M.

Tech Biotechnology Syllabus

(Approved by 110th Executive Council vide Dated 09th November 2021)

SCHOOL OF BIOTECHNOLOGY
(An Autonomous University Teaching Department)
RAJIV GANDHI PROUDYOGIKI VISHWAVIDYALAYA
(State Technological University of Madhya Pradesh)
Airport Road, Bhopal-462033
www.rgpv.ac.in; www.sobtrgpv.com
 CURRICULUM OUTLLINE

M. Tech.[BIOTECHNOLOGY]

Core Subject

SEMESTER-I SEMESTER-II
» MBT-101 Engineering Mathematics » MBT-201 IPR, Bio-safety, Bioethics
Computational Biology & Bio-simulations and Bioentrepreneurship

» MBT-102 Cell & Molecular Biology » MBT-202 Advanced Downstream

Processing

» MBT-103 Bioprocess Engineering » MBT-203 Immunotechnology

» MBT-104 Advanced Biochemistry & » MBT-204 Stem Cell Technology &
Metabolic Engineering Tissue Engineering

» MBT-105 Genomics & Genetic Engineering » MBT-205 Proteomics & Protein

Engineering

SEMESTER-III SEMESTER-IV
» MBT-301 Research Methodology » MBT-401 Dissertation
» MBT-302 Scientific Skills
» MBT-303 Project Synopsis
» MBT-304 Seminar
» MBT-305 Comprehensive Analysis
 STUDENTS ONE MONTH ENTREPRENEURSHIP/RESEARCH
TRAINING AND VISIT TO LAB, INDUSTRIES ETC
 M.Tech (Biotechnology) students shall be compulsory trained themselves in the field of
entrepreneurship and recent trends in Biotechnology by caring out one-month
Entrepreneurship/Research Training in various Industries/labs of the National / International
Repute.
 Visit to various Industries for Entrepreneurship Training viz. Fermentation, Bio-
simulations, Therapeutic, etc.
 Lab visits for Research Training to know the Recent Trends with High Throughput
Technology.

GUIDE LINES FOR PROJECT WORK

 For M. Tech. II year (III & IV Semester) students a project work shall be compulsory.
 The project shall be carried out under the supervision of departmental faculty members or in
collaboration with industry / national / international academic institutions.
 The project work shall be of one-year duration of one project divided in two semesters III &
IV.
 The project synopsis and research methodology in III semester of the same project shall be
evaluated by the two external examiners of the national / international repute.
 The seminar based on research paper that is one of the base papers of the same project shall
also be evaluated by the external examiner of national/ international standing.
 The candidate shall be required to submit the one project report printed in triplicate after
publication of one research and one review article in the peer reviewed journals at the end
of the fourth semester/ before obtaining the M.Tech degree.
 There shall be thesis evaluation by external examiner of national / international status.
 After receiving the evaluation report from the concerning examiner, suggestion/s suggested
by the concerning examiner (if any) should be incorporated in the thesis.
 Then the candidate shall be eligible for examination and defense / viva-voce of research
project at the end of the IV semester.
 ATTENDANCE
 Candidates appearing as regular students for any semester examination shall be required to
attend at least 75% of lecturers delivered and of the practical’s held, separately in each paper,
provided that a short fall in attendance up to 5% can be condoned by the Vice Chancellor of
Rajiv Gandhi Proudyogiki Vishwavidyalaya, Bhopal respectively for satisfactory reasons.

Note: If a candidate has passed a semester examination in full he/she shall not be permitted to
reappear in the examination for improvement of division/marks of any other purpose.

CRITERIA FOR PROMOTION TO HIGHER SEMESTER

According to Ordinance No.8 (A) for degree in Master of Engineering/Technology/Master of

Architecture (M.E/M.Tech/M.Arch.) for the Candidates admitted in 1st year on/after July, 2010,
under Credit Based Grading System applicable from July, 2010, the criteria for promotion to
higher semester is as follows:

 For the award of degree minimum Cumulative Grade Point Average (CGPA) required is
5.0.
 To pass a particular subject of the course the minimum required grade is D. However, the
candidate should also separately score minimum required of grade D in both mid and end
semester examinations of theory and practical parts of the subject individually.
 The distribution of weightage/marks for each component are as following :

Theory Block
i) Quizzes, assignments and regularity 10%
ii) Mid-semester tests 20%
iii) End-semester Examination 70%
Total 100%

Practical Block
i) Lab work and performance, quizzes,
assignments and regularity 40%
ii) End-semester examination 60%
Total 100%

 Project work shall be treated as practical subject.

The grades to be used and their numerical equivalents are as under:

 Credit Based Grading System

Grade % Marks range Grade Point Description of

(based on absolute performance
marks system)

A+ 91-100 10 Outstanding

A 81-90 9 Excellent

B+ 71-80 8 Very Good

B 61-70 7 Good

C+ 51-60 6 Average

C 41-50 5 Satisfactory

D 40 only 4 Marginal

F Below 40 0 Fail

I 0 Incomplete

W 0 Withdrawal
 School of Biotechnology
(An Autonomous University Teaching Department)
Rajiv Gandhi Proudyogiki Vishwavidyalaya, Airport Road, Bhopal

Programme Outcomes (POs), Program Specific Outcomes (PSOs) and

Course Outcomes (COs) of the Programmes offered by the Institution

Programme Code Programme Name Institution

MT M. Tech Biotechnology School of Biotechnology

Programme Outcomes (POs)

PO 01 An ability to Independently carry out Research /Investigation and Development Work

to solve Practical Problems.
PO 02 An ability to Write and Present a Substantial Technical Report/Document.
PO 03 Students should be able to Demonstrate a Degree of Mastery over the area as per the
specialization of the Program. The mastery should be at a level higher than the
requirements in the Appropriate Bachelor Program.
 Programme Specific Outcomes (PSOs)

PSO 01 Acquire knowledge on the fundamentals of Biotechnology for Sound and Solid base
which enables them to understand the Emerging and Advanced Engineering concepts
in Life Sciences.
PSO 02 Acquire knowledge in domain of Biotechnology enabling their applications in Industry
and Research.
PSO 03 Students will be equipped to understand three fundamental aspects in Biological
Phenomenon: a) what to seek; b) how to seek; c) why to seek?
PSO 04 Empower the students to acquire Technological Knowledge how by connecting
Disciplinary and Interdisciplinary aspects of Biotechnology.
PSO 05 Recognize the importance of Bioethics, IPR, Entrepreneurship, Communication
and Management Skills so as to use Next Generation of Industrialists.
PSO 06 Inculcate the applicative knowledge of Engineering and Applied Science
to demonstrate Research Aptitude/Skills in Emerging fields of Biotechnology.
PSO 07 Exhibit adequate proficiency of Good Lab Practices (GLP) and Good Manufacturing
Practices (GMP) in terms of Accuracy & Precision, Safety, Ethics and
Reproducibility and able to follow Standard Operating Procedures (SOP).
PSO 08 Use Research-Based Knowledge and Research Methods in the field of Biotechnology
Engineering to conduct Experiments, Analyze and Interpret the Data, Design the
Equipment’s and Processes as per the specifications and needs of Biotech Industries.
PSO 09 Create, Select, and Apply Appropriate Techniques, Resources, and Software Tools
including Prediction and Modelling to complex Engineering activities with an
understanding of the limitations.
PSO 10 Apply reasoning gained from the contextual knowledge of Biotechnological
Engineering to assess Societal, Health, Safety, Legal and Cultural issues and the
consequent responsibilities relevant to the Professional Engineering Practice.
PSO 11 Understand the impact of the Biotechnological solutions in Societal and
Environmental contexts, and demonstrate Acquired Skills for Sustainable Development.
PSO 12 Apply Ethical Principles and commit to Professional Ethics, Responsibilities and
Norms of the Biotechnology Engineering Practice.
PSO 13 Function effectively as an Individual, and as a Member or Leader in Diverse Teams,
and in Multidisciplinary Environments.
PSO 14 Communicate effectively on complex Biotechnology Engineering activities with the
Engineering Community and with Society at large, such as being able to make
Effective Presentations, Write Effective Reports and Design Documentation.
PSO 15 Demonstrate knowledge and understanding of the Biotechnology Engineering and
Management Principles and apply these to one’s own work, as a Member and Leader
in a team, to manage projects in Multidisciplinary Environments.
PSO 16 Recognize the need for, and have the preparation and ability to engage in independent
and life-long learning in the broadest context of Biotechnology Engineering and
Technological Change.

