Malaria.
Textbooks:
1. Textbook of physiology by Guyton
2. Brody's Human pharmacology: Molecular to clinical by K.P.Minneman
(2004)
3. Pharmacology by Satoshkar and Bandarkar
11

Reference books:
1. Clinical Pharmacokinetics: Concepts and Applications, M.Rowland and
T.N. Tozer, 3rd edition, Lea and Febiger, Philadelphia, 1995.
2. Pharmacokinetics and Pharmacodynamics of Biotech Drugs: Principles and
Case Studies in Drug Development - Edited by Bernd Meibohm, WILEYVCH Verlag GmbH & Co. KGaA, Weinheim, Germany 2006.
3. Basic Clinical Pharmacokinetics, Michael Winter, 4th edition, Lippincott,
Williams&Wilkins, Philadelphia, 2004.
4. Applied Biopharmaceutics and Pharmacokinetics, L. Shargel and A.B.C.
Yu, 5th edition, Appleton and Lange, Norwalk, CT, 2005.
5. Drug metabolism in drug design and development. Zhang, Zhu and
Humphreys. (2007) Wiley-Interscience.
6. Introduction to drug metabolism. Gibson and P. Skett. 3 rd Ed. (2001).
Nelson Thornes.
7. Reviews of Medical Physiology by W.F.Ganong
8. Pharmacology by Rang and Dale.
9. Medical microbiology. 24th Edition (Jawetz, Melnick and Adelberg's
Medical Microbiology) by Geo. F. Brooks. (2007)

12

M.Tech. Biotechnology I SEMESTER

ADVANCED GENETICS AND GENETIC ENGINEERING
Code : EPRBT 103

Credits : 3

No. of hours: 3 per week

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 disequilibrium and Association
mapping.
UNIT-III
Multifactorial inheritance. Heritability. Twin studies in pharmacogenetics.
Interval mapping. Polygenic models. Haplotyping.
UNIT-IV
Genetic engineering for gene therapy: Therapeutic nucleic acids.
Therapeutic genes used in clinical trials. Gene knockout and knockin. RNAi.
Methods for gene delivery. Viral vectors (Gammaretroviruses, lentiviruses,
adenoviruses, adeno-associated viruses, herpes simplex virus).
UNIT-V
Gene therapy: Gene therapy for immune system diseases. Gene therapy of
neurodegenerative diseases (Alzheimer's, Parkinson's, Huntington's and
ALS). Gene therapy of eye diseases. Gene therapy of cardiovascular
diseases. Gene therapy for cancer.
Text books:
1. J.W.Larrick and K.W.Burck. Gene therapy: applications of molecular
biology. Elsevier. 1991.
2. J-M. H. Vos. Viruses in gene therapy. Chaptman and Hall. 1995.
3. W.Weber. (2008). Pharmacogenetics. Oxford University Press.
4. Strachan and Read. (2004) Human Molecular Genetics 3, Garland Press.
Reference Books:
1. D.A.P.Evans. (1994) Genetic factors in drug therapy: Clinical and molecular
pharmacogenetics. Cambridge University Press.
13

2. I.P.Hall and M.Pirmohamed. (2006). Pharmacogenetics. Informa healthcare.

3. K.Lange. Mathematical and statistical methods for genetic analysis. 2 nd Ed.
(2003) Springer.
4. M. Giacca. Gene therapy. 2010. Springer.
5. KK Hunt, SA Vorburger and SG Swisher. Gene therapy for cancer. Humana
press (2007).
6. Genetics. Hartl and Jones, Jones and Bartlett publishers (2005)
7. Introduction to quantitative genetics, Falconer and Mckay 4th Edition.
8. Reference for case study 1) Current science. Vol.86 #1 (2004)

14

M.Tech. Biotechnology I SEMESTER

FERMENTATION AND CELL CULTURE
Course Code: EPRBT 104

Credits : 3

Hours: 3 per week

UNIT-I
Metabolic engineering: Flux control analysis, Flux control coefficients,
summation theorem, elasticity coefficient, connectivity theorem.
Genetic engineering: Genetically engineered microbes for production of
antibiotics. Production of penicillin and semisynthetic analogs of penicillin.
Production of insulin and insulin analogs. Use of humanized yeast for
glycosylation.
UNIT-II
Pharmaceutical production using plant cell culture: Production of Digoxin
from cultured cells of Digitalis lanata. Production of Shikonin from cultured
cells of Lithospermum erythrorhizon.
Biopharming: Agrobacterium mediated genetic engineering for production of
biopharmaceuticals from plants.
Engineered viral vectors for
biopharmaceutical production. Hirudin production from Brassica napus.
Edible vaccines from transgenic banana plants.
UNIT-III
Animal cell culture and its applications. Equipment and media for animal cell
culture. The insect cell-baculovirus system. Production of haematopoeitic
growth factors (thrombopoeitin and GCSF (lenograstim)), cytokines (IL2, interferon), and cytokine inhibitors (TNF inhibitors: infliximab,
adalimumab, etanercept).
UNIT-IV
Types of cell lines. Transformed human cell lines and their applications.
Embryonic stem cells and adult stem cells (hematopoietic stem cells,
neuronal stem cells) and their therapeutic applications. Organ culture of
skin.
UNIT-V
Engineering and regulatory issues in the scale up of fermentation processes:
Scale-up of manufacturing involving hazardous microbes disinfection and
inactivation procedures. Verification of inactivation process at scale.
Security of stock cultures. NIH guidelines for minimum containment
requirements for different risk level agents. Regulations for biosafety related
to production of bioprocess-based pharmaceuticals.
15

