PhD Qualifying Exam

Areas for PhD Qualifying Exam

Areas for PhD Qualifying Exam

Our current areas of research are:

   A: Environmental and Microbial Biotechnology 

   B: Parasitology and Vector Biology

   C: Bioinformatics and Computational Biology

   D: Plant Biotechnology

   E: Human Diseases and Immunology

   F: Biochemistry

   G: Molecular Biology and r-DNA technology

   H: Animal Biotechnology


General Note:
The Senate of the Institute has approved that Ph.D. qualifying examination will be conducted in two areas from the list of qualifying examination areas 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.

  • Environmental and Microbial Biotechnology

    A: Environmental and Microbial Biotechnology


    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. Molecular biology and biotechnological application of Achaea.

    Basic concept of environment and its component; Definitions and facts related to Environmental Biotechnology; Bioremediation; Biosensor technology

    Suggested Books:

    1. Tortora, G.J., Funke, B.R. and Case, C.L. 2007. Microbiology: An Introduction, 9th Ed. (First Impression 2008), Pearson Education, India.

    2. Madigan M.T., Martinko, J.M., Dunlap, P.V., Clark, D.P. (2009). Brock Biology of Microorganism, 12th Ed., Pearson International Education

    3. Environmental Biotechnology by Alan Scragg, Pearson Education Limited, UK.2005.

    4. Biotechnology, a  comprehensive treatise, ed by Rehm H J and Reed G, VCH Verleg,     

    Germany, 1999.

  • Parasitology and Vector Biology

    B: Parasitology and Vector Biology:


    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.

    Suggested Books:

    1. Parasitology and Vector Biology: William C. Marquardt, Richard S. Demaree, Robert B. Grieve Publisher Academic Press, 2000

    2. Insect Immunology: Nancy E. Beckage, 1st edition 2008, Elsevier Press.

    3. The Biology of Mosquitoes: Development, Nutrition and Reproduction, Volume 1, Sensory, Reception, and Behaviour Volume 2 and 3: By A. N. Clement (Cabi Publishing) 

    4. Malaria Immunology: 2nd edition, Perlmann, P, Troye-Blomberg, M. Karger AG press, Switzerland

    5. Insect Pathology by Vega from Elsevier 2010

  • Bioinformatics and Computational Biology

    C: Bioinformatics and Computational Biology



    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,

    Suggested Books:

    1. “Introduction to Bioinformatics” by Arther M Lesk, Oxford.

    2 “Bioinformatics Genome and sequence Analysis” by David W Mount, CSHL Press

    3. “Molecular modeling: Principles and Applications” By Andrew R Leach, Pearson Education Lim.

  • Plant Biotechnology

    D: Plant Biotechnology


    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.

    Suggested Books:

    1.                  Bhojwani, S.S. and Razdan, M.K. Plant Tissue Culture: Theory and Practices, A Revised Edition, Elsevier, Reprint 2004.

    2.                  Narayanaswamy, S. Plant Cell and Tissue Culture, Tata McGraw Hill Publishing Company Limited, 1994 (Ninth Reprint 2008).

    3.                  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). 

  • Human Diseases and Immunology

    E: Human Diseases and Immunology


    Basic Understanding of the Cause and Physiological Aspects of Hypertension, Atherosclerosis and Diabetes Type I/II.

    Cancer Classification Based on Origin; Mechanisms of Viral Oncogenesis; Proto-oncogenes (src, myc, ras and abl) & Tumor Suppressor Genes (Rb, P53); Receptor Signaling: EGFR, PDGFR, Integrin; Signal Transduction: PI3K-Ras-Akt, Wnt, NFkB, TGFβ; Immuno-evasion Strategies; Molecular Mechanism of EMT and Metastasis; Apoptosis (Extrinsic and Intrinsic), Anti-Cancer Drug Targets.

    Cell Mediated and Humoral Immunity, Antigens, Antibodies, MHC, Molecular basis of T and B cell antigen recognition and activation, Hypersensitivity, Immunity to Microbes, Immunological Tolerance, Major Cytokines, Complement system, Autoimmunity (including Type I Diabetes), Immunodeficiency, Transplantation, Basic Concepts in Vaccination.

    Suggested Books:

    1.      Essentials of Physiology, Lauralee Sherwood, 4th Edition, (2011)

    2.      Human Physiology, Stuart Ira Fox, 12th Edition, (2010)

    3.      Kuby Immnonology, Thomas J. Krindt, Riachard A. Goldsby and Barbara A. Osborne. 6th edition W.H. Freeman and Company (2007)

    4.      Basic Immunology, Abdul K Abbas and Andrew H Lichtman, (2006)

    5.      Janeway's Immunobiology, Kenneth Murphy, 8th Edition, Garland Science, (2011)

    6.   The Biology of Cancer: Robert A Weinberg. Garland Science Publisher (2007) 

  • Biochemistry

    F: Biochemistry



    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.

    Suggested Books:

    1. Campbell and Farell, Biochemistry, 5th ed., 2006, Brooks Cole Publishers.

    2. Nelson and Cox, Lehninger’s Principles of Biochemistry, 2008, 5thed, Mac Millan Publishers.

    3. "Biophysical Chemistry, Part I, Part II and Part III", Charles R Cantor and Paul R. Schimmel, W.H. Freeman and Co., New York.