PSO 17 Students after finishing this course can become entrepreneurs in the most demanding
sectors of Biotechnology such as Molecular Medicine, Biomaterials, Fermentation
Technology, Vaccinology, Genetic Engineering, etc.
 Methods of measuring attainment of PSOs
 Programme Specific Outcomes are ascertained by Periodic Review of the Teaching and
Research Activities at the Institute and Presentation of the progress at leading National and
International Journals as Research Publications.

 Further Independent Expert Reviews and Teaching Seminars are also conducted for
Evaluating the Teachers and Students for keeping the Morale and Scientific Temper and for
the whole some development of Education and Research Activities of the Department.

Course Outcomes (COs)

Semester -I

S. No. Name of the Course Code Course Outcomes

Course
01. Engineering MBT- 101 Students should be able to:
Mathematics,  Understand and apply the Mathematics &
Computational Biostatistics in various Research Areas in
Biology & Bio- Biological Sciences.
simulations  Know standard Techniques of Complex Variable
Theory to apply them with confidence and to
acquire concepts of Differential Equations and
calculus needed for solving the Problem in all
Disciplines.
 Appreciate their relevance for Investigating Specific
Contemporary Biological Questions.
 Solve the Problems of Integration and
Differentiation of functions of two variables and
know about the Maximization and Minimization of
functions of several variables.
 Understand and solve the Problems Correlation and
Regression Analysis.
 Understand and solve the Problems of Probability,
also come to know the Problems of Measures of
Central Tendency and their Applications in
Different Science and Engineering Field.
 Provide Theory and Practical Experience of the use
of common Computational Tools and Databases
which facilitate Investigation of Molecular Biology
and Evolution-Related Concepts.
 Develop an understanding of Basic Theory of these
Computational Tools.
 Gain working knowledge of these Computational
Tools and Methods.
 Analyze and Interpret Results of their study.
02. Cell & Molecular MBT- 102 Students should be able to:
Biology  Know the fact that as we go down the scale of
magnitude from Cells to Organelle to Molecules, the
understanding of various Biological Processes
becomes Deeper and Inclusive.
 Understand Membrane Transport and Cell
Signaling Mechanisms.
 Develop comprehensive understanding of Endo-
Membrane System.
 Understand Molecular Mechanisms of Prokaryotes
and Eukaryotes.
 Know the life with Molecular functionalities
Instinct of targets for control and Manipulation of
Cellular Processes for Research and Development.

Bioprocess MBT-103 Students should be able to:

03. Engineering ● Plan a Research Career or to work in the
Biotechnology Industry with strong foundation
about Bioreactor Design and Scale-up.
● Appreciate relevance of Microorganisms from
Industrial Context.
● Carry out Stoichiometric Calculations and specify
models of their growth.
● Give an account of Design and Operations of
various Bioreactors and Downstream Processes.
● Calculate Yield and Production rates in a Biological
Production Process, and also Interpret Data.
● Critically Analyze any Bioprocess from market
point of view.
● Give an account of important Microbial/Enzymatic
Industrial Processes.
● Apply Modeling and Simulation of Bioprocesses
so as to reduce costs and to enhance the Quality of
Products and Systems.

04. Advanced MBT-104 Students should be able to:

Biochemistry & ● Gain fundamental Knowledge in Biochemistry.
Metabolic ● Understand the Biochemical Principles with specific
Engineering Emphasis on different Metabolic Pathways and
Regulators.
● Understand the Molecular Basis of Various
Pathological conditions from the perspective of
Biochemical Reactions.
● Demonstrate the Knowledge of Stoichiometry and
Energetics of Metabolism.
● Apply Practical applications of Metabolic
Engineering in Chemical, Energy, Medical and
Environmental fields.
● Integrate Modern Biology with Engineering
Principles.
● Design a system, Component, or Process to meet
desired needs.
05. Genomics and MBT-105 Student should be able to:
Genetic  Describe fundamental Molecular Principles of
Engineering Genetics.
 Understand relationship between Phenotype and
Genotype in Human Genetic Traits.
 Describe the basics of Genetic Mapping.
 Understand how Gene Expression is Regulated.
 Know the basics of Genetics and Classical Genetics
covering Prokaryotic/Phage Genetics to Yeast and
Higher Eukaryotic Domains.
 Develop an ability to Design and Conduct Genetic
Engineering Experiments, as well as to Analyze and
Interpret Data.
 Demonstrate and perform various approaches to
conduct Genetic Engineering Experiments and their
applications in Biomedical Research as well as in
Biotechnology Industries.

Students should be able to:

6. Lab-I MBT-106  Perform Major Experiments in Cell Biology and
Bioprocess Engineering.
 Work well and carefully in Laboratory Environment
and with Laboratory Instruments.
 Gain Hands on Training to Spectrophotometrically
Analysis of Biomolecules.
 Demonstrate an understanding of Solving Problems
for Mass Balance and Energy Balance and Equations
Numerically.
 Access, Retrieve, and Analyze Nucleotide and Protein
Sequences using Bioinformatics Tools.
 Predict structure of Biomolecules and learn Sequence
Alignment of Biomolecules using Bioinformatics
Tools.
 Perform separation of different Organelles/Molecules
by Sucrose Density Gradient/Differential Gradient.
 Develop comprehensive concepts on various
processes in Bioreactors Mediated Microbial Process.
 Apply Engineering Principles to Address Issues in
Bioprocesses and Delineate Problems Associated with
production of Biomolecules in Bioreactor.
 Understand the scope of Cytogenetics and its
Applications.
07. Lab-II MBT-107 Students should be able to:
 Acquire Laboratory Skills Involved in Genetic
Engineering and Advanced Biochemistry.
 Understand the handling of laboratory instruments
and chemicals involved in Genetic Engineering.
 Understand the implications of rDNA techniques from
the subject area concepts, Experimentally Research
and Health-care Perspectives
 Skillfully perform basic Experiments in Genetic
Engineering and Gene Transfer Techniques.
 Perform major Basic Techniques in Biochemistry and
Basic Techniques in understanding Biomolecules and
Biophysical Techniques.
 Perform experimental foundation of Classical and
Molecular Genetics.
 Develop comprehensive concept of Genetic
Engineering including Vectors and Techniques.
 Demonstrate Microbial and Immunological
Techniques. Understand Chromosome Structure and
solve Genetic Problems.
 Demonstrate an understanding of production and
estimation of Commercially Important Molecules.
Hands on training related to Genetic Manipulation
Techniques.
 Understand the scope of Genomics with special
emphasis on Functional and Structural Genomics.
 Develop the Research Aptitude and Technical Skills
to secure a job in Genetic Engineering labs.
 Course Outcomes (COs)
Semester –II

