Last Updated: September 13, 2023

Ph.D. in Molecular Biology and Biotechnology

Course Contents

Ph.D. in Molecular Biology and Biotechnology

I. Course Title               : Plant Molecular Biology

II. Course Code            : MBB 601

III. Credit Hours          : 3+0

IV. Aim of the course

• To provide in depth knowledge of recent developments of plant molecular biology

and applications

• To discuss case studies and success stories in agriculture and industry

V. Theory

Unit I (10 Lectures)

Model Systems in Plant Biology (Arabidopsis, Rice, etc.) Forward and Reverse Genetic Approaches. Organization expression and interaction of nuclear, Mitochondrial and Chloroplast Genomes. Cytoplasmic male sterility.

Unit II (12 Lectures)

Transcriptional and Post-transcriptional Regulation of Gene Expression, Isolation of promoters and other regulatory elements, RNA interference, Transcriptional Gene Silencing, Transcript and Protein Analysis.

Unit III (12 Lectures)

Plant Developmental Processes, ABC Model of Floral Development, Role of  chormones (Ethylene, Cytokinin, Auxin and ABA, SA and JA) in plant development. Regulation of Flowering, Plant photoreceptors and light signal transduction, vernalization, Circadian Rhythms.

Unit IV (14 Lectures)

Abiotic Stress Responses: Salt, Cold, Heat and Drought. Biotic Stress Responses. Molecular Biology of Plant-pathogen Interactions, Molecular Biology of Rhizobium and Agrobacterium- Plant interaction. Role of programmed Cell Death in Development and Defense.

VI. Suggested Reading

• Buchanan, B.B., Gruissem, W. and Jones R. 2015. Biochemistry and Molecular

  Biology of Plants, 2nd edition, Wiley and Blackwell Publications.

• Slater, A., Scott, N.W., and Fowler, M.R. 2003. The Genetic Manipulation of

  Plants. Plant Biotechnology Oxford, England: Oxford University Press.

• Walker, J.M., Rapley, R. 2008. Plant Biotechnology and Genetics: Principles,

  Techniques and Applications.

I. Course Title               : Plant Genome Engineering

II. Course Code            : MBB 602

III. Credit Hours          : 3+0

IV. Aim of the course

To discuss the specialized topics and advances in field of genetic engineering and application of molecular tools in breeding of specific crops.

V. Theory

Unit I (14 Lectures)

Conventional versus non-conventional methods for crop improvement; Present status and recent developments on available molecular marker, transformation and genomic tools for crop improvement. Genetic engineering for resistance against abiotic (drought, salinity, flooding, temperature, etc) and biotic (insect pests, fungal, viral and bacterial diseases, weeds, etc) stresses; Genetic Engineering for increasing crop productivity by manipulation of photosynthesis, nitrogen fixation and nutrient uptake efficiency; Genetic engineering for quality improvement (protein, essential amino acids, vitamins, mineral nutrients, etc.); edible vaccines, etc.

Unit II (12 Lectures)

Recent developments in plant transformation strategies; Role of antisense and RNAi-based gene silencing in crop improvement; Regulated and tissue-specific expression of transgenes for crop improvement;

Unit III (12 Lectures)

Gene stacking; Pathway engineering; Marker-free transgenic development strategies; Genome editing: principles and methods, Development of genome edited plants; High throughput phenotyping of transgenic plants.

Unit IV (10 Lectures)

Field studies with transgenic crops; Environmental issues associated with transgenic crops; Food and feed safety issues associated with transgenic crops; Risk assessment of transgenic food crops.

VI. Suggested Reading

• Christou P and Klee H. 2004. Handbook of Plant Biotechnology. John Wiley &  

  Sons.

• Stewart Jr, C.N. 2016. Plant Biotechnology and Genetics: Principles, Techniques,

  and Applications. John Wiley & Sons.

• Kirakosyan A and Kaufman PB. 2009. Recent Advances in Plant Biotechnology p.

 409. Dordrecht: Springer.

I. Course Code              : MBB603

II. Course Title             : Plant Omics and Molecular Breeding

III. Credit Hours          : 3+0

IV. Aim of the course

To discuss the specialized topics and advances in field of genomics and genomics

assisted molecular breeding.

V. Theory

Unit I (12 Lectures)

Complex traits and genetic architecture, Mapping genes and QTLs, statistical concepts in QTL mapping, high-throughput genotyping using automated platforms, genetic and physical mapping of genomes, study of population structure and kinship, association genetic analysis of QTL, case studies on QTL mapping using different approaches, map-based of cloning genes and QTLs – case studies.

Unit II (12 Lectures)

Marker Assisted Breeding (MAB): Principles and methods, marker assisted foreground and background selection, marker assisted recurrent selection, whole genome selection, case studies in MAS, requirement for successful marker assisted breeding, cost of MAB.

Unit III (12 Lectures)

Concepts and methods of next generation sequencing (NGS), assembly and annotation of NGS data, genome resequencing, DNA sequence comparison, annotation and gene prediction. Genome-wide insertion mutagenesis and its use in functional genomics, transcriptome profiling using microarrays and deep sequencing, study of methylome and its significance, proteome analysis using mass spectrometry, crystallography and NMR, analysis of proteome data, study of protein- protein interactions.

Unit IV (12 Lectures)

Study of the metabolome, use of 1D/2D NMR and MS in metabolome analysis, multivariate analysis and identification of metabolite as biomarkers, study of ionome using inductively coupled plasma – mass spectroscopy (ICP-MS), correlating the data from genome, transcriptome, proteome, metabolome and ionome with phenome.

VI. Suggested Reading

• Speicher, D.W. (Ed.). 2004. Proteome analysis: interpreting the genome. Elsevier.

• Tomita, M. and Nishioka, T. (Eds.). 2006. Metabolomics: the frontier of systems  

  biology. Springer Science and Business Media

• Horst, L. and Wenzel, G. (Eds.). 2007. Molecular marker systems in plant

  breeding and crop improvement (Vol. 55). Springer Science and Business Media.

• Stewart C.N. 2008. Plant Biotechnology and Genetics: Principles, Techniques and

  Applications.

• Singh, B.D. and Singh, A.K. 2015. Marker-Assisted Plant Breeding: Principles and

  Practices Springer (India) Pvt. Ltd.

I. Course Title               : Commercial Plant Tissue Culture

II. Course Code            : MBB 604

III. Credit Hours          : 2+0

IV. Aim of the course

• To provide awareness into development of commercial scale plant tissue culture  

  units.

• To provide an insight into the commercial applications of plant tissue culture in  

  agriculture, medicine  and industry.

• To educate about bio-safety, regulatory as well as entrepreneurship opportunities.

V. Theory

Unit I (8 Lectures)

Micro-propagation of commercially important plant species; plant multiplication, hardening, and transplantation; genetic fidelity; scaling up and cost reduction; bioreactors; synthetic seeds; management and marketing.

Unit II (8 Lectures)

Production of useful compounds via, biotransformation and secondary metabolite production: suspension cultures, immobilization, examples of chemicals being produced for use in pharmacy, medicine and industry.

Unit III (9 Lectures)

Value-addition by transformation; development, production and release of transgenic plants; patent, bio-safety, regulatory, environmental and ethical issues; management and commercialization.

Unit IV (7 Lectures)

Project planning and preparation, economics (entrepreneurship, cost profit ratio), government policies (incubators, different facilitation projects, loan opportunities). Some case studies on success stories on commercial applications of plant tissue culture. Visits to some tissue culture based commercial units/industries.

VI. Suggested Reading

• Honda, H., Liu, C., Kobayashi, T. 2001. Large-Scale Plant Micropropagation. In: Zhong J.J.

et al. (eds) Plant Cells. Advances in Biochemical Engineering/ Biotechnology, vol 72. Springer, Berlin, Heidelberg.

• Bhojwani SS and Razdan MK. 1986. Plant tissue culture: theory and practice (Vol. 5). Elsevier.

