OHSU Knight Cancer Institute Graduate Program in Cancer Biology

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Cancer Biology Guidelines and Expectations

The following guidelines govern all students in the Program in Cancer Biology (CANB) and are in partnership with the requirements set forth by the Program in Molecular and Cellular Biosciences (PMCB) and the Graduate Council of the Oregon Health & Science University (OHSU) School of Medicine.

To complete the requirements for the Ph.D. degree, graduate studies in the Program in Cancer Biology must successfully complete required and elective courses, attend CANB departmental seminars, perform research and write and defend a thesis. The program requires the completion of a minimum of 135 term-hours of course credit, of which 100 hours must be in either departmental courses or conjoint courses. Generally, students are expected to enroll in 12-16 credit hours.

Structure of Cancer Biology Program

Year 1
Complete CON course requirements (CONJ 661, 662, 663, 664, 665, [one of 667, 668, 669], 650-ethics, 607-seminar series, 605, 601)
3 laboratory rotations
Present research in rotation talk forum
Attend departmental seminars
Attend PMCB seminars and journal club
Successfully complete comprehensive examination (CONJ 608A)
Select Thesis Advisor and Departmental Program
Recommended CANB courses (CANB 607, CANB 606-spring term)

Year 2
Complete PMCB CONJ course requirements
Establish a Thesis Advisory Committee (TAC)
Complete required and elective CANB courses (see below)
Successfully complete qualifying examination (CONJ 608B)
CONJ 607    PMCB seminar series
CANB 601    Engage in research in thesis laboratory
CANB 607    Attend Departmental Seminar Series
CANB 606    Participate in CANB journal club
PHPH 607    Grant Writing & Qual Exam Prep (Spring)^
Participate in Cancer Biology Research Forum

^also recommended to take Dr. Rachel Dresbeck’s Vollum writing course

Year 3+
TAC meeting at least once per year
Engage in research in thesis laboratory (CANB 601)
Attend Departmental Seminar Series (CANB 607)
Participate in CANB journal club (CANB/MGEN 606)
Participate in Cancer Biology Research Forum
Participate in the Research in Progress OHSU forum
Present your work in the Cancer Seminar series (30 minute talk)-YR3, 4 or 5

Required PCB Graduate Courses

Year 1
	CONJ 665	Development, Differentiation and Cancer (Spring)	3 credits
		Must be completed by end of year 2
Year 2
	Fall Term CANB 606	Mechanisms of Cancer Journal Club	1 credit
	CANB 607	Knight Cancer Biology Seminar Series	1 credit
	CANB 601	Research	x credits
		CANB elective courses (see list below)	x credits
		total	16 credits
	Winter Term CANB 606	Mechanisms of Cancer Journal Club	1 credit
	CANB 607	Knight Cancer Biology Seminar Series	1 credit
	CANB 601	Research	x credits
		CANB elective courses (CANB 610 is suggested, if offered)	x credits
		total	16 credits
	Spring Term CANB 606	Mechanisms of Cancer Journal Club	1 credit
	CANB 607	Knight Cancer Biology Seminar Series	1 credit
	CANB 616	Advanced Topics in Cancer Biology	4 credits
	CANB 601	Research	x credits
	PHPH 607-02	Grant Writing & Qual Exam Prep	1 credits
		total	16 credits
	Summer Term CONJ 608B	PMCB Qualifying Exam	8 credit
	CANB 601	Research	8 credits
		total	16 credits
Year 3+
	All Terms MGEN 606	Mechanisms of Cancer Journal Club	1 credit
	CANB 607	Knight Cancer Biology Seminar Series	1 credit
	CANB 601	Research	x credits
		Summer term requirement CANB 601 only

CANB Specific Course Requirements

Credit for previous course work: if a student feels that they have completed an equivalent, graduate-level course to any of the required courses, they may petition to have the course requirement waived. To petition, the student should write a memo CANB curriculum director requesting that the course requirement be waived and explaining why the student feels that the previous course is equivalent to the required course. A course outline or syllabus that indicates the subjects covered by the previous course should be included with that memo.

All students are required to enroll in and attend CANB 607^, the Knight Cancer Biology Seminar Series, throughout their graduate tenure.

Students are required to present a Departmental seminar on their thesis work during the third year of graduate studies and at least once more before graduation (usually 4th or 5th year).