Textbooks:
Glazer and Nikaido. Microbial biotechnology: Fundamentals of Applied
Microbiology. 2nd Ed. (2007)
S. Ozturk and Wei-shou Hu. Ed. Cell culture technology for pharmaceutical
and cell-based therapies (Biotechnology and Bioprocessing series). (2005)
CRC.
Biological safety: principles and practices. By Diane O. Fleming, Debra Long
Hunt. Chapter 34. Biosafety in the pharmaceutical industry. ASM Press.2000.
(For Unit-V)
References:
1. M.El-Mansi, C.F.Bryce, A.L.Demain and A.R.Allman.
Fermentation
microbiology and biotechnology. Taylor and Francis.
2. V.A.Vinci and S.R.Parekh. Ed.
Handbook of industrial cell culture:
Mammalian, microbial and plant cells. (2002). Humana Press.
3. Stephanopoulos. Metabolic engineering. (1998) Academic Press. (Unit-I)
4. Andrian Slater. Nigel W.Scott. Plant biotechnology: The genetic manipulation
of plants. (2006) 2nd Edn. Oxford press.
5. D. Balasubramanian, CFA Bryce, K.Dhamalingam, J.Green and Kunthala
Jayaraman Concepts in Biotechnology Revise edition Universities press

16

M.Tech. Biotechnology I SEMESTER

MOLECULAR BIOLOGY AND GENETIC ENGINEERING
Course Code : EPRBT 121

Credits : 0

Hours: 3 per week

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. Sitespecific, casette mutagenesis and transposon based mutagenesis. Introduction
to PCR and microarray technology. Construction and screening of a
subtractive cDNA library.
Text books:
1. H.D. Watson, T.Baker, S.P.Bell, A.Gann, M.Levine, R.Losick. Molecular Biology of
the gene.6th Ed. (2007) Benjamin Cummings.
2. Alberts et al. Molecular biology of the cell. 4th Ed. (2002) Garland publishers.
3. Molecular cell biology. Lodish et al. 5th Ed. (2003) W.H.Freeman.
References:
1. Primrose and Twyman. Principles of gene manipulation and genomics. 7th Ed. (2006)
Blackwell publishers.
2. B.Lewin. Genes-IX. 9th Ed. (2007). Jones and Bartelett publishers.
3. B.K.Nunnaly. Analytical techniques in DNA sequencing. (2005). CRC Press.
4. Current Science. Vol.86#1. (2004)

17

M.Tech. Biotechnology I SEMESTER

INTRODUCTION TO BIOCHEMICAL ENGINEERING
Code : EPRBT 122

Credits: 0

No. of hours: 6 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. LiquidLiquid 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).
18

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.Levenspiel, 3e). Interpretation of Batch Reactor
Data: Constant Volume Batch Reactor; Integral Method of Analysis;
Differential variable Volume Batch Reactor (Chapter -3, O.Levenspiel, 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.Levenspiel, 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 kineticsMicrobial kinetics, Bioreactor and its accessories, types of bioreactors in
brief Oxygen transfer in microbial systems, oxygen demand, KLa
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., 3rd edition. John
Wiley. 1999

19

M.Tech. Biotechnology I SEMESTER

APPLICABLE MATHEMATICS
Course Code: EPRBT 123 Credits : 0
Hours: 6 per week
UNIT-I
Solving simultaneous linear equations in 2 and 3 variables using matrix
inverse method and Cramers rule. Eigen values and eigenvectors of
matrices. Sums and products of trigonometric functions. Equation of line
and plane in three dimensions.
UNIT II
Differential and Integral Calculus: Methods of differentiation. Elementary
methods of integration.
Partial differentiation: Partial derivative and total derivative of functions of
more than one variable. Euler's theorem. Cartesian, cylindrical and spherical
coordinate systems and transformation rules.
Vector Calculus: Properties of Gradient, divergence and curl. Line integrals.
Area, surface and volume.
UNIT III
Representation of a complex number. Modulus and amplitude of a complex
number.
Cauchy's integral formula. Residue theorem and contour
integration.
Ordinary Differential equations: Solution of differential equations of first
order and first degree using the method of separation of variables. Brief
description of other methods of solving first order differential equations (no
numericals). Simultaneous linear equations with constant coefficients.
Cauchy's and Legendre's linear equations.
UNIT- IV
Partial differential equations: The Laplacian in cartesian and cylindrical
coordinates. Poisson's equation. Taylor series (statement only, no proof or
numericals). Elementary properties of Fourier series and Fourier transforms.
Laplace transformation of elementary functions, derivatives and integrals.
Convolution theorem. Applications to solution of ordinary differential
equations and simultaneous linear differential equations with constant
coefficients.
UNIT V
Introduction to Univariate (normal, poisson and extreme value distributions)
and multivariate distributions. ANOVA, Regression analysis. Linear
discriminant analysis. Principle components analysis. Partial least squares.
20

