PhD Program
General Overview
Time to completion: 4-5 years.
TOTAL CREDIT REQUIREMENT: 81 CREDITS.
MINIMUM: 18 GRADED CREDITS.
Learning Objectives
The Interdisciplinary Program in Pathobiology
has established learning objectives for its doctoral program.
The goal of the program is for students to:
Develop a
fundamental understanding of basic cellular and molecular processes
and techniques important in the application of basic biomedical
research to diseases of public health interest. Specifically,
this includes familiarity with the paradigms for control, prevention,
and treatment of diseases of public health importance, an understanding
of the epidemiology and diseases processes of important diseases
of national and international importance, an understanding of
how biomedical research can approach such diseases, and basic
methodologies used in this type of research, including relevant
areas of molecular biology, epidemiology, and biostatistics. Students
are also expected to develop familiarity with the major classes
of pathogens.
Become an independent scholar capable of conducting
independent research leading to the expansion of knowledge of
Pathobiology. This includes developing the skills to approach
an unfamiliar experimental system, and identify and explore important
questions concerning pathogenesis and infection.
Learn to collect, analyze, interpret, and use data for solving
problems in Pathobiology.
Develop advanced research skills and expertise
in the area of his/her research concentration.
Develop skills in communicating research findings
to scientific audiences through publications and oral presentations.
The course of study outlined below will fulfill University of
Washington regulations. In this handbook, those requirements will
not be covered exhaustively. See the appendix for a summary of
the University requirements. Students should consult with the
official Handbook and other memoranda concerning those requirements.
Ultimately, it is the student's responsibility to ensure that
s/he meets the UW and program requirements and proceeds through
the program in a timely fashion.
Required Courses
The Pathobiology Core Courses have been revised. Changes will
be implemented in the 1999-2000 academic year. Students enrolled
prior to fall 1998 should complete the old 550/551 series. Students
enrolled after fall 1998 should complete the new 550, 551, and
552 series.
| Course Number |
Course Title |
Credits |
| PABIO 550 |
Diseases of Public Health Importance and Strategies for
Control |
3 |
| PABIO 551 |
Biochemistry and Genetics of Pathogens and Their Hosts |
4 |
| PABIO 552 |
Cell Biology, Immunology and Disease |
4 |
| PABIO 553 |
Survival Skills for Scientific Research |
2 |
| EPI 511 |
Principles of Epidemiology |
4 |
| PABIO 580 |
Pathobiology Seminar |
1 |
| PABIO 581 |
Current Literature in Pathobiology |
1 |
| PABIO 582 |
Critical Thinking and Research Design |
1.5 |
| PABIO 590 |
Pathobiology Mini-Courses |
1 |
| PABIO 598 |
Didactic Pathobiology (teaching) |
2 |
| PABIO 500 |
Rotation (first-year) |
Variable |
| PABIO 600 |
Research |
Variable |
| PABIO 800 |
Doctoral Dissertation |
27 |
Plus one of these two courses
IMMUN 441
Introduction to Immunology
4
IMMUN 532
Advanced Immunology
3
*Students
are required to attend Seminar (580) and Journal Club (581) every
quarter of the academic year while enrolled. Students may be excused
for up to two quarters while writing the dissertation. Students
will give research presentations in the Graduate Research Symposium
annually after the first year. Three credits each of Seminar and
Journal Club may each be counted towards your degree.
Elective Recommendations
By Track
Students should consult a current catalog to verify course offerings.
Each student in the Ph.D. program will select a track based on
their research interests; this is done at the time of the formation
of the student-mentor partnership (third quarter of the first
year). Students should choose electives based on their track,
and whether they will follow a molecular or immunological emphasis.
Students with a molecular emphasis are required to take PABIO536
(Bioinformatics) while those with an immunological emphasis are
required to complete IMMUN532.