S. No. Name of the Course Course Code Course Outcomes

01. IPR, Bio-safety, MBT-201 Students should be able to:

Bioethics and  Understand the Professional and Ethical
Bioentrepreneurship Responsibilities.
 Have a Knowledge of Contemporary Issues.
 Understand the Ethics and Responsibility for
Biosafety and Biosecurity.
 Create awareness for the Professional
Responsibilities and Rights.
 Offer the importance of Intellectual Property
Rights for the Technologies.
 Develop an understanding of utilizing cost data in
Planning and Control.
 Apply cost concepts and cost behaviors in the
solving of management decision.
02. Advanced MBT-202 Students should be able to:
Downstream  Understand developments/ advances made in field of
Processing Microbial Technology for use of Human Welfare
and Solving Problems of the Society.
 Provide basic concept about Cellular Metabolism,
Pathway Design and Bioenergetics.
 Understand Regulatory Mechanisms and Metabolic
Modeling.
 Develop Analytical Skills to address Metabolic
Engineering Problem.
 Develop deeper understanding of the Industrial
Biotechnology and its applications.
03. Immunotechnology MBT-203 Students should be able to:
 Learn about structural features of components of
Immune System as well as their function.
 Understand development of Immune System and
Mechanisms by which our body Elicits Immune
Response.
 Predict about nature of Immune Response that
develops against Bacterial, Viral or Parasitic
Infection, and prove it by Designing new
Experiments.
 Apply knowledge of Immunology in Health and
Diagnostic Purposes.
 Utilize Immunology Principles to Design Novel
Therapeutics and New Therapeutic Strategies.
04. Stem Cell MBT-204 Students should be able to:
Technology &  Develop skills for application of Tissue Culture
Tissue Engineering  Introduce the Principles, Practices and Application
of Animal Biotechnology in Tissue Engineering,
Vaccines and Biopharmaceuticals.
 Pursue research related to Stem Cell/Animal Cell
and Tissue Culture at National and International
level.
 Contribute in Industries Related to Animal Cell
Culture as Scientists.
 Develop a solid foundation and requisite Research
Aptitude for further higher studies on Epigenetic
Analysis, Regulation of Stem Cells and
Regenerative Medicines.
 Become competent to secure a job in
Biopharmaceutical and Biomedical Industry.
05. Proteomics and MBT-205 Students should be able to:
Protein Engineering  Understand various facts of Molecular Procedures
and basics of Proteomics and Protein Engineering.
 Apply methods for functional characterization of
theRecombinant Protein Product.
 Apply selected aspects of Protein Engineering in an
Industrial Environment.
 Explain about recent advances in various faces of
Molecular Medicine which has potential to
profoundly alter many aspects of Modern Medicine.
 In practical terms, carry out Site-Specific
Mutagenesis, i.e., based on a known Amino Acid
Sequence, Replace an Amino Acid in a Soluble
Protein or Membrane Protein, Produce the Mutant
Gene.
06. Lab-III MBT-206 Students should be able to:
 Explain role of Biotechnology in Sustainable
Research and various Ethical Implications.
 Understand importance of Biosafety and Biosafety
level its necessity and legislations and Experiments
how to file Patents.
 Perform production and scale up of some
Industrially Relevant Bioactive Molecules from
Microbes.
 Demonstrate and perform various Cellular
Metabolism, Pathway Design and Bioenergetics.
 Understand regulatory Mechanisms and
Metabolic Modeling.
 Develop Analytical Skills to address Metabolic
Engineering Problem.
 Gain hands on training for Experiments related
to Properties of Enzyme.
07. Lab-IV MBT-207 Students should be able to:
 Develop comprehensive concepts of Cell and
Tissue Culture Techniques and Methodology.
 Gain fundamental concepts of in vitro
Fertilization and Animal Cloning.
 Apply applications of cell and tissue culture in
Medical Biotechnology.
 Acquire the required laboratory Skills to Perform,
Interpret and Analyze Core/Widely used Immune
Techniques.
 Perform the Techniques and Relate to Health Care,
and to Integrate the Skill into to Research and
Development.
 Understand the principle and various types of
Chromatography.
 Understand and apply the concept and application of
Electrophoresis.
 Understand, learn and perform skillfully the various
Analytical Techniques. 
 Describe role of Proteomics and Various
Associated Techniques.
 Demonstrate practical insight of Techniques and
Tools applied in Proteomics.

 Course Outcomes (COs)
Semester-III

S. No. Name of the Course Course Code Course Outcomes

01. Research MBT-301 Students should be able to:

Methodology • Select Research Methodologies based on need,
Circumstance, and Objectives of the Study.
• Understand some basic concepts of Research and
its Methodologies.
• Identify appropriate Research Topics.
• Select and define appropriate Research Problem
and Parameters.
• Prepare a Research Project Proposal to undertake
a Research.
• Organize and conduct Research in a more
Appropriate Manner.

02. Scientific Skills MBT-302 Students should be able to:

 State and elucidate some instances of Realistic
Knowledge of Scientific Databases, Science
Inquiry & Research and Scientific Development of
Assessments.
 Synthesize information from Numerous Sources
and a variety of Perspectives.
 Write a Research Report and Thesis.
 Write a Research Proposal.

03 Project Synopsis MBT-303 Students should be able to:

 Estimate the authority of information from various
sources e.g., Peer-Reviewed Journals Research
Articles or Magazines.
 Organize information systematically and formulate
questions for Research of an Appropriate Scope,
based on Information/Research Gaps or by
Reexamining Existing Information.
 Develop plans and find out the Gap in the Relevant
Research Area and to Develop a Plan to
achieve the Project's Goals.
 Break work down into Objectives and Determine
Relevant Procedures.
 Gain experience in Writing a Scientific Proposal in
the form of Synopsis with the Relevant Outcomes
and Significances of the Proposed Work.

04. Seminar MBT-304 Students should be able to:

● Prepare and Deliver Seminars to Develop
Communication Skills.
● Develop the ability to Speak and Debate with an
Appreciation.
Collaborate with others as they work on
Intellectual Research Projects.
 ● Prepare appropriately to participate effectively in
Class Discussion.
● Follow Discussions, Oral Arguments, and
Presentations, noting main points or evidence and
tracking threads through different comments.
 Confront and offer substantive replies to others
Arguments, Comments, and Questions from the
Audience.
05. Comprehensive MBT-305 Students should be able to:
Analysis  Perform Close and Critical Scientific Readings.
 Recognize the Disciplinary context for diverse
variety of Scientific Writing.
● Differentiate opinions and beliefs from
Researched Claims and Facts.

Course Outcomes (COs)

Semester -IV

S. No. Name of the Course Course Code Course Outcomes

01. Dissertation MBT-401  The purpose of this course is to help students

Organize Ideas, Material and Objectives for their
Dissertation and to begin development of
Communication Skills and to Prepare the students
to present their topic of Research and Explain its
Importance to their Fellow Classmates and
Teachers.
 Understand the basic concepts of Ethics in Proper
Conduct of Research.
 Understand about Plagiarism in Research and how
it should be avoided.
 Gain a clear idea about the importance of proper
Data Documentation.
 Students will have a clear idea about the Research
Methodologies that need to be adopted during their
Research Plagiarism, Regulatory Principles, Safety
in Research, Ethics in Stem Cell Research, Ethics
in Clinical Research, Ethics in Nanomaterials
Based Research Principles of Data Documentation,
Protocol Development, Research Questions and
Hypothesis Driven Research.
 After Completion of this course the students
should be able to demonstrate the following
abilities:
• Formulate a Scientific Question.
• Present Scientific Approach to solve the Problem.
• Interpret, Discuss and Communicate Scientific
Results in Written form.
• Gain experience in writing a Scientific
Proposal,
Thesis and Research Article.
• Learn how to Present and Explain their Research
Findings to the audience effectively.
 SEMESTER-I
MBT 101: ENGINEERING MATHEMATICS, COMPUTATIONAL BIOLOGY &
BIO-SIMULATIONS

Module-I: Integration and Differentiation

Integration

Integration by Parts, Integration by substitution, integration by Partial Fraction.

Differentiation
Derivative of a function, product rule, quotient rule and chain rule of differentiation, successive
differentiation, application of derivatives. First and second order differentiation; Maxima and
minima; Homogenous Differential Equation and Variable Separation; Linear Differential
equation with constant and variable coefficient.

Module-II: Correlation and Regression

Correlation
Types of Correlation, Coefficient of Correlation, Methods of computing Coefficient of
Correlation, Scatter diagram, Karl Pearson Correlation, Spearman Rank Correlation; Partial and
Multiple correlation.
Regression
Simple and multiple regressions, linear and nonlinear regression.

Module-III: Biostatistics
Measures of central tendencies and dispersion; Coefficient of variation
Probability- Axiomatic definition; Addition theorem; Conditional probability; Bayes’ theorem;
Random variable; Mathematical expectation. Theoretical distribution- Binomial, Poisson,
Normal and Standard normal distribution.
Sampling parameter; Static and standard error; Census and Sample methods; Method of
sampling (Probability and non-probability sampling). Null and alternative hypothesis; Type I and
type II errors; Level of significance; Large sample test; Test of significance of single and two
sample means; Test of significance of single and two proportion.
Small sample tests- F test; T test (Paired, unpaired); Chi square test goodness of fit, Analysis of
variance (ANOVA) One way and Two ways, Learning software- R statistics.

Module-IV: Essential Bioinformatics

Introduction to bioinformatics algorithms, Basic sequence and structural bioinformatics. Pairwise
and multiple sequence alignment. Methods for phylogenetic analysis and pattern recognition.
Bioinformatics databases and servers. Classification and comparison of protein structures.
Molecular mechanics, Prediction of secondary and tertiary structure from sequence. Homology
modelling of the three-dimensional structure of proteins. Molecular dynamics simulations and
molecular docking with applications to drug design.

Module-V: Computational Systems Biology and Biomolecular Simulations

Constructing computational model of a molecule, Mathematical modeling and simulating of
Biochemical Network, SBML, Creating and Visualizing a Simple Network Model, Analysis of
biological networks for feature detection, Integrating Biological Networks and Microarray
Expression data, Analyzing the network by finding sub modules.
Lab on Engineering Mathematics

a) Exercises based on biostatistics.

b) Statistical analysis through R.
c) Construction of Cladogram
d) Homology Modeling
e) Surface Analysis of a Protein Using CASTp
f) Finding the Active Site Pockets of a given Protein Molecule
g) Predict the structure of Protein-Homology Modeling
h) To check for the drug receptor interaction using docking studies
i) To calculate the absorption and distribution rate of a drug
j) To predict the toxicity of drug molecule using in silico approaches
k) Creating and Visualizing a Simple Network Model.

