Microbiology Graduate Program

Subject abbreviation: MCBL College of Natural and Agricultural Sciences

Emma L. Aronson, Ph.D. Program Director Graduate Program, 3411 Boyce Hall

• (800) 735-0717 or (951) 827-5688

microbiology.ucr.edu

Professors

James Adaskaveg, Ph.D. (Microbiology and

Plant Pathology) Emma Aronson, Ph.D. (Microbiology and

Plant Pathology) Boris Baer, Ph.D. (Entomology) Katherine A. Borkovich, Ph.D. (Plant

Pathology and Microbiology) James Borneman, Ph.D. (Microbiology and

Plant Pathology) Adler Dillman, Ph.D. (Microbioloty & Plant Pathology) Martin Garcia-Castro, Ph.D. (Biomedical Sciences) Alec Gerry, Ph.D. (Entomology) Sarjeet S. Gill, Ph.D. (Molecular, Cell and

Systems Biology) Ron Hai, Ph.D (Microbiology and Plant Pathology) Allison Hansen, Ph.D. (Entomology) Hailing Jin, Ph.D. (Microbiology and Plant

Pathology) Howard S. Judelson, Ph.D. (Microbiology and

Plant Pathology) Isgouhi Kaloshian, Ph.D. (Nematology) Lidia Kos, Ph.D. (Biomedical Sciences) Karine Le Roch, Ph.D. (Molecular, Cell and

Systems Biology) Huinan Liu, Ph.D. (Biomedical Engineering) Manuela Martins-Green, Ph.D. (Molecular,

Cell and Systems Biology) Declan McCole, Ph.D. (Biomedical Sciences) Quinn McFrederick, Ph.D. (Entomology) Ashok Mulchandani, Ph.D. (Chemical and

Environmental Engineering) Meera Nair, Ph.D. (School of Medicine) James Ng, Ph.D. (Microbiology and Plant

Pathology Leonard Nunney, Ph.D. (Evolution, Ecology

and Organismal Biology) Jessica Purcell, Ph.D. (Entomology) Caroline Roper, Ph.D.

(Microbiology and Plant Pathology) Joel L. Sachs, Ph.D. (Evolution, Ecology and

Organismal Biology) Jason E. Stajich, Ph.D., (Microbiology and

Plant Pathology) Georgios Vidalakis, Ph.D. (Microbiology and

Plant Pathology) Ian Wheeldon, Ph.D. (Chemical and

Environmental Engineering) Emma Wilson, Ph.D. (School of Medicine) Professors Emeriti

Michael Allen, Ph.D. (Microbiology and Plant

Pathology) Michael D. Coffey, Ph.D. (Microbiology and

Plant Pathology) Donald A. Cooksey, Ph.D. (Microbiology and

Plant Pathology) David E. Crowley, Ph.D. (Environmental

Sciences) Brian A. Federici, Ph.D. (Entomology) Thomas Miller, Ph.D. (Entomology) Edward Platzer, Ph.D. (Evolution, Ecology and

Organismal Biology and Nematology) A.L.N. Rao, Ph.D. (Microbiology and Plant

Pathology) Philip Roberts, Ph.D. (Nematology) Neal L. Schiller, Ph.D. (School of Medicine) Michael Stanghellini, Ph.D. (Microbiology

and Plant Pathology) Richard Stouthamer, Ph.D. (Entomology) Marylynn V. Yates, Ph.D. (Environmental

Sciences)

Associate Professors

Gregor Blaha, Ph.D. (Biochemistry) Patrick Degnan, Ph.D. (Microbiology and Plant Pathology) Emma Gachomo, Ph.D. (Microbiology and Plant Pathology) Joseph Genereux, Ph.D. (Chemistry) Juan Pablo Giraldo Gomez, Ph.D. (Botany

and Plant Sciences) Sydney I. Glassman, Ph.D. (Microbiology

and Plant Pathology) Ansel Hsiao, Ph.D. (Microbiology and Plant

Pathology) Robert Jinkerson, Ph.D. (Chemical and

Environmental Engineering) Thomas Kuhlman, Ph.D. (Physics and

Astronomy) Patricia Manosalva, Ph.D. (Microbiology and

Plant Pathology) Seán O’Leary, Ph.D. (Biochemistry) Yujie Men, Ph.D. (Chemical and Environmental

Engineering) Alexander Putman, Ph.D. (Microbiology and Plant Pathology) Samantha Ying, Ph.D. (Environmental Sciences) Assistant Professors