Track in Eukaryotic
Pathogens
| Course Number |
Course Title |
Credits |
| PABIO 548 |
Molecular & Cellular Parasitology |
3 |
| CONJ 531-544 |
Molecular Conjoint Series |
Variable |
| PABIO 536 |
Bioinformatics |
3 |
| EPI 532 |
Epidemiology of Infectious Diseases in the Third
World |
3 |
| MICROM 444 |
Medical Mycology and Parasitology |
3 |
Track in Bacterial
Pathogens
Students without
a background in bacteriology are required to take MICROM 442 (Medical
Bacteriology) or an equivalent course as a prerequisite for entry
into the Bacterial Pathogens track.
| Course Number |
Course Title |
Credits |
| PABIO 540 |
Antibiotic Resistance |
3 |
| MICROM 552 |
Pathogen Microbiology |
4 |
| MICROM 555 |
Advaned Clinical Microbiology |
2.5 |
| EPI 520 |
Infectious Diseases Epidemiology |
4 |
| EPI 529 |
Emering Infections of International Public Health
Importance |
3 |
| PABIO 568 |
Molecular Epidemiology |
2 |
Track in Viral Pathogens
Students without
a background in virology should take MICROM 450 (Molecular Biology
of Viruses) and PABIO 445 (Medical Virology) unless comparable
courses in Medical Virology and Molecular Virology have already
been taken.
Two or more of
the following are strongly recommended:
| Course Number |
Course Title |
Credits |
| IMMUN 532 |
Advanced Immunology |
3 |
| MICROM 540 |
Virology |
3 |
| CONJ 531-544 |
Molecular Conjoint |
Variable |
| EPI 520 |
Infectious Disease Epidemiology |
4 |
| EPI 530 |
AIDS: Multidisciplinary |
2 |
| EPI 524 |
Epidemiology of Cancer |
3 |
Schedule for
Coursework
For the first three quarters, students should enroll in PABIO
500 for the rotation program, as well as in other required courses.
After the student arranges for a permanent lab, s/he will enroll
in PABIO 600 for research credit.
The following example
shows the general course progression through the Ph.D. program,
assuming the students will enroll in about two regular courses
per quarter. While "elective" slots are listed, this
does not mean that students are required to take electives at
all of those slots. Students should follow either the immunological
or molecular emphasis when planning their coursework. Generally
all formal coursework should be completed by the end of the second
year. A full time course load is 10 credits per quarter. Students
desiring to enroll in more than this need approval from the Graduate
Program Director.
YEAR 1
Autumn
| Course Number |
Course Title |
| PABIO 550 |
Diseases of Public Health Importance and Strategies for
Their Control |
| IMMUN 441 |
Introduction to Immunology |
| EPI 511 |
Introduction to Epidemiology |
| PABIO 500 |
Rotation |
| PABIO 580 |
Seminar |
| PABIO 581 |
Journal Club |
Winter
| Course Number |
Course Title |
| PABIO 551 |
Biochemistry and Genetics of Pathogens and Their Hosts |
| IMMUN 532 |
Advanced Immunology or elective for molecular emphasis |
| PABIO 500 |
Rotation |
| PABIO 580 |
Seminar |
| PABIO 582 |
Critical Thinking |
Spring
| Course Number |
Course Title |
| PABIO 552 |
Cell Biology, Immunology and Disease |
| PABIO 536 |
Bioinformatics for molecular emphasis or elective for immunological
emphasis |
| PABIO 500 |
Rotation |
| PABIO 580 |
Seminar |
| PABIO 590 |
Mini-course |
| PABIO 553 |
Survival Skills |
Summer
| Course Number |
Course Title |
| PABIO 600 |
Research Credits |
| |
|
YEAR 2
Autumn
| Course Number |
Course Title |
| PABIO 580 |
Seminar |
| PABIO 581 |
Journal Club |
| PABIO 600 |
Research |
| Elective |
|
Winter
| Course Number |
Course Title |
| PABIO 600 |
Research |
| PABIO 580 |
Seminar |
| PABIO 582 |
Critical Thinking |
| 2 X Electives |
|
Spring
| Course Number |
Course Title |
| PABIO 580 |
Seminar |
| PABIO 590 |
Mini-course |
| PABIO 600 |
Research |
| 2 X Electives |
|
* Several students
have taken TC509 - Writing the Scientific Article as an elective
class and have found it very helpful when writing the dissertation.