Principle components regression. Support vector machines (No Numericals

for this unit). 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).
Text Books:
1. E. Kreyszig. Advanced engineering mathematics. (Units-III,IV & V)
2. Higher Engineering Mathematics by Dr.B.S.Grewal. (Unit-I & II)
3. Intermediate Mathematics Volume I & II (Unit I, V.Venkateswara Rao,
S.Chand& Company Ltd.
Reference Books:
1. Biological sequence analysis, Durbin, Eddy, Krogh and Mitchison (1998)
Cambridge University Press.
2. Ewens and Grant (2001) Statistical methods in bioinformatics: an
introduction. Springer verlag.
3. K.Lange. Mathematical and statistical methods for genetic analysis. 2 nd Ed.
(2003) Springer.

21

M.Tech. Biotechnology I SEMESTER

RESEARCH METHODOLOGY AND STATISTICAL METHODS
Course Code: EPRBT 124

Credits : 0

Hours: 3 per week

UNIT I
Research Process: Introduction to research methodology, objectives,
classification of research methods: Historical method, case study method,
survey method, experimental method, and other methods( field investigation
research, evaluation research, auction research, ex-post facto research,
laboratory research, business game) Definition, significance, sources,
advantages, limitations, steps involved in research.
Research Problem: sources, criteria of a good research problem, formulating
and stating the problem, common errors in selecting and formulating a
research problem.
Research Design: Definitions, need for a research design, characteristics of
good research design, components of a research design, types of research
design: descriptive, diagnostic, exploratory and experimental.
UNIT II
Sampling Methods: Introduction of sampling, probability and non
probability sampling, sampling procedures simple random, stratified,
systematic, cluster and multistage sampling, concept of sampling
distribution.
Collection and Processing of Data: Sources of data, methods of collection of
primary and secondary data, editing, coding, classification and tabulation of
data, graphical and representation of data, diagrammatic representation of
data.
UNIT III
Inferential Statistics: Basics of Statistical Inference, Sampling distribution,
Estimation Point estimation, Interval estimation, Parameter, Statistic,
Concept of a hypothesis, Research Hypothesis, Null Hypothesis, Level of
Significance, Comparison of means of two samples, Comparison of sample
proportion with population proportion, Comparison of two sample
proportions, Degrees of Freedom, Critical Value, Table value, Type I and
Type II errors, Rules for rejection & acceptance of Null Hypothesis,
Standard Error.
UNIT IV
Inferential Statistics Parametric and Non-Parametric Test: t test
Comparison of sample mean with the population mean, Comparison of
means of two independent samples, Comparison of two correlated samples
22

Z test different applications ANOVA one way ANOVA: F test, Chi

square test.
UNIT V
Correlation and Linear Regression: Introduction of correlation & regression
concepts, estimation of correlation coefficient, regression coefficients,
variance of sample estimates of the parameters, non linear regressions,
weighted and transformations in regression analysis, application of linear
regressions - standard curves in drug analysis and drug stability studies,
analysis of covariance.
Text books:
1. Santosh Gupta: Research Methodology and Statistical Techniques, Deep
& Deep Publication, 2001
2. K. P. C. Swain: A Text book of Research Methodology, 1st edition,
Kalyani Publishers, 2007.
Reference:
1. C.R.Kothari: Research Methodology Methods & Techniques, 2
edition, Wishwa Prakashan, 2000.
2. Research Methodology and Statistical Techniques Indira Gandhi
National Open University.

23

M.Tech. Biotechnology I SEMESTER

PROTEIN CHEMISTRY / PROTEIN ENGINEERING
Course Code: EPRBT 125

Credits : 0

Hours: 3 per week

UNIT- I
Biomolecules. Chemical bonding. Structure and function of proteins.
Structure and role of amino acids in protein folding. Amino acids and
proteins classification, Structural organisation of proteins. Energy status of a
protein molecule.
UNIT II
Protein folding - Hierarchic protein folding, - Defective protein folding,
- Molecular chaperones, - The HSP 70 chaperone system, - Proteasomes,
Prions, Polyketides and non-ribosomal peptides, - Combinational
manipulation of polyketides and non ribosomal peptides. Design and
construction of novel proteins and enzymes. Effect of amino acids on
structure of proteins
UNIT III
Conformation of proteins in general and enzymes in particular. Classification
and functions of Enzymes. Architecture and functions of enzymes and
coenzymes involved in disorders. Structure function relations of enzymes.
Inborn errors of metabolism and the enzymes involved in it.
UNIT- IV
Physical methods such as x-ray crystallography for determination of protein
structure. Site directed mutagenesis for specific protein function. Basic
concepts for design of a new protein/enzyme molecule. Specific examples of
enzyme engineering.
UNIT- V
Protein prefractionation and sample preparation,
Two dimensional
electrophoresis (2-D PAGE), Protein identification. Post translational
modification. Essential requirements for protein synthesis.
References:
Essential Reading :
1. J.L. Cleland and C.S. Craik, Protein Engineering: Principles and Practice,
Wiley-Liss, ISBN-13: 978-0471103547, 1 edition, February 7, 1996.
2. Biochemistry Lubert Stryer
3. Principles of Biochemistry Nelson & Cox
Supplementary Reading :
1. S. Lutz and U. T. Bornscheuer, Protein Engineering Handbook, WileyVCH, New edition ISBN-13: 978-3527318506, January 20, 2009. D.
Balasubramaniam, Bryce, Dharmalingam, Green, Jayaraman Univ. Press,
1996
24