Text (Latest Edition)

1. B.S. Grewal. Higher Engineering Mathematics, Khanna publishers.

2. P.S.S. Sunder Rao, P.H. Richard, J.Richard. An introduction to Biostatistics, Prentice
Hall of India (P) Ltd., New Delhi.
3. Gupta S.P. Statistical Methods, Sultan Chand & Sons, New Delhi.
4. Povl Krogsgaard Larsen, Tommy Liljefors and Ulf Madsen, “Textbook of Drug Design
and Discovery”, Dev Publishers & Distributors.
5. Rastogi et. al., “Bioinformatics: Methods and Applications”, Prentice Hall of India.
6. Claverie & Notredame, “Bioinformatics - A Beginners Guide”, Wiley-Dreamtech India
Ltd.
7. P. Narayanan, Bioinformatics: A Primer, New Age International Publishers.
8. Dalgaard, P. Introductory statistics with R. New York: Springer.
9. Bain, L.J. & Engelhardt, M. Introduction to probability and mathematical statistics.
Pacific Grove: Duxbury.

References (Latest Edition)

1. Rangaswamy R. A text book of Agricultural Statistics, New Age International (P) Ltd.,
New Delhi.
2. Panse V.G.Panse, P.V. Sukhatme. Statistical methods for Agricultural Workers, ICAR
Publications, New Delhi.
3. Jerrold H. Zar. Bio Statistical Analysis, Tan Prints (I) Pvt. Ltd., New Delhi.
4. Chandel, S.R.S. A Hand Book of Agricultural Statistics, Achal Prakashan Mandir,
Kanpur.
5. C.N. R. Rao. University General Chemistry, Mc Millan Publication.
6. A.S.Negi & S.C.Anand. A Text Book of Physical chemistry.
7. Rob lewis and Wynne evans. Chemistry, Palgrave foundations.
8. Relevant articles from scientific journals.
9. Peter Dalgaard Introductory Statistics with R.
 MBT 102: CELL AND MOLECULAR BIOLOGY

Module-I: Cell cycle and Genome Organization

Genome Organization in prokaryotes and eukaryotes - DNA content and C-value paradox -
methods to measure DNA content variation - Various types of DNA sequences – simple
sequences, repetitive sequences, Junk DNA or selfish DNA, tandem gene clusters, satellites
Variety of DNA structures: double helix, Z-DNA, B-DNA, Mechanism of DNA replication:
prokaryotes and eukaryotes, Overview of the cell cycle, Factors involved in cell cycle, Mitosis,
Meiosis, cell cycle control, cell check points.

Module –II: Replication and Cell Signaling Mechanisms

DNA replication models, mode of action, DNA damage, DNA repair and recombination,
Organization structures and function of ribonucleoproteins; Photoreactivation; Nucleotide
excision repair; Mismatch correction; SOS repair; Recombination: Homologous and non-
homologous; Site specific recombination; Chi sequences in prokaryotes; Gene targeting; Gene
disruption; Signal transduction, primary and secondary messengers, involvement of G proteins,
protein kinases, serine, threonine and tyrosine kinases, mechanism of signaling by steroids, cell
death.

Module – III: Prokaryotic & Eukaryotic Transcription

Prokaryotic Transcription; Regulation of transcription, Termination-Rho-dependent and
independent, Attenuation; Transcriptional regulation-Positive and negative; Operon concept-lac,
trp, ara, his, and gal operons; Transcriptional control in lambda phage; Anti-termination,
Transcript processing; Processing of tRNA and rRNA Eukaryotic transcription and regulation;
RNA polymerase structure and assembly; RNA polymerase I, II, III; Eukaryotic promoters and
enhancers; General Transcription factors; TATA binding proteins (TBP) and TBP associated
factors (TAF); Activators and repressors; Transcriptional and posttranscriptional gene silencing

Module – IV: Post Transcriptional Modifications

Processing of hnRNA, tRNA, rRNA; 5'-Cap formation; 3'-end processing and polyadenylation;
Splicing; RNA editing; Nuclear export of mRNA; mRNA stability; Catalytic RNA.
Translation & Transport
Translation machinery; Ribosomes; Composition and assembly; Universal genetic code;
Degeneracy of codons; Termination codons; Isoaccepting tRNA; Wobble hypothesis;
Mechanism of initiation, elongation and termination; Co- and post-translational modifications;
Genetic code in mitochondria; Transport of proteins and molecular chaperones; Protein stability;
Protein turnover and degradation.

Module – V: Diverse type of Oncogenesis

Viral and cellular oncogenes; Tumor suppressor genes from humans; Structure, function and
mechanism of action of pRB and p53 tumor suppressor proteins; Activation of oncogenes and
dominant negative effect; Suppression of tumor suppressor genes; DNA virus/ cell
immortalization,Oncogenes as transcriptional activators.
Case studies.

Lab on Cell & Molecular Biology

1. Isolation and Quantitation of cellular macromolecules (DNA, RNA and Protein).
2. cDNA Synthesis
 3. Transformation and Preparation of competent cells.
4. Antibiotics sensitivity test on microbial cultures
5. Agarose gel electrophoresis of DNA fragments.
6. SDS PAGE for resolution of proteins.
7. Elution of DNA from an agarose gel.
8. Preparation of metaphase Chromosome.
9. Karyotyping and banding Pattern (G-banding).
10. Preparations of blood smear for study of sex chromatin.

Text Books (Latest Edition)

1. Albert et al., Molecular Biology of the Cell, Garland.

2. G. Karp. Cell and Molecular Biology, John Wiley & Sons.
3. J.D. Watson, N.H. Hopkins, J.W Roberts, J. A. Seitz & A.M. Weiner. Molecular
Biology of the Gene, Benjamin Cummings Publishing Company Inc.
4. Benjamin Lewin. Gene IX, Jones and Barlett Publishers.

Reference Books (Latest Edition)

1. Rober A. Meyers. Encyclopedia of Molecular Cell Biology and Molecular Medicine,

Wiley-VCH Verlag GmbH & Co. KGaA.
2. J.M. Walker, R. Rapley. Molecular Biology and Biotechnology, Royal Society of
Chemistry.
3. Gabi Nindl Waite, Lee R. Waite. Applied Cell and Molecular Biology for Engineers,
McGraw Hill.
4. Thomas Pollard, Saunders. Cell Biology.
5. Dornall and Baltmore. Scientific publisher, USA.
6. Lodish et al., Molecular cell Biology. Freeman & Company.
7. Becker, Klein Smith and Hardin. The world of the cell. Pearson education Inc.
8. De Roberties F. D. P. and De Roberties Junior E.M.F. Cell and molecular biology,
Sounder, Philadelphia.
9. Relevant articles from scientific journals.
 MBT 103: BIOPROCESS ENGINEERING

Module –I: Fundamentals of Bioprocess Engineering

Microbial growth, Factors affecting growth, Growth kinetics and metabolism, Material and
energy balance calculations, Transport phenomenon (mass and energy transfer). Isolation,
screening and maintenance of industrially important microbes, Single cell Isolation, 16sRNA
analysis for characterization of Microbes; strain improvement for increased yield and other
desirable characteristics.

Module-I: Enzyme kinetics

Enzyme catalysis – general principles of catalysis; quantification of enzyme activity and
efficiency; enzyme characterization and Michaelis-Menten kinetics; relevance of enzymes in
metabolic regulation, activation, inhibition and covalent modification; single substrate enzymes;
concept of catalytic antibodies; catalytic strategies with specific examples of proteases, carbonic
anhydrases, restriction enzymes and nucleoside monophosphate kinase; zymogens.

Module –III: Bioreactors and Fermenters

Introduction to bioreactors: General design information; Selection of bioprocess equipment
(upstream and downstream); Specifications of bioprocess equipment; Batch and Fed-batch
bioreactors, Continuous bioreactors; Bioreactor operation; Sterilization; Aeration; Oxygen uptake
rate; KLa determination, Instrumentation; Culture-specific design aspects: plant/mammalian cell
culture reactors, Biosimilar production, fed-batch and perfusion reactors, Fermenters.

