Course Catalog

Course description not available.

IPR, Patent Laws & Bioethics

Internal Project Dissertation

The students are advised to work under the supervision of any one of the faculty members in the department.

Vascular Dysfunction: The primary structure, characteristics and function of Endothelial cells. Involvement of endothelial cells in inflammation and pathogenesis following pathogen attack and blood tumor barrier. Cell Signaling in primary cells.Practical: Adhesion assay, Cell death and cell cycle in primary brain cells, immunofluorescence assays, Surface Plasmon Resonance and ELISA techniques. Host Pathogen Interaction: Introduction to human diseases. Mechanism of pathogen adhesion and attack and entry into the human body. The mechanistic details and process of a few specific pathogens on primary brain cells. Practical: Cell Culture of human pathogens, co-culture and growth assays, Live cell imaging. References: Recent publications on Host pathogen Interaction and reviews will beprovided.

Description: Basic understanding of Biochemistry, Cell and Molecular Biology is prerequisite for this course offered to students in the final year of their degree program. This is designed to provide a comprehensive overview of the Chemistry, Biology and Pathology of cancer. Students opting for this course will be considered of having a specialization in modern cancer biology and therapeutics. The course is divided into two broad parts. The first part will focus on the genetic and molecular basis of cancer, while the second half will discuss the interface between cancer and medicine. The students will also be introduced to the concepts of anti-cancer drug resistance and the ever-growing need to implement personalized anti-cancer therapeutics in clinic. The use of genomics, proteomics and metabolomics tools for identification of diagnostics, predictive and prognostic cancer biomarkers will be presented. Pharmaceutical approach of anti-cancer drug discovery and concepts of clinical trials will also be discussed. Biology: Definition and pathology of cancer. Cancer is a slow growing disease. War against cancer. Cancer is a multistep process: evolution of cancer. Eight hallmarks of cancer. Inflammation and genomic instability as causes of cancer. Carcinogens/mutagens. Tumor heterogeneity. Tumor suppressors, oncogenes/oncogene addiction theory. Cancer cell signaling: PI3K and MAPK signaling. Apoptosis, autophagy, senescence and their roles in cancer. Cancer stem cells Therapeutics: Chemo, targeted, immuno and stem-cell therapies. Anti-cancer drug resistance. Biomarkers: Diagnostic, prognostic and predictive. Personalized therapies: concept, experimental tools. 2 Cancer Genomics. Functional genomics. Synthetic lethality. Clinical trials.

Course description not available.

Introduction and scope of proteomics; Protein separation techniques: ion exchange, size-exclusion and affinity chromatography techniques; Polyacrylamide gel electrophoresis; Isoelectric focusing (IEF); Two dimensional PAGE for proteome analysis; Image analysis of 2D gels; Introduction to mass spectrometry; Strategies for protein identification; Protein sequencing; Protein modifications and proteomics; Applications of proteome analysis to drug; Protein-protein interaction (Two hybrid interaction screening); Protein engineering; Protein chips and functional proteomics; Clinical and biomedical application of proteomics; Proteome database; Proteomics industry. Methods of preparing genomic DNA; DNA sequence analysis methods: Sanger Dideoxy method and Fluorescence method; Gene variation and Single Nucleotide Polymorphisms (SNPs); Expressed sequenced tags (ESTs); Gene disease association; Recombinant DNA technology: DNA cloning basics, Polymerase chain reaction, DNA fingerprinting, Human genome project and the genetic map. Introduction to systems Biology. Terms and definitions. Dynamical systems, linear stability and bifurcation analysis. Limit cycles, attractors. Genetic and biochemical networks, chemical kinetics, deterministic and stochastic descriptions. Other network types: Regulatory (e.g. fly), Signal transduction (e.g. MAP Kinase cascade in yeast), Metabolic (E coli), Neural network. Topology of genetic and metabolic networks. Software for systems biology. SBML, and open source programs eCell, Virtual Cell, StochSim,  BioNets. Quantitative models for E Coli: lac operon and lambda switch. The chemotactic module in E. Coli. Pathways and pathway inference. DAVID. Gene Ontologies. § Pathway Miner and similar Software.  SNPs and complex diseases.  Recommended Books: Genomics: The Science and Technology Behind the Human Genome Project, Cantor, C. R., Smith, C. L., Pub: John Wiley & Sons. Introduction to Genomics, Lesk, A. M., Pub: Oxford University Press. Handbook of Proteomic Method, P. M. Conn, Pub: Humana Press. Biochemistry, Berg, J. M., Tymoczko, J. L., Stryer, L., Pub: W. H. Freeman.

