BCMB 536 - GENETIC ENGINEERING

3 Credits
COURSE OBJECTIVES: To provide understanding of genetic manipulation and gene transfer in addition to
providing insights into its success in living systems.

Pre-requisite: Master’s level course in Molecular Biology.

UNIT- I - Introduction to Genetic Engineering 10h
Enzymes used in rDNA technology (Restriction enzymes, nucleases, RNA polymerases, DNA
polymerases, PNK, alkaline phosphatases, DNA ligases). Cloning Vectors for E. coli: Plasmids,
Bacteriophage λ, Filamentous phage, Cosmids, Phagemids and other advanced vectors: BAC, YAC,
P1-derived Artificial Chromosome, Shuttle vectors, Expression vectors.
UNIT- II – Gene Transfer Techniques 8h
Cloning Vectors for Eukaryotes: Vectors for cloning in yeast, Vectors for cloning in animal cells–
adenoviral vector, adeno-associated viral vectors, retroviral vectors, baculovirus vectors for cloning in
insect cells. Ligation of DNA fragments– using DNA ligases, homopolymer tailing, linkers and
adaptors. Introduction of foreign DNA into prokaryotes - Natural gene transfer methods, calcium
chloride mediated transformation, transfection with phage vectors. Introduction of foreign DNA into
animal cells - lipofection, electroporation, microinjection, microprojectile.
UNIT- III - Gene Cloning Strategies 7h
Construction of genomic and cDNA libraries. Selection and screening of recombinant clones: Methods
based on nucleic acid hybridization, finding specific clones by functional complementation. Reporter
genes. Studying protein-protein interactions-Phage display libraries, yeast two hybrid systems.
UNIT- IV – Gene Manipulation Techniques 8h
DNA sequencing methods –Sanger’s sequencing method, Next generation sequencing methods–
pyrosequencing, Polony sequencing. Polymerase chain reaction and its applications, altering genes-
Site-directed mutagenesis. DNA microarrays. Dot Blot and Slot Blot Hybridization, Fluorescence in-
situ hybridization. Analysis of DNA protein interactions-Electrophoretic mobility shift assay, Filter-
binding assay, Chromatin Immunoprecipitation (ChIP) assay, Methylation Interference assay.
UNIT- V – Expression of Engineered Proteins 7h
Engineering microbes for the production of therapeutic proteins - insulin and growth hormones.
Concepts of gene knock out technique- Cre-loxP recombination. Production of transgenic mice and
applications of transgenic mice. Gene Therapy: Gene silencing by RNA interference technology-
Genome editing by CRISPR/Cas. Necessity of bioethics in rDNA technology.

Text Books
1. Brown, T.A. (2016) Gene Cloning and DNA Analysis, Wiley-Blackwell Publishers, New Jersey.
2. Primrose, S.B. and Twyman, R. (2006) Principles of Gene Manipulation and Genomics, Wiley-
Blackwell Publishers, New Jersey.
Suggested Reading
1. Nicholl, D.S.T. (2010) An Introduction to Genetic Engineering, Cambridge University Press,
United Kingdom.
2. Glick, B.R., Pasternak, J.J., Patten, C.L., (2012) Molecular Biotechnology: Principles and
Applications of recombinant DNA, ASM Press, Washington DC.
3. Sambrook, J. and Russell, D.W. (2012) Molecular Cloning: A Laboratory Manual –a set of 3
volumes, CSHL Press, New York.
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 BCMB 537 - IMMUNOLOGY
3 Credits
Course Objectives: To understand the basic concepts in Immunology and techniques used in Immunology
research
Pre-requisite: Master’s level course in Cell Biology and Molecular Biology.

UNIT- I -Historic perspectives and introduction to immunology - 8h

History and scope of immunology; Types of Immunity-Innate/basic immunity, Acquired immunity-
natural, artificial, active and passive immunity; nature of antigens, immunogenicity, antigenicity,
epitopes; PAMPs, DAMPs; PRRs-Toll like receptors, acute phase proteins; functions of cells of
myeloid and lymphoid lineage- granulocytes, dendritic cells, macrophages, T and B lymphocyrtes;
Inflammatory response; Pathways of complement activation and its regulation

