Ph.D. Qualifying Written Exam

Ph.D. Qualifying Written Exam


Students must pass exams in 4 topics. Topics must be selected such that two of them are from one subject area and two of them could be from the remaining two subject areas or one of each*. Main subjects and the topics are listed below.
*One of the topics may be selected from the topics of other PhD programs with the approval of the student's adviser.

Subject areas and topics:

Plant Biotechnology:

  1. Plant biotechnology
  2. Plant immunity
  3. Plant molecular biology and genetics
  4. Plant nutrition
  5. Plant physiology

Molecular Biology

  1. Applied protein engineering
  2. Cell biology
  3. Immunology and signal transduction
  4. Molecular biology and biochemistry
  5. Molecular medicine


  1. Computational biology
  2. Structural biology
  3. Computational genome analysis

The faculty members of the MBGB program suggest that the following are appropriate study subjects/references for these exams. If a resource is not indicated please consult with a faculty member whos research is similar to the subject in question or the graduate area advisor.

  • Plant biotechnology exam:
    Textbook: Plant Biotechnology The genetic manipulation of plants Second Edition Adrian Slater, Nigel Scott, and Mark Fowler ISBN: 9780199282616
  • Plant immunity exam:
    The suggestion of the qualifying exam committee are to be familiar with the textbook, Plant Pathology, George N. Agrios (5th Ed), with particular emphasis on the following chapters and subjects:
    • Chapter 4 Genetics of plant disease
    • Chapter 5 How pathogens attack plants
    • Chapter 6 How plants defend against pathogens

    Also, be familiar with the book, Molecular Plant Immunity, Editor: Guido Sessa, 2013 (ISBN-13: 978-0-4709-5950-3/2013) with particular emphasis on the following chapters and subjects:
    • Chapter 1 The Rice Xa21 immune receptor
    • Chapter 2 Molecular basis of effector recoginition by plant NB-LRR
    • Chapter 3 Signal transduction pathways activated by R proteins
    • Chapter 5 Effectors of bacterial pathogens
    • Chapter 6 The roles of TAL effectors in virulance and avirulance of Xanthomonas

  • Plant physiology exam:
    Textbook: Biochemistry and Molecular Biology of Plants, 2nd Edition Bob B. Buchanan, Wilhelm Gruissem, Russell L. Jones ISBN: 978-0-470-71421-8
    • Chapter 1 Membrane Structure and Membranous Organelles
    • Chapter 11 Cell Division
    • Chapter 21 Responses to Plant Pathogens
  • Cell biology exam:
    Textbook: Molecular Biology of The Cell
    • Chapter 12 Intracellular compartments and protein sorting
    • Chapter 13. Intracellular Membrane Traffic
    • Chapter 15 Cell Signalling /Notch signaling/ Nonsense mediated decay
    • Chapter 17 Cell Cycle
    • Chapter 18 Cell Death
  • Immunology and signal transduction exam:
    Textbook: Janeway's Immunobiology (9th Ed), (or similar) with particular emphasis on the following chapters and subjects:
    • Chapters 1-10.
  • Molecular biology and biochemistry exam
    Textbook: Molecular Biology of The Cell
    • Chapter 6: How Cells Read the Genome: From DNA to Protein
      - From DNA to RNA
      - From RNA to Protein
    • Chapter 7. Control of Gene Expression
  • Molecular medicine exam
    Textbook: The Biology of Cancer (Weinberg)
    • Chapter 2: Nature of Cancer
    • Chapter 11: Multi-step Tumorigenesis
    • Chapter 14: Moving out: Invasion and Metastasis
  • Computational biology exam:
    Textbook: Setubal JoC, Meidanis Jo. Introduction to computational molecular biology. Boston: PWS Pub.
    Important material:
    • Sequence comparison
    • Database search
    • Fragment assembly of DNA
    • Physical mapping of DNA
    • Phylogenetic trees
    • Genome rearrangements
    • Structural bioinformatics
    • RNA structure prediction
    • Protein structure prediction
    • Homology modeling
    • Molecular docking
  • Structural biology exam
    • Introduction to Protein Structure Branden & Tooze
    • Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models, Gale Rhodes
    • Protein Structure and Function, Gregory Petsko