GANDHI INSTITUTE OF TECHNOLOGYAND MANAGEMENT

(GITAM)(Deemed to be University, Estd. u/s 3 of UGC Act 1956)VISAKHAPATNAM HYDERABAD BENGALURU

Accredited by NAAC with ‘A’ Grade

REGULATIONS AND SYLLABUSof

Master of Technologyin

Biotechnology(w.e.f 2015-16 admitted batch)

A University Committed to ExcellenceA University Committed to Excellence

VISIONTo become a global leader in higher education.

MISSIONTo impart futuristic and comprehensive

education of global standards education of global standards with a high sense of discipline and

social relevance in a serene and invigorating environment.

GANDHI INSTITUTE OF TECHNOLOGYAND MANAGEMENT

(GITAM)(Declared as Deemed to be University U/S 3 of UGC Act, 1956)

VISAKHAPATNAM * HYDERABAD * BENGALURU

Accredited by NAAC with ‘A’ Grade

REGULATIONS AND SYLLABUSOF

Master of Technologyin

Biotechnology(w.e.f 2015 -16 admitted batch)

A University Committed to Excellence

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M.Tech. in BiotechnologyREGULATIONS

(w.e.f. 2015-16 admitted batch)

1. ADMISSION

1.1 Admission into M.Tech. in Biotechnology program of GITAMUniversity is governed by GITAM University admission regulations.

2. ELIGIBILITY CRITERIA

2.1 A pass in B.Tech. in Biotechnology or B.Pharm or equivalent orB.Tech. Chemical Engineering or M.Sc.in Chemistry /Microbiology/ Bioinformatics / Biotechnology) with proficiency in basic Biologywith proficiency in basic 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.

2.3 The actual weightage to be given to the above items will be decidedby the authorities before the commencement of the academic year.Candidates with valid GATE score shall be exempted from appearingfor GAT (PG).

3. CHOICE BASED CREDIT SYSTEM

3.1 Choice Based Credit System (CBCS) is introduced with effect fromthe admitted Batch of 2015-16 based on UGC guidelines in orderto promote:

• Student Centered Learning• Cafeteria approach• Students to learn courses of their choice• Learning at their own pace• Inter-disciplinary learning

3.2 Learning goals/ objectives and outcomes are specified leading towhat a student should be able to do at the end of the program.

4. STRUCTURE OF THE PROGRAM

4.1 The Program Consists of

i) Core Courses (compulsory) which give general exposureto a Student in Biotechnology and subject related area.

ii) Programme electives.

iii) Open electives.

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4.2 Each course is assigned a certain number of credits depending uponthe number of contact hours (lectures/tutorials/practical) per week.

4.3 In general, credits are assigned to the courses based on thefollowing contact hours per week per semester.• One credit for each Lecture / Tutorial hour per week.• One credit for two hours of Practicals per week.• Two credits for three (or more) hours of Practicals per week.

5. MEDIUM OF INSTRUCTION

The medium of instruction (including examinations and projectreports) shall be English.

6. REGISTRATION

Every student has to register himself/herself for each semesterindividually at the time specified by the Institute / University.

7. ATTENDANCE REQUIREMENTS

7.1 A student whose attendance is less than 75% in all the courses puttogether in any semester will not be permitted to attend the end- semester examination and he/she will not be allowed to registerfor subsequent semester of study. He/she has to repeat the semesteralong with his / her juniors.

7.2 However, the Vice Chancellor on the recommendation of thePrincipal / Director of the Institute/School may condone the shortageof attendance to the students whose attendance is between 66% and74% on genuine grounds and on payment of prescribed fee.

8. EVALUATION

8.1 The assessment of the student’s performance in a Theory courseshall be based on two components: Continuous Evaluation (40marks) and Semester-end examination (60 marks).

8.2 A student has to secure an aggregate of 40% in the course in thetwo components put together to be declared to have passed thecourse, subject to the condition that the candidate must havesecured a minimum of 24 marks (i.e. 40%) in the theory componentat the semester-end examination.

8.3 Practical/ Project Work/ Industrial Training/ Viva voce/ Seminar etc.course are completely assessed under Continuous Evaluation fora maximum of 100 marks, and a student has to obtain a minimumof 40% to secure Pass Grade. Details of Assessment Procedure arefurnished below in Table 1.

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Table 1: Assessment Procedure

S.No. Component of Marks Type of Scheme of EvaluationAssessment Allotted Assessment

1 Theory 40 Continuous i) Thirty (30) marks for midEvaluation Semester examinations. Three mid

examinations shall be conducted for15 marks each; performance in besttwo shall be taken into consideration.ii) Ten (10) marks for Quizzes,Assignments and Presentations.

60 Semester-end Sixty (60) marks for Semester-endExamination examinations

Total 100

2 Practicals 100 Continuous i) Fifty (50) marks for regularity andEvaluation performance, records and oral

presentations in the laboratory.Weightage for each component shallbe announced at the beginning of theSemester.ii) Ten (10) marks for case studies.iii)Forty (40) marks for two tests of20 marks each (one at the mid-termand the other towards the end of theSemester) conducted by theconcerned lab Teacher.

3 Project work 100 Continuous i) Forty (40) marks for periodic(III Semester ) Evaluation evaluation on originality, innovation,

sincerity and progress of the work,assessed by the Project Supervisor.ii) Thirty (30) marks for mid-termevaluation for defending the Project,before a panel of examiners.iii)Thirty (30) marks for final Reportpresentation and Viva-voce, by apanel of examiners

4 Project work 50 Continuous i) Twenty (20) marks for Periodic(IV Semester) Evaluation evaluation on originality

innovation, sincerity and progress of thework, assessed by the Project Supervisor.ii) Fifteen (15) marks for mid-termevaluation for defending the Project,before a panel of examiners*.iii) Fifteen (15) marks for interim Reportpresentation and Viva-voce.

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50 Semester-end Fifty (50) marks for final ReportExamination presentation and Viva-voce assessed by

external examiners.Total 100

5 Comprehensive 100 Continuous Through five periodic Viva-voce exams forViva-voce Evaluation 20 marks each, conducted by a panel

(II Semester) of examiners. The course contentfor Viva exams shall be announced at thebeginning of the Semester.

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

9. REAPPEARANCE

9.1 A student who has secured ‘F’ grade in a Theory course shall haveto reappear at the subsequent Semester end examination held forthat course.

9.2 A student who has secured ‘F’ grade in a Practical course shall haveto attend Special Instruction Classes held during summer.

9.3 A student who has secured ‘F’ Grade in Project work / IndustrialTraining etc shall have to improve his/her report and reappear forViva – voce at the time of Special Examination to be conductedin the summer vacation.

10. SPECIAL EXAMINATION

10.1 A student who has completed his/her period of study and still has“F” grade in a maximum of three theory courses is eligible to appearfor Special Examination normally held during summer vacation.

11. BETTERMENT OF GRADES

A student who has secured only a Pass or Second class and desiresto improve his/her Class can appear for Betterment Examinationsonly in Theory courses of any Semester of his/her choice, conductedin Summer Vacation along with the Special Examinations.Betterment of Grades is permitted ‘only once’ immediately aftercompletion of the program of study.

12. GRADING SYSTEM

12.1 Based on the student performance during a given semester, a finalletter grade will be awarded at the end of the semester in eachcourse. The letter grades and the corresponding grade points areas given in Table 2.

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Table 2: Grades & Grade Points

Sl.No. Grade Grade Points Absolute Marks1 O (outstanding) 10 90 and above

2 A+ (Excellent) 9 80 to 89

3 A (Very Good) 8 70 to 79

4 B+ (Good) 7 60 to 69

5 B (Above Average) 6 50 to 59

6 C (Average) 5 45 to 49

7 P (Pass) 4 40 to 44

8 F (Fail) 0 Less than 40

9 Ab. (Absent) 0 -

12.2 A student who earns a minimum of 4 grade points (P grade) in acourse is declared to have successfully completed the course, andis deemed to have earned the credits assigned to that course, subjectto securing a GPA of 5 for a Pass in the semester.

13. GRADE POINT AVERAGE

13.1 A Grade Point Average (GPA) for the semester will be calculatedaccording to the formula:

Σ [ C x G ]GPA = ——————

Σ CWhere

C = number of credits for the course,G = grade points obtained by the student in the course.

13.2 To arrive at Cumulative Grade Point Average (CGPA), a similarformula is used considering the student’s performance in all thecourses taken, in all the semesters up to the particular point of time.

