MICROBIOLOGY

Subject abbreviation: MCBL College of Natural and Agricultural Sciences

Jason Stajich, Ph.D. Program Director Graduate Program, 1140 Batchelor Hall

• (800) 735-0717 or (951) 827-5688

microbiology.ucr.edu

James Borneman, Ph.D. Chair, Microbiology Undergraduate Steering Committee Program Office, 1223 Pierce Hall

• (951) 827-7294

cnasstudent.ucr.edu/majors

Professors James Adaskaveg, Ph.D. (Microbiology and Plant Pathology) Katherine A. Borkovich, Ph.D. (Plant Pathology and Microbiology) James Borneman, Ph.D. (Microbiology and Plant Pathology) Michael D. Coffey, Ph.D. (Microbiology and Plant Pathology) Shou-Wei Ding, Ph.D. (Microbiology and Plant Pathology) Alec Gerry, Ph.D. (Entomology) Sarjeet S. Gill, Ph.D. (Molecular, Cell and Systems Biology) Hailing Jin, Ph.D. (Microbiology and Plant Pathology) Howard S. Judelson, Ph.D. (Microbiology and Plant Pathology) Isgouhi Kaloshian, Ph.D. (Nematology) Karine Le Roch, Ph.D. (Molecular, Cell and Systems Biology) Wenbo Ma, Ph.D. (Microbiology and Plant Pathology) Ashok Mulchandani, Ph.D. (Chemical and Environmental Engineering) Leonard Nunney, Ph.D. (Evolution, Ecology and Organismal Biology) Jessica Purcell, Ph.D. (Entomology) A.L.N. Rao, Ph.D. (Microbiology and Plant Pathology) Philip Roberts, Ph.D. (Nematology) Joel L. Sachs, Ph.D. (Evolution, Ecology and Organismal Biology) Jason E. Stajich, Ph.D., (Microbiology and Plant Pathology) Richard Stouthamer, Ph.D. (Entomology) Georgios Vidalakis, Ph.D. (Microbiology and Plant Pathology) Marylynn V. Yates, Ph.D. (Environmental Sciences)

Professors Emeriti Michael Allen, 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) Dennis D. Focht, Ph.D. (Plant Pathology) Thomas Miller, Ph.D. (Entomology) Edward Platzer, Ph.D. (Evolution, Ecology and Organismal Biology and Nematology) Neal L. Schiller, Ph.D. (School of Medicine) Michael Stanghellini, Ph.D. (Microbiology and Plant Pathology)

Associate Professors Huinan Liu, Ph.D. (Biomedical Engineering) James Ng, Ph.D. (Microbiology and Plant Pathology) Caroline Roper, Ph.D. (Microbiology and Plant Pathology) Ian Wheeldon, Ph.D. (Chemical and Environmental Engineering) Emma Wilson, Ph.D. (School of Medicine)

Assistant Professors Emma Aronson, Ph.D. (Microbiology and Plant Pathology) Holly Bik, Ph.D. (Nematology) Gregor Blaha, Ph.D. (Biochemistry) Patrick Degnan, Ph.D. (Microbiology and Plant Pathology) Adler Dillman, Ph.D. (Nematology) Emma Gachomo, Ph.D. (Microbiology and Plant Pathology) Xin Ge, Ph.D. (Chemical and Environmental Sciences) Joseph Genereux, Ph.D. (Chemistry) Juan Pablo Giraldo Gomez, Ph.D. (Botany and Plant Sciences) Sydney I. Glassman, Ph.D. (Microbiology and Plant Pathology) Rong Hai, Ph.D. (Microbiology and Plant Pathology) Ansel Hsiao, Ph.D. (Microbiology and Plant Pathology) Robert Jinkerson, Ph.D. (Chemical and Environmental Engineering) Yanran Li, Ph.D. (Chemical and Environmental Engineering) Patricia Manosalva, Ph.D. (Microbiology and Plant Pathology) Quinn McFrederick, Ph.D. (Entomology) Juliet Morrison, Ph.D. (Microbiology and Plant Pathology) Meera Nair, Ph.D. (School of Medicine) Samantha Ying, Ph.D. (Environmental Sciences)

Microorganisms play key roles in ecosystems and human civilization. They can both cause and prevent a wide array of diseases in animals and plants. They are key components in the manufacturing of bread, cheese, and other food products. Microbes are involved in soil formation, global environmental processes and detoxifying contaminated environments. In addition, they contain a wealth of useful compounds and enzymes for biotechnology.