Students are also required to enroll in CANB606^^, Mechanisms of Cancer Journal Club, throughout their graduate tenure, excluding summer term.

^Students are required to attend one cancer related seminar each week during the academic year. Students can opt to attend CELL607 cancer-related seminars on weeks when CANB607 does not offer a seminar. Attendance will be monitored to evaluate student participate in the course.

^^Students can elect to take MGEN Journal club, Cancer Genetics and Genomics during the winter term in lieu of CANB606, but must get approval from the program director.

Elective Courses

CANB requires that students complete at least two elective graduate courses offered by CANB or other departments in addition to the above required PHPH 607, CONJ 665, and CANB 616. Below is a listing of some of the more popular electives taken by our students:

CANB 610, Current Topics in Cancer (2 credits, Winter Term - Alt years). Director: Maureen Hoatlin

CELL 611, Histology – The Structure and Function of Cells in Tissues (Fall Term - Alt years): Bruce Magun & Karmen Schmidt, course directors. Offered every other year. Introduction to the organization and differentiated function of the major tissues and organs of the body. Students will help develop expertise in the histological dentification of tissue and organs under the light microscope. One hour per week will deal with discussion of a paper that uses histological or histochemical analysis in combination with transgenesis or other molecular approaches.

CELL 618, Mechanisms of Development (Winter, alt years), Alex Nechiporuk, course director. Offered every other year. Topics covered include (i) signal transduction and transcriptional regulation of cell fate, (ii) RNA localization and translational control of development, (iii) asymmetric cell division, (iv) embryonic inductions, (v) signaling networks that establish the major body axes, (vi) stem cell plasticity and (vii) organogenesis.

CELL 620, Model Systems Biology (3 credits; Summer Term) Missy Wong & John Brigande, course directors. Offered every other year, even. Exploration of the history of, power of and use of key model organisms used in biomedical research. Past model systems focused on mouse, chick, zebrafish, drosophila, yeast, frog, pig, primate, human. We offer a hands-on laboratory component for real-time exposure to some of the model organisms.

MGEN 624, Gene and Cell Therapy (2 credits; winter) Hiroyuki Nakai, Cary Harding, co-directors. The course presents an introductory overview of various gene delivery systems (viral and non-viral) and cell-based approaches; advances in DNA/RNA/peptide delivery, cellular genome engineering and understanding the biology of cells as therapeutics; applications of gene delivery technologies and cell transplantation with a focus on translational research; and current issues in gene and cell therapy and regenerative medicine. The course consists of lectures by experts in the relevant fields in a lecture/paper discussion format. Students will be required to write an NIH-National Research Service Awards style research proposal on a relevant topic of their choice and expected to have an oral presentation during the course.

MBIM 610 Introduction to Immunology (2 credits; winter)
PHPH 617 Pharmacokinetics (2 credits; fall)
PHPM 524 Introduction to Biostatistics (4 credits)

Newly formed/upcoming courses

MGEN 6XX, Cancer Genetics and Genomics (1 credit; winter) Mushui Dai and Paul Spellman, co-directors. Journal club with an emphasis on cancer genetics and genomics.

Academic progress

Grade Point Average Requirements The department requires that graduate students maintain an overall 3.0 grade point average in their coursework (A = 4; B = 3; C = 2; D = 1). Courses graded on P/NP basis do not contribute to calculation of the grade point average. If a student’s cumulative grade point average drops below 3.0, the student will be placed on academic probation, requiring that he/she bring up his/her grade point average at least a 3.0 within the next 12 months. Please note that academic probation may limit the availability of some kinds of student loans or other financial aid (for further information contact Registrar’s office). Any student who fails to achieve a grade point average within the one year time limit will be subject to dismissal from the department.

Required GPA for Required Courses Students must earn a grade ≥B (3.0) in all required courses (defined in Section II). A student who receives a grade below a B must repeat that course the next available time it is offered and obtain a passing grade within 1 year. Failure to do so constitutes grounds for termination from the program.

Incomplete Grades Incomplete Grades. The grade of Incomplete can be given in circumstances beyond the control of the student (e.g. illness) that prevent completion of the course requirements by the end of the term. An Incomplete can only be given if the student is able to complete the requirements within the subsequent term.

Failing Research Credits Students failing a semester of Research credits, (i.e. receives a NP or No Pass on research) are immediately placed on academic probation. To return to good standing, the student must obtain a passing grade on the next term of Research and all subsequent terms. Failure to do so constitutes grounds for termination from the program.

