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    DEPARTMENT OF MICROBIOLOGY

    Graduate Student Handbook*

    20th Edition, 2016

    Department of Microbiology Chair and DEO, Dr. Patrick Schlievert

    Director of Graduate Studies (DGS), Dr. Tim Yahr

    Department Administrator, Jordan Keller-Wilson

    Graduate Advisory Committee Dr. John Harty

    Dr. Wendy Maury Dr. David Weiss

    Grievance Committee (Chair), Dr. Craig Ellermeier

    *This handbook has been written and edited by the Director of Graduate Studies and the Graduate Advisory Committee of the Department of Microbiology.

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    TABLE OF CONTENTS Page Table of Contents 2 Preface 4 I. The Graduate Program in Microbiology 5

    A. Introduction 5 B. Advisory Services for Graduate Students 6 C. Financial Assistance 6 D. Health Insurance 6 E. Timetable for Students Pursuing the Ph.D. Degree 7

    II. Detailed Description of Ph.D. Program Activities and Requirements 7

    A. Overview of Requirements for the Ph.D. Degree 7 B. Course and Semester Hour Requirements 8

    1. Rationale for Coursework 8 2. Semester Hour Requirements 8 3. Course Levels 8 4. Guidance in Course Selection 9 5. Academic Performance 10 6. Enrollment/Registration Procedure 10

    C. Laboratory Research Rotations 11 1. Rationale for Rotations 11 2. Selection of a Rotation Laboratory 11 3. Rotation Evaluation 12

    D. Seminars, Journal Clubs, and Lab Research Meetings 12 1. Seminars 12 2. Journal Clubs 13 3. Lab Research Meetings 13

    E. Faculty Committees for Training Graduate Students 13 1. Selection of a Mentor 13 2. Role of the Ph.D. Advisor 13 3. Composition of the Ph.D. Committee 13 4. Role of the Ph.D. Committee 14 5. Composition of the Comprehensive Examination Committee 14 6. Role of the Comprehensive Examination Committee Chair 14 7. Mandatory Annual Meeting 15 8. Annual Progress Report 15 9. Role of the Director of Graduate Studies (DGS) 16

    F. The Comprehensive Examination Protocol 16 1. The Purpose of the Comprehensive Examination 16 2. The Comprehensive Examination Process 16 3. Timetable for Completing the Exam 17 4. Composition of the Examination Committee 17 5. Submission of Possible Topics for the Exam Proposal 17 6. Abstract Preparation and Submission 17 7. Comprehensive Examination Abstract Meeting 18 8. Potential Outcomes of the Evaluation and the Student Abstract 19 9. Student Response to Outcomes 8a through 8d 19

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    Figure 1. Comprehensive Exam Flow Chart: Initial Phase 20 Figure 2. Comprehensive Exam Flow Chart: Evaluation Phase 21

    G. Preparation of the Comprehensive Examination Proposal 22 1. Timetable 22 2. General Guidelines 22 3. Scope of the Student Proposal 22 4. Composition of the Student Proposal 22 5. Pitfalls and Alternatives 26 6. Fatal Flaws to Avoid in Research Proposal 26 7. Protocol for the Proposal Defense 27 8. Alternative Outcomes of the Comprehensive Examination 28

    III. Ph.D. Thesis Research 29

    A. General 29 B. Regular Checkpoints on Student Progress 29 C. Ph.D. Dissertation Preparation and Defense 29 D. Publication Requirements for Ph.D. Students 30

    IV. Master of Science (M.S.) Degree 31

    A. Introduction 31 B. Requirements for the M.S. Degree 31 C. Matriculation into the Ph.D. Program 31

    V. Performance in Teaching 31 VI. Facilities, Equipment, and Logistic Matters 32

    A. Teaching and Research Equipment 32 B. Travel to Scientific Meetings 33 C. Departmental Administration 33 D. Radiation and Health Safety 34 E. Library Services 34 F. Computers 34 G. Grievance Review Committee 34

    APPENDIX 37

    Figure 3. Annual Progress Report Procedure 38 Graduate Training Timetable (All Years) 39 Form A. Lab Rotation Report 42 Form B. Annual Progress Report 43 Form C. Student Teaching Evaluation 45