UNIT- II -Functions of Lymphoid organs- 6h

Primary and Secondary lymphoid organs; development of T and B lymphocytes in Thymus and Bone
marrow-positive and negative selection; MHC restriction- types and significance of MHC molecules;
antigen processing and presentation to T cells- endogenous and exogenous pathways; Formation of
effecter T and B lymphocytes in the secondary lymphoid organs; Lymphocyte recirculation

UNIT- III – Humoral Immunity and Immunological Techniques- 8h

Immunoglobulins-structure, types and biological functions; Primary and Secondary immune
response; Molecular basis of antibody diversity-multiple germ-line gene segments, somatic gene
recombination, N and P nucleotide addition and somatic hypermutation; Mechanism of antigen-
antibody interaction; principle and applications of precipitation, agglutination reactions, ELISA, RIA,
Western Blotting, and immunofluorescence techniques; Hybridoma technique- principle and
methodology for production of monoclonal antibodies; Biomedical applications of murine and
humanized monoclonal antibodies

UNIT- IV – Cell Mediated Immunity- 8h

Functions of T cell subsets-Th1, Th2, Treg, CTLs, and NK cells; Mechanism of activation of T cells;
Tolerance mechanisms-central and peripheral tolerance-clonal deletion, clonal anergy; Role of
cytokines in immune regulation; T cell-B cell interaction-immunoglobulin class switching;
Mechanism of target cell killing by CTLs and NK cells-death signaling-induction of apoptosis-
intrinsic and extrinsic pathways

UNIT- IV – Immunopathology- 10h

Types and causes of hypersensitivity reactions, autoimmune diseases and immune deficiency
diseases; Transplantation immunity-types of grafts and the mechanism of graft rejection;
Applications of physical, chemical and biological immunosuppressive agents. Vaccines: conventional
vaccines-attenuated, killed and subunit vaccines; Modern vaccines- recombinant vaccines, DNA
vaccines and Edible vaccines

Text Books:
1. Punt, J., Stranford, S., Jones, P., Owen, J. (2018) Kuby’s Immunology, W. H. Freeman, New
York.
2. Murphy, K. and Weaver, C. (2016) Janeway’ s Immunobiology, Garland Science, New
York.

Suggested Reading:
1. Delves, P.J., Martin, S.J., Burton, D.R., Roitt, I.M. (2017) Roitt’s Essential
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 BCMB 538 - PROTEOMICS
3 Credits
COURSE OBJECTIVES: The course focuses on the detailed study of proteins which represent the major
proportion of functional molecules of the cell. The course will familiarize students on the application of
technologies for the analysis and quantification of proteins.
Pre-requisite: Master’s Level Course in Genetic Engineering.
UNIT- I – Introduction to Proteomics 8h
Human genome - Genomes to Proteomes - HUPO –Human Proteome Project, Branches of proteomics
- Protein extraction Methods: Subcellular fractionation, Density gradients, Ultrafiltration, - Protein
fractionation - Affinity purification –Removal of interfering compounds, salts, DNA, lipids, Protein
solubilization methods, chaotropes, detergents, etc - Sample handling and storage - Stable Isotope
Labeling with Amino acids in Culture (SILAC)
UNIT- II – Structural Proteomics 6h
Protein structure-function relationship – Disulfide bonds, Post translational modifications,
Glycosylation, Phosphorylation, other modifications, Applications - methods for detection of protein-
protein interactions - Yeast 1 and 2 hybrid systems – Phage display – Surface Plasmon Resonance
(SPR) - Fluorescence Resonance Energy Transfer (FRET).
UNIT- III – Proteomic Techniques for Analysis 10h
1D and 2-D gel electrophoresis – Mass Spectrometry – Principles - MALDITOF - RP
chromatography /Tandem mass spectrometry – Protein sequence analysis -Peptide mass finger
printing- N-terminal determination methods- Protein modification – Protein microarrays – Tissue
microarray – Infra red Protein array with Quantitative Readout (IPAQ) -- Algorithms for proteomics –
OMSSA - SEQUEST - MASCOT.
UNIT- IV – Protein expression 8h
Expression Systems –, E. coli, Yeast, Pitchia pastoris, Bacculovirus - introduction, detection and
purification of expressed transgenes - antibody capture – antibody generation and Engineering –
Protein/peptide chemical synthesis –- Protein-polynucleotide interactions Reconstitution of proteins in
lipid vesicles, - Liposomes-Peptide and protein drugs.
UNIT- V – Proteomic approach for Clinical studies 8h
Protein Biomarker Discovery and Validation - low abundance and hydrophobic proteins. High
through put techniques to identify protein molecules in sample Body fluid profiles, blood disease
profiles, diabetes profiles stroke and myocardial infarction, Alzheimer, Proteomics in Biotechnology.
Text Books
1. Twyman, R.M. (2014) Principles of Proteomics, Taylor & Francis group, New York,
USA.
2. Comai,.L, Katz, .J., Mallick, P. (2017) Proteomics: Methods and Protocols. Humana Press
Inc., New York.
Suggested Reading
1. Cathy H. Wu.C.H, Cecilia N. Arighi.C.N. and Karen E. Ross. K.E. (2017) Protein
Bioinformatics, Humana Press Inc., New York.
2. O’Connor C.D. and Homes. B. D. (2007) Proteomics, Scion Publishing Ltd., Banbury.
COURSE OUTCOME: The course will impart the knowledge of Structural Proteomics, advances in high
throughput technologies, protein engineering approaches for protein structure-function research.

