Sub-areas for Ph.D Qualifying Examination:
A: Environmental and Microbial Biotechnology
B: Parasitology and Vector Biology
C: Bio-informatics and Computational Biology
D: Plant Biotechnology
E: Cancer Biology & Chronic Diseases
F: Biochemistry & Biophysics
G: Molecular Biology & Immunology
General Note: The Senate of the Institute (160.02) has approved that Ph D qualifying examination will be conducted in two areas from the list of qualifying examination areas in the sub discipline of each department. Each student will choose two subareas; one of these must be the sub-discipline in which he/she proposes to undertake research after the consultation with his/her notional supervisor.
As per requirement, each subarea may have several sections with a total of 150/160 marks for theory and 50/40 marks for viva. The duration of each theory examination will be 3.0-4.0 hrs. Viva may be conducted separately for each sub area. A student will get a maximum of two attempts for clearing the qualifying examination (Ref clause 8.05-8.11 of academic regulation).
Course content of each area is given below:
A: Environmental and Microbial Biotechnology
Content: Microbial evolution; Chemical and molecular methods for microbial identification; microbial systematics and molecular taxonomy; Plant growth promoting microorganisms and mechanisms of colonization; Biocontrol; Microbial metabolism, Genetics of microorganisms; Factors determining microbial ecology, culture-dependent & independent analysis of microbial communities, molecular typing & DNA finger-printing, metagenomics & functional metagenomics, secretomics, stable isotope probing; Sociobiology of microorganisms: quorum-sensing, biofilm; Techniques used for study of host-microbe interaction (IVET, STM, DFI); Synthetic microorganism.
Basic concept of environment and its component; Definitions and facts related to Environmental Biotechnology; Bioremediation; Biosensor technology
- Tortora, G.J., Funke, B.R. and Case, C.L. 2007. Microbiology: An Introduction, 9th Ed. (First Impression 2008), Pearson Education, India.
- Madigan M.T., Martinko, J.M., Dunlap, P.V., Clark, D.P. (2009). Brock Biology of Microorganism, 12th Ed., Pearson International Education
- Environmental Biotechnology by Alan Scragg, Pearson Education Limited, UK.2005.
- Biotechnology, a comprehensive treatise, ed by Rehm H J and Reed G, VCH Verleg, Germany, 1999.
B: Parasitology and Vector Biology:
Content: Life cycle of parasite (Plasmodium, Trypanosoma, Leishmania, Toxoplasma, Entamoeba, Giardia), and their vectors (Mosquitoes, Sandfly, Tsetse fly); Mosquito borne viruses (Dengue, chikungunya). Taxonomy and identification of parasites and vectors; Molecular biology of parasite and vector (with special emphasis to Plasmodium-Anopheles, Dengue-Aedes); Cellular and humoral mechanisms involved in immunity to parasites; Immunomodulation in vectors; Vector parasite interactions and control strategies - Disease symptoms, Molecular approaches to diagnosis, Epidemiology, drug targets, vaccine strategies and proteomic approaches, prophylaxis, treatments to parasitic diseases and vector control measures, mechanisms of drug resistance in parasites or vectors.
Drosophila life cycle & molecular aspects may also be included as a comparative to what is known about the Anophelines & Culicines.
- Parasitology and Vector Biology: William C. Marquardt, Richard S. Demaree, Robert B. Grieve Publisher Academic Press, 2000
- Insect Immunology: Nancy E. Beckage, 1st edition 2008, Elsevier Press.
- The Biology of Mosquitoes: Development, Nutrition and Reproduction, Volume 1, Sensory, Reception, and Behaviour Volume 2 and 3: By A. N. Clement (Cabi Publishing)
- Malaria Immunology: 2nd edition, Perlmann, P, Troye-Blomberg, M. Karger AG press, Switzerland
- Insect Pathology by Vega from Elsevier 2010
C: Bioinformatics and Computational Biology:
Content: Introduction to genomic & Proteomics, Structural genomics and proteomics, Human Genome project and other sequencing projects, Biological databases and data mining, sequence similarity search and sequence alignment, Protein structure predication and structure analysis, use of software package in Bioinformatics. Biomolecular Conformations, protein folding, Forcefield, Simulation, Conformational analysis, ab initio structure prediction, comparative modeling, lattice models, usage of modeling packages,
- “Introduction to Bioinformatics” by Arther M Lesk, Oxford.
- “Bioinformatics Genome and sequence Analysis” by David W Mount, CSHL Press
- “Molecular modeling: Principles and Applications” By Andrew R Leach, Pearson Education Lim.
D: Plant Biotechnology
Content: Plant tissue culture history; Requirements to grow in vitro plants; Micro propagation, its applications and limitations; Haploid production; Meristem culture; Somaclonal variations; Somatic hybridization: Protoplast isolation and culture; somatic hybrids production; Storing plant genetic resources; Secondary metabolites.
Genetic transformation of plants; Agrobacterium mediated transfer; Ti plasmid technology; Direct gene transfer methods; Vectors for plant transformation; Molecular markers (RFLP, RAPD, AFLP, SNPs, VNTR); Designing of promoters; Stress Biology; Regulation of expression of wheat and rice seed storage protein genes, regulation and evolution of the patatin genes of potato; expression of genes controlling fatty acid biosynthesis; manipulation of cereal protein and oilseed quality, genetic manipulation of pest resistance, plant disease resistance, strategies for engineering stress tolerance, strategies for improvement of crop yield and quality; Starch, polyfructans, bioplastics, the oleosin system, custom made antibodies, edible vaccines; Public concerns over GM crops and government regulations.