** The example
above is for students entering odd years. For students entering
even years, PABIO 551 will be taken the first year and 550 will
be taken the second.
*** Students with
an immunological emphasis may wish to take CONJ 501 (autumn) prior
to IMMUN 532, as suggested by the Dept. of Immunology.
Rotation Program
First year students in the Ph.D. program participate in the laboratory
rotation program. This program is designed to provide research
experience in various projects and experimental systems that are
being investigated in the department. It will give students the
opportunity to interact with faculty, students, postdoctoral scientists,
and staff in different research groups and facilities, and assist
students in deciding in which laboratory they wish to conduct
their dissertation research. Students rotate through three labs,
one quarter each for their first three quarters.
Laboratory assignments
will be the responsibility of the GSAC. Students will be asked
to list five laboratories in which they would like to do laboratory
rotations. It is strongly encouraged that students do rotations
at more than one site. Assignment of laboratory rotations is based
on the following criteria:
Labs with available
funding will support students needing funding for the quarter
of their rotation through that lab. The students will work on
experiments related to the goals of the funded project. For students
with external funding or not needing support, the ability of the
host labs to fund the student will be ignored in making assignments,
although funding must be assured for research supplies. Like other
students, these students will rotate through three labs. The Graduate
Program Director will attempt to match students and labs according
to interest, but may need to make rotation assignments other than
those listed by the student for reasons such as space, funding,
and reasonably equitable distribution of resources.
The assignments
for first quarter will be done by the end of the first week of
school. Provisional assignments will be made at that time for
the remaining quarters. These will be confirmed with the student
midway through the first quarter. Students who wish to change
their rotation schedule will generally be allowed to do so if
the new host lab agrees and if it does not impact on the rotation
of any other students. Students will not be allowed to remain
in one lab for more than one quarter. Any changes in the rotation
schedule must be approved by the Graduate Program Director.
Students will enroll
in PABIO 500 for 3 credits for their rotation, and list the corresponding
faculty member as the professor. This faculty member will be responsible
for providing a credit/no credit grade for the student. In general,
students are expected to work approximately 20 hours a week on
their project and are expected to attend lab meetings. To receive
credit for the rotation, all students are expected to give a presentation
to the host lab on their work, write a written report on their
rotation (1-2 pages single spaced), and receive a written evaluation
from the professor using a form provided by the Pathobiology Program
Coordinator. A copy of this evaluation and the student report
will be provided to the Pathobiology Program Coordinator to be
placed in the student's file.
Students can petition
to be exempted from the rotation program. The written request
should state the basis for the request to be excused. The request
from the student should be accompanied by a letter of support
from the potential advisor. Comparable experience or compelling
reasons of funding are generally required for exemption. The petitions
will be submitted to the Graduate Program Director and the decision
to approve or not approve will rest with the Graduate Student
Advisory Committee. Students will receive a written confirmation
of the exemption. Students who wish to leave the rotation program
after commencing it must follow the same petition process.
The Graduate Program
Director will request the students to identify their dissertation
advisor during the third quarter rotation. The selection of the
dissertation advisor is a joint decision of the student and the
faculty member, who should discuss the options together. Once
a student has identified his/her dissertation advisor, s/he must
submit the Advisor Conformation Form, which has been approved
by the Chairman and the Graduate Program Director, to the Pathobiology
Program Coordinator to be placed in his/her permanent file.
TIMELINE OF
EVENTS
Year 1
1st Quarter
Orientation. Students should line up 3 rotations and start research.
3rd Quarter
In conjunction with a faculty member, decide in which lab to stay
for your dissertation research.
Year 2
1st Quarter
The three-member research advisory committee should be formed
by the beginning of this quarter. The Preliminary Research Proposal
is due October 1.
3rd Quarter
Doctoral Supervisory committee should be established. Each student
should give a 15 minute research presentation at Graduate Research
Symposium.