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 BCMB 560 - GENETIC ENGINEERING LAB
1 Credit
1. Culture of E. coli cells & plasmid isolation
2. Preparation of competent cells
3. Calcium chloride mediated transformation
4. Ligation of DNA
5. Polymerase chain reaction
6. Restriction fragment length polymorphism
7. Random amplified polymorphic DNA
8. Sub-cloning of GFP protein
Reference:
Sambrook, J. and Russell, D.W. (2012) Molecular Cloning: A Laboratory Manual –a set of 3 volumes,
CSHL Press, New York.

BCMB 561 - IMMUNOLOGY LAB

1 Credit
1. Agglutination reactions- Active agglutination- Widal Test, Blood group analysis
2. Passive agglutination reactions -Latex agglutination Test
3. Precipitation reactions on gel-double immuno diffusion
4. Single radial immunodiffusion (SRID)
5. Immunoelectrophoresis (IEP)
6. ELISA technique
7. SDS-PAGE analysis
8. Immunoblotting technique

Reference:
Gordon, J.R. (2004) A Practical Guide to cellular and Molecular Research Methods in
Immunology, Saskatchewan.

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 BCMB 443 - PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
3 Credits
COURSE OBJECTIVES: To learn basic metabolic processes plants in addition to theoretical knowledge of
various applications like tissue culture, transgenic crops and micro propagation.
Pre-requisite: Bachelor’s level course in Life Sciences.
UNIT- I - Introduction to Plant cells 9h
Photosynthesis: Chloroplast- structure and function, photosynthetic pigments and light harvesting
complexes, photo inhibition of photosynthesis, photosynthetic carbon reduction (PCR) cycle, C4
syndrome and Crassulacean acid metabolism. Oxidative respiration. Alternate electron pathways and
Respiration rate.
UNIT- II- Nitrogen metabolism & Plant hormones 9h
Physical and biological nitrogen fixation - ammonification, nitrification, denitrification. Biochemistry
and genetics of nitrogen fixation and ammonium assimilation.
Biosynthesis, physiological effects and mechanism of action of auxins, gibberellic acids, cytokinins,
abscisic acid, ethylene, brassinosteroids and polyamines.
Photomorphogenesis – phytochrome, cryptochrome and photoperiodism.
UNIT- III - Plant Stress physiology & Secondary metabolites 7h
Plant stress, plant responses to abiotic and biotic stresses, water deficit and drought resistance,
flooding, temperature stress, salt stress, ion toxicity, pollution stress and potential biotic stress (insects
and diseases).
Functions of secondary metabolites – flavonoids, alkaloids, terpenoids, anthocyanins, tannins,
steroids and lignin. Applications of secondary metabolites - drug development, biopesticides and
biofertilizers.
UNIT- IV- Introduction to plant tissue culture 8h
Media composition and preparation. Culture types - callus culture, cell suspension culture, protoplast
culture. Somatic embryogenesis, organogenesis, embryo culture and embryo rescue.
Micropropagation. Protoplast isolation, protoplast culture and fusion, selection of hybrid cells,
cybrids, somaclonal variation. Germplasm storage and cryo- preservation.
UNIT- V- Application of Plant Biotechnology 7h
Application of transgenesis in crop improvement – insect resistance, disease resistance, virus
resistance, herbicide resistance and resistance to abiotic stress. Transgenics - Bt cotton, Bt
brinjal and rice.
Text Book:
1. Taiz, L., Zeiger, E., Moller, I.M., Murphy, A. (2015) Plant Physiology and Development,
Sinclair Associates.
2. Nelson, D.L. and Cox, M.M. (2017) Lehninger Principles of Biochemistry, Macmillan Higher
Education, Basingstoke.
Suggested Reading:
1. Slater, A., Scott, N.W., Fowler, M.R. (2008) Plant Biotechnology. The Genetic Manipulation of
Plants, Oxford University Press.
2. Heldt, H.W. and Piechulla, B. (2016) Plant Biochemistry. Academic Press, Cambridge.
3. Lea, P.J. and Leagood, R.C. (1999) Plant Biochemistry and Molecular Biology, John Wiley and
Sons Ltd., New Jersey.

