I. INTRODUCTION

Aims and Objectives of the Program:

A graduate program in Experimental Pathology leading to the Ph.D. degree is offered within the School of Biological Sciences and the School of Medicine. Therefore, the degree title is “Doctor of Philosophy in the Biological Sciences with a Concentration in Experimental Pathology”. The program recruits students through the combined graduate training program in Molecular Biology, Genetics, and Biochemistry (MBGB). The MBGB program administers the first year curriculum. The application for this program can be found online. For questions about the application process, refer to the MBGB page under Prospective Students. Experimental Pathology is the study of disease, most notably human diseases and disease processes. While it is true that many programs at the University of California in Irvine have elements of their training program that pertain to human disease and disease processes, no single program makes the study of human disease the central tenet of its degree program.

Experimental pathology is an increasingly critical area of scientific research. While the National Institutes of Health has always maintained the importance of human health in its granting process, new technologies have made the study of human diseases ever more central to scientific discovery. Indeed, newer experimental approaches (e.g., transgenic mouse technologies) and knowledge bases such as the human, mouse and rat genomes, make studies on the molecular basis of human disease an exploding area of research interest and importance.

The graduate program in Experimental Pathology will feed new scientists into this ever-expanding area of human disease research. The aim of the program is to provide graduate students with the training necessary to become lead scientists studying the molecular bases of human diseases. Providing students with extensive training in molecular and cell biology, genetics, and biochemistry will prepare trainees for further concentration in Experimental Pathology. Therefore, this program is a member of the combined graduate training program in MBGB. In the first year, students are required to take the MBGB curriculum, existing of courses in proteins, nucleic acids, cell biology, and genetics. Students interested in Experimental Pathology will likely join the Experimental Pathology track within MBGB during the first year. With this strong foundation, students in the program will join the Pathology & Laboratory Medicine department in the spring or summer quarter of their first year. At this time, extensive study in human disease related research will begin in the laboratories of program faculty. Students will then have the opportunity to pursue further specialization of their training in areas including, but not limited to, neuropathology (mechanisms of neurologic disease), oncogenesis (mechanisms of human cancer), immunopathology (immunologic mechanisms of disease), molecular pathology (genetic basis of human disease), and infectious disease (molecular mechanisms of disease caused by viral, bacterial, fungal, and parasitic agents). The subsequent course work of students includes at least one didactic course per academic year concentrated in their area of research interest. These courses are outlined in greater detail below.

The objectives of this program are:

1. To provide students with the molecular and genetic knowledge necessary to understand the molecular bases of human diseases and to genetically manipulate organisms and/or cells to study these mechanisms.
2. To provide graduate students with sufficient understanding of known human disease processes to enable them to ask pertinent experimental questions to answer new and novel questions related to human disease and disease processes.
3. To provide the scientists of tomorrow, both academic and industry, with the knowledge necessary to address the important genetic and molecular causes of the most important diseases afflicting humans.

These objectives are unique among the programs within MBGB and within the University of California, Irvine.

II. THE PROGRAM.

1. Undergraduate Preparation for Admission.

Admission to the program is through the combined program in Molecular Biology, Genetics, and Biochemistry. Therefore, students are admitted by and into the MBGB program, rather than directly into this degree program concentration. As defined by MBGB:

Applicants must have completed by the time of matriculation a baccalaureate degree. The GRE General Test is required.

Applicants should have basic training in biology, physics, and chemistry. The ideal preparation includes introductory as well as some advanced courses in biology (cell biology, developmental biology, genetics, molecular biology), biochemistry, organic chemistry, physical chemistry, calculus, statistics, and physics. Demonstrated experience in laboratory research is very strongly advised.

Admission decisions are made on the basis of an overall evaluation of an applicant's preparation and potential to complete a rigorous program of advanced study in biology. Particular attention is paid to the applicant's academic experience, motivation and potential for research. The latter should be documented by reference letters from individuals in positions to judge research potential. Evaluations are based on the applicant's academic record. Graduate Record Examination scores, prior laboratory research experience, letters of recommendation, a personal statement, and a personal interview.

2. Foreign Language Requirement.

The MBGB program has no foreign language requirement nor does the Ph.D. Program in Biological Sciences.

3. Program of Study.

1. Specific Fields of Emphasis-Biological Sciences with a concentration in Experimental Pathology.
2. Plan: Doctor of Philosophy degree.
3. Unit Requirements: All students must take at least one didactic course per academic year after year 1. Students must take additional units to be enrolled on a full-time status throughout their graduate training.
4. Required and recommended courses: Students will be enrolled in the combined graduate program in Molecular Biology, Genetics, and Biochemistry during the first year of the program.