M.Tech. Biotechnology I SEMESTER

NANOBIOTECHNOLOGY
Course Code : EPRBT 126

Credits : 0

Hours: 3 per week

UNIT-I
Introduction to Nanotechnology: Size dependent properties. Size dependence
of sedimentation rate, adsorption effects, scattering of light, absorption of
electromagnetic radiation, electrical and magnetic properties. Effects of
confinement on protein stability.
UNIT II
Production of nanomaterials: Top down & bottom up strategies. Microbial
production. Thermodynamics and statistical mechanics of self-assembly and
template directed assembly: The Ising model. Cooperative transitions in
biological systems. Zimm-Bragg theory for polypeptides and base-pairing
between complementary strands of nucleic acids.
Vectors for drug delivery: Micelles, viral capsids and diatom skeletons.
Targeted drug delivery Nanobioconjugates for receptor targeting and
magnetic guidance. Controlled drug release.
UNIT III
BioNanomaterial characterization: Electron microscopy. Force microscopy.
Light Scattering. Optical tweezers and optical molasses. Localized surface
plasmon resonance.
UNIT IV
Nanomaterials for Biomedical imaging: Quantum dots. Nanomaterials for
MRI. Magnetic resonance principles, theory of relaxation, relationship
between size and relaxation properties.
Theranostics.
UNIT V
Diagnostics and Prognostics: Principles and applications of Nanoarrays and
Nanofluidics. Nanopore sequencing of DNA. BioNanomechanics:
NanoBiomotors. Mechanics of cilia and flagella. Nanobioelectronics:
Nanowires based on DNA. Molecular transistors. Voltage gated ion
channels.
Text books:
1. Neimeyer & Mirkin. Nanobiotechnology. Vol I & II.
2. Tuan Vo-Dinh. Nanotechnology in biology and medicine: Methods, devices
and applications. (2007) Taylor & Francis. (Distributed by IK.Publishers)
25

Reference books:
1. Vijay K. Varadan. Nanomedicine: Design and Applications of magnetic
nanomaterials,
nanosensors and nanosystems. (2008). Wiley Dreamtech
India.
2. Robert Freitas. Nanomedicine. Vol. I Basic capabilities.
3. Patrick Abgrall, Nam-Trung Nguyen . Nanofluidics . 2009. Artech House.
ISBN 159693350X, 9781596933507
4. G.T. Hermanson. Bioconjugate techniques. 2008. Academic Press.
5. C.M. Niemeyer. Bioconjugation protocols: strategies and methods. In
Methods in molecular biology. 2004. Humana Press. Isbn 9781588290984.
6. Challa SSR Kumar. Nanosystem characterization tools in the Life Sciences
(2006). Wiley Dreamtech India.

26

M.Tech. Biotechnology I SEMESTER

BIOELECTRONICS (FREE ELECTIVE)
Course Code: EPRBT 127 Credits: 0

Hours: 3 per week

UNIT I
Neuromorphic systems - the RF cochlea. Concepts of Cytomorphic
electronics. Brain-machine interfaces. Information, noise, energy and power.
Connections between feedback loops and circuits. Scaling laws for power in
analog circuits. Introduction to Op-amps. Applications of Op-amps.
UNIT II
Low power transimpedance
transconductance amplifiers.
Filters low pass, high pass,
and resonators. Convertors (Cochlear implants).

amplifiers and photoreceptors. Low power

Low power current mode circuits. Design of
band pass and band reject. Low power filters
A/D convertors, D/A convertors. Bionic ear

UNIT III
Biosensors and actuators. Direct electron transfer between enzymes and
electrodes. Modeling and simulation of enzyme electrodes. Hybridization
efficiency and sensitivity of oligonucleotide sensitive electrodes.
Design
and construction of glucose biosensors. Design and applications of phenol
biosensors. Screen printing methods in biosensor production.
UNIT IV
Wireless inductive power links for medical implants. Energy harvesting RF
antenna power links. Thevenin equivalent circuit models of antennas. Near
field coupling. Far field coupling. Impedance matching. Rectifier
optimization.
UNIT V
RF telemetry: Impedance modulation in coupled parallel resonators.
Impedance-modulation receiver. Pulse-width modulation receiver. Energy
efficiency of the uplink and downlink. Scaling laws for power consumption
in impedance modulation links. Rf antenna links for implants.