4th Quarter
Formal course work is usually completed by this time.
Year 3
1st Quarter
Schedule and take the general examination.
2nd Quarter
The dissertation research proposal is due.
3rd Quarter
Give a 15 minute research presentation at Graduate Research Symposium.
4th Quarter
By the end of this quarter formal course work must be completed
and students must have passed the general exam.
Year 4
3rd Quarter.
Give a 15 min. research presentation at Graduate Research Symposium
(if not presenting Ph.D. defense by this time).
Years 4-5
All Quarters
Complete dissertation research. Write dissertation. Give dissertation
defense.
* Generally students
will complete their Ph.D. in 5 years.
Note: If you
will deviate from this time line, you must have written approval
from the Chair of the Graduate Student Advisory Committee and
your Doctoral Supervisory committee (once formed).
ADVISORY COMMITTEES
A student's progress in the Ph.D. program will be followed by
several individuals. Among these are your advisor, members of
the Graduate Student Advisory Committee (GSAC) and your Ph.D.
advisory committee. In the event that you perceive you are having
problems with your academic or research program, please discuss
this with a faculty member on one of these committees.
The GSAC will monitor
your progress until the Research Advisory Committee is formed.
Please bring questions concerning course offerings and curriculum
to them. Current members of the GSAC are Dr. Lee Ann Campbell
(chair), Dr. Jean Feagin, and Dr. Paul Lampe. One of these individuals
will serve as your primary GSAC advisor.
Formation of
the Research Advisory Committee:
The Research Advisory Committee, which should be formed by the
start of the second year, will consist of your research advisor
and two other members (at least one of these should be from the
Department). The Committee will review the preliminary research
proposal and provide guidance. The members of this Committee will
also be part of the Supervisory Committee. This committee meets
every six months. For each Committee meeting, the students should
prepare a brief written report (1-2 pages) documenting their progress.
The committee will complete a brief report (Appendix G) regarding
your progress after each meeting. You, your advisor and the GSAC
will all receive copies of this report. If you do not receive
a copy, please contact the Pathobiology Program Coordinator.
Formation of
the Supervisory Committee:
The major advisor will write a letter to the department chairperson
for approval to nominate a member of the supervisory committee.
Typically, the Doctoral Supervisory Committee consists of 5 members,
including the advisor (usually serving as chair), at least 2 other
faculty members from the department, and the Graduate Faculty
Representative. This last individual is appointed by the Dean
of the Graduate School. The supervisory committee can also include
one non-graduate faculty member. All members except the Graduate
Faculty Representative have voting privileges. The committee should
be formed 4 months prior to the General Examination. This committee
meets every six months to monitor progress. It is the responsibility
of the student to arrange these meetings. For each Committee meeting
the student should prepare a brief written report (1-2 pages)
documenting his/her progress. The Committee will document your
progress as above.
Preliminary
Research Proposal
The Preliminary Research Proposal is due October 1 of the second
year.
The requirement
for the Preliminary Research Proposal has several goals, including:
- stimulating
familiarity with the literature in the specific research area
at the outset of the research.
- generating a
logical plan for experiments during the subsequent year.
- providing experience
in writing formal proposals.
The proposal should
contain the following in this order:
- A brief synopsis
of background and significance of the project.
- A summary of
preliminary experiments.
- A description
of the experimental plan for the next year, which optimally
will form the basis of the preliminary data for the dissertation
proposal.
- Appropriate
references, including titles.
Students are encouraged
to consult with their advisor and research advisory committee
during the preparation of the proposal. The experiments should
be designed such that when they are complete, the student will
have a clear idea of the experiments that will comprise the dissertation
research. Appropriate references should be cited, although the
list does not need to be exhaustive. This proposal should be 3-4
single spaced pages, excluding references. The proposal is turned
in to the Pathobiology Program Coordinator and to members of the
Research Advisory committee. The committee in turn will discuss
the proposal and experimental options with the student.