Isolation of DNA, cDNA synthesis, chemical synthesis of DNA by phosphoramidite method. Introduction of DNA into living cells, Introduction to gene cloning and its uses, tools and techniques: plasmids and other vectors, DNA, RNA, cDNA. Enzymes used in genetic engineering. Restriction endonucleases and restriction mapping, DNA ligase, DNA polymerase-I, reverse transcriptase, Sl nuclease, terminal nucleotide transferase, alkaline phosphatase, polynucleotide kinase, polynucleotide phosphorylase. Production of proteins from cloned genes: gene cloning in medicine (Pharmaceutical agents such as insulin, growth hormones, recombinant vaccines), gene therapy for genetic diseases. Cloning vectors- salient features, plasmid vectors, phage vectors, cosmids, phagemids (Lambda and M13 phages), viral vectors (SV40, Baculo and CMV), artificial chromosomes BAC, YAC and MAC.   Ligation of DNA to vectors – cohesive end, blunt end, - homopolymer tailing, linkers and adaptors. Gene transfer techniques- transformation, transfection, microinjection, electroporation, lipofection and biolistics. Reporter gene assay, selection and expression of r-DNA clones. Polymerase Chain Reaction, PCR variations and their applications DNA sequencing - chemical, enzymatic and NGS methods. Salient features of human genome project. Applications of genetic engineering in agriculture, animal husbandry, medicine and industry.   Recommended Books: Recombinant DNA Technology, Watson, J. D., Pub: W. H. Freeman. Gene cloning and DNA analysis, Brown, T. A., Pub: Wiley Blackwell A John Wiley & Sons, Ltd. Principles of Gene manipulation: an introduction to Genetic Engineering, Primrose, Old R. W., Primrose, S.B., Pub: Blackwell Science Ltd.

Basic techniques of cell, tissue and organ culture. Primary culture and subculture of cells. kinetics of cell growth. Properties of normal and transformed cells. Role of carbondioxide, serum and other supplements in cell culture. Different types of culture media- natural media, BSS, MEM, serum free media. Different methods for the estimation of cell viability and cytotoxicity. Applications of cell culture. Stem cells – Embryonic and adult stem cells. Isolation and culture of stem cells. Induced pluripotency of stem cells. Stem cell markers. Stem cell plasticity and differentiation. Application of stem cells in medicine. Apoptosis- mechanism and significance with reference to degenerative diseases – Parkinson’s disease, stroke and diabetes. Organ culture and tissue engineering: Organ cultures, histolytic cultures, three dimensional cultures, organotypic cultures. Production of bio-artificial skin, liver and pancreas. Tissue engineering- cell source and culture, culture of cells, design engineering of tissues, tissue modeling. Embryonic stem cell engineering. Production of monoclonal antibodies, Production of Transgenic Animals -Mouse, sheep, cattle and fish by microinjection, retroviral vector method and embryonic stem cell method. Animal cloning-Somatic cell nuclear transfer and embryonic stem cell nuclear transfer methods. Bio pharming and gene knockout. Recommended books: Culture of Animal cells; A manual of Basic techniques (6th ed.), Freshney, R. I., Pub: Wiley-Blackwell. Molecular Biotechnology: Principles and Applications of Recombinant DNA, Glick, B. R., Pasternak, J. J., Pub: ASM Press. Elements of Biotechnology, Gupta, P. K., Pub: Rastogi & Co. Concepts of Biotechnology, Balasubrahmanian, et al., Pub: University press.         