27

Text books:
1. Rahul Sarpeshkar. Ultra low power bioelectronics: fundamentals,
biomedical applications and bio-inspired systems. (2010). Cambridge
University Press.
2. P.N.Bartlett. Bioelectrochemistry: Fundamentals, Experimental Techniques
and Application. John Wiley and Sons. (2008) (Chapter 8: Modeling
Biosensor responses).
3. R.B.Northrop. Analysis and Application of Analog Electronic Circuits to
Biomedical Instrumentation. 2nd Edition. (2012) Taylor and Francis.
Reference books:
1. The art of electronics. Horowitz and Hill. Cambridge University Press.
2. Jonathan Cooper, Anthony Cass. Biosensors: a practical approach. 2nd ed.,
Vol.268 of Practical approach series (2004). Oxford University Press.
3. Pethig, Ronald R. & Smith, Stewart. Introduction to Bioelectronics: For
Engineers and Physical Scientists. (2012). John Wiley and Sons.
Prerequisites:
1. Basic Electronics, Process dynamics and Control.

28

M.Tech. Biotechnology I SEMESTER

PHARMACOLOGY AND GENETIC ENGINEERING
LABORATORY
Course Code: EPRBT 111

Credits : 2

Hours: 6 per week

Minimum of 10 experiments from the following:

1. Determination of clotting time and effect of anticoagulant on coagulation
time.
2. Recording of systemic arterial blood pressure and effect of posture on blood
pressure.
3. Determination of lung volumes and capacities.
4. Recording of 12 lead ECG.
5. Study of simple muscle twitch (SMT).
6. Study of fatigue in skeletal muscle.
7. MTT assay for cell viability
8. Scatchard plots.
9. Plasmid isolation and Restriction.
10. Ligation.
11. Transformation of E.coli.
12. Construction and screening of a cDNA library.
13. DNA sequencing.
14. Molecular weight determination by electrospray Mass spectrometry.
15. Peptide mapping of proteins.
16. Edman sequencing of polypeptide.
17. Polypeptide sequencing using Mass spectrometry.
18. PCR.
19. DNA arrays for gene expression.

Note: If equipment for conducting experiments is not available, data obtained

from databases or simulation may be used.
Text book:
1. Molecular cloning. Vol.I, II and III. Sambrook, Fritsch and Maniatis.

29

M.Tech. Biotechnology I SEMESTER

FERMENTATION AND CELL CULTURE Laboratory
Course Code: EPRBT 112 Credits : 2
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.

Hours: 6 per week

Production and isolation of penicillin

Production and isolation of streptomycin
Media and sterilization techniques for Plant tissue culture
Development of callus from explants of Catharanthus roseus
Extraction and isolation of vinblastine/vincrystine
Extraction of quinolone alkaloids from Cinchona officinalis bark
Media and equipment for Animal cell culture
Separation and culture of human lymphocytes
Maintenance of cancer and Haematopoietic cell lines and testing of
bioactivity of plant extracts on these cell lines
Production, isolation and/or Characterization of antibodies

M.Tech. Biotechnology I SEMESTER

SEMINAR
Course Code

: EPRBT 113

Credits : 3

Hours: 3 per week

30

M.Tech. Biotechnology II SEMESTER

PHARMACOINFORMATICS
Code : EPRBT201

Credits : 3

No. of hours: 3 per week

UNIT-I
Similarity score matrices (PAM, BLOSUM), sequence alignment using
dynamic programming Needleman-Wunsch algorithm for global
alignment, Smith-waterman algorithm for local alignment, Multiple sequence
alignment methods of multiple sequence alignment, multidimensional
dynamic programming, multiple sequence alignment by profile HMM
tranining.
UNIT-II
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.
UNIT-III
Prediction of RNA secondary structure: Nussinov folding algorithm, energy
minimization and Zuker folding algorithm, covariance models. Introduction
to immunoinformatics. Principles of B-cell and T-cell epitope prediction.
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
Informatics based methods for prediction of pharmacokinetic properties:
ClogP, Intestinal membrane permeability, Blood-brain-barrier permeability,
toxicity. Integrated Models for prediction of absorption, distribution,
metabolism and elimination. One-compartment model, two compartment
models and multi-compartmental models.
Text books:
1. Biological sequence analysis. Durbin, Eddy, Krogh and Mitchison.
(Cambridge University Press). (For Units I,II and III)
2. AR Leach and VJ Gillet. An introduction to chemoinformatics. Springer.
(2007)
31

Reference books:
1. Clinical Pharmacokinetics: Concepts and Applications, M.Rowland and
T.N. Tozer, 3rd edition, Lea and Febiger, Philadelphia, 1995.
2. Molecular modeling, Principles and applications, Andrew R. Leach, 2nd
Ed.(2007) Prentice Hall (Unit IV)
3. Computational Molecular Biology: An algorithmic approach Pavel,
A.Pevzner. (PHI)
4. Bioinformatics, D.Mount
5. Database Management systems: C.J.Date
6. A practical guide to the analysis of gene and proteins. Baxevanis. 3 rd Ed.
(2005) Wiley, (Unit IV and Unit V)