Core requirements-year 1: During the first year, students are required to take four core courses that cover fundamental concepts in molecular and cell biology, genetics and biochemistry, as follows:

Fall Quarter: Protein Structure and Function (Mol Bio 204)

Winter Quarter: Structure and Biosynthesis of Nucleic Acids (Mol Bio 203)
    AND: Cell Biology (Dev Bio 231B)
        OR Molecular, Cellular, & Developmental Neurobiology (Dev Bio 231D).
    AND: T.A. Training Workshop (Dev Bio 202B)
        OR: Cell Biology (Dev Bio 231B)
        OR: Molecular, Cellular & Developmental Neurobiology (Dev Bio 231D)
        OR: System Cell Biology (Dev Bio 232)

Spring Quarter: Regulation of Gene Expression (Mol Bio 206)
    AND: Responsible Conduct of Research (MMG 250)
        OR: Molecular Genetics (Mol Bio 207)
        OR: Developmental Genetics (Dev Bio 210)

Graduate students may take elective courses relevant to their area of specialization. Certain tracks may have specific recommendations for elective courses.

Students are also required to do two laboratory rotations in two different laboratories during the first year. The requirement for two different laboratory rotations may be waived for students in the Medical Scientist Training Program. Students are encouraged to do at least three rotations in laboratories that provide exposure to diverse research topics and a wide variety of experimental approaches. Such varied research opportunities provide a rewarding academic experience. Students select a thesis mentor and laboratory at the completion of the Spring Quarter in the first year and begin work to complete a Ph.D. thesis based upon their own original laboratory research.

In addition, students who choose to join the program leading to a Ph.D. in Biological Sciences with a concentration in Experimental Pathology are required to take the following course in Experimental Pathology: Path 225: Molecular Mechanisms of Human Disease. This course is offered every Spring Quarter of odd years. This course may be taken at any time during the course of the student’s training but should be completed in the first two or three years of the program.

Core-elective courses: From the following list, and any other core-elective courses suggested by participating faculty and approved by the graduate advisor, each student will take at least one core-elective in the first year and complete a total of two core-electives by the end of the second year. Students are required to take a minimum of one didactic core-elective course for five years of graduate training. In the case of completion of all graduate requirements prior to five years, no additional coursework will be required. After five years, no additional didactic course work is required. Path 230-236 are courses derived from the medical school pathology course.

Biochem 212: Signal Transduction and Growth Control
Dev Bio 231B: Molecular, Cellular & Developmental Neurobiology (if not taken year 1)
Mol Bio 217A: Cancer Biology I
Mol Bio 217B: Cancer Biology II
Mol Bio 218: Clinical Cancer for Basic Scientists
M&MG 215: Molecular Immunology
M&MG 222: Molecular Pathogenesis of Viral Infections
Path 221/M&MG 221: Immunopathogenic Mechanisms of Disease
Path 225/M&MG 225: Molecular Mechanisms of Human Disease
Path 230: Principles of Experimental Pathology
Path 231: Pathology of Cardiovascular Diseases
Path 232: Pathology of Pulmonary Diseases
Path 233: Pathology of Renal Diseases
Path 234: Pathology of Gastrointestinal Diseases
Path 235: Pathology of Genitourinary Diseases
Path 236: Graduate Neuropathology
Path 271AB: Molecular Physiology & Disease

Throughout the training program, students who are doing their thesis research under the Experimental Pathology concentration are required to enroll in Path 200 for research credit, under their research advisor, and Path 203, a literature review course. Students are also required to participate in the Pathology & Laboratory Medicine department research seminar series, Path 204, which has research in progress presentations from faculty, postdoctoral fellows, and graduate students. This seminar series currently meets twice monthly. As the graduate program grows, the seminar series will become more frequent.

Teaching Component: Per the MBGB Program-all students in the MBGB program are required to teach during their first and second years of study. Students enroll in Mol Bio 399 (University Teaching) and teach in either undergraduate lecture or undergraduate laboratory courses within either the Departments of Developmental and Cell Biology or Molecular Biology and Biochemistry. In general, students are teaching assistants in a total of three courses. Previously, teaching assistant activity has been entirely in year two of the students’ graduate program. More recently, students begin by teaching in the Spring Quarter of their first year and, additionally, in the Fall and Winter Quarters of their second year. This is arranged by MBGB in coordination with the respective departments. All students in Experimental Pathology are subject to the same teaching requirements as other MBGB students.