Students earning a degree will be prepared to continue studies at the graduate level, earn teaching credentials, or enter professional schools in medicine, pharmacy, optometry, den- tistry, veterinary medicine, and clinical laboratory science among others. Students will also be trained for technical careers in medicine, agricul- ture, biotechnology and environmental fields. For information on how to select elective coursework for specific career paths, visit the CNAS Under- graduate Academic Advising Center.

Students in the Microbiology major can obtain either B.A. or B.S. degrees. The B.S. degree offers students with a strong interest in the natural sciences an opportunity to emphasize this aspect of their education. The B.A. degree is available to students who wish to obtain a broader background in the humanities and social sciences than is required of students in the B.S. program.

See the Undergraduate Studies section for requirements that all students must satisfy.

See Degree Requirements, College of Natural and Agricultural Sciences, in the Undergraduate Studies Section, for requirements that students must satisfy.

Some of the following requirements for the Microbiology major may also fulfill the College’s breadth requirements. Consult with an advisor for course planning.

• 1. Core Curriculum (72-77 units)

Students must complete all required core curriculum courses with a grade of “C-” or better and with a cumulative GPA in the courses of at least 2.0. Grades of “D” or “F” in two required courses, either separate courses or repetitions of the same course, are grounds for discontinuation from the major.

• a) BIOL 005A, BIOL 05LA or BIOL 020,

BIOL 005B, BIOL 005C

• b) CHEM 001A,CHEM 001B,CHEM 001C,

CHEM 01LA, CHEM 01LB, CHEM 01LC

• c) 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

• d) PHYS 002A or PHYS 002HA, PHYS 002B or PHYS 002HB, PHYS 002C or

PHYS 002HC, PHYS 02LA or PHYS 02HLA, PHYS 02LB or PHYS 02HLB, PHYS 02LC or PHYS 02HLC

• e) MATH 007A or MATH 009A, MATH 007B

or MATH 009B

• f) STAT 100A

• g) BCH 100, or BCH 110A or BCH 110HA

and BCH 110B or BCH 110HB

• 2. Upper-Division Requirements (37 units)

• a) Major Core (19 units): BIOL 102, BIOL 107A, MCBL 121/BIOL 121, MCBL 121L/BIOL 121L, MCBL 125

• b) Major Electives. A minimum of 18 units

from the following to be selected in consultation with a faculty advisor: BIOL 128/CBNS 128, BIOL 157, BIOL 158, CBNS 101, ENSC 120/NEM 120, MCBL 120/BIOL 120/PLPA 120, MCBL 120L/ BIOL 120L/PLPA 120L, MCBL 122/BIOL 122, MCBL 123/BIOL 123/PLPA 123, MCBL 124/BIOL 124, MCBL 126, MCBL 141/ENSC 141, MCBL 1902, MCBL 1972, PLPA 134/BIOL 134, PLPA 134L/ BIOL 134L

• 3. Other Requirements

For the Bachelor of Science degree, an additional 16 units in upper-division microbiology courses and/or substantive courses in a field or fields related to the major. Acceptable courses include BCH 162, BIOL 107B, BIOL 109, BIOL 119, ENSC 133/MCBL 133, MCBL 198-I3; a more complete list of acceptable courses is available at the CNAS Undergraduate Academic Advising Center.

For the Bachelor of Arts degree, the foreign language requirement may be fulfilled by completing level-four coursework or by demonstrating the equivalent proficiency in one foreign language.

