Courses

MC 206 (AUG) 2.0
RNA Biology
Mechanisms and machinery of transcription in prokaryotes and eukaryotes. RNA splicing and editing. Catalytic RNAs. RNA-protein recognition and interactions. Transcriptional and translational regulation of gene expression. Ribosome heterogeneity. RNA granules and liquid liquid phase separation. mRNA decay in prokaryotes and eukaryotes. RNA modifications. RNA viruses & viroids, and their biology (Negative sense RNA Viruses, Positive Sense RNA Viruses, Retroviruses, Double Stranded RNA Viruses & Viroids). Small RNAs: biogenesis, and their modes of action in regulation of gene expression and chromatin architecture.

Instructors
Saibal Chatterjee (Coordinator), Purusharth Rajyaguru

References

Flint SJ, Enquist L, Racaniello V, Rall GF, Skalka AM. Principles of Virology. 4th ed. ASM Press; 2015. ISBN-10: 1555819338;
Knipe DM, Howley PM . Fields Virology. 6th ed. Lippincott: Williams and Wilkins; 2013. ISBN-10: 1451105630;
For general RNA Biology: Any standard text book and The RNA World by Gesteland, Cech, and Atkins

MC 205 (AUG) 2:0
Pathogen – Host interactions and immune evasion mechanisms
The vertebrate host has evolved numerous mechanisms to shield itself against the onslaught of the myriad pathogens around it. The host uses toll like receptors to recognize pathogens, and deploys effective weapons from its impressive arsenal to eliminate pathogens. This course will utilize multiple host-pathogen pairs as models to demonstrate the innumerable mechanisms utilized by pathogens of viral, bacterial and parasitic origin to subvert the host and enhance their own survival. Secretion systems of bacteria: Type I, II, III, IV, V overview of ABC exporters and importers, Plant Pathogen interactions (Xanthomonas Citrobactor, Erwinia); Virulence gene expression, intracellular pathogenesis; Signaling by the bacterial components; Innate and adaptive immunity to bacterial pathogens; Quorum sensing, biofilm formation and its role in pathogenesis.
Functional mimicry of host complement proteins, secretion of chemokine and cytokine –like molecules, inhibition of NF-κB and apoptosis, inhibition of serine proteases of the host antigen presenting cells to suppress antigen presentation, inhibition of inflammatory responses of the host seen in poxviruses, inhibition of MHC class I presentation of viral antigens by adenoviruses, inhibition of host secretory pathway by herpes viruses, prevention of phagosome acidification and other macrophage functions by Mycobacterium tuberculosis, antigenic variation and suppression of TH1 responses by protozoan pathogens will all be covered.
Viral infectious cycle; Induction, regulation and mechanisms of Antiviral innate Immunity; Strategies of Viral evasion and antagonism of antiviral immunity; Mechanisms of Viral Pathogenesis. Interferon (IFN) is the cornerstone of antiviral innate immunity in mammalian cells. We will discuss detection of viral pathogens as foreign entity by mammalian cells, subsequent Interferon (IFN) induction and signaling, antiviral mechanisms of IFN Stimulated Genes (ISGs), Viral evasion and antagonism of IFN mediated immune response.

Instructors
Shashank Tripathi (Coordinator), Dipshikha Chakravortty and Balaji KN

References

David G. Russell and Siamon Gordon,Phagocyte-Pathogen Interactions: Macrophages and the Host Response to Infection,ASM Press,2009. Knipe,D.M.

MC 203/DB 203 (AUG) 3:0
Essentials in Microbiology
Fascinating world of microbes; Principles of microscopy; Microbial taxonomy, Microbial diversity, evolution and genomics; Mechanisms of horizontal gene transfer including genome transplantation, Microbes as model systems of development, Microbes as bioreactors and sensors; bioremediation; bacterial cell structure and function; Bacterial physiology and nutrition; Bacteriophages, Plasmids and Transposons; Understanding and combating bacterial pathogenesis; Antibiotics- mechanisms of drug resistance and mode of action; Quorum sensing and biofilms; Host-pathogen interactions and mechanisms of immune surveillance; PRR and their role in pathogenesis; TH subsets and modulation by pathogens; Diagnostics and vaccine development; Origin of cellular life; Biogeography of microbial diversity (is everything everywhere?); Host associated and free-living microbes; Mechanisms of microbial interactions; Causes, consequences, and evolution of physiological heterogeneity in bacterial populations; Bacterial predation, and survival strategies.