Module –IV: Scale up and scale down processes

Scale up and scale down issues: Scale up methods in three classes, Effect of scale on
oxygenation, mixing, sterilization, pH, temperature, Inoculum development, nutrient availability
and supply; Bioreactor scale-up based on constant power consumption per volume, mixing time,
impeller tip speed (shear), mass transfer coefficients, four step scale down procedure, pilot plants
studies.

Module –V: Description of industrial processes

Microbial processes for production of organic acids (citric acid, acetic acid), amino acids
(Lysine, isoleucine, glutamic acid, Arginine), antibiotics (Penicillin, Cephalosporin C,
actinomycin), alcohol, enzymes. Recombinant protein production in microbes e.g. recombinant
insulin; Waste treatment.
Case studies

Lab on Bioprocess Engineering

1. Microbial growth and product formation kinetics.

2. Conventional filtration.
3. Effects of inhibitor on microbial growth.
4. Enzyme immobilization techniques.
 5. Bioconversion using immobilized enzyme preparation.
6. Bioconversion in batch.
7. Mixing and agitation in fermenters.
8. Protein precipitation and its recovery.
9. Membrane based filtration-ultra filtration in cross flow modules and micro filtration.
10. Experiments on KLa determination.

Text Books (Latest Edition)

1. Shuler M. and Kargi F. Bioprocess Engineering: Basic Concepts, Prentice Hall, Englewood
Cliffs, NJ.
2. Doran P., Bioprocess engineering principles, Academic Press.
Reference Books (Latest Edition)
1. Ratledge C., Kristiansen B. Basic Biotechnology, Cambridge University Press.
2. Harrison R. et al., Bioseparations Science and Engineering, Oxford University Press.
3. Harris and Angal S. Protein Purification Methods, Ed. IRL Press at Oxford University
Press.
4. Belter P.A., Cussler E.L., and Hu Wei-Shou. Bioseparations-Downstream Processing for
Biotechnology, Wiley-Interscience Publication.
5. Bailey J. E. and Ollis D. F. Biochemical Engineering Fundamentals, Mc-Graw Hill, Inc.
6. Scopes R. K., Berlin. Protein Purification: Principles and Practice, Springer.
7. Biotol series. Product Recovery in Bioprocess Technology, Butterworth Heinemann Ltd.
8. Relevant articles from Bioprocess journals.
MBT-104: ADVANCED BIOCHEMISTRY& METABOLIC ENGINEERING
Module-I: Enzymes & Bioenergetics
Enzymes
Enzyme classification. Active site, energy of activation, transition state hypothesis, lock and key
hypothesis, induced fit hypothesis. Enzyme activation, various types of enzyme inhibition and
identification using double reciprocal plot. Introduction to Allosteric enzymes.
Definition of holoenzyme, apoenzyme, coenzyme, cofactor, prosthetic group and their examples.
Concept of ribozyme, multiple forms, isozymes and abzymes.
Bioenergetics
TCA cycle and glycolitic cycle, biological order and energy, coupled reaction, electrochemical
potential and redox reaction, osmosis, dialysis, Donnan equilibrium, membrane transport,
Mitochondrial electron transport chain, oxidative phosphorylation, chemical coupling,
conformation coupling and chemiostatic theories for oxidative phosphorylation, uncouplers and
inhibitors of respiratory chain.

Module-II: Analytical Techniques

Electrophoretic methods of separation, Paper and gel electrophoresis, Different variants of
polyacrylamide gel electrophoresis (PAGE) like native and SDS-PAGE, 2D-PAGE, capillary
electrophoresis.
Spectrophotometry: Principles and applications, UV-VIS, Fluorescence, IR and FTIR, Raman,
NMR and FTNMR, ESR and X-Ray spectroscopy.
Hydrodyanmic methods of separation of biomolecules such as viscosity and sedimentation-their
principles, variants and applications.
Tracer techniques in biology: Concept of radioactivity, radioactivity counting methods, concept
of α, β and γ emitters, scintillation counters, γ-ray spectrometers, autoradiography, applications
of radioactive tracers in biology
Microscopy – Bright field, Dark field, Phase contrast and Fluorescence microscopy,
Transmission and scanning, freeze fracture techniques, specific staining of biological materials.

Module-III: Biochemical calculations

Mole concept, Determination of mole wt. by gram molecular volume relationship, problems
based on mole concept, Solutions, colligative properties, Methods of expressing concentrations,
strength, Normality, Molarity & Molality, ppm. Standardization of solutions, Colloids, pH,
buffer systems, dissociation constant, pK value, Preparation of standard solution of acids and
bases, problems related to acid base titrations, volumetric experiments-acidimetry, alkalimetry,
permanganometry, dichrometry, iodometry.

Module-IV: Metabolomics Fundamentals &its Applications

Metabolic pathway databases: ENZYME, EcoCys, MetaCys & KEGG. Metabolite isolation and
analysis by Mass spectrometry, metabolite library, HPLC-capillary electrophoresis coupled with
Mass spectrometry; Metabolome informatics, data integration and mining. Applications of
Metabolomics to biology: Metabolic adaptations during starvation and metabolic profile in
organs. Detoxification and biotransformation of Xenobiotics.
Module -V: Metabolic Engineering
Importance of metabolic engineering, comprehensive models for cellular reactions,
stoichiometry of cellular reactions, reaction rates, dynamic mass balance, yield coefficients and
linear rate equations, the black box model, elementary balance, heat balance, control of
transcription initiation, control of translation, regulation at the whole cell level, branch point
classification, enhancement of product yield and productivity, extension of substrate range,
extension of product spectrum and novel products, improvement of cellular properties. Metabolic
pathways synthesis algorithm, case study- lysine biosynthesis, restriction on the maximum yield,
theory, sensitivity analysis, direct flux determination from transient intensity measurements,
metabolic isotopic steady state experiments.

Lab on Advanced Biochemistry & Metabolic Engineering

1. Extraction of lipids; Separation of lipids using thin layer chromatography.
2. Determination of enzymatic activities and determination of Km, Vmax.
3. Assay of enzyme activity and specifc activity.
4. Immobilization of enzymes by adsorption and covalent binding.
5. Protein precipitation and its recovery.
6. Membrane based filtration- ultrafiltration in cross.
7. Estimation of Amino Acids.
8. Analyzing the enzyme activity.
9. Study the effect of pH and Temperature on enzyme activity.
10. Starch digestion by salivary amylase and products.
11. Study of metabolic pathways using databases MetaCyc & KEGG.
12. Fatty acid extraction from Arabidopsis seedlings.

Text Books (Latest Edition)

1. Principles of Biochemistry - L. Stryer (W.H. Freeman & Co.).
2. Principles of Biochemistry - A.L.Lehninger, D.W.Nelson & M.M.Cox (Macmillan).
3. Tietz Textbook of Clinical Chemistry - Brutis&Ashwood W.B., Saunders Company.

Reference Books (Latest Edition)

1. Biochemistry - D.Voet & J.G.Voet (John Willey).
2. Harper’s Illustrated Biochemistry - R.K. Murray et al. (McGraw Hill).
3. Outline of Biochemistry - Conn & Stump (John Willey & Sons).
4. Protein Science - A.M. Lesk (Oxford Univ. Press).
5. The Enzyme – Dixan& Webb.
6. Keith Wilson & John Walker, Principles & Techniques of Practical Biochemistry,
Cambridge University, Press.
7. Varley’s Practical Clinical Biochemistry Vol. I & II.
8. Pathway Analysis and Optimization in Metabolic Engineering by Néstor V. Torres and
Eberhard O. Voit.
9. Metabolic Engineering: Principles and Methodologies by Gregory N. Stephanopoulos,
Aristos A. Aristidou, and Jens Nielsen.
10. Relevant articles from scientific journals.
 MBT 105: GENOMICS AND GENETIC ENGINEERING
Module-I: Genetic engineering tools
Restriction Enzymes; The range of DNA manipulative enzymes (Nucleases, Ligases,
Polymerases, Modifying enzymes, Topoisomerases); Cohesive and blunt end ligation (Linkers,
Adaptors, Homopolymer tailing); Labeling of DNA (Radioactive and Non- radioactive);
Plasmids; Bacteriophages; M13 mp vectors; pUC19 and Bluescript vectors, Phagemids; Lambda
vectors; Cosmids; Artificial chromosome vectors (YACs; BACs); Animal Virus derived vectors
SV-40; Expression vectors (pMal, GST, pET-based vectors); Protein purification (His-tag, GST-
tag, MBP-tag); Inclusion bodies; Baculovirus vector system, Yeast vectors, Shuttle vectors;
Cloning of PCR products; Cloning vectors for direct cloning of PCR parts.