Bryan Brown, Ph.D. (Molecular Cell and

Systems Biology) Elizabeth Brauer, Ph.D. (Microbiology and

Plant Pathology) Sonali Chaturvedi, Ph.D. (Microbiology and

Plant Pathology) Tibo Duran, Ph.D. (Microbiology and

Plant Pathology) Ahmed El-Moghazy, Ph.D. (Microbiology and

Plant Pathology) Fatemeh Khodadadi, Ph.D. (Microbiology and

Plant Pathology) Juliet Morrison, Ph.D. (Microbiology and

Plant Pathology) Olakunle Olawole, Ph.D. (Microbiology and

Plant Pathology) Jason A. Rothman, Ph.D. (Microbiology and

Plant Pathology) Tingting Xiang, Ph.D. (Bioengineering) Jiue-in Yang, Ph.D. (Nematology)

The Graduate Program in Microbiology is an interdisciplinary program with participating faculty from the departments of Evolution, Ecology and Organismal Biology, Molecular, Cell, and Systems Biology, Chemical and Environmental Engineering, Chemistry, Entomology, Environmental Sciences, Microbiology and Plant Pathology, and the Division of Biomedical Sciences. Faculty research interests are concentrated in several disciplines in the areas of basic and applied microbiology. These disciplines include the following:

• Microbial Pathogenesis

• Environmental Microbiology and Ecology

• Microbial Evolution, Genomics, and

Metagenomics

• Molecular and Cellular Microbiology

Admission For admission into the graduate program in Microbiology, a student must have a B.A. or B.S. degree from an accredited institution and an academic record that satisfies the minimum admission standards established by the UCR Graduate Division.

Although no specific undergraduate degree specialization is required, applicants should have an adequate background in the physical and biological sciences, including the following or equivalent courses:

CHEM 001A, CHEM 001B, CHEM 001C (General Chemistry), CHEM 008A and 08LA or CHEM 08HA and CHEM 8HLA, CHEM 008B and CHEM 08LB or CHEM 08HB and CHEM 8HLB, CHEM 008C and CHEM 08LC or CHEM 08HC and CHEM 8HLC (Organic Chemistry), BCH 110A or BCH 110HA, BCH 110B or BCH 110HB (Biochemistry), MATH 007A or MATH 009A, MATH 007B or MATH 009B (Calculus), STAT 010 or STAT 120A (Statistics), BIOL 102 (Genetics), BIOL 121A/MCBL 121A, BIOL 121L/MCBL 121L (Microbiology), BIOL 107A or BCH 110C (Molecular Biology)

This list is intended to represent the minimum background required for students wishing to pursue a graduate degree in Microbiology. Additional course work and laboratory experience in microbiology, biochemistry or genetics is highly desirable. However, upon the recommendation of the graduate advisory committee, occasionally a student may be admitted into the graduate program with one or more course work deficiencies; such students must satisfy these course work deficiencies usually within the first and no later than within the second year of graduate study.

Curriculum The program is designed to prepare students for teaching and research careers in colleges and universities, as well as basic and applied research in private, industrial and government laboratories. To attain this goal, a three-tiered set of coursework has been designed: See Master’s Degree and Course Work section under Doctoral Degree.

Ph.D. and M.S. students must attend one seminar per week each quarter, when offered, in programs collaborating with Microbiology. The seminar course must be chosen from the following list: MCBL 250, PLPA 250. Other seminar courses may be approved by the graduate advisor. Students are also required to present one seminar during their tenure in the program. The seminar can be either on the student’s thesis research or related topics and can be presented in any of several program student seminar series.

M.S. students must fulfill the requirements for Plan I (Thesis) or Plan II (Comprehensive Examination) of the Graduate Council. All students must complete at least 11 units of 200-level coursework, which can include the microbiology core courses and/or other microbiology courses chosen in consultation with the student advisory committee. Non-microbiology courses can also be used for this 200-level coursework requirement with approval from the student’s advisory committee and the graduate advisor. Plan I requires 36 units, of which 24 must be in graduate level courses. Of the 24, a maximum of 12 may be in graduate research for the thesis. The student must also submit and defend an acceptable research thesis. For the Plan II Masters, the Comprehensive Examination option, students must complete 36 units total, of which at least 24 must be in 200-level coursework, which should include the microbiology core courses and/or other microbiology courses chosen in consultation with the student advisory committee. Of the 24 200- level units, a maximum of 6 units may be in graduate research, but no research units are required for this option. The student must also pass a comprehensive exam created from relevant material from at least 3 of the 200-level microbiology courses that the student has already completed, usually the 3 microbiology core courses.

