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 3rd 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 4th 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).

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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 semester’s 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 student’s 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:

Σ [ C x G ]

GPA = ----------------

Σ 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 student’s 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 1st semester (after admission) of M.Tech.

Course Code Name of the Course Instruction hours Maximum marks Credits

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, Bloom and Roth.

3) Reviews of Medical Physiology by W.F.Ganong

4) Pharmacology by Rang and Dale.

5) Medical microbiology. 24th Edition (Jawetz, 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. 3rd Ed. (2001). Nelson Thornes.


ADVANCED GENETICS AND STATISTICS

Code : EPRBT 103

Credits : 3 No. of hours: 4 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: 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. 2nd Ed. (2003) Springer. 8) Genetics. Hartl and Jones, Jones and Bartlett publishers (2005) 9) Introduction to quantitative genetics, Falconer and Mckay 4th Edition. Reference for case study 1) Current science. Vol.86 #1 (2004)

M.Tech Biotechnology I Semester MOLECULAR BIOLOGY AND GENETIC ENGINEERING

ELECTIVE Course Code : EPRBT 121

Credits : 3 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. 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.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.

Reference:

4. Primrose and Twyman. Principles of gene manipulation and genomics. 7th Ed. (2006) Blackwell publishers.

5. B.Lewin. Genes-IX. 9th Ed. (2007). Jones 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: Fourier’s 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: Fick’s 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, 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

M.Tech Biotechnology I Semester 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 Stem cells and adult stem cells 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. 2nd 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.

M.Tech Biotechnology I Semester PHARMACOLOGY AND GENETIC ENGINEERING LABORATORY



Minimum of 10 experiments from the 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 from databases or simulation may be used.

Textbook:

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

M.Tech Biotechnology I Semester 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 1st Semester SEMINAR



M.Tech Biotechnology 2nd Semester

PHARMACOINFORMATICS

Code : EPRBT201 Credits : 3 No. of hours: 4 per week

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, 2nd 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. 3rd Ed. (2005) Wiley, (Unit IV

and Unit V)

M.Tech Biotechnology 2nd 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 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.

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 polymorphism at 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. John 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. 2nd 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. 7th Ed.(2006) Blackwell

publishers.


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) Burger’s Medicinal Chemistry, 6th 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. 7th 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.


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.

M.Tech Biotechnology 2nd 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


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.


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 BioJava. To create 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 2nd Semester SEMINAR



M.Tech Biotechnology 3rd 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, 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.

Recommended 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. 4th Ed. (2005). Oxford University Press. 4) Poul Krogsgaard-Larsen et al. (2002) Textbook of drug design and discovery. Taylor and Francis

publishers.

M.Tech Biotechnology 3rd 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. 3rd edition. Lea and

Febiger, 1986. 2. Encyclopedia of Pharmaceutical Technology. 3rd edition. (2006). Informa Healthcare. 3. Good manufacturing practices for pharmaceuticals. 6th edition.(Drugs and pharmaceutical

sciences. (2006). Informa Healthcare.

M.Tech Biotechnology 3rd Semester MOLECULAR MODELING LABORATORY



Generating 3D representations from 2D 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.

M.Tech Biotechnology 3rd 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.

M.Tech Biotechnology 3rd Semester PROJECT



M.Tech Biotechnology 4th 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.

m. tech biotechnology

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