I. Course Title               : Plant Microbe Interaction

II. Course Code             : MBB 605

III. Credit Hours           : 2+0

IV. Aim of the course

To discuss the specialized topics and advances in field of plant microbe interaction for understanding their potential in enhancing crop growth and development.

V. Theory

Unit I (8 Lectures)

Microbial communities in the soil and atmosphere, Community dynamics and population interactions with particular reference to plant–microbe and microbe interactions leading to symbiotic, associative, endophytic and pathogenic interactions, effects of microorganisms on plants, effects of plants on micro organisms .Recognition processes and signal exchange, Molecular aspects of Plant Growth Promoting Rhizobacteria (PGPR), Symbiotic diazotrophs: Rhizobia and association with legumes. Mycorrhizal associations: Ectomycorrhizae, Endomycorrhizae with particular emphasis to AM fungi, Ectendomycorrhizae. Bio-control agents and their action, endophytes associations

Unit II (8 Lectures)

Enzymes, toxins, pili, siderophores, secretion systems of microbes and plants determining soil health, nutrient availability and uptake defense responses in plants: pamp-triggered immunity, effect or-triggered susceptibility, qualitative resistance, r genes, structure and function, effector-triggered immunity, regulation of plant cell death, plant hormones in immunity, Plant parasite interactions and its molecular basis and impact on plant functions including photosynthesis, respiration, nitrogen metabolism and translocation

Unit III (8 Lectures)

Quorum sensing in bacteria, understanding microbiome, phytobiomes, dynamics, Applied and ecological aspects of symbioses and pathogen defense, techniques to study plant microbe interaction including microbe tagging, metagenomics and use of organismal databases to identify genes involved in interactions. Industrial application of agriculturally important microbes.

Unit III (8 Lectures)

Resistance mechanisms against attack by plant pathogens, gene-for-gene interactions; induced resistance; non-host resistance. Systemic Acquired Resistance

(SAR) and Induced Systemic Resistance (ISR), Plant and microbial gene expression and signal exchange, specific regulators for different interactions including transgenic plants. Recognition mechanism and signal transduction during plant- pathogen interaction

VI. Suggested Reading

• Rangaswamy, G. Bhagyaraj. 1993. Agricultural Microbiology, Prentice Hall India.

• Stacey, G., and Keen, N.T. (Eds.). 1996. Plant-microbe interactions. Springer  

 Science & Business Media.

• Dickinson M. 2005. Molecular Plant Pathology. Bios Scientific Press, Taylor and

 Francis group.

• Kosuge T and Nester EW. 1989. Plant-Microbe Interactions: Molecular and Genetic

 Perspectives.Vols I-IV. McGraw Hill.

• González MBR and Gonzalez-López J. (Eds.). 2013. Beneficial plant-microbial  

 interactions: ecology and applications. CRC press.

I. Course Title                : RNA Biology

II. Course Code            : MBB 606

III. Credit Hours           : 1+0

IV. Aim of the course

To discuss the specialized topics and advances in the field of Plant RNAs, their structure and role in cellular regulation and scope for crop improvement.

V. Theory

Unit I (4 Lectures)

RNA structure, functional evolution: RNA structure, types of RNA and function; Genome evolution- RNA as genetic material to regulatory molecule, Non-Coding RNAs, structure, function and regulation

Unit II (4 Lectures)

RNA synthesis, processing and regulation: transcription and its regulation in prokaryotes and eukaryotes; RNA splicing and editing; Translation and its regulation in prokaryotes and eukaryotes

Unit III (4 Lectures)

Genome regulation: Prokaryotic- attenuation, ribozymes, aptamers, riboswitches, CRISPER-Cas; eukaryotic-Exon skipping, nonsense-mediated decay, RNAi, Long non-coding RNA.

Unit IV (4 Lectures)

Epigenetic regulation. RNA-based gene silencing technologies and their applications for crop improvement

VI. Suggested Reading

• Elliott, D., and Ladomery, M. 2017. Molecular biology of RNA. Oxford University   

 Press.

• Rao, M.R.S. (Ed.) 2017. Long Non-Coding RNA Biology, Springer,

• Donald, C.R., Hannon, G., Ares, M. and Nilsen, T.W. 2011. RNA: A Laboratory

  Manual, CSHL Press.

• Maas, S. (Ed.). 2013. RNA Editing: Current Research and Future Trends. Horizon

  Scientific Press.

I. Course Title               : Plant Hormones and Signaling

II. Course Code             : MBB 607

III. Credit Hours           : 2+0

IV. Aim of the course

To provide in-depth knowledge of plant hormone and their role in plant growth and

development.

V. Theory

Unit I (12 Lectures)

Hormone Biosynthesis, Metabolism and its Regulation: Auxin biosynthesis and metabolism, Gibberellin biosynthesis and Inactivation, Cytokinin biosynthesis and metabolism, Ethylene biosynthesis, Abscisic acid biosynthesis and metabolism, Brassinosteroid biosynthesis and metabolism. Salicylic acid and jasmonate biosynthesis and metabolism.

Unit II (12 Lectures)

Functioning of hormones in plant growth and development: Transport of Auxins, Induction of vascular tissues by Auxin, Hormones and the regulation of water balance, seed development and germination, Hormonal control of day length and senescence.

Unit III (12 Lectures)

Action of Hormones: Hormones in defense against insects and disease; Role of jasmonates, salicylic acids and peptide hormones for defense, growth, development

and reproduction; Methods of plant hormone analysis. NPR 1 dependent Salicylic acid signaling, PAMP and effect or triggered immunity, systemic acquired resistance

and SA signaling.

Unit IV (12 Lectures)

Hormone Signal Transduction: Auxin metabolism, transport and signal transduction, Cytokinin types, synthesis, metabolism, transport and signal transduction, Gibberellin biosynthesis, transport, signal transduction in stem elongation & Leaf Growth, Ethylene metabolism, perception and signaling in seedling growth and development, Ethylene signal transduction in fruits and flowers, Abscisic acid metabolism, transport and signal transduction in nuclear gene expression and stomatal responses. Brassinosteroid biosynthesis, catabolism and signal transduction. Strigalactone biosynthesis, transport and signaling in plant parasitism and symbiosis. Methods of Plant Hormone Analysis: Quantitative analysis of plant hormones based on LC/MS.

VI. Suggested Reading

• Davies Jr. F. et al. 2017. Hart Mann and KRster’s. Plant Propagation: Principles

  and Practices. Pearson.

I. Course Title       : Computational and Statistical tools in Biotechnology

II. Course Code     : MBB 608

III. Credit Hours   : 2+1

IV. Aim of the course

To provide information on basic principles of computational biology and statistical tools used for data analysis

V. Theory

Unit I (8 Lectures)

Basic molecular biology; introduction to the basic principles of structure/function analysis of biological molecules; genome analysis; different types and classification

of genome databases (e.g. HTGS, DNA, Protein, EST, STS, SNPs, Unigenes, etc.) Unit II (8 Lectures)

Statistical Techniques: MANOVA, Cluster analysis, Discriminant analysis, Principal

component analysis, Principal coordinate analysis, Multidimensional scaling; Multiple regression analysis; Likelihood approach in estimation and testing; Resampling techniques – Bootstrapping and Jack- knifing; Markov Models. Hidden

Markov Models, Bayesian estimation and Gibbs sampling

Unit III (8 Lectures)

DNA sequence retrieval system, various DNA and protein sequence file formats, Basic concepts of similarity searching and sequence alignments, pair wise and multiple sequence alignments, DNA sequence analysis, different gene prediction models and gene annotation tools,

Unit IV (8 Lectures)

Protein sequence analysis and structure prediction, comparative genome analysis, phylogenetic analysis, gene expression analysis tools, programming languages and

their applications in bioinformatics

VI. Practical (16)

• Different Types of Databases and Database Search and Retrieval,

• DNA and Protein Sequence Analysis,

• Similarity Searching and Multiple Alignments,

• Gene Annotation,

• Phylogenetic Analysis,

• Sequence Analysis,

• Protein Structure Prediction,

·   Analysis of Microarray Data,

• Programming Languages in Bioinformatics.