Pre-Qualifying Graduate Students: A pre-qualifying graduate student is required to notify and meet with his/her mentor, graduate education committee director (GPD) and graduate program coordinator (GDC) immediately upon receiving a failing grade on the research credits in any one term. The GPD will suggest a course of action that the student must follow in correcting his/her academic performance.

Post-Qualifying Graduate Students: A post-qualifying graduate student (in consultation with his/her mentor, GPD and GPC) is required to schedule a Thesis Advisory Committee (TAC) meeting immediately upon receiving a failing grade on his/her research credits in any one term. This TAC meeting must take place within two weeks of receipt of the failing grade on the research credits. The mentor and TAC will suggest a course of action that the student must follow in correcting his/her research performance.

Student Salaries/Stipends

In the first year, students graduate research assistant salary is supported by the PMCB program. When students enter the CANB graduate program and select a faculty mentor, the faculty mentor becomes responsible for financial support of the student’s graduate research assistant salary. Once a student has passed their Qualifying Examination and advanced to PhD candidacy they are eligible for a stipend increase. Eligibility for this increase and continuing financial support of salary/stipend is dependent on timely and appropriate progress in course work and research, and is established in accordance with the Graduate Council recommendations.

Thesis Advisory Committee

Within six months upon declaration of a dissertation laboratory, students in consultation with their mentor should nominate a Preliminary Thesis Advisory Committee (PTAC). The following guidelines for the PTAC/TAC will be followed:

1) This committee should consist of the mentor and at least three other OHSU Graduate Faculty members. One member must be from outside of CANB. At least one member other than the advisor must be experienced in advising a Ph.D. thesis student (i.e. he/she must have mentored at least one student who has successfully completed their Ph.D.)

2) Members of this committee should be chosen based on their research area of technical expertise. The main purpose of this committee is to provide the student with guidance periodically during thesis research. Members of this committee may also subsequently serve on the Thesis Examination Committee. In this way, these faculty members will be familiar with research and will have the opportunity to communicate possible concerns they may have about the students work to pre-empt problems prior to Dissertation Defense.

3) The TAC membership must be approved by the CANB graduate education committee. A memo nominating the TAC membership should be sent to the chair of the Graduate Education Committee.

4) Students must meet with their TAC within 6 months after passing the Qualifying Examination and at least once a year after the initial meeting. TAC meetings will usually involve an oral presentation by the student encompassing thesis research goals and progress.

5) Students who have not established a TAC will not be allowed to take the qualifying examination.

6) During the initial meeting, one member of the committee will be selected to serve as chair of the committee. Following each committee meeting, the chair should prepare a brief memo evaluating the student’s progress which should be sent to the Graduate Education Committee Chair. A copy of the memo will be archived in the student’s file in the program office.

Ph.D Qualifying Examination

The purpose of the Qualifying examination in CANB is two-fold. First the examination will determine if the student has acquired sufficient knowledge and skills to pursue his or her Ph.D. thesis work. Second, the exam will provide the student with the opportunity to practice the preparation of a research proposal. Before taking the candidacy examination, the student must have completed the CANB course requirements. In the event that a course is not offered before the end of the second year, and the student is otherwise prepared to take the candidacy examination, the examination may proceed without completion of the course and with approval from the Graduate Education Committee. However, the required course must be taken prior to the thesis defense.

Format of the Examination:

The qualifying examination will consist of written research proposal prepared by the student within his or her general area of research, but not directly on the student’s research project, followed by an oral examination.

Note: CANB guidelines are in accordance with PMCB written guidelines with minor differences that are outlined and bolded.

Written examination: The qualifying examination will consist of written research proposal prepared by the student within his or her general area of research, but not directly on the student’s research project, followed by an oral examination. The written proposal should use the general format of the "Research Plan" section of an NIH NRSA Grant, which is detailed below. The research plan should have the substance and content, including original thinking, appropriate for such an application. That is, it shall be formatted in the following sections:

1. Format: Use an Arial, Helvetica, Palatino Linotype, or Georgia typeface, a black font color, and a font size of 11 points or larger. Type density must be no more than 15 characters per inch and no more than six lines per inch. At least one-half inch margins should be used.