Dissertation
Research Proposal
The dissertation research proposal should be done by the first
quarter of the third year. The student is encouraged to consult
with his/her advisor during the preparation of the proposal, and
also to discuss the proposal with the Thesis committee as needed.
The proposal should contain the following, in this order:
Specific Aims.
A list of the specific aims of the research which will form the
basis of the Ph.D. thesis. These aims outline the goals of the
research. Typically there will be 3-5 specific aims. The aims
may include those aims which are already complete at this time.
The goal of this list is to provide the committee with an overall
picture of what the body of work comprising the Ph.D. dissertation
shall be. This section should be one half to one single spaced
page.
Background. This
section will summarize the relevant literature and point out the
significance of the general problem addressed by the dissertation
research. This section may also present information which supports
the approaches employed in the proposed experiments.
Preliminary Results.
This section should contain the preliminary data which the student
has already obtained. Such information may fall into two categories
(not mutually exclusive): 1) information which may not form part
of the eventual dissertation, but provides support for the experimental
approach; and 2) experiments which are directed at the specific
aims outlined in I. and which will be part of the dissertation.
Experimental Plan.
In this section, the experiments which will address the specific
aims are outlined. Sufficient detail should be included that the
committee is convinced of the feasibility of the approach and
the student's competence to undertake the experiments. This includes
the identification of appropriate control experiments. Throughout
the proposal, references should be cited where appropriate (although
the list need not be exhaustive). The total document should be
about 6-8 single spaced pages, excluding the reference list. The
Dissertation Research Proposal will be submitted to the formal
Doctoral Supervisory committee. The committee will discuss the
proposal with the student and will advise the student of alternative
experimental approaches when applicable.
A copy of the approved Dissertation Research Proposal should be
provided to the Pathobiology Program Coordinator for inclusion
in the student's file.
General Examination
General Examination
The General Examination consists of two parts: written and oral.
These are described briefly below:
Written examination: The written exam is given
at the end of the first year. All members of a graduate class
will take this exam at the same time.
The goals are to test mastery of the following: general knowledge/understanding
of important concepts; ability to synthesize information and logically
present material in a written format; ability to interpret and
critique primary literature.
Five subject areas to be covered, each with an
emphasis on health and human disease:
M olecular Biology with Biochemistry emphasis
M olecular Biology with Genetics emphasis
C ell Biology
P ublic Health
I mmunology
A closed book format will be used. Students will be provided
with laptop computers, without internet access, for the examinations.
Students can also choose to write the answers long hand, but anonymity
can not be guaranteed. All students will be tested at the same
time and the exam will be proctored.
Questions will be solicited from all faculty members; final selection
of questions will be made by the exam committee comprised of the
instructors of the core courses (550, 551, 552) and two additional
faculty to be chosen. Multiple questions may be included for each
topic. The format of the questions can vary - long answer, short
answer, data analysis, literature critique, etc. The format of
the topic can also vary students may be required to answer all
questions, select one of two or three questions, etc. The content
of the exams for each topic will be formulated based on the questions
submitted and the expertise of the exam committee. Decisions about
the format of the questions and the format of the exam will be
made by the exam committee with input from faculty submitting
questions.
The exam will be given at the end of first year on 2.5 consecutive
days, at the end of June or in early July. The examination for
each topic area will take approximately 2-3 hours, and students
may not have additional time unless there is a disability consideration.
Grading of the questions will be performed by faculty, overseen
by the exam committee. For each topic area, two faculty will independently
grade the responses without knowledge of the identity of the student;
these will be scored as Pass/Not Pass. The author of the question
will usually be one of the graders. Responses with discordant
grades will be graded by two additional faculty.
Students who do not achieve a Passing grade in any topic will
be required to re-take an examination on the specific topic, usually
within three months unless remedial course work is required. Failure
to successfully complete the follow-up examination may result
in dismissal from the program, after input from the prospective
mentor, the Graduate Student Advisory Committee, the Associate
Chair and the Chair.