Introduction to Bioinformatics, Review on Biological Databases concept: Primary, secondary and composite databases, Nucleotide Sequence databases (EMBL, GenBank, DDBJ) Protein Databases –(UNIPROT, PIR, TREMBL), Protein family/domain databases (PROSITE, PRINTS, Pfam,), Metabolic & Pathway databases (KEGG), Structural databases (PDB). Structural Bioinformatics: Classification of protein structures, Primary, Secondary and Tertiary structures, Quaternary structure, Protein folding concept, Potential energy map and Ramachandran plot. Secondary structure prediction methods, Classification of Three Dimensional Structures of Proteins, Motifs, Folds and Domains, Classification of Three Dimensional Structures in PDB (HSSP, SCOP, FSSP, CATH).  Structural Alignment Methods, Homology Modeling, fold recognition and ab initio methods. Computer aided drug design (CADD), Molecular Docking. Genomics: The Human Genome, Comparative Genomics (Comparative genomics of Model organisms), gene identification methods, primary gene expression analysis. Primary Sequence Analysis: Sequence alignment, Homology concept, pairwise sequence alignment, multiple sequence alignment, Phylogenetic Analysis, concept of SNP and snip analysis. Books: Bioinformatics–Sequence, Structure and Databanks, Higgins, D., Taylor, W., Pub: Oxford University Press, Incorporated. Bioinformatics: A practical guide to the analysis of genes and proteins, Baxevanis, A. D., Ouellette, B.F.F., Pub: John Wiley and Sons Inc. Bioinformatics: Sequence and Genome Analysis, Mount, D.W., Pub: Cold Spring Harbor Laboratory Press. Structural Bioinformatics, Ed: Bourne, P. E., Weissig, H., Pub: Wiley-Blackwell.

Nature of genetic material, organization of genetic material in prokaryotes and eukaryotes. Structure of chromatin, fine structure of the gene. Different kinds of genes- split genes, overlapping, assembled, polyprotein & nested genes. Gene amplification and polytene chromosome. C - Value paradox, mitochondrial & plastid genomes. DNA replication – Types of DNA polymerases. Mechanism of DNA replication. Enzymes and accessory proteins involved in DNA replication. Replication of telomeres and its significance. Differences in prokaryotic and eukaryotic DNA replication and regulation. DNA damage and repair. Transcription in prokaryotes and eukaryotes. Mechanism of transcription, Types of RNA polymerases and promoter-polymerase interactions. Transcriptional factors. Processing of mRNA, tRNA and rRNA. RNA editing and transport. Translation in prokaryotes and eukaryotes: Genetic code, translational machinery, mechanism of initiation, elongation and termination. Regulation of translation, co and post translational modifications. Leader sequences & protein targeting. Regulation of gene expression in prokaryotes and eukaryotes- the operon concept, negative & positive control and attenuation. Role of enhancers, cis-trans elements, DNA methylation and chromatin remodeling in gene expression. Environmental regulation of gene expression. RNAi and gene silencing. Recommended Books: Biochemistry (5th ed.), Stryer, L., Pub: freeman-Toppan. Genes VIII, Lewin, B., Pub: Oxford. Cell and Molecular Biology (7th ed.), De Roberties, E,D.P., De Robertis, E. M. F.,  Pub: Saunders College publisher. Molecular Biology, Frefielder, D., Pub: Narosa Publishing House Pvt. Limited, Molecular Biology of the Gene, Watson, J. D., et. al., Pub: Benjamin. Molecular Biology, Weaver, R. F., Pub: McGraw-Hill.

Properties and importance of water, intra and intermolecular forces, non-covalent interactions- electrostatic, hydrogen bonding, Vander Waals interactions, hydrophobic and hydrophilic interactions. Disulphide bridges. pH, pK, acid base reactions and buffers. Carbohydrates: Different carbohydrates and with examples of glucose, galactose, sucrose, starch and glycogen. Carbohydrates metabolism: Glycolysis, Kreb’s Cycle and oxidative phosphorylation. Gluconeogenesis, Pentose phosphate pathway, Glyoxylate cycle. Proteins: Classification and properties of amino acids, Classification based on structure and functions, structural organization of proteins (primary, secondary, tertiary and quaternary structures), biosynthesis of protein. Enzymes and enzyme kinetics. Michaelis-Menten equation, significance of Km , Vmax and Kcat. Lineweaver – Burk plot. Biosynthesis and degradation of aromatic and branched chain amino acids. Nucleic acids: Structure and properties of nucleic acids. Different forms of DNA-A, B, Z. Circular DNA and DNA supercoiling. Different types of RNA- mRNA, and non coding RNA – tRNA, rRNA, snRNA, miRNA and siRNA. Synthesis and regulation of purine nucleotides by de novo pathway. Salvage of purine nucleotides. Synthesis and regulation of pyramidine nucleotides. Formation of deoxyribonucleotides and their regulation. Degradation of purines and pyrimidine nucleotides, disorders of nucleotide metabolism Lipids: Classification, structure, properties and functions of fatty acids, triglycerides, phospholipids, sphingolipids, cholesterol and eicosanoids- prostaglandlins. Saturated and unsaturated fatty acids - synthesis, β-oxidation and regulation. Ketone bodies. Synthesis of triacylglycerides, phospholipids, and cholesterol. Vitamins: Source, structure, biological role and deficiency disorders of vitamins . Recommended Books: Lehninger Principles of Biochemistry (5th ed.), Nelson, D., Cox, D., Pub: Macmillan Pub. Biochemistry (6th ed.), Stryer, L., Pub: Freeman-Tappan. Text Book of Biochemistry by West, E. S., Todd, W. R., Bruggen, J. T V., Pub: Mac Milan. Principles of Biochemistry by White, A., Handler, P., Smith, E. L., Pub: McGraw Hill. Harper's Biochemistry, Murray, R. K., et al., 27 ed., Pub: Langeman Biochemistry (3rd ed.), Voet, D., Voet, J. G., Pub: John Wiley. Biochemistry, Mathews, et. al., Pub: Pearson         