13.3 CGPA required for classification of class after the successfulcompletion of the program is shown in Table 3.

Table 3: CGPA required for award of Class

Class CGPA Required

First Class with Distinction > 8.0*

First Class > 6.5

Second Class > 5.5

Pass Class > 5.0

* In addition to the required CGPA of 8.0 or more, the student must havenecessarily passed all the courses of every semester in first attempt.

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14. ELIGIBILITY FOR AWARD OF THE M.Tech. DEGREE

14.1 Duration of the program: A student is ordinarily expected tocomplete the M.Tech. program in four semesters of two years.However a student may complete the program in not more thanfour years including study period.

14.2 However the above regulation may be relaxed by the ViceChancellor in individual cases for cogent and sufficientreasons.

14.3 A student shall be eligible for award of the M.Tech. Degreeif he / she fulfills all the following conditions.

a) Registered and successfully completed all the coursesand projects.

b) Successfully acquired the minimum required credits asspecified in the curriculum corresponding to the branchof 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.

15. DISCRETIONARY POWER

Not withstanding anything contained in the above sections, theVice Chancellor may review all exceptional cases, and give hisdecision, which will be final and binding.

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M.Tech. in BiotechnologyDepartment of Biotechnology

Effective from academic year 2015-2016 admitted batch

Semester II

S.No. Course Course Category L T P CCode Title

1 EBT702 Molecular Diagnostics PC(CE) 4 0 0 4

2 EBT704 Modeling and Simulationof Drug ManufacturingProcesses PC(CE) 4 0 0 4

3 EBT706 Biotechnology in DrugDevelopment PC(CE) 4 0 0 4

4 EBTXXX Program Elective – II PE(PE) 4 0 0 4

5 EBTXXX Program Elective – III PE(PE) 4 0 0 4

6 EIDXXX Open Elective – II OE(OE) 3 0 0 3

7 EBT722 Modeling and Simulationlaboratory PC(CE) 0 0 3 2

8 EBT792 Technical Seminar PC(CE) 0 0 3 2

9 EBT794 Comprehensive Viva PC(CE) 2

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Semester I

S.No. Course Course Category L T P CCode Title

1 EBT701 Physiology andPharmacology PC(CE) 4 0 0 4

2 EBT703 Advanced Genetics andGenetic engineering PC(CE) 4 0 0 4

3 EBT705 Molecular Modeling PC(CE) 4 0 0 4

4 EBT707 Pharmacoinformatics PC(CE) 4 0 0 4

5 EBTXXX Program Elective – I PE(PE) 4 0 0 4

6 EIDXXX Open Elective – I OE(OE) 3 0 0 3

7 EBT721 Pharmacology and GeneticEngineering laboratory PC(CE) 0 0 3 2

8 EBT723 Pharmacoinformatics andBiological programminglaboratory PC(CE) 0 0 3 2

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Semester III

S.No. Course Course Category L T P CCode Title

1 EBT891 Project Work PP(PW) 16 8

Semester IV

S.No. Course Course Category L T P CCode Title

1 EBT892 Project Work PP(PW) 32 16

Number of Credits

Semester I II III IV Total

Credits 27 29 8 16 80

Open Elective - I

S.No. Course Course Category L T P CCode Title

1 EID741 BioJava OE(OE) 3 0 0 3

2 EID743 Bioelectronics OE(OE) 3 0 0 3

3 EID745 Research Methodology OE(OE) 3 0 0 3

Open Elective-II

S.No. Course Course Category L T P CCode Title

1 EID742 BioPerl OE(OE) 3 0 0 3

2 EID744 Nanobiotechnology OE(OE) 3 0 0 3

3 EID746 Management of Technologyand Innovation OE(OE) 3 0 0 3

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PROGRAMME ELECTIVES

Programme Elective-I

S.No. Course Course Category L T P CCode Title

1 EBT741 Regulatory issues inDrug Design andDevelopment PE (PE) 4 0 0 4

2 EBT743 PharmaceuticalBiotechnology PE (PE) 4 0 0 4

3 EBT745 Fermentation andCell culture PE(PE) 4 0 0 4

Programme Elective-II

S.No. Course Course Category L T P CCode Title

1 EBT742 Cancer Biology PE(PE) 4 0 0 4

2 EBT744 Screening and TargetValidation PE(PE) 4 0 0 4

3 EBT 746 Clinical Biochemistryand Diagnostics PE(PE) 4 0 0 4

Programme Elective-III

S.No. Course Course Category L T P CCode Title

1 EBT748 Protein Chemistry PE(PE) 4 0 0 4

2 EBT750 Stem cells and Tissueengineering PE(PE) 4 0 0 4

3 EBT752 Advanced Instrumentalmethods of analysis PE(PE) 4 0 0 4

Remedial courses

S.No. Course Course Category L T P CCode Title

1 EBTXXX Engineering Mathematics Remedial 4 0 0 0Course

2 EBTXXX Introduction to BiochemicalEngineering ORMolecular Biology andGenetic Engineering Remedial 4 0 0 0

Course

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EBT701: PHYSIOLOGY AND PHARMACOLOGY L T P C

4 0 0 4Module I 8 hoursPhysiology of central nervous system, Parkinson’s, Alzheimer’s and Huntington’sdiseases. Molecular basis of muscle contraction, neuromuscular junction, DMDand Myasthenia gravis. Physiology of endocrine glands: Pituitary; dwarfism andgigantism. Thyroid; hyper and hypothyroidism. Adrenal gland; Addison’s andCushing’s diseases. Pancreas. Diabetes mellitus. Drugs, targets and mode of actionof drugs.

Module II 8 hoursPhysiology of GI tract, motility disorders. Functional physiology of kidney,common diseases. Physiology of heart, cardiac cycle, vascular diseases;atherosclerosis and aneurysms. Arrhythmias; Bradycardia and tachycardia.Functional physiology of the respiratory system, asthma and COPD. Drugs,targets and mode of action of drugs.

Module III 8 hoursPhysiology of the immune system, autoimmunity, autoimmune diseases and HIV.Molecular basis of cancer. Tumor pathology, classification, major anti-cancerdrugs. Infectious diseases; Tuberculosis and malaria. Drugs, targets and modeof action of drugs.

Module IV 8 hoursMechanisms, 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. Conceptof Adverse drug reactions and drug interactions. Drug transporters in drugdisposition, interaction and resistance.

Module V 8 hoursComputational Approaches in Phamacokinetics: Bioequivalence and bioavailabilitystudies. Estimation of pharmacokinetic parameters. WagnerNelson calculation ofbioavailability and Assessment of bioavailability, Physiology-BasedPharmacokinetic (PBPK) Modelling.

Text Book(s)

1. J. E. Hall, Guyton and Hall Textbook of medical physiology, 12/e, Saunders,2010.

2. K. Minneman, Brody's Human Pharmacology: Molecular to Clinical, 4/e,Mosby, 2004.

3. R.S.Satoskar, S.D. Bhandarkar, S. S. Ainapure, Pharmacology andPharmacotherapeutics, 23/e, Indian Pharmacological Society, 2014.

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References

1. B. Meibohm, Pharmacokinetics and Pharmacodynamics of Biotech Drugs:Principles and Case Studies in Drug Development, WILEY-VCH, 2006.

2. M. Winter, Basic Clinical Pharmacokinetics, 4/e, Lippincott, 2004.3. L. Shargel and A.B.C. Yu, Applied Biopharmaceutics and Pharmacokinetics,

5/e, Appleton and Lange, 2005.4. D. Zha, M. Zhu and W. G. Humphreys (Eds.), Drug Metabolism in Drug

Design and Development, Wiley, 2007.

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EBT702: MOLECULAR DIAGNOSTICS L T P C

4 0 0 4

Module I 8 hoursNucleic acid extraction. Nucleic acid amplification methods. Hybridization basedmethods. Next-generation sequencing methods. Lab-on-a-chip approach tomolecular diagnostics.

Module II 8 hoursMolecular diagnosis for genetic diseases: Thrombofilia, Cystic fibrosis,Huntington disease, X-linked mental retardation, Ataxias.

Module III 8 hoursMolecular diagnostics for evaluation of cancer. Gene expression analysis fortumor profiling. Molecular diagnostics for hematopoietic disorders. Moleculardiagnosis for cervical carcinoma.

Module IV 8 hoursMolecular diagnosis for Hepatitis C Virus, Cytomegalovirus, multiple respiratorysyndrome virus. Molecular diagnostics for streptococcus and tuberculosis.Molecular diagnosis for HLA typing.