4. Preliminary Examination.

At the end of the first year, students must demonstrate proficiency by passing a preliminary qualifying exam. The purpose of this exam is to verify that you have completed the goals of the MBGB first-year program. These are:

1. to establish a foundation of knowledge in the relevant disciplines
2. to acquire an understanding of research methods including the responsible conduct of research
3. to sharpen your critical thinking abilities so that you are ready to begin thesis research in which you will take major responsibility for the design, conduct and publication of Ph.D. - level research projects

The possible outcomes of the exam are:

1. Pass.
2. Fail with an opportunity to retake the exam within one month (same committee). Possible outcomes are 1 and 3 on this list.
3. Fail.

The committee decision is referred to the Program Director for action. Students who pass the exam will normally move immediately to departmental Ph.D. Programs.

5. Thesis and Dissertation.

During the second year of the program, students will begin thesis research in the laboratory of faculty within Experimental Pathology. Once sufficient research progress has occurred, usually within the second year in Experimental Pathology (third year in the graduate program), the student will Advance to Candidacy. The student will prepare a twenty-five page (double-spaced) written proposal for dissertation research and orally defend this proposal before the Advancement to Candidacy Committee. This committee will consist of five faculty members, one of whom must not hold an appointment in the Department of Pathology & Laboratory Medicine and at least three, including the thesis mentor, must hold appointments in the Department of Pathology & Laboratory Medicine. After successful Advancement to Candidacy, a Doctoral Committee will be formed, selected from the Advancement to Candidacy committee. The composition of this committee will be at least three members, a majority of which must be from the Department of Pathology & Laboratory Medicine. All five members of the Advancement to Candidacy committee can be selected for the dissertation committee. The purpose of the committee is to guide the student’s progress towards completion of the dissertation. When the student’s thesis advisor and the remaining members of the Doctoral Committee determine that a sufficient body of original research has been completed, the student will prepare the thesis for a public defense before the Doctoral Committee.

6. Final Examination.

The student’s oral defense of the dissertation before the doctoral committee constitutes the final examination.

7. Sample Program.

Due to the number of electives and the diverse nature of Experimental Pathology training, no set program will exist. For example, some students may choose a heavy emphasis on neuropathology, with elective courses in neuroanatomy, neurological development, and neuropathology. Other students may specialize in the pathogenesis of cancer with a heavy emphasis on genetics, cell signaling, and cell and cancer biology. Nevertheless, a general program overview can be offered as demonstrated below.

Year 1 (As determined by the MBGB Program):

Fall Quarter: Protein Structure and Function (Mol Bio 204)

Winter Quarter: Structure and Biosynthesis of Nucleic Acids (Mol Bio 203)
    AND: Cell Biology (Dev Bio 231B)
        OR Molecular, Cellular, & Developmental Neurobiology (Dev Bio 231D).
    AND: T.A. Training Workshop (Dev Bio 202B)
        OR: Cell Biology (Dev Bio 231B)
        OR: Molecular, Cellular & Developmental Neurobiology (Dev Bio 231D)
        OR: System Cell Biology (Dev Bio 232)

Spring Quarter: Regulation of Gene Expression (Mol Bio 206)
    AND: Responsible Conduct of Research (MMG 250)
        OR: Molecular Genetics (Mol Bio 207)
        OR: Developmental Genetics (Dev Bio 210)

Summer Quarter: Qualifying examination.

Year 2:
Fall Quarter: University Teaching (Mol Bio 399); Research in Experimental Pathology (Path 200A); Advanced Studies in Experimental Pathology (Path 203A); Seminars in Experimental Pathology (Path 204).
Winter Quarter: University Teaching (Mol Bio 399); Path 200B, Path 203B, Path 204.
Spring Quarter (odd years): Path 200C, Path 203C, Path 204, and Molecular Mechanisms of Human Disease (Path 225/MMG 225).
Spring Quarter (even years): Path 200C, Path 203C, Path 204.

Year 3:
Fall Quarter: Path 200A, Path 203A, Path 204.
Winter Quarter: Path 200B, Path 203B, Path 204.
Spring Quarter (odd years): Path 200C, Path 203C, Path 204, and Molecular Mechanisms of Human Disease (Path 225/MMG 225).
Spring Quarter (even years): Path 200C, Path 203C, Path 204.
Fall, Winter, or Spring Quarter: One elective course.
Summer Quarter: Advancement to Candidacy.

Year 4:
Fall Quarter: Path 200A, Path 203A, Path 204.
Winter Quarter: Path 200B, Path 203B, Path 204.
Spring Quarter: Path 200C, Path 203C, Path 204.
Fall, Winter, or Spring Quarter: One elective course.