COURSE OUTCOME: Basic knowledge of plant physiology and various metabolic processes and applications
for crop improvement and micro propagation.

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 BCMB 543 – STEM CELL AND REGENERATIVE BIOLOGY
3 Credits
COURSE OBJECTIVES: The course will focus on the biology and mechanism involving stem cells, their
applications in replacing, regenerating and engineering human cells for translational regenerative medicine
and ethical issues associated with the same.
Pre-requisite: Master’s level course in Cell Biology.

UNIT- I – Introduction to Stem Cells 6h

Definition and Criteria for Stem Cells; Pluripotent, Multipotent and Totipotent Stem cells; Primordial
germ cells, Embryonic stem cells; Amniotic fluid derived stem cells; Cord blood stem cells.

UNIT- II – Stem Cell Biology and Mechanisms 10h

Molecular Basis of Pluripotency, Mechanisms of Self Renewal, Role of LIF/JAK/STAT,
Nodal/Activin/TFGβ, FGF/MAP kinase pathways, Chromatin signature of pluripotent cells, Cell cycle
regulators in Stem cells; Stem cell niches, Change of phenotype and differentiation, Senescence of
Dividing somatic cells, aging and stem cell renewal, Quiescent Stem Cells.

UNIT- III –Tissue and Organ Development 10h

Differentiation in early development, Potency, Commitment, Polarity and the specification of
asymmetric divisions, induction, competence determination and differentiation, morphogenetic
gradients, cell fate and cell lineages, Epigenetic silencing and lineage commitment; Cellular
differentiation of the nervous system, Progenitors in adult brain, Epithelial stem cells; Adult
progenitor cells, Mesenchymal stem cells, Plasticity; De-differentiation, Cancer stem cells.

UNIT- IV – Stem Cell Technology 8h

Characteristics and characterization of Human Pluripotent Cells; Fluorescence and Magnetic bead
assisted cell sorting, Derivation, characterization and maintenance of Murine and Human Embryonic
Stem Cells, Differentiation of embryonic stem cells; Derivation of induced pluripotent stem cells;
Derivation and differentiation of Human Embryonic Germ Cells; Genomic Reprogramming, Fate
Mapping of Stem Cells.

UNIT- V – Stem Cells in Regenerative Therapeutics 6h

Neural stem cells in Neurodegenerative diseases; Hematopoietic stem cell transplantation; Epithelial
stem cells and burns; Stem cells and heart disease; Pancreatic stem cells and diabetes; Liver stem cells
and cell therapy for liver disease; Embryonic stem cells in tissue engineering, Examples of stem cells
in Clinical Trials and translational therapeutics, stem cell banking, Ethical concerns in stem cell
research.

Text Books:
1. Lanza, R. and Atala, A. (2013) Essentials of Stem Cell Biology, Academic Press, California.
2. Huang, N.F., L'Heureux, N., Song, L. (2018) Engineering Stem Cells for Tissue Regeneration.
World Scientific Publishing Company
Suggested Reading:
1. Scott, C.T. (2006) Stem Cell Now, Pearson Education, New Jersey.
2. Marshak, D.R., Gardner, R.L., Gottlieb, D. Lanza, R., Atala, A (ED.) (2001) Stem Cell Biology.
Cold Spring Harbor Press, New York.

COURSE OUTCOME: The course will provide the basic understanding of stem cell biology and
their applications in translational therapeutics.

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