Module V 8 hoursQuality control. Assurance. Identification and standards. Regulatory issues inmolecular diagnostics. Ethical considerations in molecular diagnostics.

Text Book(s)1. C.A. Burtis, D.E. Bruns Tietz, Fundamentals of clinical chemistry and

molecular diagnostics, 7/e, Saunders, 2014.2. L. Buckingham, Molecular Diagnostics: fundamentals, methods and clinical

applications, F.A. Davis Company, 2011.

References1. G.P. Patrinos, W.J. Ansorge, Molecular Diagnostics, 2/e, Elsevier publications,

2010.2. W.W. Grody, R.M. Nakamura, F.L. Kiechle, C. Storm, Molecular diagnostics:

techniques and applications for the clinical laboratory, 1/e, Academic press,2009.

3. D.E. Bruns, E.R. Ashwood, C.A. Burtis, Fundamentals of moleculardiagnostics, Elsevier-Saunders. 2007.

4. C.A. Burtis, D.E. Bruns, eds. Tietz Fundamentals of clinical chemistry andmolecular diagnostics, 7/e, Saunders-Elsevier, 2015.

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EBT703: ADVANCED GENETICS AND GENETICENGINEERING

L T P C4 0 0 4

Module 8 hoursGenetic polymorphism. Genetic variability in drug metabolizing enzymes, drugtransporters and drug receptors. Immunogenetic polymorphisms. Methods forgenotyping.Case study: Host genetics and tuberculosis susceptibility.

Module II 8 hoursMonogenic traits: Mendelian pedigree patterns. Linkage analysis, Pedigreeanalysis. Hardy-Weinberg Law. Allele frequency estimation for two alleles andthree alleles at a locus. Linkage disequilibrium and Association mapping.

Module III 8 hoursMultifactorial inheritance. Heritability. Twin studies in pharmacogenetics. Intervalmapping. Polygenic models. Haplotyping.

Module IV 8 hoursGenetic engineering for gene therapy: Therapeutic nucleic acids. Therapeuticgenes used in clinical trials. Gene knockout and knockin. RNAi. Methods forgene delivery. Viral vectors (Gammaretroviruses, lentiviruses, adenoviruses, adeno-associated viruses, herpes simplex virus).

Module V 8 hoursGene therapy: Gene therapy for immune system diseases. Gene therapy ofneurodegenerative diseases (Alzheimer's, Parkinson's, Huntington's and ALS).Gene therapy of eye diseases. Gene therapy of cardiovascular diseases. Genetherapy for cancer.

Text Book(s)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.

References1. D.A.P.Evans, Genetic factors in drug therapy: Clinical and molecular

pharmacogenetics, Cambridge University Press, 1994.2. I.P.Hall and M.Pirmohamed, Pharmacogenetics, Informa healthcare, 2006.3. K.Lange, Mathematical and statistical methods for genetic analysis, 2/e,

Springer, 2003.

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EBT704: MODELING AND SIMULATION OF DRUGMANUFACTURING PROCESSES

L T P C4 0 0 3

Module I 8 hoursMathematical modeling. Compartmental models. Models with memory. Modelswith time delay. Parameter estimation. Model validation. Modeling of dynamicalsystems. Stability of dynamical systems.

Module II 8 hoursModeling and simulation of Unit processes used in bulk drug manufacture: Batchreactor and CSTR. Downstream processing calculations for sedimentation,centrifugation, solvent extraction, distillation, adsorption, crystallization.Environmental assessment and Economic assessment.

Module III 8 hoursTablet manufacture: Machine theory, design and process troubleshooting of tabletcompression. Modeling and simulation of granulation scale-up. Modeling andsimulation of coating. Modeling and simulation of packaging techniques.

Module IV 8 hoursIntroduction to Good manufacturing practices (GMP). Biosafety: Process safetyand reaction hazard assessment. Criticality classes. Reaction heat, adiabatictemperature rise, MTSR, gas evolution. Safety testing. Risk assessment ofbiological hazards.

Module V 8 hoursPilot plant design. Fermenter design calculations. Pilot plant operation(simulations). Plant design calculations for the Penicillin production system. Plantdesign calculations for production of insulin.

Text Book(s)1. James Swarbrick, Encyclopedia of Pharmaceutical Technology, Marcel

Dekker, 2002.2. David J. am Ende, Chemical Engineering in the pharmaceutical industry: R&D

to manufacturing, John Wiley and Sons, 2011.

References1. Joseph D. Nally, Good manufacturing practices for pharmaceuticals, 6/e, CRC

Press, 2006.2. Leon Lachman, The theory and practice of industrial pharmacy, CBS

Publishers & Distributors, 2009.

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EBT705: MOLECULAR MODELINGL T P C4 0 0 4

Module I 8 hoursQuantum chemistry for Modeling of small molecules: Variation method and Timeindependent Perturbation theory. Ab initio methods for molecules: Hartree-FockSCF method.Introduction to semi-empirical methods: Huckel molecular orbital theory. Pariser-Parr-Pople method. CNDO, AM1 and PM3.

Module II 8 hoursForce fields for molecular modeling. Free energy calculations. Potentials of meanforce. 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.

Module III 8 hoursConformational analysis: Geometry optimization using steepest descent andconjugate gradients. Distance geometry. Monte-carlo simulation. Moleculardynamics and simulated annealing. Prediction of transmembrane segments inmembrane proteins.Protein 3D structure prediction: Comparative modeling. Threading and Foldprediction. Methods based on minimization of energy.

Module IV 8 hoursLigand based drug design: SAR, QSAR and 3D-QSAR. Partial least squares andMolecular field analysis (COMFA). 3D-pharmacophores. Deriving 3Dpharmacophores (Constrained systematic search, Ensemble distance geometry,Ensemble molecular dynamics, genetic algorithms, clique detection, maximumlikelihood).

Module V 8 hoursReceptor based drug design: Computational methods for identification of plausiblebinding sites. Molecular Docking (rigid body and flexible docking). Receptor basedde novo ligand design.

Text Book (s)1. A.R. Leach, Molecular modeling. Principles and applications, 2/e, Prentice

Hall, 2001.2. P. E. Bourne and H. Weissig, Structural Bioinformatics, Wiley-Liss, 2003.

References1. P. Krogsgaard-Larsen, Textbook of drug design and discovery, Taylor and

Francis, 2002.2. P. Atkins and R. Friedman, Molecular quantum mechanics, 4/e, Oxford

University Press, 2005.

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EBT706: BIOTECHNOLOGY IN DRUGDEVELOPMENT

L T P C4 0 0 3

Module I 8 hoursIntroduction to metabolomics. Metabolic markers for drug development.Metabolic engineering: Flux control analysis, flux control coefficients, summationtheorem, elasticity coefficient and connectivity theorem. Modeling of metabolicpathways.

Module II 8 hoursApplications of proteomics for target selection and lead optimization. Proteinexpression profiles. Analysis of data from 2DGE experiments. Analysis of datafrom Mass spectrometry: Peptide sequencing using mass spectrometry - spectrumgraphs. MS for protein identification via database search. Spectral convolution.Spectral alignment.

Module III 8 hoursProtein function: Use of sequence patterns, motifs and profiles. Patternrepresentation methods: consensus, regular expressions, profiles. Protein proteininteractions: Methods (phage display, yeast two-hybrid technique, protein arrays)and Tools for analysis of protein-protein interaction.

Module IV 8 hoursTarget selection in drug development. Applications of structural genomics fortarget selection. Applications of functional genomics for target selection. Markergenes and polymorphism at the genomic level. DNA Microarrays for detectingSNPs. Data and algorithms for inference of gene regulatory networks.

Module V 8 hoursStructural genomics: Gene prediction – frequentist approaches, model basedapproaches and similarity based approaches. Genome assembly and annotation.Comparative genomics: Genome alignment and Genome rearrangements. Sortingby reversals. The breakpoint graph. Interleaving graphs and hurdles. Dualitytheorem for genomic distance.

Text Book (s)1. S. R. Pennington and M. J. Dunn, Proteomics, Viva books, 2002.2. G. Stephanopoulos, A. A. Aristidou and J. Nielsen, Metabolic engineering:

Principles and methodologies, Academic Press, 1998.3. S. P. Hunt and R. Livesey, Functional genomics. A practical approach, IK

Publishers, 2004.