- Bhojwani, S.S. and Razdan, M.K. Plant Tissue Culture: Theory and Practices, A Revised Edition, Elsevier, Reprint 2004.
- Narayanaswamy, S. Plant Cell and Tissue Culture, Tata McGraw Hill Publishing Company Limited, 1994 (Ninth Reprint 2008).
- Hammond, J. Mc Garvey, P. and Yusibov, Plant Biotechnology. Springer Verlag, Berlin, NY (1999), 2nd Printing 2000.
- Adrian Slater, Nigel W. Scott, and Mark R. Fowler: Plant Biotechnology: The Genetic manipulation of plants (Second edition). Oxford University Press (2008).
E: Cancer Biology & Chronic Diseases
Content: Cancer Classification, Carcinogens and Tumor Viruses, Signal Transduction & Cancer, Proto-oncogenes & Tumor Suppressor Genes, Cell Cycle Control & Cancer, Apoptosis, Necrosis & Autophagy, Telomerase & Cancer, Metastasis, Treatment of Cancer (e.g., anti-cancer drugs).
Inflammation and Stress, Free Radicals in Biology of Diseases, Risk Factors, Prevalence, and Prevention of Common Chronic Diseases, Genetics of Common Chronic Diseases and Epidemiology, Diseases of Cardiovascular system (Cardiomyopathies, Hypertension and Stroke etc) related to a) Altered homeostasis causing metabolic syndrome, Atherosclerosis, Obesity and Diabetes, b) Neurological Disorders (Alzheimer and Parkinson's disease etc) c) Liver and kidney d) Treatments and Prevention Options
- The Biology of Cancer: Robert A Weinberg.Garland Science Publisher .2007
- Molecular Biology of Cancer: Mechanisms, Targets, and Therapeutics:- Lauren Pecorino, Third Edition.Oxford University Press 2012.
- Text book of medical physiology, Guyton and Hall
- Human Physiology, Stuart Ira Fox
F: Biochemistry and Biophysics
Content: Organization of cells; Biomolecules (proteins, carbohydrates, lipids, nucleic acids); Enzymes: structure, isolation/purification, kinetics and mechanism of action; Biochemical energetics; Metabolic pathways: Carbohydrate metabolism, Biological oxidations, Lipid metabolism, Photosynthesis, Metabolism of nitrogen.
Physical principles in the biological and biomimetic molecular systems; Conformational and energetical properties of biomolecules like amino acids, proteins, nucleotides, nucleic acids as well as biomimetic systems like monolayers and bilayers; Related physical phenomena in these systems like structural transitions, protein folding, membrane equilibria; Principles of major experimental techniques applied to understand these physical problems.
- Campbell and Farell, Biochemistry, 5th ed., 2006, Brooks Cole Publishers.
- Nelson and Cox, Lehninger’s Principles of Biochemistry, 2008, 5th ed, Mac Millan Publishers.
- "Biophysical Chemistry, Part I, Part II and Part III", Charles R Cantor and Paul R. Schimmel, W.H. Freeman and Co., New York.
- “Principals of Physical Biochemistry” Kensal E. van Holde, W. C. Johnson and P.S. Ho John, 2nd Ed. Pearson Prentice Hall
G: Molecular Biology and Immunology
Content: The Interrupted Gene, The Content of Genome, Clusters and repeats, Chromosome and Controlling chromatin structure, DNA replication, DNA - protein interactions, RNA transcription and control, mRNA Stability and Localization, Catalytic RNA, RNA processing, translation, mechanism of gene expression in prokaryotes and eukaryotes, signal transduction, Phage Strategies: Control of lytic cascades in T4, T7 and lambda phage, Maintenance of lysogeny, Repressor synthesis and binding, Balance between lysogeny and lytic cycle, Eukaryotic and prokaryotic Transcription Regulation: Mechanism of action of activators and repressor, Interaction of activators with basal apparatus, Methylation of histones and DNA, DNA binding domains, Zinc fingers, steroid receptors, leucine zipper, Histone acetylation and modification, Yeast GAL genes, Epigenetic Effects: Histone methylation and phosphorylation, Regulatory RNA: Riboswitch, Regulate gene expression, by noncoding RNA, Attenuation and regulation by small RNA molecules,Gene silencing and RNA interference, antisense RNA
Introduction to immune system, cell mediated and humoral immunity, Antigens, Antibodies, MHC, molecular basis of T and B cell antigen recognition and activation, hypersensitivity, Immunity to microbes and diseases caused by humoral and cell mediated immune responses, Immunological tolerance, Cytokines - types and mechanisms, Complement system, autoimmunity, immunodeficiency, Transplantation, Antibody engineering, basic concepts in vaccination, tools in immunology.
- Lewin’s Genes X: by Jocelyn Krebs, Elliott Goldstein and Stephen Kilpatrick; (10thEd), Jones & Bartlett Publication, 2011
- Molecular Biology of Gene: Watson, Baker, Bell, Gann, Lavine & Losick (5th Ed), Pearson Education.
- Thomas J. Krindt, Riachard A. Goldsby and Barbara A. Osborne. (2007), Kuby Immnonology 6th edition W.H. Freeman and Company, New York.
- Abbas, Lichtman, Pillai, 6th Ed. Cellular and Molecular Immunology, Harcourt Brace & Company Asia, Saunders.