2. Page 1: Specific Aims. State concisely the goals of the proposed research and summarize the expected outcome(s), including the impact that the results of the proposed research will exert on the research field(s) involved.
List succinctly the specific objectives of the research proposed, e.g., to test a stated hypothesis, create a novel design, solve a specific problem, challenge an existing paradigm, or address a critical barrier to progress in the field.

3. Pages 2-7: research proposal (six pages). Organize the Research Strategy in the specified order using the instructions provided below. Start each section with the appropriate section heading — Significance and Approach. Cite published experimental details in the Research Strategy section and provide the full reference in the Bibliography and References Cited section that is not included in the page limit.
(i) Significance (about ½ page)
a. Explain the importance of the problem or critical barrier to progress in the field that the proposed project addresses.
b. Explain how the proposed project will improve scientific knowledge, technical capability, and/or clinical practice in one or more broad fields.
c. Describe how the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field will be changed if the proposed aims are achieved.
(ii) Approach
d. Describe the overall strategy, methodology, and analyses to be used to accomplish the specific aims of the project. Include how the data will be collected, analyzed, and interpreted.
e. Discuss potential problems, alternative strategies, and benchmarks for success anticipated to achieve the aims.
f. Note that the page limitations may preclude a detailed presentation of all the methods used in the proposal. However, the candidate should be prepared to discuss them fully during the oral presentation, if asked.

Before embarking on preparation of a research proposal, the student will submit two abstracts of approximately 300 words each to the Graduate Student Coordinator (GSC) who will then distribute copies to the Graduate Education Committee. The abstracts should describe specific research problems which have been designed by the student and which may not include the student's thesis research project. The abstracts will be reviewed and the Graduate Education Committee will select one topic for development. If the Graduate Education Committee deems none of the proposals suitable, the student will present additional proposals. During the preparation of the proposal, the student is encouraged to seek constructive criticism by others, but is not permitted to ask members of the qualifying exam committee, their advisor or any other faculty member to review the qualifying exam proposal or a draft of the proposal, and then provide feedback about the scientific content of the proposal. As outlined in the PMCB academic guidelines, students may discuss topics and proposed experiments with all sources (fellow students, post-doctoral fellows, faculty, and visiting scientists), but none of them may be involved in any aspect of the student’s written proposal. Students may also seek general assistance in scientific writing and proofreading. However, it must be remembered that the written proposal is an examination, and must represent the student’s ideas and development of the research topic.

Oral examination: A period of 2.5 hours should be scheduled for the examination. The oral examination will probe the breadth of the student’s knowledge and also the depth of the student’s understanding of his/her research proposal. The student is expected to begin the oral examination by giving a short (20-30 minute) formal presentation summarizing the written proposal. Audio-visual aids may be used. Questions from the Qualifying Examination Committee should focus primarily on issues pertaining to the proposal; however, the student is responsible for all areas of cellular and molecular biology that have been covered during the first two years of graduate study. Therefore, students also should expect questions on general knowledge in addition to questions relating to the scientific background pertinent to their areas of specialization, as well as more general issues related to the proposed experiments. Student should be prepared to discuss the rationale for the proposed study, the strengths and limitations of the proposed experimental strategies and the potential pitfalls and alternative.

Following the student’s short presentation, the qualifying examination committee will question the student on all areas of cancer biology relating to the proposal. The chairman of the committee will establish the length and format of the questioning period, and will determine when the exam has concluded.

Defined Categories:
Pass (unconditional)
Pass (conditional)
Fail (Retry)
Fail (Final)

Students who pass the examination conditionally will be required to complete additional work (e.g. rewriting of the proposal, re-examination by the Examination Committee on basic knowledge). The additional work, and date by which it must be completed, will be specified in writing by the chair of the Examination Committee. Upon the recommendation of the Examination Committee, a student who fails the candidacy examination may be given the option of taking a second examination. The second Examination Committee will either pass the student or recommend that the student not be admitted to candidacy for the Ph.D. degree in the Program of Cancer Biology.

Timing of the Examination
Each student is expected to complete the qualifying examination by no later than the end of the summer term (this is not true for a re-examination) of their second year in the program, in compliance with the PMCB requirements.

On or before July 13 of their second year, students must submit two abstracts to the Graduate Student Coordinator, who will make copies and distribute them to the Graduate Education Committee members.

July 19: the GEC will select a Qualifying Examination Committee (QEC) responsible for conducting the student’s qualifying examination. A chair of the QEC will be designated. The student is notified of the names of the panel members.