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References1. T. A. Brown, Genomes, Bios scientific, 2002.2. S. Kohane, A. Kho and A. J. Butte, Microarrays for an integrative genomics,

MIT Press, 2002.3. P. A. Pevzner, Computational Molecular Biology:An algorithmic approach,

2/e, PHI, 2004.

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EBT707: PHARMACOINFORMATICSL T P C4 0 0 4

Module I 8 hoursSimilarity score matrices (PAM, BLOSUM), sequence alignment using dynamicprogramming – Needleman-Wunsch algorithm for global alignment, Smith-waterman algorithm for local alignment, Multiple sequence alignment – methodsof multiple sequence alignment, multidimensional dynamic programming

Module II 8 hoursMolecular phylogenetics: introduction to binary trees. Phylogenetic treeconstruction using weighted parsimony and neighbor-joining, Probabilistic modelsof evolution – Jukes cantor model and Kimura model. Prediction of RNAsecondary structure: Nussinov folding algorithm, energy minimization and Zukerfolding algorithm, covariance models.

Module III 8 hoursData base concepts – Introduction to SQL-DDL and SQL-DML- Creation ofdatabases – Searching database using SQL – Introduction to MySQL.

Module IV 8 hoursChemoinformatics: Pharmacology databases, structure databases, Moleculardescriptors. Molecular similarity. 2D substructure searching. 3D databasesearching. Pharmacophore keys. Introduction to database filters, Lipinski Ruleof Five, In silico ADMET; QSAR approach, Knowledge - based approach.

Module V 8 hoursLigand based design of compounds; Structure based design of compounds,Chemoinformatics tools for drug discovery.

Text Book(s)1. Durbin, Eddy, Krogh and Mitchison Biological sequence analysis. Cambridge

University Press, 2003.2. AR Leach and VJ Gillet. An introduction to chemoinformatics. Springer. 2007.

References1. M.Rowland and T.N. Tozer Clinical Pharmacokinetics: Concepts and

Applications, 3/e, Lea and Febiger publications, 1995.2. Andrew R. Leach, Molecular modeling, Principles and applications, 2/e,

Prentice Hall 2007.

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EBT721: PHARMACOLOGY AND GENETICENGINEERING LABORATORY

L T P C0 0 3 2

Minimum of 10 experiments from the following:1. Determination of clotting time.2. Recording of systemic arterial blood pressure and effect of exercise and

posture on blood pressure.3. Determination of lung volumes and capacities.4. Recording of 12 lead ECG.5. Study of simple muscle twitch (SMT) (Demonstration).6. Isolation of plasmid DNA and visualization by horizontal gel

electrophoresis.7. Restriction Digestion of ? DNA.8. Ligation of ? EcoRI digest.9. Transformation of E.coli by a – complementation.10. DNA sequencing (Demonstration).11. Edman sequencing of polypeptide (Demonstration).12. Polymerase Chain Reaction.13. Production, recovery and estimation of penicillin14. Development of callus from explants of Catharanthus roseus and

extraction of alkaloids15. Characterization of antibodies: Sandwich ELISA and ODD.

Note: If equipment for conducting experiments is not available, simulationmay be used.

Text Book(s)

1. J. Sambrook, E. F. Fritsch and T. Maniatis, Molecular Cloning: ALaboratory Manual, Volumes 1, 2 and 3, Cold Spring Harbor LaboratoryPress, 1989.

2. S. Fox, A Laboratory Guide to Human Physiology: Concepts andClinical Applications, McGraw-Hill, 2010.

3. P. F. Stanbury, A. Whitaker and S. J. Hall Principles of FermentationTechnology, Butterworth-Heinemann, 1999.

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EBT722: MODELING AND SIMULATIONLABORATORY

L T P C0 0 3 2

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

Biotransformation of drugs, microsomal and non-microsomal mechanisms.Factors influencing enzyme induction and inhibition.

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

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EBT723: PHARMACOINFORMATICS ANDBIOLOGICAL PROGRAMMING LABORATORY

L T P C0 0 3 2

Minimum of 10 experiments from the following:Tools for Pharmacoinformatics1. Biological Databases with Reference to Expasy and NCBI2. Sequence similarity searching using BLAST3. Pair-wise sequence alignment algorithms4. Multiple Sequence and Phylogenetic Analysis5. RNA Secondary Structure prediction algorithms6. Energy minimisation & geometry optimization for proteins & peptides7. Homology Modeling Using Modeller8. Integrating Biological Networks and Microarray expression data9. Studies on Drug-Receptor Interaction using AutoDock10. Prediction of Pharmacokinetics in drug design process11. Toxicity prediction of a drug molecule

BioPerl experiments1. Perl program to Convert DNA sequence into RNA sequence2. Perl program to get anti-parallel and complementary strand of a given DNA

strand3. Perl program to join two different sequences of a given DNA4. Perl program to open NCBI database file by File-handle5. Perl program to convert Fasta format to GenBank format6. Perl program to count the bases present in DNA molecule7. Perl program to translate RNA to amino acid sequence

BioJava Experiments1. Write Java/BioJava code to create pair-wise sequence alignment using

Needleman-Wunsch and Smith-Waterman algorithms2. Write Java/BioJava code to create Multiple Sequence Alignment for the given

sequences3. Write Java/BioJava code to translate RNA to amino acid sequence

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EBT741: REGULATORY ISSUES IN DRUG DESIGNAND DEVELOPMENT

L T P C4 0 0 4

Module I 8 hoursQuality control: GMP. Purity determination as per ICH guidelines.

Module II 8 hoursIntellectual Property: Concepts and Fundamentals, Mechanisms for protectionof Intellectual Property- patents, copyright, trademark; factors affecting choiceof IP protection; penalties for violation, Role of IP in Pharma Industry.Trade related aspects of Intellectual Property Rights: Intellectual Property andInternational Trade: Concepts behind WTO (World Trade Organization),WIPO(World Intellectual Property Organization) GATT (General Agreement on Tariffand Trade), TRIPs (Trade Related Intellectual Property Rights), TRIMS (TradeRelated Investment Measures) and GATS (General Agreement on Trade inServices); Protection of plant and animal genetic resources; biological materials;gene patenting. Case studies and examples.

Module III 8 hoursNuts and Bolts of patenting, copyright and trademark protection: Criteria forpatentability, types of patents; Indian Patent Act, 1970. Filing of a patentapplication: 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 andguidelines, fee structure, time frames, jurisdiction aspects. Types of patentapplications- provisional, non-provisional, PCT and convention patentapplications; 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.

Module IV 8 hoursPatenting by research students, lecturers and scientists- University/organizationalrules. Thesis, Research Paper Publication, credit sharing by workers, financialincentives; Useful information sources for patents related information.Significance of copyright protection for researchers; Indian Copyright Law anddigital technologies- Berne convention, WIPO copyright treaty (WCT), WIPOperformance and Phonograms Treaty (WPPT); Protection for computer databases,multimedia works; Trademarks legislation and registration system. Meaning oftrademark, criteria for eligibility. Trade secrets-scope, modalities and protection.

Module V 8 hoursTechnology Development/Transfer/Commercialization related aspects: Drugrelated 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.

23

Managing technology transfer (TOT). Compulsory Licensing, access to medicineissues; 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 projectreport, financial appraisal. Business models. Case Study: Antiretroviral drugs.

Text Book(s)1. M.A.Voet, The Generic Challenge: Understanding Patents, FDA and

pharmaceutical life-cycle management, 2/e, Brown Walker Press, Boca Raton,USA, 2008.

2. Marc S. Gross, S. Peter Ludwig, Robert C. Sullivan, Biotechnology andPharmaceutical Patents: Law and Practice, Aspen Publishers, 2007.

24

EBT742: CANCER BIOLOGYL T P C4 0 0 4

Module I 8 hoursCharacteristics of human cancer; causes of cancer; the epidemiology of humancancer, types of cancers, Principles of chemical and physical carcinogenesis.

Module II 8 hoursThe biochemistry and cell biology of cancer: historical perspectives, growthcharacteristics of malignant cells, modification of extra-cellular matrix components,mechanisms of cancer cell proliferation versus differentiation, cell cycle regulation,apoptosis, growth factors, overview of signal transduction pathways importantin cancer. Angiogenesis. Biology of tumor metastasis

Module III 8 hoursMolecular genetics of cancer: split genes and RNA processing, geneticrecombination, gene amplification, cis-acting regulatory elements: promoters andenhancers, transcription factors, DNA methylation, molecular genetic alterationsin cancer cells, oncogenes, tumor suppressor genes, basic concepts of cancer stemcells.