VII. Suggested Reading

• Xiong J. 2012. Essential Bioinformatics, Cambridge University Press.

• Andreas, D.B., and Ouellette B.F.F., (Eds) 2004. Bioinformatics: A Practical Guide   

  to the Analysis of Genes and Proteins 3rd Edition, Wiley Interscience.

• Mount D. 2004. Bioinformatics: Sequence and Genome Analysis, 2nd Edition. By,

  CSHL Press.

• Augen J. 2004. Bioinformatics in the Post-Genomic Era: Genome, Transcriptome,  

  Proteome, and Information-Based Medicine.

• Galperin M.Y. and Koonin E.V. (Eds) 2003. Frontiers in Computational Genomics.
 

M.Sc. in Molecular Biology and Biotechnology

*Core Courses; # New Courses

Course Contents

M.Sc. in Molecular Biology and Biotechnology

I. Course Title              :           Principles of Biotechnology

II. Course Code          :           MBB 501

III. Credit Hours        :           3+0

IV. Aim of the course

• To understand the basics of Molecular biology, plant and microbial Biotechnology

• Importance and applications in agriculture, case studies and success stories

• Public education, perception, IPR and related issues

 V. Theory

Unit I (12 Lectures)

History, scope and importance of Biotechnology; Specializations in Agricultural Biotechnology: Genomics, Genetic engineering, Tissue Culture, Bio-fuel, Microbia Biotechnology, Food Biotechnology etc. Basics of Biotechnology, Primary metabolic pathways, Enzymes and its activities.

Unit II (16 Lectures)

Structure of DNA, RNA and protein, their physical and chemical properties. DNA function: Expression, exchange of genetic material, mutation. DNA modifying enzymes and vectors; Methods of recombinant DNA technology; Nucleic acid hybridization; DNA/RNA libraries; Applications of gene cloning in basic and applied research, Plant transformation: Gene transfer methods and applications of GM crops.

 Unit III (8 Lectures)

Molecular analysis of nucleic acids -PCR and its application in agriculture and industry, Introduction to Molecular markers: RFLP, RAPD, SSR, SNP etc, and their applications; DNA sequencing, different methods; Plant cell and tissue culture techniques and their applications. Introduction to genomics, transcriptomics, ionomics, metabolomics and proteomics. Plant cell and tissue culture techniques and their applications.

 Unit IV (12 Lectures)

Introduction to Emerging topics: Genome editing, gene silencing, Plant microbial interactions, Success stories in Biotechnology, Careers and employment in biotechnology. Public perception of biotechnology; Bio-safety and bioethics issues; Intellectual property rights in biotechnology.

VI. Suggested Reading

• Watson JD, Baker TA, Bell SP, Gann A, Levine M and Losick R. 2014. Molecular Biology of the Gene,

7th edition, Cold Spring Harbor Laboratory Press, New York

• Brown T A. 2010. Gene Cloning and DNA analysis an Introduction 6th edition, Wiley Blackwell

• Primrose SB and Twyman R. 2006. Principles of gene Manipulation 7th edition, Wiley Blackwell

Restructured and Revised Syllabi of Post-graduate Programmes Vol. 2668

• Singh BD. 2012. Biotechnology: Expanding Horizons 4th edition, Kalyani publisher, New

Delhi, India

  I. Course Title             :          Fundamentals of Molecular Biology

II. Course Code          :           MBB 502

III. Credit Hours        :          3+0

IV. Aim of the course

• To understand the basics of DNA, RNA, structure, types and chromatin assembly.

• To get insights into the Central Dogma, basic cellular processes, role of mutation 

  and recombination.

• To understand different levels of gene regulation and the pathways involved.

V. Theory

Unit I (8 Lectures)

Historical developments of molecular biology, Nucleic acids as genetic material, Chemistry and Nomenclature of nucleic acids; Structure of DNA: primary structure; secondary structure, Forms of DNA: A,B, Z and their function; Structure and Types of RNA Genome organization in prokaryotes and eukaryotes; DNA Topology; DNA re-association kinetics, Types of repeat sequences.

Unit II (10 Lectures)

Central dogma of Molecular Biology; DNA replication- Classical experiments, Models of DNA replication; DNA replication, Origin and Steps in DNA replication - initiation, elongation and termination; Enzymes and accessory proteins and its mechanisms; Eukaryotic DNA replication in brief. Types of DNA damages and mutations; DNA repair mechanisms, Recombination: Homologous and non-homologous, Genetic consequences.

Unit III (8 Lectures)

Prokaryotic transcription, initiation, elongation and termination, promoters, Structure and function of eukaryotic RNAs and ribosomal proteins. Eukaryotic transcription – RNA polymerase I, II and III, Elongation and Termination, Eukaryotic promoters and enhancers, Transcription factors, Post transcriptional processing, Splicing: Catalytic RNAs, RNA stability and transport, RNA editing.

 Unit IV (10 Lectures)

Genetic code and its characteristics, Universal and modified genetic code and its characteristics, Wobble hypothesis; Translational machinery; Ribosomes in prokaryotes and Eukaryotes. Initiation complex formation, Cap dependent andCap independent initiation in eukaryotes, Elongation: translocation, trans-peptidation and termination of translation; Co- and Post-translational modifications of proteins;

Translational control; Protein stability -Protein turnover and degradation.

 Unit V (12 Lectures)

Gene regulation in prokaryotes, Constitutive and Inducible expression, small molecule regulators; Operon concept: lac and trp operons, attenuation, anti termination, stringent control. Gene regulation in ukaryotes– regulatory RNA and RNA interference mechanisms, Silencers, insulators, enhancers, mechanism of

silencing and activation; Families of DNA binding transcription factors: Helixturn-helix, helix-loop-helix etc. Epigenetic regulations

VI. Suggested Reading

• Nelson DL and Cox M.M. 2017. Lehinger’s Principles of Biochemistry, 7th edition, W HFreeman

Publication New York.

• Krebs, J.E., Goldstein, E.S., Kilpatrick, S.T. 2017. Lewin’s Genes XII 12th edition, Jones &Bartlett

Learning publisher, Inc.

• Watson, J.D., Baker, T.A., Bell, S.P., Gann, A., Levine, M and Losick R. 2014. Molecular Biology of the

Gene, 7th edition, Cold Spring Harbor Laboratory Press, New York.

• Alberts, B. 2017. Molecular Biology of the Cell 5th edition, WW Norton & Co, Inc.

• Allison, L.A. 2011. Fundamentals of Molecular Biology.2nd Edition, John Wiley and Sons.

I. Course Title             :           Molecular Cell Biology

II. Course Code           :           MBB 503

III. Credit Hours         :           3+0

IV. Aim of the course

• To understand the basics structure and function of plant and animal cell

• To get insights into the basic cellular processes, transport, signalling, cell movement, cell division and

general regulation mechanisms.

V. Theory

Unit I (8 Lectures)

Origin of life, History of cell biology, Evolution of the cell: endo-symbiotic theory, tree of life, General structure and differences between prokaryotic and eukaryotic cell; Similarities and distinction between plant and animal cells; different kinds of cells in plant and animal tissues.

Unit II (8 Lectures)

Cell wall, cell membrane, structure and composition of bio-membranes, Structure and function of major organelles: Endoplasmic reticulum Ribosomes, Golgi apparatus, Mitochondria, Chloroplasts, Lysosomes, Peroxisomes, Micro-bodies, Vacuoles, Nucleus, Cyto-skeletal elements.

Unit III (12 Lectures)

Membrane transport; Diffusion, osmosis, ion channels, active transport, mechanism of protein sorting and regulation of intracellular transport, trans membrane and vesicular transport - endocytosis and exocytosis; General principles of cell communication: hormones and their receptors, signaling through G-protein couple dreceptors, enzyme linked receptors; signal transduction mechanisms and regulation, Cell junctions, Cell adhesion, Cell movement; Extracellular matrix.