Normative Time to Degree 6 quarters

Ph.D. students must meet all requirements of the Graduate Council. Students satisfactorily complete the core class requirements and a program of courses approved by the student advisory committee. The Ph.D. degree is awarded upon passing the preliminary and qualifying examinations and demonstrating an ability to carry out original research by preparing and submitting an acceptable dissertation.

Students enrolled in the Ph.D. program are expected to become actively engaged in a research project no later than the end of their first year, and research progress is monitored by the student’s advisory committee until the student advances to candidacy and a dissertation committee is appointed. The program stresses the importance of innovative and independent laboratory research as the major component of the student’s education.

Course Work The program is designed to prepare students for teaching and research careers in colleges and universities, as well as basic and applied research in private, industrial and government laboratories. To attain this goal, a three- tiered curriculum has been designed whereby students are expected to complete the following:

• 1. A core sequence of classes in microbiolo

gy: MCBL 202 (Microbial Pathogenesis and Physiology), BIOL 221/MCBL 221 (Microbial Genetics), and MCBL 211 (Microbial Ecology)

• 2. A selection of at least one elective gradu

ate (200-level) course in microbiology or other relevant field(s) chosen in consultation with the student’s major professor and the advisory committee in order to develop depth in particular areas of specialization.

• 3. Research training in specific areas of

microbiology (at least 6 units of MCBL 297 or MCBL 299).

Students fulfill their professional development training by enrolling in PLPA 265, a 3 unit course that covers a range of topics including careers in microbiology, CV preparation, skills on giving scientific presentations, strategies for success in the candidacy examination and graduate school, data acquisition, management and ownership, policy and regulation, and intellectual property.

Preliminary Examination The preliminary examination, consisting of a written, comprehensive examination is based on general microbiology and required material in the student’s area of specialization. If a student fails this examination, the advisory committee recommends either additional course work in specific areas of weakness, transfer to a terminal M.S. degree program, or withdrawal from the program. The preliminary examination may only be repeated once and must be passed for the student to continue in the Ph.D. program. The preliminary examination is normally taken in the spring quarter of the second year.

Oral Qualifying Examination After completion of the preliminary examination, the qualifying committee is established, and the oral qualifying examination is normally taken no later than the eighth quarter (year three) of academic work, not counting summer quarters.

A qualifying committee is nominated by the graduate advisory committee and submitted to the graduate dean for approval. Suggestions of potential members of the qualifying committee may be submitted to the advisory committee by the student and the student’s major professor. The qualifying committee is composed of five faculty members: three with expertise in the area of specialization in microbiology, one representing a different area from microbiology, and one outside member. The student’s major professor may not serve on the qualifying committee. Prior to the oral qualifying examination, the student submits a written dissertation research proposal to the members of the qualifying committee. The oral examination covers the student’s area of specialization and research field and must be passed for the student to continue in the program. Upon successful completion of the qualifying examination, the student is advanced to candidacy. The qualifying examination may be repeated only once.

The Oral Qualifying Exam can be taken in one of the following modes: In-Person or Hybrid. The student and their advisor will discuss which mode best suits the circumstances, with the advisor making the determination. If the student or one of the other committee members protests the decision, the Program Director will make the final determination. Students taking the exam In-Person are expected to present on campus with all committee members physically present. If Hybrid is chosen, the student is expected to present the exam on campus in a video enabled room that supports some members physically present and others remotely.

Dissertation and Final Oral Examination The dissertation committee is nominated by the graduate advisor for approval by the graduate dean (upon successful completion of the qualifying examination) and is composed of the student’s major professor and at least two other faculty members suggested by the student and the student’s major professor. Before approval of the dissertation, the student is expected to present orally the dissertation research at an announced defense seminar.

The Final Defense can be taken in one of the following modes: In-Person or Hybrid. The student and their advisor will discuss which mode best suits the circumstances with the advisor making the determination. If the student or one of the other committee members protests the decision, the Program Director will make the final determination. Students taking the exam In-Person are expected to present on campus with all committee members physically present. If Hybrid is chosen, the student is expected to present the exam on campus in a video enabled room that supports some members physically present and others remotely.

Teaching Requirement Two quarters of teaching experience is required, which may be satisfied by serving as a teaching assistant in any of the microbiology courses listed.

Foreign Language Requirement None

Normative Time to Degree 15 quarters