Module IV 8 hoursTumor immunology and diagnosis: mechanisms of the immune response to cancer,role of gene rearrangement in the tumor response, heat shock proteins asregulators of the immune response, immunotherapy, categories of tumor markers,gene expression microarrays in cancer diagnosis, proteomics in cancer diagnosis,circulating endothelial cells and endothelial progenitor cells, molecular imaging,haplotype mapping in cancer diagnosis

Module V 8 hoursCancer treatment and prevention: patient–tumor interactions, fever and infection,sequelae of cancer treatment, molecular mechanisms of aging and its prevention,diet and cancer prevention, chemoprevention, antioxidants, protease inhibitors,histone deacetylase inhibitors, statins, multi-agent chemoprevention.

Text Book(s)1. R.W. Ruddon, Cancer Biology, 4/e, Oxford University Press, 2007.2. R.A. Weinberg, The Biology of Cancer, Garland Science, 2007.

References1. Roger J.B. King, Cancer Biology, 1/e, Longman publishres, 1996.2. Raymond. W. Ruddin, Cancer Biology, 3/e, Oxford University Press, 1995.

25

EBT743: PHARMACEUTICAL BIOTECHNOLOGYL T P C4 0 0 4

Module I 8 hoursBiomolecules. Chemical bonding. Structure and function of proteins. Structureand role of amino acids in protein folding. Amino acids and proteins classification,Structural organization of proteins. Energy status of a protein molecule.

Module II 8 hoursProtein folding, Hierarchic protein folding, Defective protein folding, Molecularchaperones, The HSP 70 chaperone system, Proteasomes, Prions, Polyketidesand non-ribosomal peptides, Combinational manipulation of polyketides and nonribosomal peptides. Design and construction of novel proteins and enzymes.Effect of amino acids on structure of proteins

Module III 8 hoursConformation of proteins in general and enzymes in particular. Classification andfunctions of Enzymes. Architecture and functions of enzymes and coenzymesinvolved in disorders. Structure function relations of enzymes. Inborn errors ofmetabolism and the enzymes involved in it.

Module IV 8 hoursPhysical methods such as x-ray crystallography for determination of proteinstructure. Site directed mutagenesis for specific protein function. Basic conceptsfor design of a new protein/enzyme molecule. Specific examples of enzymeengineering.

Module V 8 hoursProtein prefractionation and sample preparation, Two dimensional electrophoresis(2-D PAGE), Protein identification. Post translational modification. Essentialrequirements for protein synthesis.

Text Book(s)1. J.L. Cleland and C.S. Craik, Protein Engineering: Principles and Practice, 1/

e, Wiley-Liss, 1996.2. David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry,

6/e, W. H. Freeman, 2012.3. J.M. Berg, J.L. Tymoczko, L. Stryer, Biochemistry, 6/e, W.H. Freeman, 2006.

References1. S. Lutz and U. T. Bornscheuer, Protein Engineering Handbook, Wiley-VCH,

2009.2. D. Voet, J.G. Voet, Biochemistry, 3/e, John Wiley, 2004.3. E.S.West, W.R. Todd, H.S. Mascon, J.T. Van Bruggen, Text Book of

Biochemistry, 4/e, Oxford and IBH Publishers, 1974.

26

EBT744: SCREENING AND TARGET VALIDATIONL T P C4 0 0 4

Module I 8 hoursExperimental methods for binding studies: Use of linear and non-linear Scatchardplots for studies of ligand-receptor binding. The Hill plot. Surface plasmonresonance.

Module II 8 hoursNMR spectroscopy. Chemical shifts, chemical exchange and relaxation. Use ofNMR spectroscopy for structure determination of small molecules – applicationof chemical shift, J-coupling and relative areas. The Nuclear Overhauser effect.2D and 3D NMR spectroscopy principles. Structure determination ofmacromolecules and complexes. Determination of binding sites for weaklyinteracting ligands. Screening by NMR.

Module III 8 hoursPrinciples of MRI. Spin echo and gradient echoes. MR angiography. Echo planarimaging for cardiac applications. Applications of MRI for drug design anddevelopment.X-ray crystallography for target and lead characterization. Small moleculestructure determination using direct methods. Phase determination of largemolecules using MIR, MAD and molecular replacement. The Laue method.

Module IV 8 hoursCombinatorial chemistry: Principles of combinatorial synthesis. Design ofcombinatorial libraries. Measures of diversity of a combinatorial library.Characterization of combinatorial libraries. High throughput screening. Highthroughput screening for lead discovery. Tools for high throughput screening.Assay technologies.

Module V 8 hoursUses of comparative genomics. Gene expression profiling for target validation.Algorithmic approaches to clustering gene expression data. Gene knockout fortarget validation. Animal models for important therapeutic areas.

Text Book(s)1. D. J. Abraham and D. P. Rotella, Burgers medicinal chemistry, Drug discovery

and development, 7/e, Wiley, 2010.2. P. M. Carroll and K Fitzgerald, Model organisms in drug discovery, Wiley,

2003.References1. R. Mannhold, H. Kubinyi and G. Folkers, High throughput screening in drug

discovery, Wiley-VCH, 2006.2. B. W. Metcalf and S. Dillon, Target validation in drug discovery, Academic

Press, 2006.3. C. R. Cantor and P. R. Schimmel, Biophysical Chemistry, W.H.Freeman,

1980.

27

EBT745: FERMENTATION AND CELL CULTUREL T P C4 0 0 4

Module I 8 hoursMetabolic engineering: Flux control analysis, flux control coefficients, summationtheorem, elasticity coefficient, connectivity theorem. Genetic engineering:Genetically engineered microbes for production of antibiotics. Production ofpenicillin and semisynthetic analogs of penicillins. Production of insulin andinsulin analogs. Use of humanized yeast for glycosylation.

Module II 8 hoursPharmaceutical production using plant cell culture: Production of Digoxin fromcultured cells of Digitalis lanata. Production of Shikonin from cultured cells ofLithospermum erythrorhizon.Biopharming: Agrobacterium mediated genetic engineering for production ofbiopharmaceuticals from plants. Hirudin production from Brassica napus. Ediblevaccines from transgenic banana plants.

Module III 8 hoursAnimal cell culture and its applications: Equipment and media for animal cellculture. Insect cell Baculovirus system. Production of haematopoeitic growthfactors, cytokines, cytokine inhibitors.

Module IV 8 hoursCell lines: Transformed human cell lines and their applications. Embryonic stemcells and adult stem cells; hematopoietic and neuronal stem cells and theirtherapeutic applications. Organ culture of skin.

Module V 8 hoursEngineering and regulatory issues: Scale-up of fermentation process involvinghazardous microbes. Disinfection and inactivation procedures. Verification ofinactivation process. Security of stock cultures. NIH guidelines for minimumcontainment requirements for different risk level agents. Regulations for biosafetyrelated to production of bioprocess based pharmaceuticals.

Text Book(s)1. S. S. Ozturk and W. Hu (Eds), Cell culture technology for pharmaceutical

and cell based therapies, CRC press, 2005.2. N. Okafor, Modern industrial microbiology and biotechnology, Science

publishers, 2007.

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References1. E.M.T. El Mansi, C.F. C. Bryce, A.L. Demain and A.R.Allman (eds),

Fermentation microbiology and biotechnology, 3/e, CRC Press, 2012.2. A. N. Glazer and H. Nikaido, Microbial biotechnology: Fundamentals of

Applied Microbiology, 2/e, Cambridge press, 2007.3. A. Slater, N.W. Scott, Plant biotechnology: The genetic manipulation of plants,

2/e, Oxford press, 2006.4. D. O. Fleming and D. L. Hunt, Biological safety: principles and practices,

ASM Press, 2000.

29

EBT746: CLINICAL BIOCHEMISTRY ANDDIAGNOSTICS

L T P C4 0 0 4

Module I 8 hoursMaintenance of Clinical laboratory, Composition of Blood, Serum and Plasma.Collection and preservation of samples and sampling methods. Digestive systemdisorders: functions and methods of evaluation, pancreatic exocrine functions andmethods of evaluation. Plasma proteins: properties, functions, variations duringdisease. Plasma lipid and lipoproteins, variations during disease

Module II 8 hoursDetermination of constituents of Blood: Determination of haemoglobin,determination of bilirubin, determination of cholesterol, determination of creatineand creatinine, determination of urea, determination of sugar, determination ofcalcium and Amylase.