Unit IV (10 Lectures)

Chromatin structure, Cell division and regulation of cell cycle; Mechanisms of cell division, Molecular event sat M phase, mitosis and cyto-kinesis, Ribosomes in relation to cell growth and division, Extracellular and intracellular Control of Cell Division; abnormal cell division: cancer- hall marks of cancer and role of on cogenes and tumor suppressor genes in cancer development - Programmed cell death (Apoptosis).

Unit V (10 Lectures)

Morphogenetic movements and the shaping of the body plan, Cell diversification, cell memory, cell determination, and the concept of positional values; Differentiated cells and the maintenance of tissues and organ development; Stem cells: types and applications; Basics of Animal development in model organisms (C. elegans; Drosophila); Plant development.

VI. Suggested Reading

• Alberts, B. 2017. Molecular Biology of the Cell 5th edition, WW Norton & Co, Inc.

• Lodish, H., Berk, A., Kaiser, C.A., Krieger, M., Bretscher, A., Ploegh, H., Amon, A., Martin,K.C., 2016.

Molecular Cell Biology 8th Edition. W.H. Freeman & Co. New York.

• Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., Hopkin, K., Johnson, A., Walter, P., 2013

Essential of Cell Biology, WW Norton & Co, Inc.

• Cooper, G.M. and Hausman, R.E. 2013. The cell: A Molecular Approach 6th edition, Sinauer

Associates, Inc.

 I. Course Title             :          Techniques in Molecular Biology I

II. Course Code          :           MBB 504

III. Credit Hours        :           0+3

IV. Aim of the course

• To get a basic overview of molecular biology techniques, good lab practices and recombinant DNA technology

• To get a hands on training in chromatography, protein analysis, nucleic acid analysis, bacterial and phage genetics

 V. Practicals

• Good lab practices, preparation of buffers and reagents.

• Principle of centrifugation and spectrophotometry.

• Growth of bacterial culture and preparation of growth curve, Isolation of Genomic DNA from bacteria.

• Isolation of plasmid DNA from bacteria.

• Growth of lambda phage and isolation of phage DNA.

• Isolation and restriction of plant DNA (e.g. Rice / Moong / Mango / Merigold).

• Quantification of DNA by (a) Agarose Gel electrophoresis and (b) Spectrophotometry

• PCR using isolated DNA.

• PAGE Gel electrophoresis.

• Restriction digestion of plasmid and phage DNA, ligation, Recombinant DNA construction.

• Transformation of E. coli and selection of transformants

• Chromatographic techniques

a. TLC

b. Gel Filtration Chromatography,

c. Ion exchange Chromatography,

d. Affinity Chromatography

• Dot blot analysis, Southern hybridization, Northern hybridization.

• Western blotting and ELISA.

• Radiation safety and non-radio isotopic procedure.

VI. Suggested Reading

• Sambrook, J., and Russell, R.W. 2001. Molecular Cloning: A Laboratory Manual 3rd Edition,

Cold spring harbor laboratory press, New York.

• Wilson, K., and Walker, J., 2018. Principles and Techniques of Biochemistry and Molecular

Biology 8th edition, Cambridge University Press.

• Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA and Struhl K. 2002.

Short Protocols in Molecular Biology 5th edition, Current Protocols publication.

 I. Course Title            :           Omics and Systems Biology

II. Course Code           :           MBB 505

III. Credit Hours         :           2+1

IV. Aim of the course

• To get a basic overview of genomics, proteomics, ionomics and metabolomics

• To get a primary information on the application of omics science across the industry

V. Theory

Unit I (8 Lectures)

Different methods of genome sequencing, principles of various sequencing chemistries, physical and genetic maps, Comparative and evolutionary genomics, Organelle genomics, applications in phylogenetics, case studies of completed genomes, preliminary genome data analysis, basics of ionomics analysis, different methods

Unit II (6 Lectures)

Protein-basics: primary-, secondary- and tertiary structure, Basics of X-ray crystallography and NMR, Principal and Applications of mass spectrometry, Proteomics: Gel based and gel free, Basics of software used in proteomics, MASCOT,PD-Quest, etc., Study of protein interactions, Prokaryotic and yeast-based expression system and purification

Unit III (6 Lectures)

Metabolomics and its applications, Use of 1D/2D NMR and MS in metabolome analysis, Multivariate analysis and identification of metabolite as biomarkers, Study of ionome using inductively coupled plasma – mass spectroscopy (ICP-MS), X-Ray Fluorescence (XRF), Neutron activation analysis (NAA), Data integration using genome, transcriptome, proteome, metabolome and ionome with phenome.

 Unit IV (6 Lectures)

Introductory systems Biology - The biochemical models, genetic models and systems model, Molecules to Pathway, Equilibrium binding and cooperatively – Michaelis Menten Kinetics, Biological oscillators, Genetic oscillators, Quorum Sensing, Cell cell communication, Drosophila Development, Pathways to Network, Gene regulation at a single cell level, transcription network, REGULATORY CIRCUITS, Negative and positive auto-regulation, Alternative Stable States, Bimodal Switches, Network

building and analysis

VI. Practical (12)

• Isolation of HMW DNA and brief overview of sequencing, Primary information on genome data

analysis.

• BSA Standard curve preparation, Extraction of protein and estimation methods.

• Quantification of proteins from different plant tissues using spectrophotometry.

• 2-D Gel Electrophoresis, 2-D Image analysis.

• Experiments on protein-protein interaction (Yeast 2-hybrid, Split Ubiquitin  

  system).

• Demonstration on MALDI-TOF.

• Demonstration on ICP-MS, AAS, Nitrogen estimation using various methods.

VII. Suggested Reading

• Primrose, S.B. and Twyman, R. 2006. Principles of Gene Manipulation 7th edition, Wiley Blackwell

• Wilson, K., and Walker, J. 2018. Principles and Techniques of Biochemistry and Molecular Biology 8th

Edition, Cambridge University Press.

I. Course Title             :           Plant Genetic Engineering

II. Course Code          :           MBB 506

III. Credit Hours        :           3+0

IV. Aim of the course

• To get a basic overview of molecular cloning, vectors and genomic library construction.

• To get an overview of PCR and its applications, sequencing, gene knockouts, transgenics etc.

V. Theory

Unit I (10 Lectures)

Historical background, Restriction Enzymes; DNA Modifying enzymes, ligase, T4DNA polymerase, Polynucleotide kinaseetc, Cohesive and blunt end ligation; Labeling of DNA: Nick translation, Random priming, Radioactive and non-radioactive probes, Hybridization techniques: Northern, Southern and Colony hybridization, Fluorescence in situ hybridization; Chromatin Immuno precipitation; DNA-Protein

Interactions: Electromobility shift assay.

Unit II (14 Lectures)

Plasmids; Bacteriophages; M13, Phagemids; Lambda vectors; Insertion and Replacement vectors; Cosmids; Artificial chromosome vectors (YACs; BACs); Animal Virus derived vectors-SV-40; Expression vectors; pMal, pET-based vectors; Protein purification; His-tag; GST-tag; MBP-tag, etc.; Baculovirus vectors system, Plant based vectors, Ti and Ri plasmids as vectors, Yeast vectors, Shuttle vectors. Transformation; Construction of libraries; Isolation of mRNA and total RNA; cDNA and genomic libraries; cDNA and genomic cloning, Jumping and hopping libraries, Protein-protein interactive cloning and Yeast two hybrid system; Phage display; Principles in maximizing gene expression; Codon optimization for heterologous expression. Introduction of DNA into mammalian cells; Transfection techniques

Unit III (12 Lectures)

Principles of PCR, Primer design, DNA polymerases, Types of PCR – multiplex, nested, reverse transcriptase, real time PCR, touchdown PCR, hot start PCR, colony PCR, cloning of PCR products; T- vectors; Applications of PCR in gene recombination, Site specific mutagenesis, in molecular diagnostics; Viral and bacterial detection; Mutation detection: SSCP, DGGE, RFLP, Oligo Ligation Assay.