• 4. Bachelor of Science Sample Program

Freshman Year Fall Winter Spring

BIOL 005A, BIOL 005LA, or BIOL 020, BIOL 005B 5 4

CHEM 001A, CHEM 001B, CHEM 001C, 4 4 4

CHEM 01LA, CHEM 01LB, CHEM 01LC 1 1 1

ENGL 001A, ENGL 001B 4 4

Humanities/Social Sciences 4

MATH 009A, MATH 009B 4 4

NASC 093 2

Total Units 15 14 17

Sophomore Year Fall Winter Spring

STAT 100A 5

BIOL 005C 4

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

4 4 4

Elective 4

Humanities/Social Sciences 4

PHYS 002A or PHYS 002HA, PHYS 002B or PHYS 002HB, PHYS 002C or PHYS 002HC

4 4 4

PHYS 02LA or PHYS 02HLA, PHYS 02LB or PHYS 02HLB, PHYS 02LC or PHYS 02HLC

1 1 1

Total Units 13 17 14

Junior Year Fall Winter Spring

BCH 100 4

Humanities/Social Sciences 4 4 4

BIOL 102 4

MCBL 121 4

MCBL 121L 3

PHIL 0094 4

Major Electives & Other Reqs 7

Elective 4 4

Total Units 16 16 14

Senior Year Fall Winter Spring

BIOL 107A 4

MCBL 125 4

Major Electives & Other Reqs. 8 8 7

MCBL 197 3 3 3

ENGL 001C 4

Total Units 15 15 14

Notes:

1 Some students will take courses in summer session to (i) reduce the unit load during the normal academic year (ii) complete the degree requirements in less than four years or (iii) enable the acquisition of a minor or double major in four years.

2 No more than 4 units of either MCBL 190 or MCBL 197 can be applied toward the Major Electives unit requirement, unless approved by the Microbiology Steering Committee.

3 No more than 4 units can be applied toward the Other Requirements unit requirement, unless approved by the Microbiology Steering Committee.

4 Students are encouraged to take a class in ethics.

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 Me-

ta-genomics

• • 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. In addition, all applicants must submit results of the GRE General Test (verbal, quantitative and analytical) at the time of application.

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 100A or STAT 120A (Statistics), BIOL 102 (Genetics), BIOL 121A/ MCBL 121A, BIOL 121L/MCBL 121L (Micro- biology), 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 experi- ence in microbiology, biochemistry or genetics is highly desirable. However, upon the recom- mendation 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.

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 microbi-

ology: MCBL 201 (Functional Diversity of Prokaryotes) or MCBL 202 (Microbial Pathogenesis and Physiology), BIOL 221/MCBL 221 (Microbial Genetics), and MCBL 211 (Microbial Ecology)

• 2. A selection of elective courses in micro-

biology and other relevant fields 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

The program stresses the importance of innova- tive and independent laboratory research as the major component of the student’s education.

In addition to the above course work, students must attend one seminar per week each quarter in programs collaborating with Microbiology. Stu- dents 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.

Upon entering the program, a student advisory committee is appointed for each student to help plan a program of study. The committee consists of the student’s major professor, who serves as chair, and two other professors from the program with expertise in the student’s area of interest. Graduate students must meet at least annually with their advisory committee to plan their courses; however, students are encour- aged to meet with their committee more often. Minutes of the meeting, prepared by the chair, are approved by the rest of the committee and then placed in the student’s file. In addition, prior to advancement to candidacy, students present the advisory committee with a written summa- ry of their research progress and plans at the beginning of each academic year.

M.S. students must fulfill the requirements for Plan I (Thesis) of the Graduate Council. They must complete the core series of courses and three additional graduate level courses chosen in consultation with the student advisory commit- tee. Plan I requires 36 units, of which 24 must be in graduate level courses. No more than 6 units of MCBL 290 level courses may be used to sat- isfy this unit requirement. The student must also submit an acceptable research thesis. The M.S. thesis committee, consisting of three members, which may be the same as the student advisory committee, is nominated by the graduate advi- sor after consultation with the student. The com- mittee, once approved by the graduate dean, becomes responsible for the student’s academic guidance and evaluation. The master’s degree is conferred at the end of the academic quarter in which all requirements have been satisfied.

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 ad- visory committee. The Ph.D. degree is awarded upon passing the preliminary and qualifying ex- aminations 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 re- search 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 com- mittee is appointed.

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 aca- demic 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 represent- ing 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.

Dissertation and Final Oral Examination The dissertation committee is nominated by the graduate advisor for approval by the gradu- ate 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.

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