Module III 8 hoursSpecial tests: Thymol turbidity test, Determination of prothrombin time, BenceJones proteins, Amniotic fluid composition and biochemical tests, Hormonalanalysis using RIA methods.

Module IV 8 hoursCerebrospinal fluid: Functions and their variation in diseases. Kidney: Functionand composition of urine, investigation of renal disorders. Liver: Liver functionsand function tests, Liver diseases: Jaundice, Hepatitis, Gallstones, Cirrhosis andfatty liver. Clinical chemistry of new born, clinical enzymology: Isoenzymes inhealth and disease.

Module V 8 hoursEndocrine disorders of pancreas: Diabetes mellitus, Hypoglycemia and Glucosetolerance tests, Thyroid: Hypo and Hyper thyroidism, BMR and tests for thyroidfunctions. Pituitary clinical syndromes.

Text Book(s)1. J. E. Hall and A. C. Guyton, Guyton and Hall, Textbook Of Medical

Physiology, 12/e, Saunders Elsevier, 2011.2. R. Chaterjee, Text book of Medical Biochemistry, 8/e, JP Medical Limited,

2012.

References1. C. A. Burtis, E. R. Ashwood, Teitz, Fundamentals of Clinical Chemistry,

6/e, Elsevier, 2008.2. Chakravarti, Bhattacharya, A hand book of Clinical pathology, Academic

publishers, 1976.

30

EBT748: PROTEIN CHEMISTRYL T P C4 0 0 4

Module I 8 hoursBiomolecules. Chemical bonding. Structure and function of proteins. Structureand role of amino acids in protein folding. Amino acids and proteins classification,Structural organization of proteins. Energy status of a protein molecule.

Module II 8 hoursProtein folding, Hierarchic protein folding, Defective protein folding, Molecularchaperones, The HSP 70 chaperone system, Proteasomes, Prions, Polyketidesand non-ribosomal peptides, Combinational manipulation of polyketides and nonribosomal peptides. Design and construction of novel proteins and enzymes.Effect of amino acids on structure of proteins

Module III 8 hoursConformation of proteins in general and enzymes in particular. Classification andfunctions of Enzymes. Architecture and functions of enzymes and coenzymesinvolved in disorders. Structure function relations of enzymes. Inborn errors ofmetabolism and the enzymes involved in it.

Module IV 8 hoursPhysical methods such as x-ray crystallography for determination of proteinstructure. Site directed mutagenesis for specific protein function. Basic conceptsfor design of a new protein/enzyme molecule. Specific examples of enzymeengineering.

Module V 8 hoursProtein prefractionation and sample preparation, two dimensional electrophoresis(2-D PAGE), Protein identification. Post translational modification. Essentialrequirements for protein synthesis.

Text Book(s)1. J.L. Cleland, C.S. Craik, Protein Engineering: Principles and Practice, 1/e,

Wiley-Liss, 1996.2. David L. Nelson, Michael M. Cox, Lehninger Principles of Biochemistry,

6/e, W. H. Freeman, 2012.3. J.M. Berg, J.L. Tymoczko, L. Stryer, Biochemistry, 6/e, W.H. Freeman, 2006.

References1. S. Lutz and U. T. Bornscheuer, Protein Engineering Handbook, Wiley-VCH,

2009.2. D. Voet, J.G. Voet, Biochemistry, 3/e, John Wiley, 2004.3. E.S.West, W.R. Todd, H.S. Mascon and J.T. Van Bruggen, Text Book of

Biochemistry, 4/e, Oxford and IBH Publishers, 1974.

31

EBT750: STEM CELLS AND TISSUE ENGINEERINGL T P C4 0 0 4

Module I 8 hoursBasic biology of stem cells; Types & sources of stem cell with characteristics:embryonic, adult, cancer stem cells, induced pluripotent stem cells; signalingmechanisms of stem cell self renewal and differentiation

Module II 8 hoursHistory and scope of tissue engineering. Organization of cells into higher orderedstructures. Composition and diversity of ECM, receptors for extracellular matrixmolecules. Matrix molecules and their ligands. Preparation of ECM, Biologicactivities of ECM, scaffolds, Commercially available scaffolds composed ofextracellular matrix, Cell differentiation and migration

Module III 8 hoursBiomaterials in cell culture: Cell culture: harvest, selection, expansion, anddifferentiation, Cell nutrition, Natural Polymers in tissue engineering applications,Biomaterial scaffold properties. Models as Precursors for Prosthetic Devices,Quantitative Aspects, cell tissue mechanics, Mechano-chemical control of cellfate switching

Module IV 8 hoursScaffold design and fabrication: Degradable polymers and Bioceramics for tissueengineering. Principles of Scaffold design. Scaffold fabrication technologies:Foaming, sintered microspheres, solvent casting, phase separation, Electro-spinning. Textile technologies for fiber and fabrics. Solid free form fabrication.

Module V 8 hoursBioreactors for tissue engineering: 2D and 3D cell culture. Key functions ofbioreactors in tissue engineering, Bioreactor design and development, Bioreactorsas 3D in vitro model Systems, Bioreactors in clinical applications, Tissueengineering of skin, bone, cartilage, nervous system, lung, liver and pancreas.

Text Book(s)1. Clemens A. van Blitterswijk, Peter Thomsen. Tissue engineering. 1/e,

Academic press series in biomedical engineering. 20082. Robert.P.Lanza, Robert Langer and L. William Chick, Principles of tissue

engineering, 3/e, Elsevier Publishers, 2007.

References1. Challa SSR Kumar. Tissue, cell and organ engineering. Wiley-publishers, 2006.2. PO Palsson and PA Bhatia. Tissue engineering. Prentice Hall publishers, 2009.3. Y. Ikada. Tissue engineering: fundamentals and applications. Elsevier

publishers, 2006.

32

EBT752: ADVANCED INSTRUMENTAL METHODSOF ANALYSIS

L T P C4 0 0 4

Module I 8 hoursThe Transmission Electron microscope. Wavelength of electrons. Resolution ofthe electron microscope. Collimation of electron beam. Image formation and dataanalysis. Sample preparation. Vacuum requirements. The Scanning Tunnelingmicroscope. Atomic force microscopy. Scanning modes in AFM. Magnetic forcemicroscopy. Near field scanning optical microscope.

Module II 8 hoursMicroarrays: Types of microarrays. Fabrication of microarrays – Roboticspotting and light-directed combinatorial systhesis. Microarray design andMicroarray data analysis. Applications of microarrays – SNP analysis, differentialexpression, Diagnostics and Prognostics.

Module III 8 hoursMicrofluidics: Fundamentals of fluid mechanics in the micro- and nanoscale.Electrokinetic effects in micro- and nanochannels. Zeta potential. Mixing inmicroscale. Fabrication of microfluidic channels using glass, silicon and polymers.Pumps, Valves and Sensors for microfluidic systems. Microfluidics for diagnosticand prognostic applications. Lab-on-a-chip devices. Integrated microfluidiccircuits.

Module IV 8 hoursOptical methods: Scattering: Rayleigh scattering. Use of scattering to obtainparticle 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 - Principles and applications.

Module V 8 hoursPrinciples of magnetic resonance. Theory of relaxation. FTNMR. Spin echo.Pulsed field gradients and Gradient echos. Principles of Magnetic resonanceimaging. MR angiography. MR-spectroscopy. Diffusion tensor imaging. MRbased reporter genes. MRI markers. MR based Theranostics.

Text Book(s)1. R. W. Brown, Y. N. Cheng, E. M. Haacke, M. R. Thompson, R. Venkatesan,

Magnetic Resonance Imaging: Physical Principles and Sequence Design, 2/e, Wiley-Blackwell, 2014.

2. P. Abgrall, N. Nguyen, Nanosystem characterization tools in the Life Sciences,Artech House, 2009.

References1. S.S.R.C. Kumar, Nanosystem characterization tools in the Life Sciences,

Wiley Dreamtech India, 2006.

33

EBT792: TECHNICAL SEMINARL T P C0 0 3 2

34

EBT794: COMPREHENSIVE VIVAL T P C

2

35

EBT891: PROJECT WORKL T P C0 0 16 8

36

EBT892: PROJECT WORKL T P C0 0 32 16

37

EID741: BIOJAVAL T P C3 0 0 3

Module I 8 hoursJava: Introduction, variables and data types, expressions and arithmetic operators,decision constructs arrays, Input & Loop constructs, class & objects,programming demo.