Unit IV (12 Lectures)

Genetic transformation of plants: DNA delivery – Agro bacterium mediated method. Direct DNA delivery – chemical mediated electroporation and particle bombardment. Vectors and transgene design - Promoters and Marker genes. Chloroplast transformation. Development of marker-free plants. Analysis of transgenic plants– molecular and Biochemical assays, genetic analysis - Identification of gene integration site - Advance methods – cis genesis, in tragenesis and targeted genome modification – ZFN, TALENS and CRISPR. Application of transgenic technology.

 VI. Suggested Reading

• Brown, T.A. 2010. Gene Cloning and DNA Analysis an Introduction. 6th edition, Wiley

Blackwel.

• Primrose, S.B. and Twyman, R. 2006. Principles of Gene Manipulation 7th edition, Wiley

  Blackwell.

• Sambrook, J., and Russell, R.W. 2001. Molecular cloning: A laboratory manual 3rd Edition,

Cold spring harbor laboratory press, New York.

• Wilson, K., and Walker, J. 2018. Principles and Techniques of Biochemistry and Molecular

Biology 8th Edition, Cambridge University Press.

I. Course Title             :           Techniques in Molecular Biology II

II. Course Code          :           MBB 507

III. Credit Hours        :           0+3

IV. Aim of the course

• To get a basic overview of molecular biology techniques, good lab practices and molecular markers.

• To get a hands on training in RNAi, microarrays, yeast2 hybrid and immunological techniques.

V. Practicals

Construction of gene libraries (cDNA and Genomics).

• Synthesis and cloning of cDNA.

• Real time PCR and interpretation of data.

• Molecular markers

i. RAPD.

ii. SSR.

iii. AFLP / ISSR and their analysis.

• Case study of SSR markers - construction of linkage map.

• QTL analysis using genotypic data based on SSR.

• SNP identification and analysis.

• Microarray studies and use of relevant software.

• Proteomics

i. 2D gels,

ii. Mass spectrometry

• RNAi - designing of construct, phenotyping of the plant.

• Yeast 1 and 2-hybrid interaction.

• Generation and screening of mutants.

• Transposon mediated mutagenesis.

• Immunology and molecular diagnostics: Ouchterlony double diffusion, Immuno precipitation, Radiation

Immuno diffusion, Immuno electrophoretic, Rocket Immuno electrophoretic, Counter Current

Immuno electrophoretic, ELISA, Latex Agglutination, Immuno histo chemistry.

VI. Suggested Reading

• Wilson, K., and Walker, J. 2018. Principles and Techniques of Biochemistry and Molecular

   Biology 8th Edition, Cambridge University Press

• Bonifacino, J. S., Dasso, M., Harford, J. B., Liipincott-Schwartz, J., and Yamada, K. M.

   2004. Short Protocols in Cell Biology. John Wiley & Sons, New Jersey

• Hawes, C., and Satiat-Jeunemaitre, B. 2001. Plant Cell Biology: Practical Approach. Oxford

University Press, Oxford

 • Sawhney, S.K., Singh, R. 2014. Introductory Practical Biochemistry, Alpha science international

limited

 I. Course Title             :           Introduction to Bioinformatics

II. Course Code          :           MBB 508

III. Credit Hours        :           2+1

IV. Aim of the course

• To get a basic overview of computational techniques related to DNA, RNA and protein analysis.

• To get a hands on training in software’s and programs used to analyse, assemble or annotate genomes, phylogenetics, proteomics etc.

V. Theory

Unit I (8 Lectures)

Bioinformatics basics, scope and importance of bioinformatics; Biological databases for DNA and Protein sequences -PIR, SWISSPROT, Gen-Bank, DDBJ, secondary database, structural databases –PDB,SCOP and CATH, Specialized genomic resources, Microarray database.

Unit II (10 Lectures)

Bioinformatics Tools Facilitate the Genome-Wide Identification of Protein-Coding Genes, Sequence analysis, Sequence submission and retrieval system-SEQUIN, BANKit, SAKURA, Webin, Sequence alignment, pair wise alignment techniques, multiple sequence alignment; Tools for Sequence alignment- BLAST and its variants; Phylogenetic analysis- CLUSTAL X, CLUSTAL W, Phylip, Tcoffee

Unit III (10 Lectures)

Sequencing of protein; Protein secondary structure prediction- Chousfasman, GOR Method, Protein 3DStructure Prediction: Evaluation of models- Structure validation and refinement - Ramachandran plot, Force field calculations, SAVES. Protein function prediction- sequence and domain based, Primer designing- principles and methods. Drug discovery, Structure Based Drug Design- Rationale for computer

aided drug designing, basic principles, docking, QSAR.

VI. Practical (12 Lectures)

• Usage of NCBI resources

• Retrieval of sequence/structure from databases and submission

• Different Databases, BLAST exercises.

• Assembly of DNA and RNA Seq data

• Annotation of assembled sequences, Phylogenetics and alignment

• Visualization of structures, Docking of ligand receptors

• Protein structure analysis and modelling

VII. Suggested Reading

• Attwood, T.K., and Parry-Smith, D. J. 2004. Introduction to Bioinformatics, Pearson

Education (Singapore) Pvt. Ltd.

• David Edwards (Ed.) 2007. Plant Bioinformatics: Methods and Protocols. Humana Press,

  New Jersey, USA.

• Mount, D.W. 2004. Bioinformatics: Sequence and Genome Analysis. 2nd Revised edition

Cold Spring Harbor Laboratory Press, U.S.

• Pevsner J. 2009. Bioinformatics and Functional Genomics, 2nd edition, Wiley-Blackwell.

I. Course Title             :           Plant Tissue Culture

II. Course Code          :           MBB 509

III. Credit Hours         :           2+1

IV. Aim of the course

• To provide insight into principles of plant cell culture and genetic transformation.

• To get a hands on training in basic plant tissue culture techniques, callusing, micro propagation and analysis.

V. Theory

Unit I (12 Lectures)

History of plant tissue culture, principle of Totipotency; Tissue culture media; Plant hormones and morphogenesis; Direct and indirect organogenesis; Direct and indirect somatic embryogenesis; Applications of plant tissue culture; National certification and Quality management of TC plants; Genetic Fidelity testing and Virus indexing methods – PCR, ELISA

Unit II (12 Lectures)

Micropropagation of field and ornamental crops; Virus elimination by meristem culture, meristem tip culture and micro grafting; Androgenesis and gyno genesis -production of androgenic and gynogenic haploids - diploidization; Protoplast culture- isolation and purification; Protoplast culture; Protoplast fusion; Somatic hybridization - Production of Somatic hybrids and Cybrids;, Wide hybridization -

embryo culture and embryo rescue techniques; Ovule, ovary culture and endosperm culture.

Unit III (12 Lectures)

Large-scale cell suspension culture - Production of alkaloids and other secondary metabolites- techniques to enhance secondary metabolite production, Somaclonal and game to clonal variations – causes and applications; Callus culture and in vitro screening for stress tolerance; Artificial seeds, In vitro germplasm storage and cryo-preservation. Commercial Tissue Culture: Case studies and success stories,

Market assessment; project planning and preparation, economics, government policies

VI. Practical (12)

• Preparation of stocks - macronutrients, micronutrients, vitamins and hormones, filter sterilization of

hormones and antibiotics. Preparation of Murashige and Skoogmedium.

• Micro-propagation of plants by nodal and shoot tip culture.

• Embryo culture to overcome incompatibility, Anther culture for haploid production.

• Callus induction in tobacco leaf discs, regeneration of shoots, root induction, role of hormones in

morphogenesis.

• Acclimatization of tissue culture plants and establishment in greenhouse.

• Virus indexing in tissue culture plants. (Using PCR and ELISA).