Oral Examination: The oral exam is generally
taken during the third year and is administered by the Doctoral
Supervisory Committee. The Doctoral Supervisory Committee must
be formed at least 4 months prior to the oral examination. The
Program Coordinator will contact the Dean of the Graduate School
requesting approval of the oral examination. This request must
be received by the Dean’s Office at least 3 weeks prior
to the proposed date of the oral exam. The student will reserve
a room for the exam for a period of 3 hours. The Dean will provide
a warrant to the Department permitting the student to take the
examination. The examination should not be scheduled at a time
that would compromise the student’s participation in the
annual Graduate Research Symposium.
Content of the Oral Examination: The oral exam
will cover the following areas:
· The student’s research area. In depth knowledge,
including familiarity with both background literature and current
research, is required. This would include knowledge of specifics
as well as generalizations. It would encompass an understanding
of research findings and their importance, as well as critical
questions that are unresolved. The student should be able to critically
evaluate this body of work.
· Areas related to the student’s research. A moderate
level of knowledge regarding this body of work is required. Familiarity
with literature, current research, and important questions is
expected, but the depth of specific knowledge is not expected
to be as complete as for the directly related areas.
· Areas not directly related to the student’s research,
but covered in Pathobiology coursework. It is generally considered
that these areas will have been covered by the written examination
and will not comprise a significant portion of the oral examination.
The students are encouraged to meet with committee members to
gain input on general emphasis areas for the oral exam. However,
by program policy, students are not to be provided with questions
or the definition of specific areas of questioning in advance.
Committee members mat wish to suggest certain readings, although
the examination is not restricted to those readings.
Dissertation
Format: The dissertation must be written in the format
required by the Graduate School. The format is specified in the
booklet entitled "Style and Policy Manual for Thesis and
Dissertations" which should be obtained from the Graduate
School.
Dissertation:
The dissertation must be of such quality that at least one published
article with the student as the first author results. At least
one article must have been submitted for publication before the
final examination.
Appointment
of the Reading Committee: When the Supervisory Committee determines
that the student is ready for the final examination, the Reading
Committee should be appointed. The chairperson of the Supervisory
Committee will request the Dean of the Graduate School to approve
the three-member Reading Committee who will normally be members
of the Supervisory Committee.
Final Examination:
After the Reading Committee is established officially, a request
for approval to conduct the Final Examination will be signed by
the all members of the Supervisory Committee and submitted to
the Dean of the Graduate School. This letter should be presented
to the Graduate School at least 3 weeks prior to the Final Examination
date. The dissertation presentation is open to the public. Following
this presentation, the Ph.D. candidate will meet with the supervisory
committee. Each member will question the student on any aspect
of his dissertation. If the final exam is passed, the warrant
is signed and returned to the Graduate School immediately. The
student has 60 days to make any necessary corrections and submit
the dissertation to the Graduate School.
Teaching Practice
Students obtain training in teaching at the University level through
enrollment and participation in PABIO 598, Didactic Pathobiology
for one quarter. The requirement of Didactic Pathobiology (PABIO
598) for the Ph.D. degree is intended to provide the student with
a meaningful teaching experience in a guided environment. Two
credits are required. The student can fulfill the requirement
via a number of different avenues, as listed below.
The student can
fulfill the requirement via a number of different avenues, as
listed below:
Act as a Teaching
Assistant for a lab course (2 credits).
Act as a Teaching Assistant for a lecture course (2 credit).
Act as a Teaching Assistant for a lab course in another dept.
(2 credits).
Act as a Teaching Assistant for a weekly discussion section (2
credits).
Organize a readings course under the supervision of a faculty
member (2
credits).
This could be 2
- 3 students working together.
The Pathobiology
Program Coordinator will maintain a list of teaching opportunities
and copies of the TA requests from course organizers. Students
should consult with the appropriate course organizer for additional
specifics about the Teaching Assistantship. They may sign up for
PABIO 598 only with the approval of the relevant course organizer.
Because teaching slots are limited, students are urged to make
the necessary arrangements well in advance. Students should consult
with the faculty organizer of specific courses prior to enrolling
in PABIO 598. The course organizer will inform the students of
the specific requirements for teaching in a given course.