Module II 8 hoursFile handling, strings and object references, regular expressions, appletprogramming, Java applets, graphical models, managing Input / Output files inJava.

Module III 8 hoursBioJava: Java as a language for Bioinformatics, symbols and symbol Lists,locations, sequences and features.

Module IV 8 hoursSequence I/O basics, Changeability, Mutability and Events, ProbabilityDistributions and Hidden Markov Models using BioJava

Module V 8 hoursTranscription, translation and reverse complementation of given sequences usingBioJava

Text Book(s)1. Balaguruswamy, Programming with Java – A Primer, Tata Mc Graw Hill,

2004.2. H.Bal and J.Hujol, Java for Bioinformatics and Biomedical applications,

Springer, 2006.

38

EID742: BIOPERLL T P C3 0 0 3

Module I 8 hoursPerl: Variables, operators and functions. Regular expressions. Pattern matching.Data structures. Arrays. Modules. Example programmes: Program to findrestriction sites, Program to convert genbank format file to Fasta format.

Module II 8 hoursBioperl's objects, Accessing sequence data from local and remote databases usingBioperl, Transforming formats of database/ file records, Manipulating sequences,Searching for “similar'' sequences, Parsing BLAST and FASTA reports with Searchand SearchIO.

Module III 8 hoursSearching for genes and other structures on genomic DNA (Genscan), Developingmachine readable sequence annotations, Manipulating clusters of sequences(Cluster, ClusterIO), Representing non-sequence data in Bioperl: structures, treesand maps

Module IV 8 hoursBioperl alphabets, Auxilliary Bioperl Libraries, Database classes. Connecting toDatabases.

Module V 8 hoursBioPerl example programmes: Translate given DNA sequence to predict possiblepolypeptides using BIOPERL, Program to convert genbank format file to Fastaformat using BIOPERL.

Text Book(s)1. James D. Tisdall, Beginning Perl for Bioinformatics, Oreilly and Associates,

2001.2. Cynthia Gibas and Per Jambeck, Developing bioinformatics computer skills,

Oreilly and Associates, 2000.3. Rex A Dwyer, Genomic Perl, Cambridge University Press, 2001.

39

EID743: BIOELECTRONICSL T P C3 0 0 3

Module I 8 hoursNeuromorphic systems - the RF cochlea. Concepts of Cytomorphic electronics.Brain-machine interfaces. Information, noise, energy and power. Connectionsbetween feedback loops and circuits. Scaling laws for power in analog circuits.Introduction to Op-amps. Applications of Op-amps.

Module II 8 hoursLow power transimpedance amplifiers and photoreceptors. Low powertransconductance amplifiers. Low power current mode circuits. Design of Filters– low pass, high pass, band pass and band reject. Low power filters andresonators. Convertors - A/D convertors, D/A convertors. Bionic ear (Cochlearimplants).

Module III 8 hoursBiosensors and actuators. Direct electron transfer between enzymes and electrodes.Modeling and simulation of enzyme electrodes. Hybridization efficiency andsensitivity of oligonucleotide sensitive electrodes. Design and construction ofglucose biosensors. Design and applications of phenol biosensors. Screen printingmethods in biosensor production.

Module IV 8 hoursWireless inductive power links for medical implants. Energy harvesting RF antennapower links. Thevenin equivalent circuit models of antennas. Near field coupling.Far field coupling. Impedance matching. Rectifier optimization.

Module V 8 hoursRF telemetry: Impedance modulation in coupled parallel resonators. Impedance-modulation receiver. Pulse-width modulation receiver. Energy efficiency of theuplink and downlink. Scaling laws for power consumption in impedancemodulation links. Rf antenna links for implants.

Text Book(s)1. R. Sarpeshkar, Ultra low power bioelectronics: fundamentals, biomedical

applications and bio-inspired systems,Cambridge University Press, 2010.2. P.N.Bartlett. Bioelectrochemistry: Fundamentals, Experimental Techniques

and Application, John Wiley and Sons, 2008.3. R.B.Northrop. Analysis and Application of Analog Electronic Circuits to

Biomedical Instrumentation. 2/e, Taylor and Francis, 2012.

References1. J.M. Cooper, J. Cooper, A.E.G. Cass, Biosensors: a practical approach. 2/

e, Volume 268 of Practical approach series, Oxford University Press, 2004.2. P. Ronald, R. Smith, Stewart, Introduction to Bioelectronics: For Engineers

and Physical Scientists, John Wiley and Sons, 2012.

40

EID 744: NANOBIOTECHNOLOGYL T P C3 0 0 3

Module I 8 hoursIntroduction to Nanotechnology: Size dependent properties. Size dependence ofsedimentation rate, adsorption effects, scattering of light, absorption ofelectromagnetic radiation, electrical and magnetic properties. Effects of confinementon protein stability.

Module II 8 hoursProduction of nanomaterials: Top down & bottom up strategies. Microbialproduction. Thermodynamics and statistical mechanics of self-assembly:Cooperative transitions in biological systems. Zimm-Bragg theory forpolypeptides and base-pairing between complementary strands of nucleic acids.Vectors for drug delivery: Micelles, viral capsids and diatom skeletons. Targeteddrug delivery – Nanobioconjugates for receptor targeting and magnetic guidance.Controlled drug release.

Module III 8 hoursBioNanomaterial characterization: Electron microscopy. Force microscopy. LightScattering. Optical tweezers. Localized surface plasmon resonance.

Module IV 8 hoursNanomaterials for Biomedical imaging: Quantum dots.Nanomaterials for MRI. Magnetic resonance – principles, theory of relaxation,relationship between size and relaxation properties.Theranostics.

Module V 8 hoursDiagnostics and Prognostics: Principles and applications of Nanoarrays andNanofluidics. Nanopore sequencing of DNA.BioNanomechanics: NanoBiomotors. Mechanics of cilia and flagella.Nanobioelectronics: Nanowires based on DNA. Molecular transistors. Voltagegated ion channels.

Text Book(s)1. Y Xie, The nanobiotechnology handbook, CRC, 2012.3. C. A. Mirkin and C. M. Niemeyer, Nanobiotechnology II: More concepts

and applications, Wiley-VCH, 2007.

References1. T.Vo-Dinh, Nanobiotechnology in biology and medicine: methods, devices

and applications, CRC, 2007.

41

EID745: RESEARCH METHODOLOGYL T P C3 0 0 3

Module I 8 hoursResearch Process: Introduction to research methodology, objectives, classificationof research methods, Historical method, case study method, survey method,experimental method, and other methods (field investigation research, evaluationresearch, laboratory research). Definition, significance, sources, advantages,limitations and steps involved in research. Research Problem: Sources, criteriaof a good research problem, formulating and stating the problem. Research Design:Definition, characteristics, components and types of research design: descriptive,diagnostic, exploratory and experimental.

Module II 8 hoursSampling Methods: Introduction; probability and non probability sampling.Sampling procedures; simple random, stratified, systematic, cluster and multistagesampling. 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 diagrammaticrepresentation of data.

Module III 8 hoursInferential Statistics: Basics of statistical inference; Point and interval estimation,parameter and statistic. Concept of a hypothesis; Research hypothesis, nullHypothesis, Type I and Type II errors, rules for rejection and acceptance ofnull hypothesis, levels of significance, degrees of freedom, critical value, tablevalue and standard error. Comparison of means of two samples, comparison ofsample proportion with population proportion and comparison of two sampleproportions.

Module IV 8 hoursInferential statistics: Parametric and non parametric tests. Student ‘t’ test,comparison of sample mean with the population mean, comparison of meansof two independent samples, comparison of two correlated samples, Z- test,ANOVA; one way ANOVA and applications. F-test, Chi-square test, analysisof covariance.

Module V 8 hoursCorrelation and linear regression: Introduction of correlation and regressionconcepts, estimation of correlation coefficient, regression coefficients, varianceof sample estimates of the parameters, application of linear regressions, standardcurves in drug analysis and drug stability studies.

Text Book(s)1. C. R. Kothari and G. Garg, Research Methodology: Methods and techniques,

3/e, New Age International, 2014.

42

References1. S. Gupta, Research methodology and statistical techniques, Deep publication,

2001.2. K. P. C. Swain, A text book of research methodology, Kalyani publishers,

2007.