Module- II: Genomic Analysis

Insertion of Foreign DNA into Host Cells; Construction of libraries; Isolation of mRNA and total
RNA; cDNA synthesis and cloning; genomic libraries; Expression cloning; jumping or hopping
libraries; Southwestern and Farwestern cloning; Protein-protein interactive cloning and Yeast
two hybrid system; Phage display; Hybridization Techniques (Colony Hybridization,
Fluorescence in situ Hybridization); DNA-Protein Interactions (EMSA-Electrophoretic mobility
shift Assay; DNaseI footprinting, Chromatin Immunoprecipitation), Microarray.

Module- III: PCR and Its Applications

Primer design; Fidelity of thermostable enzymes; Types of PCR (multiplex PCR, nested PCR,
reverse transcriptase PCR, real time PCR, touchdown PCR, hot start PCR, colony PCR);PCR in
gene recombination (Deletion; addition; Overlap extension; and SOEing, Site specific
mutagenesis); PCR in molecular diagnostics; Viral and bacterial detection; PCR based
mutagenesis, Mutation detection: SSCP, DGGE, RFLP, Oligo Ligation Assay (OLA), MCC
(Mismatch Chemical Cleavage, ASA (Allele-Specific Amplification), PTT (Protein Truncation
Test).

Module-IV: Post Genomic analysis

Enzymatic DNA sequencing; Chemical sequencing of DNA; Automated DNA sequencing; RNA
sequencing, Next Generation Sequencing using Sequencer; Chemical Synthesis of
oligonucleotides; Gene silencing techniques; siRNA & stRNA technology, CRISPER; Micro
RNA; Construction of siRNA vectors; Principle and application of gene silencing; Gene
knockouts; Creation of knock-out mice; Identification and classification using molecular
markers- ribosomal typing/sequencing; Metagenomics, codon optimization.

Module- V: Genetic engineering applications

Gene therapy in Disease models (Cancer, Diabetes, AIDS, Thalassaemia); Somatic and germ-
line therapy- in vivo and ex vivo; Suicide gene therapy; Gene replacement; Gene targeting;
Transgenics; cDNA and intragenic arrays; Differential gene expression and protein array.

Case studies

Lab on Genomics and Genetic Engineering

 1. Cloning using pUC18 and pBR 322.
2. Transformation of recombinant plasmid in to host.
3. Non-radioactive Random Primer labeling.
4. Blotting techniques: (Southern, Western, Northern).
5. Southern hybridization with genomic DNA with non radioactive labeled probe detection.
6. RFLP analysis of the PCR product.
7. Introduction of DNA into mammalian cells; Transfection techniques.
8. Preparation of genomic DNA library in plasmid vector.
9. Real Time PCR.
10. Gene expression microarray and Tissue microarray.
11. Single gene sequencing and Targeted gene sequencing using Sequencer.
12. Methylation analysis by sequencing.

Text Books (Latest Edition)

1. S.B. Primrose, R.M. Twyman and R.W. Old. Principles of Gene Manipulation. S.B.
University Press.
2. Brown TA, Genomes. Garland Science.
3. G. Wesley Hatfield and Pierre Baldi. DNA Microarrays and Gene Expression: From
Experiments to Data Analysis and Modeling.
4. Steen Knudsen. Guide to Analysis of DNA Microarray Data.

Reference Books (Latest Edition)

1. J. Sambrook and D.W. Russel. Molecular Cloning: A Laboratory Manual, CSHL.

2. Robert G. Kunz. Nanotechnology: Environmental Implications and Solutions by Louis
Theodore.
3. Challa S. S. R. Kumar. Biological and Pharmaceutical Nanomaterials.
4. David S. Goodsell, Bionanotechnology: Lessons from Nature.
5. Challa S.S.R. Kumar, Josef Hormes, Carola Leuschner. Nanofabrication Towards
Biomedical Applications: Techniques, Tools, Applications, and Impact.
6. Rheis. Analysis of genes and genome.
7. Technical Literature from Stratagene, Promega, Novagen, New England Biolab etc.
8. Relevant articles from scientific journals.
 SEMESTER-II

MBT 201: IPR, BIOSAFETY, BIOETHICS AND

BIOENTREPRENEURSHIP
Module-I: Patent filing procedures
Introduction to Intellectual Property. Introduction to Patents; Types of patent applications
National & PCT filing procedure; Time frame and cost; Status of the patent applications filed;
Precautions while patenting – disclosure/non-disclosure; Financial assistance for patenting -
introduction to existing schemes. Patent licensing and agreement Patent infringement- meaning,
scope, litigation, Deliberate Testing-Transgenic testing, Centers in India for Testing, Overview
of search engine, Indian Patents.

Module-II: Biosafety & Bioethics

Introduction; Principles of laboratory Biosafety and Biosecurity; Risk assessment: Occupational
health hazards and laboratory associated infections (LAIs); Laboratory biosafety level criteria
and biosafety laboratory design; Primary containment for biohazards: Selection, installation and
used of biosafety cabinets; Decontamination and disinfection; Safe working practices in biorisk
areas and waste management of biohazards; Biosafety guidelines - Government of India;
Definition of GMOs & LMOs.
Bioethics: Institutional Biosafety Committee (IBSC), Institutional Animal Ethics Committee
(IAEC), Review Committee for Genetically Modified organisms (RCGM), Genetic Engineering
Approval Committee (GEAC) etc. for GMO applications in food and agriculture; Environmental
release of GMOs. Handling and transportation of infectious material and genetically modified
products.

Module-III: Fundamentals of Entrepreneurship & HR

Meaning & types of entrepreneurship, Characteristic of an entrepreneur; barriers & challenges to
entrepreneurship. Business idea generation & evaluation, Making a bankable business plan..
Statutory and legal requirements for starting a company/venture; Stages of entrepreneurial life
cycle & management; Succession planning, Support mechanism for entrepreneurship in India,
Management. Leadership skills; Managerial skills; Organization structure, Team building,
Performance Appraisal; Rewards in small scale set up. Negotiation & Crises management

Module-IV: Accounting and Finance

Sources of finance for capital expenditure and for working; Budget planning and cash flow
management; Basics in accounting practices: concepts of balance sheet, P&L account, and
double entry bookkeeping; Estimation of income, expenditure, profit, income tax etc.

Module –V: Marketing

Definition & Functions of Marketing, Identifying needs of customers including gaps in the
market, Product life cycle & Designing Marketing Mix Strategies, Understanding Segmentation,
Targeting, Positioning, branding.

Case studies
 Lab on IPR, Biosafety and Bioentrepreneurship

1. Filing of patents
2. Grant writing for revenue generation.
3. Project writing for revenue generation.

Text Books (Latest Edition)

1. BAREACT, Indian Patent Act 2005, Acts & Rules, Universal Law Publishing Co. Pvt. Ltd.
2. Kankanala C. Genetic Patent Law & Strategy, 1st Edition, Manupatra Information Solution
Pvt. Ltd.
3. Shkula. S. M. Advanced Accountancy, Masherwari, Sahitya Bhawan, Agra.
4. Kotler. P. Marketing Management, Prentice Hall of India Limited.
5. Staton. E.J. Fundamentals of Marketing Tata McGraw Hill.

Reference Books (Latest Edition)

6. M. K. Sateesh I. K. International Pvt. Ltd. Bioethics and Biosafety.

7. Frederic H. Erbisch, Karim M. Maredia. Intellectual property rights in agricultural
biotechnology, CAB International publication, USA.
8. Rajmohan Joshi. Biosafety and Bioethics, Gyan Publishing House.
9. Relevant articles from scientific journals.

Important Links:
1. http://www.w3.org/IPR/
2. http://www.wipo.int/portal/index.html.en
3. http://www.ipr.co.uk/IP_conventions/patent_cooperation_treaty.html
4. www.patentoffice.nic.in
5. www.iprlawindia.org/ - 31k - Cached - Similar page
6. http://www.cbd.int/biosafety/background.shtml
7. http://www.cdc.gov/OD/ohs/symp5/jyrtext.htm
8. http://web.princeton.edu/sites/ehs/biosafety/biosafetypage/section3.html
 MBT 202: ADVANCED DOWNSTREAM PROCESSING
Module-I: Introduction and Cell disruption
Role of downstream processing, unit operations in downstream processing, factors to affecting
design of downstream process. Costing, physical and chemical principles in downs stream
processing. Cell disruption: unit operations in recovery of intracellular products, Different
methods of cell disruption, advantages, disadvantages.