• Plan of a commercial tissue culture unit.

VII. Suggested Reading

• Razdan, M.K. 2003. Introduction to plant tissue culture, 2nd edition, Oxford publicationsgroup

• Butenko, R.G. 2000. Plant Cell Culture University Press of Pacific

• Herman, E.B. 2008. Media and Techniques for Growth, Regeneration and Storage, Agritech

Publications, New York, USA.

• Bhojwani, S.S and Dantu P. 2013. Plant Tissue Culture – An Introductory Text. Springer

Publications.

• Gamborg, O.L and G.C. Philips (eds.). 2013. Plant Cell, Tissue and Organ culture-Lab Manual.

  Springer Science & Business media

I. Course Title             :           Microbial/ Industrial Biotechnology

II. Course Code          :           MBB 510

III. Credit Hours        :           2-+1

IV. Aim of the course

To familiarize about the various microbial processes/systems/activities, which have been used for the development of industrially important products/processes.

 V. Theory

Unit (8 Lectures)

Introduction, scope and historical developments; Isolation, screening and genetic improvement (involving classical approaches) of industrially important organisms.

Unit II (8 Lectures)

Primary metabolites, production of industrial ethanol as a case study; Secondary metabolites, bacterial antibiotics and non-ribosomal peptide antibiotics as case study; Recombinant DNA technologies for microbial processes; Strategies for development of industrial microbial strains with scale up production capacities; Metabolic pathway engineering of microbes for production of novel product for industry.

Unit III (8 Lectures)

Microbial enzymes, role in various industrial processes, production of fine chemicals for pharmaceutical industries; Bio-transformations, Bio- augmentation with production of vitamin C as a case study; Bioreactors, their design and types; Immobilized enzymes-based bioreactors; Microencapsulation technologies for immobilization of microbial enzymes.

Unit IV (8 Lectures)

Environmental Biotechnology, bio treatment for pollution control, treatment of industrial and other wastes, biomass production involving single cell protein; Bioremediation of soil; Production of eco-friendly agricultural chemicals, bio- pesticides, bio-herbicides, bio-fertilizers, bio-fuels, etc.

VI. Practical

• Isolation of industrially important microorganisms, their maintenance and improvement.

• Lab scale production of industrial compounds such as alcohol, beer, citric acid, lactic acid

and their recovery.

• Study of bio-reactors and their operations.

• Production of bio-fertilizers.

• Experiments on microbial fermentation process of antibiotics, bio-pigments, dairy products,

harvesting purification and recovery of end products.

• Immobilization of cells and enzymes, studies on its kinetic behavior, growth analysis and

biomass estimation.

• Determination of mass transfer coefficient.

VII. Suggested Reading

• Waites, M.J., Morgan, N.L., Rockey, J.S., Higton, G. 2001. Industrial Microbiology: An

Introduction, Wiley-Blackwell.

• Slater, A., Scott, N.W., & Fowler, M.R. 2003. The Genetic Manipulation of Plants. Plant

  Biotechnology Oxford, England: Oxford University Press.

• Kun, L.Y. (Ed.). 2003. Microbial biotechnology: principles and applications. World Scientific

  Publishing Company.

I. Course Title             :           Molecular Plant Breeding

II. Course Code          :           MBB 511

III. Credit Hours        :           2-+1

IV. Aim of the course

• To familiarize the students about the use of molecular biology tools in plant breeding.

• To provide a hands on training in data analysis, diversity analysis and mapping of genes and QTLs.

V. Theory

Unit I (8 Lectures)

Inheritance of qualitative and quantitative traits. Heritability – its estimation, Population structure of self- and cross-pollinated species, Factors affecting selection efficiency. Development of different kinds of segregating populations – F2, F3,BC1F1, BC1F2, BC4F2, RIL (Recombinant Inbred Lines), AIL (Advanced Inter crossed Lines), DH (Di-haploid population), NIL (Near Isogenic lines), NAM (Nested

Association Mapping), MAGIC (Multi-parent Advanced Generation Inter cross population).

Unit II (8 Lectures)

Causes of sequence variation and its types, Types of molecular markers and development of sequence based molecular markers – RFLP, AFLP, SCARs, CAPS,SSRs, STMS, SNPs InDel and DARTseq; Inheritance of markers, Linkage analysis using test cross, F2, F3, BC1F1, RIL. Construction of genetic map, Mapping genes for qualitative traits; Genotyping by sequencing and high-density chip arrays.

 Unit III (8 Lectures)

QTL mapping using structured populations; Association mapping using unstructured populations; Genome Wide Association Studies (GWAS),Principle of Association mapping– GWAS-SNP genotyping methods, DART array sequencing, Illumina’s Golden Gate Technology, Genotyping by sequencing methods- Fluidigm; GBS, Illumina Hi seq- Nano pore sequencing, Principles and methods of Genomic Selection, Fine mapping of genes/QTL; Development of gene based markers; Allele mining by

TILLING and Eco-TILLING.

 Unit IV (8 Lectures)

Tagging and mapping of genes. Bulk segregant and co-segregation analysis, Marker assisted selection (MAS); Linked, unlinked, recombinant, flanking, peak markers. Foreground and background selection; MAS for gene introgression and pyramiding: MAS for specific traits with examples. Haplo type concept and Haplo type-based breeding; Genetic variability and DNA fingerprinting. Molecular markers in Plant

variety protection, IPR issues, hybrid purity testing, clonal fidelity testing and transgenic testing.

VI. Practical

• Construction of linkage map.

• QTL analysis using the QTL cartographer and other software.

• SNP data analysis using TASEEL.

• Detection of haplo type block using SNP data –pLink software.

• Genotyping by sequencing methods –Illumina genotyping platform.

• Marker assisted breeding – MABB case studies quality traits in rice/maize.

• Genome Assisted Breeding in model crops, Genomic Selection models using them orphological and SNP data

 VII. Suggested Reading

• Acquaah, G. 2007. Principles of Plant Genetics and Breeding, Blackwell Publishing Ltd.

USA.

• Weising, K., Nybom, H., Wolff, K., and Kahl, G. 2005. DNA Fingerprinting in Plants:

Principles, Methods and Applications, 2nd ed. Taylor and Francis Group, Boca Raton, FL.

• Halford, N. 2006. Plant Biotechnology-Current and future applications of genetically modified

crops, John Wiley and Sons, England.

• Singh, B. D. and Singh, A. K. 2015. Marker-Assisted Plant Breeding: Principles and Practices

Springer (India) Pvt. Ltd.

•  Boopathi, NM. 2013. Genetic Mapping and Marker Assisted Selection: Basics, Practice and

Benefits.Springer India. p293.

I. Course Title : IPR, Bio-safety & Bioethics

II. Course Code : MBB 512

III. Credit Hours : 2+0

IV. Aim of the course

• To familiarize the students about ethical and bio-safety issues in plant biotechnology.

• To provide a hands-on training in data analysis, diversity analysis and mapping of genes and QTLs.

V. Theory

Unit I (10 Lectures)

IPR: historical background in India; trade secret; patent, trademark, design & licensing; procedure for patent application in India; Patent Cooperation Treaty(PCT); Examples of patents in biotechnology-Case studies in India and abroad; copyright and PVP; Implications of IPR on the commercialization of biotechnology products, ecological implications; Trade agreements- The WTO and other international agreements, and Cross border movement of germplasms.

Unit II (8 Lectures)

Bio-safety and bio-hazards; General principles for the laboratory and environmental bio-safety; Bio-safety and risk assessment issues; handling and disposal of biohazards; Approved regulatory laboratory practice and principles, The Cartagena Protocol on bio-safety; Bio-safety regulations in India; national Bio-safety Policy and Law; Regulations and Guidelines related to Bio-safety in other countries

Unit III (8 Lectures)

Potential concerns of transgenic plants – Environmental safety and food and feed safety. Principles of safety assessment of Transgenic plants – sequential steps in risk assessment. Concepts of familiarity and substantial equivalence. Risk -Environmental risk assessment – invasiveness, weediness, gene flow, horizontal gene transfer, impact on non-target organisms; food and feed safety assessment –toxicity and allergenicity. Monitoring strategies and methods for detecting transgenics.