43

EID746: MANAGEMENT OF TECHNOLOGY ANDINNOVATION

L T P C3 0 0 3

Module I 8 hoursIntroduction & History of Innovation, Sources of Innovation, Types and Patternsof Innovation, Standards

Module II 8 hoursBattles and Design Dominance, Choosing Innovation Projects, CollaborationStrategies, Product Innovation

Module III 8 hoursOrganizing for Innovation, Managing the New Product Development, Process& Teams, The Interactive and non-linear nature of Innovation, InnovationMeasurement Technology

Module IV 8 hoursTransfer and Diffusion: Protecting Innovation, Intellectual Property Rights,Interactive Learning and Networks of Innovation:

Module V 8 hoursTechnology Platforms; Firms Taxonomy. Dynamics of Technological Change andInnovation, Systems of Innovation, case studies

Text Book(s)1. P. Trott,Innovation Management and New product Development, Prentice

Hall, 20022. J. Cagan, and C.M. Vogel, Creating Breakthrough Products: innovation from

product planning to program approval, Prentice Hall, 20023. J. Goldenberg, and D. Mazursky, Creativity in product Innovation”,

Cambridge University Press, 2002.

References1. D. Mann, Hands-On Systematic Innovation, CREAX Press, 2002.2. J.E.M. Klostermann, and A. Tukker, Product Innovation and Eco-Efficiency,

Kluwer Academic Press, 1998.3. M. French, Invention and Evolution: Design in Nature and Engineering,

Cambridge University Press, 1994.4. B. Rogers, Creating Product Strategies, London, Intl. Thomson Business Press,

1996.

44

EBTXXX: ENGINEERING MATHEMATICSL T P C4 0 0 0

Module I 8 hoursSolving simultaneous linear equations in 2 and 3 variables using matrix inversemethod and Cramer’s rule. Eigen values and eigenvectors of matrices. Sums andproducts of trigonometric functions. Equation of line and plane in threedimensions.

Module II 8 hoursDifferential and Integral Calculus: Methods of differentiation. Elementarymethods of integration. Partial differentiation: Partial derivative and total derivativeof functions of more than one variable. Euler's theorem. Cartesian, cylindricaland spherical coordinate systems and transformation rules. Vector Calculus:Properties of Gradient, divergence and curl. Line integrals. Area, surface andvolume.

Module III 8 hoursRepresentation of a complex number. Modulus and amplitude of a complexnumber. Cauchy's integral formula. Residue theorem and contour integration.Ordinary Differential equations: Solution of differential equations of first orderand first degree using the method of separation of variables. Brief descriptionof other methods of solving first order differential equations (no numericals).Simultaneous linear equations with constant coefficients. Cauchy's and Legendre'slinear equations.

Module IV 8 hoursPartial differential equations: The Laplacian in cartesian and cylindricalcoordinates. Poisson's equation. Taylor series (statement only, no proof ornumericals). Elementary properties of Fourier series and Fourier transforms.Laplace transformation of elementary functions, derivatives and integrals.Convolution theorem. Applications to solution of ordinary differential equationsand simultaneous linear differential equations with constant coefficients.

Module V 8 hoursIntroduction to Univariate (normal, poisson and extreme value distributions) andmultivariate distributions. ANOVA, Regression analysis. Linear discriminantanalysis. Principle components analysis. Partial least squares. Principlecomponents regression. Support vector machines (No Numericals for this unit).Markov chains. Hidden markov models. Viterbi algorithm, Parametric estimationfor HMM's (Baum-Welch and Viterbi training). EM algorithm. (Numericalproblems only for Markov chains).

Text Book(s)1. E. Kreyszig. Advanced engineering mathematics, 10/e, Willey, 20102. B.S.Grewal, Higher Engineering Mathematics, 43/e, Khana Publishers, 2014.3. V.Venkateshwara Rao, N. Krishna Murthy, B.V.S.S. Sarma, Intermediate

Mathematics, Volume I & II , S.Chand, 2003

45

EBTXXX: INTRODUCTION TO BIOCHEMICALENGINEERING

L T P C4 0 0 0

Module I 8 hoursFluid Mechanics : Properties of Fluids, Types of Fluids, Laminar and TurbulentFlow, Basic equations of fluid flow: Conservation of mass, conservation of energy,Boundary Layer, Hagen-Poiseuille equation, Flow through porous media,Fluidization.

Module II 8 hoursConduction: Fourier’s Law of Heat Conduction, Conduction through a compositeplane wall. Conduction through resistances in parallel. Convection: Definitionsof Natural convection and forced convection, individual heat transfer coefficients,correlations for calculation of heat transfer coefficients, Heat Transfer with phasechange, overall heat transfer coefficient, LMTD. Radiation: Black body Radiation,Radiation from the sun. (Note: Problems may come from conduction througha composite plane wall only)

Module III 8 hoursDiffusion: Fick’s Law, Diffusivity of fluids, Steady State diffusion of fluids. Interphase Mass Transfer: Mass Transfer coefficient, relation between mass transfercoefficients, overall mass transfer coefficient. Absorption: Choice of solvent forabsorption, material balance for counter current

Module IV 8 hoursDistillation: 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 singlestage extraction operation.(Note: Distillation problems may be given on Mc-Cabe-Thiele method only).

Module V 8 hoursChemical Reaction Engineering & Bioreactor Design: Kinetics of Homogeneousreactions, single and multiple reactions. Elementary & Non elementary reactions;molecularity and order of reactions; representation of reactions; testing kineticmodels. Temperature-dependent term of a rate equation. Interpretation of BatchReactor Data: Constant Volume Batch Reactor; Integral Method of Analysis;Differential variable – Volume Batch Reactor. Simple problems based on the threechapters. Single Ideal Reactors: Performance equations for batch reactors, FedBatch reactors, MFR and PFR.

Text Book(s)1. Salil K. Ghosal, Siddhartha Datta, Introduction to Chemical Engineering, Tata

Mc Graw Hill Education, 2011.2. Octave Levenspiel, Chemical Reaction Engineering, 3/e, John Wiley & Sons

(Asia), 1999.

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EBTXXX: MOLECULAR BIOLOGY AND GENETICENGINEERING

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Module I 8 hoursGenome 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.

Module II 8 hoursReview of transcription and translation. Regulatory mechanisms.Posttranscriptional regulatory mechanisms. SnRNPs. Spliceosome structure andfunction. Posttranslational regulatory mechanisms. MicroRNAs. RNAi. Casestudy: Transcriptional regulation in mycobacteria.

Module III 8 hoursMajor signal transduction pathways and regulation of the Cell cycle. Transportmechanisms. Regulatory mechanisms of metabolic and signal transductionpathways: feedback and feedforward controls. Case study: Signal transductionsystems of mycobacteria.

Module IV 8 hoursMethods: DNA sequencing by Sanger's method. High throughput DNAsequencing methods. Protein sequencing by Edman degradation and by Massspectrometry. Oligonucleotide synthesis. Solution phase and solid phase peptidesynthesis.

Module V 8 hoursReview of transformation, transduction and conjugation in bacteria. Restrictionand ligation. Construction and screening of libraries. Site-specific, casettemutagenesis and transposon based mutagenesis. Introduction to PCR andmicroarray technology.

Text Book(s)1. H.D. Watson, T.Baker, S.P.Bell, A.Gann, M.Levine, R.Losick. Molecular

Biology of the gene, 6/e, Benjamin Cummings, 2007.2. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter,

Molecular biology of the cell, 4/e, Garland publishers, 2002.

References1. H. Lodish, A. Berk, S. L. Zipursky, P. Matsudaira, D. Baltimore and J. Darnell,

Molecular cell biology, 5/e, W.H.Freeman, 2003.2. J.D. Watson, R.M. Meyers, A.A. Caudy and J.A. Witkowski, Recombinant

DNA: genes and genomes - A short course, 3/e, W.H. Freeman and Co, 2007.3. S.B. Primrose, R. Twyman, B. Old, Principles of gene manipulation, 6/e,

Wiley-Blackwell, 2001.

Chandrahas Bhavan - Institute of Technology, Visakhapatnam Campus

Institute of Technology, Hyderabad Campus

Sir Visweswaraiah Bhavan - Institute of Technology, Bengaluru Campus

Gandhi Nagar Campus, Rushikonda,Visakhapatnam-530 045, A.P. INDIAPhones: 91-0891-2795311,2840501 EPABX:91-891-2790101 Fax:91-891-2795311

A Publication of GITAM University Press

GANDHI INSTITUTE OF TECHNOLOGY AND MANAGEMENT (GITAM)