Module-II: Solid-liquid separation and Pre-treatment

Sedimentation, stokes law, flocculation, coagulation, air flotation, types of filtration process and
equipments; cross flow filtration, batch and continuous filtration, filter media, Darcy's equation,
compressibility, centrifugation. Various types of centrifuges; Centrifugation theory;
Determination of molecular weight and particle size from centrifugation data Importance of pre-
treatment, role of filter aids. Advantages and disadvantages of using filter aids.

Module-III: Solvent-Solvent Extraction & Adsorption

Factors affecting liquid-liquid extraction process, partition or distribution coefficient, selectivity
of extraction, batch and continuous extraction, types of column. Super critical fluid extraction
and its advantages & disadvantages, applications of super critical fluid extraction, revered
micellar extraction, aqueous two phase extraction. Membrane separation.

Adsorption, Henry’s law, Graham's law. Langmuir adsorption isotherm; Equilibrium relationship
for adsorption; Adsorbate; Adsorbate; Freundlich adsorption isotherm.

Module-IV: Chromatography
Different classifications of chromatography, retention time, retention volume, capacity factor or
the retention ratio, column efficiency, number of theoretical plates, resolution, peak asymmetry,
band broadening, Principles and applications of Paper, Thin layer & HPTLC, Gas, Gas-liquid,
Liquid chromatography, HPLC and FPLC, GC-MS, ion exchange chromatography, hydrophobic
interaction chromatography, size exclusion chromatography, affinity chromatography, ion
suppression reversed phase chromatography, Ultra-filtration, Large Scale filtration.

Module-V: Crystallization & Drying

Crystallization theory; Rate of nucleation and rate of crystal growth; Particle size distribution of
crystals; Batch and continuous crystallizers. Drying of bioproducts; Drying mechanism; Freeze
drying; Supercritical drying; Natural air drying; Spray drying; Equipment for drying;
Equilibrium moisture content of bioproducts.

Lab on Advanced Downstream Processing

1. Enzyme purification and estimation of enzyme kinetics.

2. Conventional filtration
3. Centrifugation in batch and continuous centrifuges
4. Cell disruption
5. Protein precipitation and its recovery
6. Ion-exchange chromatography
 7. Membrane based filtration-ultra filtration in cross flow modules and micro filtration

Text Books (Latest Edition):

1. Process Biotechnology Fundamentals by S. N. Mukhopadhyay

2. Bioprocess Engineering Principles by Pauline M. Doran
3. Principles of Fermentation Technology Biotol series by Peter F. Stanbury, Allan
Whitaker, Stephen J.

Reference Books (Latest Edition):

1. Biotol Series: Biotechnological Innovations in Chemical Synthesis by J.A. M. van Balken

2. Biotol Series, Product recovery in Bioprocess Technology by Butterworth Heinemann
3. Industrial sterilization by Richards
4. Relevant articles from scientific journals.
 MBT 203 : IMMUNOTECHNOLOGY

Module-I: Introduction
Immunology- fundamental concepts and anatomy of the immune system, Immune memory,
Immune tolerance; Phagocytosis; Complement and Inflammatory responses; Haematopoesis;
Mucosal Immunity; Antigens - Immunogens, Haptens; Major Histocompatibility Complex -
MHC genes, MHC and immune responsiveness and disease susceptibility, HLA typing.

Module-II: Hybridoma Technology & Antibody Engineering

Hybridoma techniques and monoclonal Ab production- myeloma cell lines, fusion of myeloma
cell lines with Ab producing B cells, fusion methods, selection and screening methods, for
positive hybrids, -cloning methods- production and purification and characterization of MAb.
Application of MAb in biomedical research, in clinical diagnosis and treatment. Production of
human MAb and their applications. Production of polyclonal Ab with different type of Ag: Ag
preparation and modification, adjuvants, dose and route of Ag administration, collection of sera.
Antibody genes and antibody engineering- chimeric and hybrid monoclonal antibodies; Catalytic
antibodies and generation of immunoglobulin gene libraries.
Module-III: Immunotechniques-Antigen-Antibody interactions
Immunoprecipitation- Mancini Method, Ouchterloney Method, Immune Electrophoresis, Rocket
Immunoelectrophoresis, Crossed Immunoelectrophoresis, Agglutination and Complement
Mediated Immune Reactions; Advanced Immunological Techniques - RIA, ELISA, Western
Blotting, ELISPOT and ELAST Assay, Peptide Based Immuno Binding Assay, Peptide
Mapping, Epitope Mapping, Flurosence and Photo Illuminance Based Immunoassay, DELPHIA
and SLFIA, Concept of Immunohisto / Cyto-chemistry, Immunofluorescence, Flow Cytometry
and Immunoelectron Microscopy; Detection of Molecules in living cells, in situ localization by
Techniques such as FISH and GISH. Surface plasmon resonance, Biosenor assays for assessing
Ligand–Receptor Interaction, CMI Techniques- Lymphoproliferation Assay, Mixed Lymphocyte
Reaction, Cell Cytotoxicity Assays.

Module-IV: New generation Vaccines: Immunobiotechnology

Vaccines and Vaccination, types and stages of vaccine production including new generation
vaccines. Tumor immunology. Active and passive immunization; Live, killed, attenuated, sub
unit vaccines; Vaccine technology- Role and properties of adjuvants, recombinant DNA and
protein based vaccines, mRNA Vaccine, plant-based vaccines, reverse vaccinology; Peptide
vaccines, conjugate vaccines, industrial vaccine production, Phases of Clinical trials of Vaccines.

Module –V: Clinical Immunology

Hypersensitivity – Type I-V; Autoimmunity; Types of autoimmune diseases; Mechanism and
role of CD4+ T cells; MHC and TCR in autoimmunity; Treatment of autoimmune diseases;
Transplantation – Immunological basis of graft rejection; Clinical transplantation and
immunosuppressive therapy; Tumor immunology – Tumor antigens; Immune response to tumors
and tumor evasion of the immune system,Cancer immunotherapy;Immunodeficiency-Primary
immunodeficiencies, Acquired or secondary immunodeficiencies.
Case studies

Lab on Immunotechnology:
1. Single Radial Immuno Diffusion.
 2. Double diffusion.
3. Rocket Immunoelectrophoresis.
4. Counter- Current Immunoelectrophoresis.
5. Characterization of Immunoglobulins by SDS-PAGE.
6. Antibody titre by ELISA method.
7. Isolation of Lymphocytes from human blood and Culture
8. Culturing and maintenance of cell lines
9. Immunoblotting, Dot blot assays.
10. Abs Production.

Text Books ( Latest Edition)

1. Kuby, RA Goldsby, Thomas J. Kindt, Barbara, A. Osborne. Immunology.
2. Brostoff J, Seaddin JK, Male D, Roitt IM. Clinical Immunology, Gower Medical
Publishing.
Reference Books( Latest Edition)
1. Janeway et al., Immunobiology, Current Biology publications.
2. Paul. Fundamental of Immunology, Lippencott Raven.
3. Goding. Monoclonal antibodies, Academic Press.
4. P. Delves, S. Martin, D. Burton and I. Roitt. Essential Immunology, Eleventh Edition
(2006) Wiley-Blackwell Publishers, UK.
5. J. Kuby. Immunology, W H Freeman & Co Publishers.
6. Hay F.C. and Westwood O.M.R. Practical immunology, Wiley-Blackwell Publishers.
7. E. Benjamin, G. Sunshine, and S. Leskowitz. Immunology - A Short Course, Wiley-Liss
Publishers, New York.
8. D.P. Stites, J.D. Stobo and J.V. Wells. Basic and Clinical Immunology, Appleton &
Lange Publishers.
9. Relevant articles from scientific journals.
 MBT 204 : STEM CELL TECHNOLOGY & TISSUE ENGINEERING

Module-I: Introduction to Stem Cells

Stem Cells: Definition, Classification and Sources, Blastocyst Culture, Xeno-free Derivation and
Cryopreservation, Properties and Applications of Embryonic Stem Cells, Characterization of
Human Embryonic Stem Cells, Stem Cells and their Developmental Potential. Culture,
Subcloning, Spontaneous and Controlled Differentiation of Human Embryonic Stem Cells, in
vivo and in vitro Differentiation of Human Embryonic Stem Cells, Feeder-free Culture of Human
Embryonic Stem Cells,

Module-II: Human Stem cells research & Ethics

Generation and Expansion of pluripotent Stem cells, Epigenesis in Pluripotent Cells,
Organogenesis, Mammalian Nuclear Transfer Technology, Novel Strategies for the mobilization
of HSC, GMP: clinical scale production of MSCs; Ethical considerations, stem cell religion
consideration, Stem Cell based therapies: pre clinical regulatory consideration and patient
advocacy, Intellectual property issues surrounding Human Embryonic Stem cells study.