History, evolution and development of microbiology. Diversity of microorganisms- scope and importance. Characterization and identification of bacteria based on morphology, physiology, biochemistry, ecology, chemotaxonomy and molecular systematics. Bergey’s manual – classification of bacteria, fungi, algae and archea.   The study of microbial structure by use of light, phase, fluorescent and electron microscopy. Preparation and staining of specimens. Microbial nutrition, nutritional types, requirements, design and types of nutrient media, microbial growth- principles, kinetics and methods. The influence of environmental factors on growth. Microbial control- definition, methods of sterilization, physical methods and chemical agents. Isolation of pure cultures- spread plate, streak plate and pour plate.   Classification of general features of cyanobacteria and importance of Spirulina, Rickettsia, Chlamydia, Mycoplasma, Archaebacteria. Methanogenic and Halophilic bacteria. General account and economic importance of algae and fungi. Clinically important bacteria and protozoans. Distribution of microbes in nature.   History and development of viruses. Nature, origin and evolution of viruses. Nomenclature, recent classification (ICTV) structure and characteristics of viruses. Isolation, cultivation and identification of viruses. Biological and chemical properties of viruses. Animal, plant and bacterial viruses and their interactions with hosts. Virus replication and genome expression. Process of infection- animal, plant and bacterial cells. Molecular mechanisms of viral pathogenesis with respect to poliovirus, rotavirus, herpes virus, retroviruses.   Transmission of viruses (Direct and Indirect) persistence of viruses and their mechanism. Purification and inactivation of viruses- physical and chemical methods. Virus ecology and epidemiology, scope and concepts of epidemiology. Bacterial recombination, transformation, conjugation and transduction. Mapping of prokaryotic genome and tetrad analysis, insertion sequences, transposons and mechanism of transposition, retro transposons, plasmids.   Recommended Books: Microbiology: Concepts and Applications, Pelczar, M. J., Chan, E. C. S., Krieg, N. R., Pub: Mcgraw hill International Book Company. Brock Biology of Microorganisms (9th edition), Brock, T. D., Madigan, M. T., Pub: Prentice Hall International.  Introduction to Microbiology, Ross, Pub: Addison-Wesley Educational Publishers. Prescot’s Microbiology, Willey, J., Sherwood, L., Woolverton, C., Pub: MacGraw Hill. Microbiology: An Introduction, Oortora, G. J., Funke, B. R., Case, C. L., Pub: Pearson Benjamin Cummings.

Unit I: Basic Cell, Molecular Biology and Genetics Prokaryotes and Eukaryotes, Introduction to Microbiology, Cell organelles, Biochemistry of macro molecules (Carbohydrates, Lipids, Proteins and Nucleic acids), Principles of Genetics (mendelian inheritance, concept of gene, Mutation, chromosomal abberations), Cell cycle, Cell division. Central Dogma of Molecular Biology (Replication,Transcription,Translation and Gene expression), Introduction to Genomics, Transcriptomics and Proteomics, Basics of cloning, Cancer, Biosensors, Bio artificial organs. Applications of engineering in biology. Instrumental techniques: Microscopy, Centrifugation, PCR, Gel Electrophoresis