Instructors
Amit Singh (Coordinator), Samay Pande, Dipshika Chakravortty

References

Stanier, R.V.,Adelberg E.A and Ingraham J.L., GENERAL MICROBIOLOGY, Macmillan Press, Fourth edition;
Westriech, G.A. and Lechmann M.D., MICROBIOLOGY, Macmillan Press, Fifth Edition;
Atlas R.M., MICROBIOLOGY: FUNDAMENTALS AND APPLICATIONS, Macmillan Press Second Edition;
Goldsby, R. A.,Kindt T. J., Osborne B. A., Kuby J., IMMUNOLOGY, W. H. Freeman & Company, New York;
Travers, J., Shlomchik, W., IMMUNOBIOLOGY, Garland Science publishing, New York

MC 212 (AUG) 2:0
Advances in Cell Biology
Concepts: Prokaryotic and eukaryotic membrane structure, composition, organization and transport; Organelle structure, function and their biogenesis includes nucleus, endoplasmic reticulum, Golgi, endosomes, lysosomes and lysosome-related organelles, autophagosomes, peroxisomes, mitochondria and chloroplasts; Protein trafficking in-and-out of the organelles; Cytoskeletal elements and organization; Cell adhesion and junctions; Intra and extra cellular signaling; Cell cycle, cell division (asymmetric and symmetric) and stem cells; Cell death and protein homeostasis pathways and Cellular diseases. Methods: Introduction and evolution of light microscopy; Electron microscopy; Cytohistochemistry; Flowcytometry; Pulse-chase and subcellular fractionation; Proteomics and Protein-protein interaction approaches and genome-wide RNAi or small molecular screens to study the various cellular pathways.

Instructors
Subba Rao Gangi Setty (Coordinator), Sachin Kotak

References

Molecular Biology of The Cell, Fifth edition, Alberts et al.

MC 207 (AUG) 3:0
Molecular Biology
Genome organisation, structure and complexity. Chromatin structure and remodelling. Protein nucleic acids interactions. DNA replication in prokaryotes and eukaryotes:general rules, mechanisms, andregulation. DNA modifications in epigenetic control of biologicalprocesses.DNA repair and recombination.Mechanisms and machinery of transcription in prokaryotes and eukaryotes.RNA splicing and editing.Catalytic RNAs.Transcriptional and translational regulation of geneexpression. Protein splicing and repair.Small RNAs: biogenesis, and their modes of action in regulation of gene expression and chromatin architecture. Group discussions and seminars on current topics in MolecularBiology

Instructors
Umesh Varshney (Coordinator), V Nagaraja

References

Lewin’s Genes X, Lewin,B.,Krebs,J.E.

MC 208 (AUG) 2:0
Principles of Genetic Engineering
Growth and maintenance of bacteriophages and bacterial strains containing plasmids. Enzymes used in genetic engineering. Vectors used in molecular cloning and expression of genes, promoter analyses, and gene targeting in bacterial, mammalian, human, and plant systems. DNA, RNA, and protein isolation, purification, and fractionation methods. Radioactive and nonradioactive labelling of nucleic acids and proteins, and detection. Nucleic acids hybridisation methods. Transformation and transfection methods. Gene and cDNA cloning methods. In vitro genome packaging systems and construction of genomic DNA and cDNA libraries. Detection and characterisation methods for genes and chromosomes. Nucleic acids sequencing methods. Methods for protein analysis, protein-nucleic acid, and protein-protein interactions. Site-specific mutagenesis in vitro and in vivo. Random mutagenesis methods in vitro and in vivo. Polymerase chain reaction (qualitative and quantitative), methods, and applications. Antisense technology and RNA silencing techniques. DNA and Protein microarrays. Methods to generate transgenic bacteria/animals/plants. Methods of Genome Editing; ZFN, TALEN and CRISPR/Cas Systems, Genome wide Screening, Gene Drives. Ethical and Safety issues of Genome Editing. Applications of Genetic Engineering Methods in Medicine and Agriculture.