Year 5:
Fall Quarter: Path 200A, Path 203A, Path 204.
Winter Quarter: Path 200B, Path 203B, Path 204.
Spring Quarter: Path 200C, Path 203C, Path 204.
Fall or Winter: One elective course.
Spring Quarter: Dissertation Defense.

8. Normative Time from Matriculation to Degree.

The normative time from matriculation to completion of the Doctoral degree is five years (before the beginning of the 16th academic quarter*). The first year is in the MBGB program and the remaining four years in the Department of Pathology & Laboratory Medicine doing thesis work in the laboratory of Experiment Pathology faculty. Students may also perform thesis work in the laboratories of affiliate faculty, currently including faculty from the Departments of Molecular Biology and Biochemistry, Physiology and Biophysics, Developmental & Cell Biology, and Biological Chemistry. As indicated above, the normative time from matriculation to advancement to candidacy (i.e., pre-candidacy) is three years (before the beginning of the 10th academic quarter) and the normative time to the Ph.D. in candidacy, two years. All students are required to defend their theses by the end of their seventh year (before the beginning of the 22nd academic quarter).

*The 10th academic quarter would be the beginning of the fourth year, so normative time to advancement would be during the third year of graduate school, including the summer of the third year. Similarly the 16th and 22nd academic quarters would be before the beginning of the 6th and 8th years.

III. COURSES

1. Courses Offered in Pathology & Laboratory Medicine.

Path 200A, 200B, 200C: Research in Experimental Pathology - Taught by Pathology & Laboratory Medicine Faculty.

Path 203A, 203B, 203C: Advanced Studies in Experimental Pathology - Taught by Pathology & Laboratory Medicine Faculty.

Path 204: Experimental Pathology Research Seminar - Attendance and participation in the departmental research seminar series.

Path 221: Immunopathogenic Mechanisms of Disease. Taught by A.J. Ouellette, Ph.D. Joint listed as MMG 221. 3 units, Winter quarter in even numbered years.

Path 225: Molecular Mechanisms of Human Disease. Taught by W.E. Robinson, Jr., M.D, Ph.D. Joint listed as MMG 225. 3 units, Spring quarter in odd numbered years.

Path 230D: Principles of Experimental Pathology - Taught by the faculty of the Department of Pathology & Laboratory Medicine. 4 units, Fall quarter.

Path 231A: Pathology of Cardiovascular Diseases - Taught by the faculty of the Department of Pathology & Laboratory Medicine. 2 units, Fall quarter.

Path 232A: Pathology of Pulmonary Diseases - Taught by the faculty of the Department of Pathology & Laboratory Medicine. 1.5 units, Fall quarter.

Path 233A: Pathology of Renal Diseases - Taught by the faculty of the Department of Pathology & Laboratory Medicine. 1 unit, Fall quarter.

Path 234A, 234B: Pathology of Gastrointestinal Diseases - Taught by the faculty of the Department of Pathology & Laboratory Medicine. 2 units, Fall through Winter quarters.

Path 235A, 235B: Pathology of Genitourinary Tract Diseases - Taught by the faculty of the Department of Pathology & Laboratory Medicine. 2 units, Fall through Winter quarters.

Path 236B: Graduate Neuropathology - Taught by the faculty of the Department of Pathology & Laboratory Medicine. 1.5 units, Winter quarter.

Path 271AB: Molecular Physiology & Disease - Taught by the faculty of the Department of Physiology and Biophysics. Joint listed as Pharm 271AB and Physio 271AB. 4 units, 271A is Fall of even numbered years and 271B is Fall of odd numbered years.

NB: Path 230-236 are sections of the second year medical school pathology course, 508ABC. Graduate students may take portions of the course for credit as indicated by these courses. The students will, in addition to attending the class sections, work in small groups with a faculty member and will discuss experimental approaches to the medical problems taught in the course. Each student will submit written hypotheses, aims, and experimental approaches relevant to a pathologic problem of current import. Student evaluations will be made based on attendance, students’ participation in the discussions and the quality of their written experimental plans.

2. Supporting Courses.

BC 212: Signal Transduction and Growth Control
DB 210: Developmental Genetics
DB 231B: Cell Biology
DB 231D: Cellular, Molecular, & Developmental Neurobiology
MBB 204: Structure and Functions of Proteins
MBB 203: Structure and Biosynthesis of Nucleic Acids
MBB 206: Regulation of Gene Expression
MBB 207: Molecular Genetics
MBB 399: University Teaching
MMG 215: Molecular Immunology
MMG 221: Immunopathogenic Mechanisms of Disease
MMG 222-: Molecular Pathogenesis of Viral Infections