Unit IV (6 Lectures)

Field trails – Bio-safety research trials – standard operating procedures, labelling of GM food and crop Bio-ethics- Mankind and religion, social, spiritual &environmental ethics; Ethics in Biotechnology, labeling of GM food and crop; Biopiracy

VI. Suggested Reading

• Goel, D. and Parashar, S. 2013. IPR, biosafety, and bioethics.

• Joshi, R. 2006. Biosafety and Bioethics.

• Nambisan, P. 2017. An Introduction to Ethical, Safety and Intellectual Property Rights Issues

in Biotechnology.

I. Course Title             :           Immunology and Molecular Diagnostics

II. Course Code          :           MBB 513

III. Credit Hours        :           3+0

IV. Theory

Unit I (6 Lectures)

Immunity and its classification; Components of innate and acquired immunity; Lymphatic system; Hematopoiesis; Organs and cells of the immune system- primary, secondary and tertiary lymphoid organs Descriptions of Antigens - immunogens, hapten and adjuvants.

Unit II (12 Lectures)

Immunoglobulins-basic structure, classes & subclasses of immunoglobulins, antigenic determinants; Multigene organization of immunoglobulin genes; B-cell receptor; Immunoglobulin super-family; Principles of cell signaling; Basis of self and non-self discrimination; Kinetics of immune response, memory; B cell maturation, activation and differentiation; Generation of antibody diversity; T-cell maturation, activation and differentiation and T-cell receptors; Functional T Cell Subsets; Cell mediated immune responses, ADCC; Cluster of Differentiations (CDs), Cytokines properties, receptors and therapeutic uses.

Unit III (8 Lectures)

Phagocytosis; Complement and Inflammatory responses; Major Histo compatibility Complex - MHC genes, MHC and immune responsiveness and disease susceptibility, HLA typing; Antigen processing and presentation- endogenous antigens, exogenousantigens, non-peptide bacterial antigens and super-antigens; Cell-cell co-operation, Hapten-carrier system

Unit IV (10 Lectures)

Precipitation, agglutination and complement mediated immune reactions; Advanced immunological techniques – RIA, ELISA, Western blotting, ELISPOT assay, immuno fluorescence, flow cytometry and immuno electron microscopy; Surface plasm on resonance, Biosen or assays for assessing ligand –receptor interaction, CMI techniques- lympho proliferation assay, Mixed lymphocyte reaction, Cell Cyto-toxicity assays, Apoptosis, Transgenic mice, Gene knock outs

Unit V (12 Lectures)

Active and passive immunization; Live, killed, attenuated, sub unit vaccines; Vaccine technology- Role and properties of adjuvants, recombinant DNA and protein based vaccines, plant-based vaccines, Antibody genes and antibody engineering- chimeric and hybrid monoclonal antibodies, Immunity to Infection, Bacteria, viral, fungal and parasitic infections, Hypersensitivity – Type I-IV; Autoimmunity; Types of autoimmune diseases, MHC and TCR in autoimmunity; Transplantation, Immunological basis of graft rejection, immunosuppressive therapy; Tumor immunology – Tumor antigens.

V. Suggested Reading

• Owen J.A., Punt, J., & Stranford, S. A. 2013. Kuby immunology (p. 692). New York: WH

  Freeman.

• Kenneth, M., and Weaver, C. 2017. Janeways Immunobiology, 9th Edition, New York, USA:

Garland Science, Taylor & Francis publisher.

• William, P. 2013. Fundamental of Immunology, 7th edition, Lippencott, William and Wilkins

publisher.

I. Course Title             :           Nano Biotechnology

II. Course Code          :           MBB 514

III. Credit Hours        :           2+1

IV. Aim of the course

Understanding the molecular techniques involved in structure and functions of nano-biomolecules in cells such as DNA, RNA and proteins.

V. Theory

Unit I (8 Lectures)

Introduction to Nanotechnology - Nano materials - Self-assembly to artificial assembly for creation of useful nanostructures – Bottoms up and Top down approach (Nanorods, nano cages, nanotubes, quantum dots, nano wires, metal/ polymer-based nanostructures) – Preparation and Characterization of nano particles (particle size analyzer, microscopy, viz. electron microscopy, atomic force microscopy, etc).

Unit (8 Lectures)

Cell structure – Bio macromolecules: Types, Structure, Dynamics and interaction with water – Cellular nano machines – cellular transducers, membrane channels, membrane transporters, Membrane motors – Creation of bio-nanostructures (Nanoliposomes, Nano micelles, Nanomotors, etc).

Unit III (8 Lectures)

Chemical, physical and biological properties of biomaterials and bio response: biomineralization, biosynthesis, and properties of natural materials (proteins, DNA, and polysaccharides), structure-property relationships in polymeric materials(synthetic polymers and structural proteins); Aerosol properties, application and dynamics; Statistical Mechanics in Biological Systems,

Unit (8 Lectures)

Nano particular carrier systems; Micro- and Nano-fluidics; Drug and gene delivery system; Micro fabrication, Biosensors, Chip technologies, Nano- imaging, Metabolic engineering and Gene therapy.

VI. Practical

• Isolation of enzymes and nucleic acids involved in biosynthesis of nano materials

• Synthesis of Gold/silver Nano particles by biogenic methods, Synthesis of micelles and inverse micelles

• Synthesis of Carbon Nano-materials by Chemical Vapor Deposition and Sputtering technique

• Preparation of thiolate silver nano particles, Purification and measurement of carbon nano materials

• Zinc selenide quantum dot preparation, Synthesis of Iron Oxide Nano particle

• Thin film preparation by spin coating technique, Synthesis of Nickel metal nano particle by urea

decomposition method

• Synthesis of Zinc Oxide nano particle

VII. Suggested Reading

• Nalwa, H.S. 2005. Handbook of Nano structured Biomaterials and Their Applications in    

Nano biotechnology. American Scientific Publications.

• Niemeyer C.M. and Mirkin C.A. (Eds) 2005. Nano biotechnology: Concepts Applications and

Perspectives, Wiley Inter-science publications.

• Cao, G., and Wang, Y. 2004. Nanostructures and Nano materials: Synthesis, Properties and

  Applications, Imperial College Press.

I. Course Title             :           Environmental Biotechnology

II. Course Code          :           MBB 515

III. Credit Hours        :       3+0

IV. Aim of the course

To apprise the students about the role of biotechnology in environment management

for sustainable eco-system and human welfare.

 V. Theory

Unit I (8 Lectures)

Basic concepts and environmental issues; types of environmental pollution; problem sarising from high-input agriculture; methodology of environmental management; air and water pollution and its control; waste water treatment - physical, chemical and biological processes; need for water and natural resource management.

Unit II (8 Lectures)

Microbiology and use of micro-organisms in waste treatment; biodegradation; degradation of Xeno biotic, surfactants; bioremediation of soil & water contaminated with oils, pesticides and toxic chemicals, detergents etc; aerobic processes (activated sludge, oxidation ditches, trickling filter, rotating drums, etc); anaerobic processes: digestion, filtration, etc.

 Unit III (8 Lectures)

Renewable and non-Renewable resources of energy; energy from solid waste; conventional fuels and their environmental impact; biogas; microbial hydrogen production; conversion of sugar to alcohol; gasohol; biodegradation of lignin and cellulose; bio-pesticides; bio-fertilizers; composting; vermi culture etc.

 Unit IV (8 Lectures)

Treatment schemes of domestic waste and industrial effluents; food, feed and energy from solid waste; bioleaching; enrichment of ores by microorganisms; global environmental problems: ozone depletion, UV-B, greenhouse effects, and acid rain; biodiversity and its conservation; biotechnological approaches for the management environmental problems.