32

M.Tech. Biotechnology II SEMESTER

PROTEOMICS AND GENOMICS FOR TARGET IDENTIFICATION
Code : EPRBT 202

Credits : 3

No. of hours: 3 per week

UNIT-I
Protein expression profiles. Analysis of data from 2DGE experiments.
Analysis of data from Mass 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. Modeling
of metabolic pathways. Protein protein interactions: Methods (phage display,
yeast two-hybrid technique, protein arrays) and Tools for analysis of proteinprotein interaction.
UNIT-III
Gene prediction frequentist approaches, model based approaches and
similarity based approaches. Genome assembly and annotation. Fragment
assembly. Mapping, Interval graphs.
UNIT-IV
Marker genes and polymorphism at the genomic level. DNA Microarrays for
detecting SNPs. Data and Algorithms for inference of gene regulatory
networks. Modeling of signal transduction pathways and Gene regulatory
networks.
UNIT-V
Comparative genomics: Genome alignment and Genome rearrangements.
Sorting by reversals. The breakpoint graph. Interleaving graphs and hurdles.
Duality theorem for genomic distance.
Text books:
1. S.R.Pennington and M.J.Dunn. Proteomics. Viva books. New delhi, 2002.
2. Hiroaki kitano. Foundations of sytems biology. Mit press. (2001)
3. Primrose and Twyman. Principles of gene manipulation and genomics. 7th
Ed.(2006) Blackwell publishers.
33

References:
1. Computational Molecular Biology:An algorithmic approach Pavel,
A.Pevzner (PHI).
2. Charles R. Cantor, Cassandra L.Smith (1999) Genomics: the science and
technology behind the human genome project. John wiley and sons (asia)
pvt. ltd. Singapore.
3. Kohane, IS., Kho, A and Butte, A.J. 2002. Microarrays for an integrative
genomics. Barnes and Nobles, MIT press.
4. T.A.Brown. Genomes. 2nd edition. Bios scientific. 2002.
5. Villas-Boas. Neilsen. Smedgard. Hansen, Roessner-Tunali. Metabolome
analysis an introduction.
6. Functional genomics. A practical approach. S.P.Hunt and R.Livesey. (IK
Publishers). 2004.

34

M.Tech. Biotechnology II SEMESTER

SCREENING AND TARGET VALIDATION
Code : EPRBT 203

Credits : 3

No. of hours: 3 per week

UNIT-I
Experimental methods for binding studies: Use of linear and non-linear
Scatchard plots for studies of ligand-receptor binding. The Hill plot. SPR.
UNIT-II
NMR. Chemical shifts, chemical exchange and relaxation. Use of NMR for
structure determination of small molecules application of chemical shift, Jcoupling 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. Algorithmic approaches to clustering gene expression data. Gene
knockouts, Gene traps and gene knockdown in mice for target validation.
Animal models for important therapeutic areas.
Text books:
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). WileyVCH (Unit IV)
35

3. O.Zerbe, R.Mannhold, H.Kubinyi and G.Folkers. BioNMR in drug research.

Methods and principles in medicinal chemistry. Vol. 16. (2006). WileyVCH. (Unit II)
References:
1. B.W.Metcalf and S.Dillon. Target validation in drug discovery.(2006)
Academic Press.
2. Burgers Medicinal Chemistry, 6th Edition, Vol.I and II (Unit-I, II, III,IV)
3. Villas-Boas. Neilsen. Smedgard. Hansen, Roessner-Tunali. Metabolome
analysis an introduction (Unit III)
4. I.Pelczer. NMR in Ligand screening: Theory, methods and applications.
(2006). Oxford University Press.
5. N. Beckmann. In vivo MR techniques in drug discovery and development.
(2006). Informa healthcare.
6. Primrose and Twyman. Principles of gene manipulation and genomics. 7th
Ed.(2006) Blackwell publishers. (Unit V)
7. Model Organisms in Drug Discovery by Pamela M.Carroll and Kevin
Fitzgerald (2003) (Unit V)
8. D.Leon and S.Markel. Insilico strategies in drug target identification and
validation.(2006). Drug discoveries series. CRC.

36

M.Tech. Biotechnology II SEMESTER

BIOLOGICAL PROGRAMMING: BIOPERL, JAVA AND BIOJAVA
Code : EPRBT 204

Credits : 3

No. of hours: 3 per week

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.
Text 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 Primer by Balaguruswamy, Tata Mc Graw Hill,
New Delhi.
6. Java for Bioinformatics and Biomedical applications.
H.Bal &
J.Hujol(2006) Springer.
37