July 26: The QEC notifies the student in writing of selection of the examination topic and the acceptance or of any weaknesses or specific suggests for improvement to their proposal.

August 6: students must have their examination dates scheduled. Examinations must be completed at least ten days before the beginning of the Fall term.

Students submit their final written proposal to the QEC and their thesis advisor at least one week prior to the Examination date. Students must submit a letter to the QEC from their thesis advisor describing the advisor’s role during preparation of the proposal (see “Role of Thesis Advisor and Other Faculty” in the PMCB guidelines).

A student who is asked to repeat the candidacy examination will be expected to do so within 2 months of the initial examination.

Examination committee
The Graduate Education Committee will appoint a 5-member examination committee for each student based on the topic to be presented by the student and, as they see fit, the nominations of the student involved. Names of the examiners nominated by the student should be submitted to the Graduate Education Committee together with the abstracts of his or her proposals. The student's thesis advisor may not serve on the examining committee, but may attend the examination as an observer. The Graduate Education Committee is charged with maintaining uniformity for the candidacy examinations. To this end, each examination committee will have at least one member of the Curriculum or Graduate Education Committee.

Preparation, Submission and Oral Defense of Thesis

Preparation and Submission of Thesis. All instructions and guidelines adopted by the Graduate Council By-Laws shall be carefully followed. The thesis should represent the equivalent of at least two publications in significant, peer-reviewed journals; fulfillment of this requirement will be determined by the TAC.

Oral Defense of Thesis. The composition of the Oral Thesis Examining Committee should be suggested by the student and mentor and must be approved by the CANB Graduate Education Committee. After these approvals are obtained, final approval of the composition of this committee must be obtained from the Associate Dean for Graduate Studies.

CANB requires that the Thesis Advisory Committee must meet to review and approve the proposed thesis research before a thesis defense can be scheduled. The chair of the Thesis Advisory Committee should send a memo to the Program Coordinator giving approval of the thesis project and approval for scheduling the oral thesis defense.

Time Limit for Completing Degree Requirements. It is the School of Medicine Graduate Council policy that students must complete all requirements for Ph.D. within 7 years of matriculation. Students that do not complete degree requirements within this deadline may be dismissed from the graduate program. Students, mentors and the TAC should consider this deadline when evaluating thesis research goals and progress.

Exceptions. No exceptions from the policies and procedures described in these guidelines can be made without approval by the CANB faculty. In matters related to coursework, exceptions must be approved by the CANB graduate education committee before review and consideration for approval by the CANB faculty.

Ethical and Professional Behavior

CANB graduate students are expected to maintain high ethical standards. Graduate students should demonstrate honesty in all aspects of research activities. Students should learn about and avoid sources of error in scientific research. It is essential that students do not misrepresent scientific findings or misappropriate credit. All graduate students are required to take a course concerning ethics and science. Students should show cooperation, responsibility and respect in working with other students and faculty. Students should be considerate of the cultural and individual diversity of their colleagues. CANB graduate students will be held to the standards of the OHSU workplace and be in compliance with research integrity through courses on the Big Brain, in addition to CON650, Practice & Ethics of Science.

Non-compliance

Non-compliance with any of the CANB requirements can and will result in the revocation of certain program privileges, academic probation and possible dismissal from the graduate program.

MISCELLANEOUS

Grievances The procedure for handling grievances is outlined in the OHSU Graduate Studies Handbook.

Extracurricular Employment or Enrollment in Degree Granting Programs The Program in Cancer Biology considers employment as a graduate student in the Ph.D. program to represent full time employment. Students are strongly discouraged from seeking outside employment or concurrent enrollment in other degree granting programs. Any student wishing to pursue outside employment or enrollment in a degree granting program must submit a written request to the TAC, mentor, the Director of Graduate Education and the Graduate Education Committee. The student must receive written authorization from the above entities prior to accepting employment or enrollment in a degree granting program. Failure to do so may result in academic probation. If the student is unsure if his/her intended activity falls into this category, he/she is advised to discuss the matter with his/her mentor.

Contacts

Director of the Cancer Biology Graduate Program: Matt Thayer

Directors of Graduate Education: Phil Stork (Qual Exam), Missy Wong (TAC)

Directors of the Curriculum Committee: Rosie Sears, Maureen Hoatlin

Graduate Student Coordinator: Jeni Wroblewski