Ph.D. Qualifying Written Exam

Ph.D. Qualifying Written Exam

LISTEN

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 - Selim Çetiner
  2. Plant immunity - TBD
  3. Plant molecular biology and genetics - Zehra Sayers and Selim Çetiner
  4. Plant nutrition - İsmail Çakmak
  5. Plant physiology - Levent Öztürk

Molecular Biology

  1. Cell biology - Cavit Ağca
  2. Immunology and signal transduction - TBD
  3. Molecular biology and biochemistry - Hüveyda Başağa
  4. Gene regulation and disease - Cavit Ağca

Bioinformatics

  1. Computational biology - Ogün Adebali and Öznur Taştan
  2. Structural biology - Zehra Sayers

Integrative Biology

  1. Animal physiology - Christopher Mayack
  2. Animal behavior - Christopher Mayack
  3. Integrative biology - Christopher Mayack
  4. Neurobiology - Nur Mustafaoğlu

Bioengineering:

  1. Biosensors - Nur Mustafaoğlu
  2. Tissue engineering - Nur Mustafaoğlu
  3. Genetic Engineering - Christopher Mayack


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
    • Chapters 10 - 19
  • 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
    Biochemistry;
    • Amino acids peptides and proteins, their structure and function
    • Enzymes
    • Carbohydrates and lipids and nucleic acids (their structures and functions)
    • Nucleic acids and their functions
    • Membranes and transport
    • Bioenergetics and metabolism (electron transport chain and ox phosphorylation)
    Textbook:
    Principles of Biocemistry (David Nelson and Michael Cox) recent edition or any Biochemistry text book.

    Molecular Biology;
    • Biosignaling
    • Transcription
    • Apoptosis and autophagy
    • Regulation of gene expression
    • Principles of methods used in molecular biology
    Textbook: Any recent biochemistry or molecular biology textbook and recent articles from literature.
    For the molecular bio, it will be an open book exam. Students will be asked to comment on an article from literature in terms of hypothesis, methodology used and suggestions for furthering the research.
  • 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:
    • Biological sequence analysis. Probabilistic models of proteins and nucleic acids, edited by R. Durbin, S. Eddy, A. Krogh, and G. Mitchinson. 1998. Cambridge: Cambridge University Press
    • Altuna Akalın, Computational Genomics with R, https://compgenomr.github.io/book/stats.html (Not the coding part but the concepts)
  • Structural biology exam:
    Textbooks:
    • 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
  • Integrative Biology exam
  • Animal Physiology exam:
    Textbook:
    • Animal Physiology 4th Edition
      by Richard W. Hill (Author), Gordon A. Wyse (Author), Margaret Anderson (Author)
      Publisher: Sinauer Associates is an imprint of Oxford University Press; 4th edition (September 13, 2016)
      Language: English
      Loose Leaf: 828 pages
      ISBN-10: 1605355941
      ISBN-13: 978-1605355948
  • Animal Behavior exam:
    Textbook:
    • Animal Behavior
      2nd Edition
      Authors: Michael Breed Janice Moore
      eBook ISBN: 9780128016831
      Paperback ISBN: 9780128015322
      Imprint: Academic Press
      Published Date: 1st February 2015
      Page Count: 552
  • Integrative Organismal Biology exam:
    Textbook:
    • Editor(s): Lynn B. Martin Cameron K. Ghalambor H. Arthur Woods
      First published:14 November 2014
      Print ISBN:9781118398784 |Online ISBN:9781118398814 |DOI:10.1002/9781118398814
      Copyright © 2015 John Wiley & Sons, Inc
  • Neurobiology exam:
    Textbook:
    • From Neuron to Brain by Author A. Robert Martin, David A. Brown, Mathew E. Diamond, Antonino Cattaneo, Francisco F. De-Miguel, and Foreword by John Nicholls ISBN: 9781605354392
  • Biosensors exam:
    Textbooks:
    • Biosensors: Essential, Gennady Evtugyn, Springer ISBN 978-3-642-40241-8
    • Handbook of Immunoassay Technologies by Sandeep K. Vashist and John H.T. Loung ISBN 978-0-12-811762-0
  • Tissue Engineering exam:
    Textbook:
    • Principles of Tissue Engineering by Robert Lanza, Robert Langer, Joseph Vacanti eBook ISBN: 9780128214015, Hardcover ISBN: 9780128184226
  • Genetic Engineering exam:
    Textbook:
    • An Introduction to Genetic Engineering 3rd Edition by Desmond S. T. Nicholl (Author), Publisher : Cambridge University Press; 3rd edition (June 1, 2008)
      Language : English
      Paperback : 347 pages
      ISBN-10 : 0521615216
      ISBN-13 : 978-0521615211
  • Gene regulation and disease exam:
    TBA