M.Tech. Biotechnology II SEMESTER

ADVANCED INSTRUMENTAL METHODS OF ANALYSIS
Course Code: EPRBT 221

Credits : 3

Hours: 3 per week

UNIT I
The Transmission Electron microscope. Wavelength of electrons. Resolution
of the electron microscope. Collimation of electron beam. Image formation
and data analysis. Sample preparation. Vacuum requirements. The Scanning
Tunneling microscope. Atomic force microscopy. Scanning modes in AFM.
Magnetic force microscopy. Near field scanning optical microscope.
UNIT II
Microarrays: Types of microarrays. Fabrication of microarrays Robotic
spotting and light-directed combinatorial systhesis. Microarray design and
Microarray data analysis. Applications of microarrays SNP analysis,
differential expression, Diagnostics and Prognostics.
UNIT III
Microfluidics: Fundamentals of fluid mechanics in the micro- and
nanoscale. Electrokinetic effects in micro- and nanochannels. Zeta potential.
Mixing in microscale. Fabrication of microfluidic channels using glass,
silicon and polymers. Pumps, Valves and Sensors for microfluidic systems.
Microfluidics for diagnostic and prognostic applications. Lab-on-a-chip
devices. Integrated microfluidic circuits.
UNIT IV
Optical methods: Scattering: Rayleigh scattering. Use of scattering to obtain
particle number. Use of scattering to determine size distribution. Mie
Scattering. Raman scattering and resonance raman scattering.
Quantum dots relationship between particle size and absorption properties.
Optical tweezers - Measurement of forces between nanoparticles with
optical tweezers.
UNIT V
Principles of magnetic resonance. Theory of relaxation. FTNMR. Spin echo.
Pulsed field gradients and Gradient echos. Principles of Magnetic resonance
imaging. MR angiography. MR-spectroscopy. Diffusion tensor imaging.
MR based reporter genes. MRI markers. MR based Theranostics.
Text books:
1. Challa SSR Kumar. Nanosystem characterization tools in the Life
Sciences (2006). Wiley Dreamtech India.
2. Patrick Abgrall, Nam-Trung Nguyen . Nanofluidics . 2009. Artech
House. ISBN 159693350X, 9781596933507
3. Principles of MRI. Brown and Venkatesan.
38

M.Tech. Biotechnology II SEMESTER

MOLECULAR DIAGNOSTICS
Course Code: EPRBT 222

Credits : 3

Hours: 3 per week

UNIT I
Nucleic acid extraction. Nucleic acid amplification methods. Hybridization
based methods. Next-generation sequencing methods. Lab-on-a-chip
approach to molecular diagnostics.
UNIT II
Quality control. Assurance. Identification and standards. Regulatory issues
in molecular diagnostics. Ethical considerations in molecular diagnostics.
UNIT III
Molecular diagnosis for genetic diseases: Thrombofilia, Cystic fibrosis,
Huntington disease, X-linked mental retardation, Ataxias.
UNIT IV
Molecular diagnostics for evaluation of cancer. Gene expression analysis
for tumor profiling. Molecular diagnostics for hematopoietic disorders.
Molecular diagnosis for cervical carcinoma.
UNIT V
Molecular diagnosis for Hepatitis C Virus, Cytomegalovirus, multiple
respiratory syndrome virus. Molecular diagnostics for streptococcus and
tuberculosis. Molecular diagnosis for HLA typing.
Text books:
1. Molecular diagnostics: techniques and applications for the clinical laboratory.
By Wayne W. Grody, Robert M. Nakamura, Frederick L. Kiechle
2. Fundamentals of molecular diagnostics. By David E. Bruns, Edward R.
Ashwood, Carl A. Burtis. Elsevier Health sciences

39

M.Tech. Biotechnology II SEMESTER

TISSUE ENGINEERING
Course Code: EPRBT 223

Credits : 3

Hours: 3 per week

UNIT I
History and scope of tissue engineering. Organization of cells into higher
ordered structures. Composition and diversity of ECM, receptors for
extracellular matrix molecules. Matrix molecules and their ligands.
Dynamics of cell ECM interaction and its relevance for tissue engineering.
UNIT II
Morphogenesis. Morphogenetic dynamics. Cell differentiation and
migration. Mechanical and chemical determinants of tissue development.
Engineering principles for the design of replacement tissues and organs.
Biomaterials for tissue engineering. Biomaterial scaffold properties. Effects
of pore size and interconnectivity. Surface modification of biomaterials.
UNIT III
Scaffold design and fabrication: Degradable polymers and Bioceramics for
tissue engineering. Principles of Scaffold design.
Scaffold fabrication
technologies: Foaming, sintered microspheres, solvent casting, phase
separation, Electrospinning. Textile technologies for fiber and fabrics. Solid
free form fabrication.
UNIT IV
Bioreactors for tissue engineering: 2D and 3D cell culture. Bioreactors for
cell seeding. Bioreactors for enhanced mass transport. Kinetics and transport
in tissue engineering molecular interaction with cells, molecular and cell
transport through tissue.
UNIT V
Tissue engineering for skin transplantation. Tissue engineering of musculoskeletal system (cartilage, bone, tendons and ligaments), cardiovascular
system (blood vessels and hear valves) and nervous system. Animal and
human trials of engineered tissues.
Text books:
1. Clemens A. van Blitterswijk, Peter Thomsen. Tissue engineering. Academic
Press series in biomedical engineering. Academic Press, 2008
2. Y. Ikada. Tissue engineering: fundamentals and applications. AP/Elsevier.
2006.
3. Challa SSR Kumar. Tissue, cell and organ engineering. Wiley-VCH. 2006.
4. PO Palsson and PA Bhatia. Tissue engineering. Prentice Hall 2004/Dorling
Kindersely 2009.
40

M.Tech. Biotechnology II SEMESTER

PHARMACOINFORMATICS LABORATORY
Code : EPRBT 211

Credits : 2

Hours: 6 per week

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.