    4. “Principals of Physical Biochemistry” Kensal E. van Holde, W. C. Johnson and P.S. Ho John, 2nd Ed. Pearson Prentice Hall

  • Molecular Biology and r-DNA technology

    G: Molecular Biology and r-DNA technology


    Content:                                                                                                                                                           Eukaryotic chromosome and its Organization(Chromosome and chromatin structure the Content of Genome, Clusters and repeats); DNA replication (Prokaryote and eukaryote), Transcription, its control and post-transcriptional modifications; Translation, its control and post-translational modifications; Regulation of gene expression in prokaryotes and eukaryotes (Epigenetic modifications like DNA methylation Histone methylation ,acetylation and phosphorylation, DNA binding domains, Zinc fingers, steroid receptors, leucine zipper, Yeast GAL genes) Eukaryotic cell cycle control and regulation( basic regulation of cell cycle, Signal transduction pathways: MAP-Kinase Jak-Stat, PI3Kinase, Notch, Wnt and Integrin/E-Cadherin); 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); Regulatory RNA Biology (Riboswitch, Regulate gene expression by noncoding RNA, Attenuation and regulation by small RNA molecules, Gene silencing and RNA interference, antisense RNA)



    Plasmids as cloning vehicles; plasmid copy number control mechanism, Cosmids; Restriction enzymes, Ligation, Linkers, Adaptors Homo -polymer tailing; Different cloning strategies in gram negative and gram positive bacteria; Screening of Recombinant molecules; Expression vectors and protein purification; PCR, Reverse transcription-PCR (RT-PCR); Site directed mutagenesis; Nucleotide sequencing; Basic Techniques in Recombinant DNA Technology with emphasis on Electrophoresis, Blotting Techniques (Western, Southern, Northern Blotting), DNA and protein microarrays, DNA mediated transformation, viral transduction and electroporation.

    Suggested Books:

    1. Lewin’s Genes X: by Jocelyn Krebs, Elliott Goldstein and Stephen Kilpatrick;  (10thEd), Jones & Bartlett Publication, 2011  

    2. Molecular Biology of Gene: Watson, Baker, Bell, Gann, Lavine&Losick (5th Ed), Pearson Education.

    3. Principle of gene manipulations and genomics, S B Primrose and R.M. Twyman, 7th ed. 2006.

    4. Recombinant DNA Principles & Methodologies, James J. Green &Vengalla B. Rao.   Marcel  DekkerInc - 1998.

    5. Molecular biology of the Cell, Bruce alberts et al 5th Edition Garland Science.

  • Animal Biotechnology

    H: Animal Biotechnology


    Cell and Tissue Culture: Uses, Advantages and Disadvantages; Primary Cell Culture; Characteristics of Cells in Culture; Sterilization & Media Preparation; Transformation & Immortalization; Cryopreservation; 3D Culture Method; Tissue Engineering; Cell Based Assays (Principle and procedure: Viability, Cyto-toxicity, Staining and Visualization, Flow Cytometry); Scaling Up; Therapeutic & Bio-technological Aspects of Cell Culture.

    Basic Characteristic of Embryonic Stem Cells and Adult Stem Cells; IPSCs; Transcriptional and Epigenetic Control of Stem Cells; Therapeutic and Reproductive Cloning Procedure; Cancer Stem Cells, Basics to Culture of Stem Cells; Current Status of Stem Cell Therapy.

    Identification of Major Mouse Strains (Congenic, Syngenic and Allogenic); Transgenic Production Basics (Process of pronuclear microinjection and Blastocyst injection); Mouse Knock-out (homologous recombination / dominant negative strategy), Gene Trap, Hypomorphic and Conditional Knockout Strategies (Cre-loxP and FLP/FRT).


    Suggested Books:

    1.      Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications, Freshney, R.I., Willey-Blackwell Press, 6th Edition (2010)

    2.      Animal Cell Culture – Concept and application, Sheelendra M. Bhatt, Narosa Publishing House, New Delhi, (2011)

    3.      Animal Cell Technology, Asok Mukhopadhyay. I. K. International Publishing House Pvt. Ltd. (2009)

    4.      Essentials of Stem Cell Biology, Robert Lanza, 2nd Edition, Academic Press, (2009)

    5.      Stem Cells: Basics and Applications, Deb & Totey, Tata McGraw Hill. (2009)

    6.      Principles of Gene Manipulation and Genomics, Sandy B. Primrose, Richard Twyman, (2009)

    7.      Gene Targeting & Embryonic Stem Cells, Edited by Thomson & McWhir, Taylor & Francis, (2008)

    Transgenic Animal Technology: A Laboratory Handbook, Carl A Pinkert. 2nd Edition, (2002)

MOU Signed with National Institute of Health, USA

BITS, Pilani has signed a MOU with National Institute of Health, USA for research collaboration in the area of epigenetics and human health. The collaboration is aimed at students and faculty exchange programme for completing doctoral thesis work.


An Institution Deemed to be University estd. vide Sec.3 of the UGC Act,1956 under notification # F.12-23/63.U-2 of Jun 18,1964

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