Instructors
Shashank Tripathi (Coordinator), Subba Rao G

References

J. Sambrook and D. W. Russell, Molecular Cloning: A Laboratory Manual, 3rd Edn: Vol. I, II, & III, Cold Spring Harbor Laboratory Press; (2) J. J. Greene and V. B. Rao. Recombinant DNA Principles and Methodologies. CRC Press; (3) S. B. Primrose and R. M. Twyman. Principles of Gene Manipulation and Genomics, 7th Ed., Blackwell Publishing; (4) Fred Ausubel and Others. Current Protocols in Molecular Biology. Wiley; (5) Gurbachan S. Miglani, Genome Editing: A Comprehensive Treatise. Alpha Science International Ltd.; CRISPR 101: A Desktop Resource Created and Compiled by Addgene May 2017 (2nd Edition) www.addgene.org. Information will also be taken from the original papers, which describe the principles and methods.

MC 202 (JAN) 2:0
Developmental Genetics
Logic and techniques of molecular genetic analysis. Understanding interaction networks using genetics and genomics. Illustrating the application of genetic analysis to specific developmental pathways in model eukaryotes and prokaryotes. Some examples are genetic and epigenetic mechanisms of cell fate determination and signaling pathways in development, embryo and organ patterning, regulation of organ size and shape, stem cell homeostasis and developmental plasticity using Drosophila and Arabidopsis as model organisms. Development in unicellular prokaryotes and eukaryotes. Genetics of the evolution of life cycle in the lab.

Instructors
Samay Pande (Coordinator), Upendra Nongthomba, Utpal Nath

References

Current Opinion in Genetics and Development/ Cell Biology/ Plant Biology; • (2) Trends in Genetics/ Cell Biology/ Biochemistry; • (3) Principles of Development by Wolpert and co-authors; • (4) Mechanisms in Plant Development by Leyser and Day; • (5) Plant Physiology by Taiz and Zeiger; • (6) Ecological Developmental Biology by Scott Gilbert and David Epel; • (7) R. V. Stanier, E. A. Adelberg and J. L. Ingraham, General Microbiology, Macmillan Press.

MC 210/RD 206 (JAN) 2:0
Molecular Oncology
Introduction to Cancer Biology: Immortalization, transformation, metastasis; Causes of Cancer: initiators and promoters, carcinogens, tumor viruses, sporadic and familial cancer; Genetic alterations: mutation, deletion, insertion, aneuploidy, chromosome translocation and Gene amplification; multistep carcinogenesis model; Cancer diagnosis and treatment; Cell cycle and cancer: cell cycle checkpoints, G1/S checkpoint, G2/M checkpoint, cyclins and cyclin dependent kinases, CDK inhibitors – p16, p21 and p27; Oncogenes: growth factors, growth factor receptors, G protein/signal transduction, tyrosine and serine/threonine kinases and transcription factors; Tumor suppressor genes: p53, RB, BRCA1, BRCA2, APC and WT1; Mismatch repair, Telomerase, DNA methylation, Protein phosphorylation/ dephosphorylation and degradation events; Transformation by RNA and DNA tumor viruses: Adenovirus, Simian Virus 40 and Human papilloma virus, Oncogene-tumor suppressor interactions; Apoptosis and cancer, Cancer as a tissue: stroma, angiogenesis; Cancer stem cells; Cancer gene therapy.

Instructors
Kumar Somasundaram (Coordinator), Annapoorni Rangarajan

References
The Biology of Cancer, 2nd Edition (2014) by Robert A. Weinberg

MC 211 (JAN) 3:0
Molecular basis of Ageing and Regeneration
Mechanisms of Ageing and Regeneration; Model systems for studying Ageing and Regeneration; Role of cellular processes such as transcription, translation, posttranslational modifications; Signalling mechanisms; Cellular Senescence; Genetic basis of Ageing and longevity; Ageing and Diseases; Organ Senescence; Obesity/Diabetes/Cardiovascular diseases/Muscle degeneration; Interventions to delay ageing and/or enhance life span

Instructors
Nagalingam Ravi Sundaresan (Coordinator), Varsha Singh, Purusharth Rajyaguru

References
Principles of Regenerative Biology by Bruce Carlson. http://www.sciencedirect.com/science/book /9780123694393 2. Regeneration –Developmental Biology by Scott F Gilbert (6th edition) 3. Hand book of the Biology of Aging,Seventh Edition,by Edward J. Masoro,Steven N. Austad,2010 4. Molecular Biology of Aging (Cold Spring Harbor Monograph Series).