41

M.Tech. Biotechnology II SEMESTER

BIOLOGICAL PROGRAMMING LABORATORY
Code : EPRBT 212

Credits : 2

No. of hours: 6 per week

Use Perl/Bioperl:
1.
2.
3.
4.

To convert sequence information between different formats.

To predict possible translations for a polynucleotide sequence.
For sequence alignment and
To create and access a local database.

Use Python/Biopython to display molecular structure.

Use of Java/BioJava to create a web-interface.
Write a program to 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.

M.Tech. Biotechnology II SEMESTER r

SEMINAR
Course Cod : EPRBT 213

Credits : 3

42

Hours: 3 per week

M.Tech. Biotechnology III SEMESTER

MOLECULAR MODELING AND LEAD OPTIMIZATION
Course Code: EPRBT 301

Credits : 3

Hours: 3 per week

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
function 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, maximum likelihood).
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.
Text books:
1. Molecular modelling. Principles and applications. - Andrew R. Leach. 2nd Ed.
(2007). Prentice Hall.
2. Structural Bioinformatics. Ed. P.E. Bourne and H.Weissig. (2003). Wiley-liss.
3. Molecular quantum mechanics. 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.
43

M.Tech. Biotechnology III SEMESTER

MODELING AND SIMULATION OF DRUG MANUFACTURING
PROCESSES
Course Code : EPRBT 302

Credits : 3

Hours: 3 per week

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.
UNIT-II
Modeling and simulation of Unit processes used in bulk drug manufacture:
Batch reactor and CSTR. Downstream processing calculations for
sedimentation, centrifugation, solvent extraction, distillation, adsorption,
crystallization. Environmental assessment and Economic assessment.
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. Modeling and simulation of packaging
techniques.
UNIT-IV
Introduction to Good manufacturing practices (GMP). Biosafety: Process
safety and reaction hazard assessment. Criticality classes. Reaction heat,
adiabatic temperature rise, MTSR, gas evolution. Safety testing. Risk
assessment of biological hazards.
UNIT-V
Pilot plant design. Fermenter design calculations. Pilot plant operation
(simulations). Plant design calculations for the Penicillin production system.
Plant design calculations for production of insulin.
Text books:
1. Leon Lachman et al Theory and practice of industrial pharmacy. 3rd edition.
Lea and Febiger, 1986.
2. Encyclopedia of Pharmaceutical Technology. 3rded.(2006). Informa Healthcare.
3. Chemical Engineering in the pharmaceutical industry: from R&D to
manufacturing. Ed. David J. am Ende. Chapter 11. Process safety and reaction
hazard assessment. John Wiley and Sons, 2011.
Reference:
1. Good manufacturing practices for pharmaceuticals. 6th edition.(Drugs and
pharmaceutical sciences. (2006). Informa Healthcare.

44

M.Tech. Biotechnology III SEMESTER

MOLECULAR MODELING LABORATORY
Course Code: EPRBT 311

Credits : 2

Hours: 6 per week

1. Generating 3D representations from 2D descriptions of small

molecules.
2. Use of molecular mechanics for geometry optimization of a small
molecule.
3. Evaluate energy of a small molecule using
CNDO/MINDO/MNDO/AM1/PM3
4. Evaluate energy of a small molecule using ab initio QM with 631G
basis set.
5. Calculate solvent accessible surface area.
6. Polypeptide conformational analysis using monte-carlo and molecular
dynamics methods.
7. Secondary structure prediction. Servers: PHD, PSIPRED
8. Prediction of transmembrane helices.
9. Comparative modeling of a small protein.
10. Docking of a polypeptide ligand into a protein.
11. QSAR.
12. 3D-QSAR.
13. CoMFA.
14. SXRs for ADMET.

45

M.Tech. Biotechnology III SEMESTER

MODELING AND SIMULATION LABORATORY
Course Code: EPRBT 312

Credits : 2

Hours: 6 per week

1. Modelling of dynamical systems. Parameter estimation. Simulation.

Stability of dynamical systems.
2. Modeling of metabolic pathways. Comparison of metabolic pathways.
3. Modeling of signal transduction pathways and networks.
4. Whole cell simulations.
5. Representation of signal transduction pathways using Systems biology
markup language.
6. Ease of formulation.
7. Modeling and simulation of bioprocesses:
8. Biotransformation
mechanisms.

of

drugs,

microsomal

and

non-microsomal

9. Factors influencing enzyme induction and inhibition.

10. Modeling and simulation of unit operations used in bulk drug
manufacture.
M.Tech. Biotechnology III SEMESTER
PROJECT
Course Code : EPRBT 313

Credits : 10

Hours: 15 per week

M.Tech. Biotechnology III SEMESTER

INDUSTRIAL TRAINING REPORT
Course Code: EPRBT 314

Credits : 2

M.Tech. Biotechnology IV SEMESTER

PROJECT
Course Code : EPRBT 411

Credits : 20

46

Hours: 35 per week