Module-III: Cancer Stem Cells & Regenerative Medicine

Purification and characterization of cancer stem cells, therapeutic implications of cancer stem
cells: Preventative and therapeutic strategies for cancer stem cells, Targeting acute myelogenous
leukemia stem cells, targeting cancer stem cell pathways: Hedgehog/GLI signaling, Notch
signaling pathway, Wnt; Stem Cell therapy for Neurodegenerative Diseases: Parkinson’s,
Alzheimer, Spinal Cord injuries and other brain syndromes, Tissue system failures, Diabetic
Cardiomycopathy, kidney failure, liver failure, Leukemia, transplantation.

Module-IV: Fundamentals of Animal Tissue Engineering and Applications

Introduction, basic requirements for tissue engineering; Cell culture media and reagents. Types
of culture & Culture Techniques: Primary culture & secondary culture; Continuous cell lines;
Suspension cultures; cell, tissue and organ cultures, Commercial scale production of animal cell,
Testing of toxicity of environmental pollutants in cell culture; Cell line engineering (GS and
DHFR system). Application of animal cell culture for in vitro testing of drugs; Application of
cell culture technology in production of human and animal vaccines and pharmaceutical proteins.

Module-V: Fundamentals of Plants Tissue Engineering and Applications

Virus free culture, Protoplast culture, Somatic cell cloning and hybridization; Cyto-
differentiation; Organogenesis; Somatic embryogenesis; Artificial seed production;
Micropropagation; Somaclonal variation; Androgenesis Germplasm conservation and
cryopreservation, Protoplast isolation; Somatic hybridization, Cybrids. Applications of tissue
culture in agriculture, horticulture and forestry.

Case studies

Lab on Stem Cell Technology:

1. Preparation of feeder cell culture.

2. Culturing of Stem cell line.
3. Isolation of cells from blastocyst.
4. Growing mesenchymal stem cell.
 5. Preservation of cord blood.
6. Stem cell isolation from umbilical cord.
7. Types of cleavage, invertebrates, vertebrates,and permanent preparations – stains of
stages of blastula
8. Development of Amphibian – Gestulation – Metamorphosis
9. Sex determination – Drosophila (Prescribed assignments with problems in genetic)
10. Stem cells –Identification of cells by staining of bone marrow – (Animal example)

Text Books (Latest Edition)

1. Ariff Bongso, Eng Hin Lee. Stem cells from Bench to Bedside. World Scientific
Publishing Co. Pte. Ltd.
2. Stewart Sell. Stem cells Hand Book. Humana Press. Totowa, New Jersy.

Reference Books (Latest Edition)

3. S.F.Gillert, Sinauer. Developmental Biology, Associates inc., Massachuselts.
4. Ethan Bier. The coild spring Cold Spring Harbor Lab Press, New York.
5. Freshney, R. I. Culture of Animal Cells. Wiley-Liss.
6. Masters, J. R. W. Animal Cell Culture – Practical Approach, Oxford Univ. Press.
7. Basega, R. Cell Growth and Division: A Practical Approach. IRL Press.
8. Butler, M and Dawson, M. Cell Culture Lab Fax, Eds., Bios Scientific
Publications Ltd., Oxford.
9. Clynes, M. Animal Cell Culture Techniques. Springer.
10. Mather, J.P and Barnes, D. Methods in Cell Biology, Animal Cell Culture Methods.
Academic Press.
11. Marshak. Cold spring Harbar Symposium Publication.
12. Scott F. Gilbert. Development Biology.
13. Relevant articles from scientific journals.
 MBT 205: PROTEOMICS & PROTEIN ENGINEERING

Module-I: Architecture of Proteins

Amino acids, classification of proteins, Protein Structure: primary, secondary, tertiary and
quaternary. Protein folding, thermodynamics and kinetics of protein folding, Protein Stability:
protein stability & associated factors. Detection, identification and quantification of amino acids
and proteins, In-silico protein modeling.

Module-II: Control of Protein Function

Mechanisms of Regulation, Protein Interaction Domains, Regulation by Location, Effector
Ligands: Competitive Binding and Cooperativity, Conformational Change and Allostery, Protein
Switches Based on Nucleotide Hydrolysis, GTPase Switches: Small Signaling G Proteins, Signal
Relay by Heterotrimeric GTPases, Protein Synthesis, Motor Protein Switches, Regulation by
Degradation, Control of Protein Function by Phosphorylation, Regulation of Signaling Protein
Kinases: Activation Mechanism, Cdk Activation, Two-Component Signaling Systems in
Bacteria, Control by Proteolysis, Protein trafficking.

Module-III: Protein – Protein Interactions

Charting protein–protein interactions: Topoisomerase-based cloning, Univector plasmid-fusion
system, Two-hybrid analysis protein-protein interactions in yeast, viral, bacteria systems. Use of
phage display to detect protein-ligand interactions, Detecting interactions by protein fragment
complementation assays.

Module-IV: Protein Engineering & Protein Design

Outline of bioengineering of macromolecules a multidisciplinary approach; Methods to alter
primary structure of protein: site directed mutagenesis; examples of engineered proteins, protein
design, principles and examples. Steps involved in protein engineering and protein modeling to the
desired needs. Protein characterization: Amino acids sequencing, Peptide finger mass printing,
Mass Intact protein, Glycan analysis.

Module –V: Techniques: Protein engineering

Physical methods of determining the three-dimensional structure of proteins (X-ray
crystallography, Nuclear magnetic resonance spectroscopy, Cryoelectron microscopy, Neutron
diffraction, Optical spectroscopic techniques, Vibrational spectroscopy, Raman spectroscopy),
Use of 2-D PAGE, sensitivity and resolution and representation of 2-D gels, multiplexed analysis
to show expression profiles; circular dichroism (CD), MALDITOF and MALDITOFTOF,
special strategies for qualitative and quantitative analysis. Protein array for expressional analysis,
profiling and functional analysis, application of proteomics to medicine.
Case studies.

Lab on Proteomics &Protein Engineering

1. Using absorbance coefficients and extinction coefficients to estimate protein concentration

2. Protein quantitation when contaminating nucleic acids are present
3. The nitric acid method for protein estimation in biological samples
4. Quantitation of Tryptophan in Proteins
5. The CAT (chloramphenicol acetyltransferase) Assay
6. Use of Luciferase in a reporter assay
 7. In vitro translation - Determining amino acid incorporation
8. Casting Immobilized pH Gradients (IPGs)
9. Carboxymethylation of cysteine using iodoacetamide/iodoacetic acid
10. Analyzing Protein Phosphorylation
11. SDS PAGE and Western Blotting

Text Books (Latest Edition)

1. TE Creighton. Protein Function A Practical Approach, 2005. W.H. Freeman & Company.
New Edition.
2. Thomas E Creighton, Creighton. Proteins: Structures and Molecular Properties, W.H.
Freeman & Company. New Edition.
3. N J Darby, T E Creighton. Protein Structure (In Focus), W.H. Freeman & Company. New
Edition.

Reference Books (Latest Edition)

1. Charles J Dutton, Mark A Haxell, Hamish A. I. McArthur and Richard G. Wax Marcel
Dekker. Peptide Antibiotics - Discovery, Modes of Action, and Applications.
2. Peter Goodenough. Protein Engineering II CPL Press.
3. Lilia Alberghina. Protein Engineering for Industrial Biotechnology, CRC Press.
4. Loïc Faye and Véronique Gomord. Recombinant Proteins From Plants - Methods and
Protocols, Humana Press.
5. Sheldon J Park, Jennifer R Cochran. Protein Engineering And Design, CRC Press.
6. Paul R Carey. Protein Engineering and Design, Academic Press.
7. Paul Wrede, Gisbert Schneider, Walter De Gruyter. Concepts in Protein Engineering and
Design: An Introduction.
8. Nediljko Budisa, Wiley-VCH Verlag GmbH. Engineering
9. The Genetic Code: Expanding The Amino Acid Repertoire For The Design Of Novel
Proteins.
10. Relevant articles from scientific journals.