Structural organization of flower, initiation and differentiation of floral organs, structure and development of anther, microsporogenesis, structure and type of ovule, megasporogenesis, types of embryo sac. Plant water relationship, mineral nutrition, Solute transport, Role of growth regulators. Photosynthesis-light and dark phases of photosynthesis. Role of ATP and NADPH in carbon dioxide assimilation, factors influencing photosynthesis, photosynthesis of CAM plants. Role of plants in converting radiant energy into chemical energy. Respiration of chlorophyllous tissues in C3 and C4 plants. Regulation of photorespiration, photo periodism and flowering. Plant development: structure of plant body; fundamental differences between animal and plant development; embryogenesis – classical and modern views using Fucus and Arabidopsis as models; axis specification and pattern formation in angiosperm embryos; organization and homeostasis in the shoot and root meristems; patterning in vegetative and flower meristems; growth and tissue differentiation in plants; evolution of developmental mechanisms in plants.

Introduction to Vertebrates and Invertebrates: General characters, classification of up to different phyla from protozoa to echinoderms with special reference to protozoa and arthropod. Type study of human pathogens: Plasmodium vivax, Trypanosoma gambiense, Entamoeba histolytica, Faciola hepatica, Tenia solium and Ascaris lumbricoides. Introduction to model systems: C.elegans, Drosophila and zebra fish.   Recommended Books: Modern Text book of Zoology: Invertebrates, Kotpal, R.L., Pub: Rastogi. Invertebrate Zoology, Anderson, D. T., Pub: Oxford University Press.

Course Summary IT has changed the Biologists thought process, revolutionary processing speed and advancement in data storage and mining methods has completely changed the Biotechnology  and new branches emerged like “-Omics” technologies. The class is hands-on, project-oriented to give better understanding of IT applications in Biology. The course is designed to introduce the most important and basic computer concepts. It also involves case studies and applications in which Bioinformatics tools and algorithms can be used. The course will introduce students to altogether a new world of Biology which includes many new terminologies and concepts in Bioinformatics. This course will enable student aware of programming methods in Perl and linux which they can use in Bioinformatics analysis. Detailed Contents Introduction to computers:Overview and functions of a computer system, Computer generations with characteristic features, computer organization, CPU, ALU, memory hierarchy, registers, I/O devices, storage devices. Types of Processing: Batch, Real-Time, Online, Offline. Introduction to operating systems:  Operating System concept, Variants of Unix, Linux operating system and command line applications. Computer Networking: Introduction to networking: Associated hardware devices, gadgets (Router, Switch etc.), Network Topologies and Protocols LAN, WAN and MAN, World Wide Web (WWW) Network security: fire walls. Concepts in text-based searching Medline, bibliographic databases. Algorithms, Flowcharts & Programming concepts:  Algorithms: Concepts & definitions, Converting algorithms to flowcharts, Comparing algorithms, flowcharts & programs, Algorithms solving Biological problems, Basic PERL Programming. Computers in Biology: Nature of Biological data, Biological Databases, pubmed, Overview of Bioinformatics, sequence alignment, Major Bioinformatics Resources: NCBI, EBI & ExPASY. References Introduction to Bioinformatics- Attwood Bioinformatics -David Mount Developing Bioinformatics Computer Skills- Cynthia Gibas Introduction to Bioinformatics- Arthur M Lesk Fundamentals of Computers, -V Rajaraman, PHI. Introduction to computers - Peter Norton Computer Fundamentals – P.K. Sinha  

Cancer Biology

Environment Science

Cancer And Its Therapies

Advanced Molecular and Cell Biology

Computational Biology

Vascular Dysfunction: The primary structure, characteristics and function of Endothelial cells. Involvement of endothelial cells in inflammation and pathogenesis following pathogen attack and blood tumor barrier. Cell Signaling in primary cells. Practical: Adhesion assay, Cell death and cell cycle in primary brain cells, immunofluorescence assays, Surface Plasmon Resonance and ELISA techniques. Host Pathogen Interaction: Introduction to human diseases. Mechanism of pathogen adhesion and attack and entry into the human body. The mechanistic details and process of a few specific pathogens on primary brain cells. Practical: Cell Culture of human pathogens, co-culture and growth assays, Live cell imaging.

Advanced Biostatistics

Synthetic Biology

Microbial Technology