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    PREFACE The University of Iowa General Catalog (https://registrar.uiowa.edu/general-catalog), and the Manual of Rules and Regulations of the Graduate College (http://www.grad.uiowa.edu/graduate-college-manual), contain useful information about requirements for advanced degrees at the University. Since regulations and practices vary among departments, this handbook provides specific information about graduate student training in the Department of Microbiology. The handbook is organized into the following major sections: I. The Graduate Program in Microbiology II. Detailed Description of Ph.D. Program Activities and Requirements III. Ph.D. Thesis Research IV. Master of Science (M.S.) Degree V. Performance in Teaching VI. Facilities, Equipment, and Logistical Matters There is also an Appendix containing a suggested graduate training timetable, a diagram of the annual progress report procedure, and copies of various report forms.

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    I. THE GRADUATE PROGRAM IN MICROBIOLOGY A. Introduction

    1. Training and Degrees Offered: The Department of Microbiology offers research training for the Doctor of Philosophy (Ph.D.), Master of Science (M.S.), and Bachelor of Science (B.S.) degrees. Students will typically be admitted for Ph.D. training without the necessity of also writing a M.S. thesis. However, the M.S. can be a degree objective, a tool for improving writing skills, or a terminal degree for Ph.D. candidates who do not fulfill all of the demands for the Ph.D. degree. Both degrees require the writing and defending of a thesis on a research topic. The objectives of the graduate program in microbiology are to facilitate the education of students so that they:

    a. gain basic information about microbiology and immunology, and become experts in specific areas of microbiology and immunology,

    b. become technically able to investigate new problems and successfully acquire knowledge about new problems, and

    c. can communicate acquired knowledge to peers in the field. The specific areas included in the program are: immunology, bacterial genetics and physiology, pathogenic bacteriology, virology, parasitology, and bioinformatics. Several of these areas involve interdisciplinary training within and outside the Department, so that students receive a broad background of information during their course of study.

    2. Requirements for the Ph.D. Degree: To achieve the Ph.D. degree, a student must: a. successfully complete the necessary course and rotation requirements, b. pass the comprehensive examination, c. demonstrate research ability and write a dissertation, d. present a research seminar before the faculty, and satisfactorily defend the

    dissertation research before the student's Ph.D. Committee, and e. be a first author on a peer-reviewed manuscript accepted for publication.

    3. Student Teaching: Since students are expected to become qualified in the teaching

    of microbiological topics, all students will serve as teaching assistants for at least part of two semesters during their graduate training. Students are typically placed in general courses for which all are expected to have academic competence. In some cases students will be assigned to specialized courses for which they have special aptitude and training. Graduate teaching assistant duties range from teaching laboratory sections in general courses, preparing laboratories in advanced courses, grading of examinations, and in special cases, presenting formal lectures. All teaching activities are evaluated and a report/evaluation may be added to the student’s file (see page 31 and Form C, page 45).

    4. Expectations and Performance during the First Year: As established by the Graduate College and the Department of Microbiology, all students must maintain the minimum grade point average of 3.0 to continue study in the Ph.D. program (see page 10). An average of

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    All first year students are required to satisfactorily complete three rotations. Two of these rotations may be in the same laboratory. Students entering with an M.S. degree or in the M.D./Ph.D. program can petition the Graduate Advisory Committee (GAC) to do only two rotations. The opportunity to study in a particular laboratory, either as a rotation or as part of a degree research project, is a privilege that needs to be taken seriously. Rotating students are expected to keep regular and reliable schedules, and to be working in the laboratory between classes. Rotation evaluations are made by the mentor and an unsatisfactory rotation report can result in a "U" (unsatisfactory) grade in MICR:7261. Unsatisfactory performance in one or more rotations can lead to dismissal from the program. B. Advisory Services for Graduate Students: The Director of Graduate Studies (DGS), in collaboration with the GAC, will help incoming students plan a program of studies for the first year, taking into account the student’s background and scientific interests. To facilitate this process, it is important that new students arrive on campus at least one week before classes begin to attend an Orientation Session with the GAC and meet with the DGS. The latter will serve as the student’s official advisor until the student selects a Ph.D. advisor. Prior to the Orientation Session, incoming students should familiarize themselves with the range of research interests of the departmental faculty. This information is available on the Departmental Website http://www.medicine.uiowa.edu/microbiology. The GAC encourages students to meet and become acquainted with faculty members and their research. This usua