MC 213 (JAN) 2:0
Basic and Applied Virology
Viruses are omnipresent, in and outside of us in the environment, however in recent past they have assumed great public health significance. In last few decades viral pathogens like human immunodeficiency virus (HIV) and hepatitis viruses have caused substantial mortality, morbidity and economic loss all over the world. Moreover, in last one decade we have seen frequent emergence of viral pandemics and outbreaks potential e.g. SARS CoV2, H1N1 Swine Flu, Zika and Ebola. This course is designed to give an overview of fundamental concepts in virology, explain biology and pathogenesis of major viral pathogens and give introduction to applied aspects of virology.

Instructor
Shashank Tripathi

References

Fields Virology, 6th Edition, Edited by David M. Knipe and Peter M. Howley. Philadelphia, PA, USA. Lippincott Williams & Wilkins;
Principles of Virology, 2 Volume Set, 4th Edition, S. Jane Flint, Vincent R. Racaniello, Glenn F. Rall, Anna Marie Skalka, Lynn W. Enquist; ISBN: 978-1-683-67335-4.

UG Courses

UB 102 (JAN)
INTRODUCTORY BIOLOGY II (MICROBIOLOGY, CELL BIOLOGY AND GENETICS)
Introduction to the microbial world and its diversity; importance of microbes in exploration of basic principles of biology; bacterial growth and its modulation by nutrient availability in the medium; structure and function of a bacterial cell; structure of cell wall; isolation of auxotrophs; introduction to viruses – life cycles of temperate and lytic bacteriophages, structure and function of extra-chromosomal elements and their applications in molecular microbiology.
Introduction to cell biology, eukaryotic cells and their intracellular organization; introduction to the light microscopes and other methods of studying intracellular organelles; further studies on endoplasmic reticulum, Golgi apparatus, lysosomes, mitochondria, nucleus (organization and function), plasma membrane structure and its function, the cytoskeleton, the cell cycle.
Mendelian genetics (segregation and independent assortment); sex determination and sex linkage in diploids; cytoplasmic inheritance; pedigrees, markers, mapping and genetic disorders; gene frequencies and Hardy- Weinberg principle.
Light microscopy, identification of microorganisms, staining techniques (Gram’s, acid fast), bacterial plating, tests for antibiotic resistance, cell media and tissue culture; cell counting, immunostanining for actin, microtubules, DNA and identifying interphase and various mitotic phases; Drosophilcrosses using red eye and white eye mutants, observation of Barr body in buccal mucosa cells, preparation of mitotic/polytene chromosomes from Drosophila larvae; and karyotyping using human metaphase plate photos.
Dipshikha Chakravortty, Sachin Kotak and Arun Kumar
References:

Berg, J. M., Tymoczko, J. L. and Styrer, L., Biochemistry, W. H. Freeman & Co., 6th Edition, 2006.
Stanier, R. Y., Adelberg, E. A. and Ingraham, J. L., General Microbiology, MacMillan Press, 5th Edition, 2007.
Alberts, B., Molecular Biology of the Cell, Garland Science, 5th Edition, 2008.
Strickberger, M. W., Genetics, Prentice-Hall, India, 3rd Edition, 2008.
Daniel, H., Essential Genetics: A genomics perspective, Jones & Bartlett, 3rd Edition, 2002.
Strachan, T. and Read, A. P., Human Molecular Genetics, Garland Science, 3rd Edition, 2004.

UB 201(AUG)
INTRODUCTORY BIOLOGY III (MOLECULAR BIOLOGY, IMMUNOLOGY AND NEUROBIOLOGY)
Molecular biology (central dogma, DNA repair, replication, transcription, genetic code and translation); examples of post-transcriptional and post-translational modifications; genetic methods of gene transfer in bacteria.
Introduction to the immune system – the players and mechanisms, innate immunity, adaptive responses, B cell receptor and immunoglobulins, T cell activation and differentiation and Major Histocompatibility Complex encoded molecules.
Overview of the nervous system, ionic basis of resting membrane potential and action potentials, neurodevelopment, neurotransmitters, sensory systems, motor systems, learning and memory, attention and decision making.
UB 201L
M13 infection, plaque assay, preparation of bacterial competent cells, transformation, transduction, conjugation, β -galactosidase assay. Immune organs and isolation of cells from lymph node, spleen and thymus; lymphocyte and macrophage activation studies, nitrite detection, ELISA and cell cycle analysis; gross anatomy of the human brain; staining of mouse brain sections; generation of action- potential; psychophysical and cognitive neurobiology experiments.
Umesh Varshney, Dipankar Nandi, Kavita Babu and Sridharan Devarajan
References:

Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Scott, M. P., Bretscher, A., Ploegh, H. and Matsudai-
Kindt, T., Goldsby, R. and Osborne, B. A., Kuby Immunology, W. H. Freeman Publishers, 6th Edi- tion, 2006.
Bear, M., Connors, B. and Paradiso, M., Neuroscience: Exploring the Brain, Lippincott Williams & Wilkins, 3rd Edition, 2006.

UB 205(JAN)
INTRODUCTORY PHYSIOLOGY
Mammalian Physiology: Introduction to physiology, internal environment, control of internal environment by feedback systems, renal physiology, body fluids and kidneys, urine formation by the kidneys, principles of membrane transport, transporters, pumps and ion channels, cell signalling and endocrine regulation, hormonal regulation of energy metabolism, hormonal regulation of calcium metabolism, hormonal control of reproduction in males and females, pregnancy and lactation; structure of heart, cardiac muscle contraction, cardiac cycle, electric conductivity of heart, regulation of cardiac homeostasis, structure and function of arteries and vein, blood pressure, blood flow, capillary exchange, physiology of lymphatic system.
Plant Physiology: Plant cell structure and cell wall, water uptake, photosynthesis and photorespiration, secondary metabolites, phytochrome and light signalling, hormone signalling in plants, control of flowering, stress physiology.
N. Ravi Sundaresan and C. Jayabhaskaran
References:

Hall, J. E., Guyton and Hall Textbook of Medical Physiology, Elsevier, 12th Edition, 2011.
Jameson, J. L. and De Groot, L. J., Endocrinology, Elsevier, 6th Edition, 2010.
Taiz, L. and Zeiger, E., Plant Physiology, Sinauer Associates, 5th Edition, 2010.

UB 301L (AUG)
EXPERIMENTS IN MICROBIOLOGY AND ECOLOGY
There are two sets of practical experiments for Biology majors:
In the first part, students will get a hands-on experience in understanding the basic concepts of microbiology. The topics include the microbial growth curve, microbial nutritional requirements, genetic engineering techniques, plasmid isolation, creation of genetic knock out in bacteria, bacterial infection in cell culture system, estimation of infection by colony forming unit (CFU) analysis and fluorescence technique.
In the second part, students will explore key concepts in Ecology, Evolution and Behavior using field methods, laboratory manipulations and computer simulations. Students will design many of their own experiments and will utilize different modes of scientific communication, including oral presentations and documentaries. Topics include niche and population dynamics, competition and predation, trophic interactions, evolution and adaptation, natural and sexual selection, and conservation. This module also includes a mandatory field trip where students develop an independent research project.
Dipshikha Chakravortty, Maria Thaker and Kartik Shanker

UB 302 (JAN):
DEVELOPMENTAL BIOLOGY
Introduction, history and concepts of developmental biology; the current understanding on the mechanisms of development using model organisms including invertebrates, vertebrates and plants; general principles for the making of a complex, multicellular organismfrom a single cell; the creation of multi-cellularity (cellularization, cleavage), reorganization into germ layers (gastrulation), cell type determination; creation of specific organs, (organogenesis); molecular mechanisms underlying morphogenetic movements, differentiation, and interactions during development; fundamental differences between animal and plant development; embryogenesis in plant – classical and modern views; 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; stem cells and regeneration; evolution of developmental mechanisms
Usha Vijayraghavan, Ramray Bhat, and Utpal Nath
References:

Wolpert, L. and Tickle, C., Principles of Development, Oxford University Press, 4th Edition, 2010.
Gilbert, S. F., Developmental Biology, 9th edition, Sinauer Associates, 2010.
Slack, J. M. W., Essential Developmental Biology, John Wiley & Sons, 3rd Edition, 2012. •
Leyser, O. and Day, S., Mechanisms in Plant Development, Willey-Blackwell, 2003. •
Taiz, L. and Zeiger, E., Plant Physiology, 5th edition, Sinauer Associates, 2010. •
Alberts, B., Molecular Biology of the Cell, Garland Science, 5th Edition, 2008.