 VI. Suggested Reading

• Evans, G. M. and Furlong, J. C. 2010. Environmental Biotechnology: Theory and Application.

2nd edition, Wiley-Blackwell.

• Jordening HJ and Winter J. 2006. Environmental Biotechnology: Concepts and Applications.

  Wiley-VCH Verlag.

 I. Course Title            :           Bio-entrepreneurship

II. Course Code          :           MBB 516

III. Credit Hours        :           1+0

IV. Aim of the course

The objective of this course is to teach students about fundamentals of entrepreneurship, launching a venture or a start up in biotechnology-based theme.

V. Theory

Unit I (4 Lectures)

Scope in biotechnology; types of bio-industries – bio-pharma, bio-agri, bio-services and bio-industrial; Importance of entrepreneurship; introduction to bio-entrepreneurship – biotechnology in a global scale; –skills for successful entrepreneur–creativity, leadership, managerial, team building, decision making;

opportunities for bio-entrepreneurship- entrepreneurship development programs of public and private agencies (MSME, DBT, BIRAC, Start-up & Make in India)

Unit II (4 Lectures)

Business plan preparation; business feasibility analysis by SWOT, socio-economic costs benefit analysis; funds/ support from various agencies; statutory and legal requirements for starting a company/ venture.

Unit III (4 Lectures)

Entry and exit strategy; identifying needs of customers; Market linkages, branding issues; developing distribution channels - franchising; policies, promotion, advertising; branding and market linkages for ‘virtual start-up company’. Pricing strategy.

Unit IV (4 Lectures)

Knowledge centers e.g., in universities, innovation centres, research institutions(public & private) and business incubators; R&D for technology development and upgradation; assessment of technology development; managing technology transfer;

VI. Suggested Reading

• Adams, D.J. and Sparrow, J.C. 2008. Enterprise for Life Scientists: Developing Innovation and  

Entrepreneurship in the Biosciences. Bloxham: Scion.

• Shimasaki, C.D. 2014. Biotechnology Entrepreneurship: Starting, Managing, and Leading Biotech  

Companies. Amsterdam: Elsevier. Academic Press is an imprint of Elsevier.

• Onetti, A., and Zucchella, A. 2014. Business Modeling for Life Science and Biotech Companies:  

Creating Value and Competitive Advantage with the Milestone Bridge.Routledge.

• Jordan, J. F. 2014. Innovation, Commercialization, and Start-Ups in Life Sciences. London: CRC

Press.

• Desai, V. 2009. The Dynamics of Entrepreneurial Development and Management. New Delhi:

Himalaya Pub.House.

I. Course Title             :           Stress Biology and Genomics

II. Course Code          :           MBB 517

III. Credit Hours        :           2+0

IV. Aim of the course

To provide advanced knowledge on genomics with reference to abiotic stress tolerance

and biotic stress resistance in plants tolerance.

V. Theory

Unit I (10 Lectures)

Different kinds of stresses (biotic and abiotic) and adaptation strategies: Plant cell as a sensor of environmental changes; role of cell membranes in signal perception; Ways of signal transduction in cells and whole plants as a response to external factors. Abiotic stresses affecting plant productivity – Drought, salinity, water logging, temperature stresses, light stress and nutrient stress; Drought stress – Effects on

plant growth and development; Components of drought resistance; Physiological, biochemical and molecular basis of tolerance mechanisms; Biotic stress (insect and pathogen) resistance mechanism.

Unit II (12 Lectures)

Strategies to manipulate drought tolerance – Osmotic adjustment and Osmo protectants - synthesis of proline, glycine betaine, poly amines and sugars; ROS and antioxidants; hormonal metabolism - ABA signaling; signaling components– transcription factors. Water logging stress – effects on plant growth and metabolism; adaptation to water logging, tolerance mechanisms -hormones and flooding tolerance. Strategies for improving submergence tolerance. Salinity stress– effects on physiology and metabolism of plants, SOS pathways and ion homeostasis, Strategies to improve salinity tolerance in plants. Water logging stress– effects on plant growth and metabolism; tolerance mechanisms. Physiological and biochemical changes – High & Low temperature tolerance mechanisms -molecular basis of thermo tolerance. Morphological and physiological changes in plants due to high and low light stresses - photo oxidation -plastid development.

Characters of helio phytes and scio phytes – solar tracking – sieve effect and light channeling. Heavy metal stress – Al and Cd stress - effects on plant growth and development, biotech Strategies to overcome heavy metal stress Nutrient stress effects on plant growth and development. Genetic manipulation strategies to overcome the stress effects.

Unit III (10 Lectures)

Genomics; transcriptomes, small RNAs and epigenomes; functional genomics; transfer of tolerance/resistant genes to model plants and validation of gene function.

Different techniques for the functional validation of genes.

Signaling pathway related to defense gene expression, R proteins, RNAi approach and genes from pathogens and other sources, coat protein genes, detoxification genes, transgenic and disease management. Bt proteins, resistance management strategies in transgenic crops, ecological impact of field release of transgenic crops.

Bioinformatics approaches to determine gene function and network in model plants under stress.

VI. Suggested Reading

• Buchanan, B.B., Gruissem, W. and Jones R. 2015. Biochemistry and Molecular Biology of

Plants, 2nd edition, Wiley and Blackwell Publications.

• Sarwat, M., Ahmad, A., Abdin, M.Z. 2013. Stress Signaling in Plants: Genomics and

Proteomics Perspective, Volume 1, Springer.

• HeribertHirt. 2010. Plant Stress Biology: From Genomics to Systems Biology, John Wiley.

• Pandey, G.K. 2015. Elucidation of Abiotic Stress Signaling in Plants, Stringer.

 I. Course Title            :           Gene Regulation

II. Course Code          :           MBB 518

III. Credit Hours        :           2+0

IV. Aim of the course

To understand the basics of gene regulation including a wide range of mechanisms that are used by organisms to increase or decrease the production of specific gene products in terms of time, space, conditions or their combinations.

V. Theory

Unit I (8 Lectures)

Transcriptional regulation – Regulatory proteins, Activators and Repressors, Binding of RNA polymerase, Allosteric regulation, DNA looping, Cooperative binding, Anti termination, Combinatorial control – Regulation of lac, trp and ara Operons. Gene regulation in Lambda phage – lytic or lysogenic establishment.

Unit II (10 Lectures)

Regulatory sequences – Promoters, Enhancers, Silencers, Insulators, Locus Control Region. Activator proteins and their binding sites, DNA binding domain –

Homeo domain, Zinc containing proteins, Leucine Zipper Motif, Helix-Loop-Helix,HMG proteins. Recruitment of RNA polymerase to promoter region, Nucleosomes and their modifiers. Signal integration. Signal transduction and transcriptional regulation. Gene Silencing. Epigenetic gene regulation.

Unit III (10 Lectures)

Regulation by RNA in prokaryotes and eukaryotes, RNA as defense agents. Riboswitches. Gene Silencing by RNA - siRNA & miRNA – synthesis and function. Non-coding RNAs their impact, categories and role in gene regulation, chromatin assembly etc.

Unit IV (4 Lectures)

Negative auto-regulation, Positive auto-regulation, Bistable and Bimodal switch, Oscillating pattern of gene expression.

VI. Suggested Reading

• Nelson, D. L. and Cox, M. M. 2017. Lehinger’s Principles of Biochemistry, 7th edition, W H

Freeman Publication New York

• Krebs, J. E., Goldstein, E. S., Kilpatrick, S. T. 2017. Lewin’s Genes XII 12th edition, Jones &

Bartlett Learning publisher, Inc

• Watson, J. D., Baker, T. A., Bell, S. P., Gann, A., Levine,M., &Lonick, R. 2014. Molecular

Biology of the Gene, 7th Edition, Cold Spring Harbor Laboratory Press, New York.

• Gardner, E. J., Simmons MJ and Snustad, D.P. 2006. Principles of Genetics (2006) eighth

Edition. Wiley

Under Graduate Courses