Microbiology

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

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

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

Environmental Engineering) 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) Adler Dillman, Ph.D. (Nematology) Xin Ge, Ph.D. (Chemical and Environmental

Sciences) 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) Rong Hai, Ph.D. (Microbiology and Plant

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

Plant Pathology) Quinn McFrederick, Ph.D. (Entomology) Yujie Men, Ph.D. (Chemical and Environmental

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

Pathology)

Assistant Professors

Patrick Degnan, Ph.D. (Microbiology and

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

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

Plant Pathology) Joseph Genereux, Ph.D. (Chemistry) Robert Jinkerson, Ph.D. (Chemical and

Environmental Engineering) Yanran Li, Ph.D. (Chemical and Environmental

Engineering) Juliet Morrison, Ph.D. (Microbiology and

Plant Pathology) Jason A. Rohman, PhD. Jiue-in Yang, Ph.D. (Nematology) 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.

The Microbiology major is unique because it offers research based capstone course (MCBL 125) that trains students to become research scientists. The major also offers many laboratory courses enabling students to obtain highly valuable skills.

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, dentistry, veterinary medicine, and clinical laboratory science among others. Students will also be trained for technical careers in medicine, agriculture, biotechnology and environmental fields. For information on how to select elective coursework for specific career paths, visit the CNAS Undergraduate Academic Advising Center. Students in the Microbiology major can obtain either B.A. or B.A. degrees or both B.S. and M.S. in our combined program. 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 (72-73 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 and CHEM 01LA or CHEM 01HA

and CHEM 1HLA, CHEM 001B and CHEM 01LB or CHEM 01HB and CHEM 1HLB, CHEM 001C and CHEM 01LC or CHEM 01HC and CHEM 1HLC

• c) CHEM 008A and CHEM 08LA or CHEM 08HA and CHEM 08HLA, CHEM 008B and

CHEM 08LB or CHEM 08HB and CHEM 08HLB, CHEM 008C and CHEM 08LC or CHEM 08HC and CHEM 08HLC

• d) PHYS 002A and PHYS 02LA or PHYS 02HA and PHYS 02HLA, PHYS 002B and

PHYS 02LB or PHYS 02HB and PHYS 02HLB, PHYS 002C and PHYS 02LC or PHYS 02HC and PHYS 02HLC, or PHYS 040A, PHYS 040B, PHYS 040C

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

or MATH 009B

• f) STAT 010

• g) BCH 100 or BCH 100H or BCH 110A or

BCH 110HA

• 2. Upper-Division Requirements (37-38 units)

• a) Major Core (19-20 units): BIOL 102, BIOL 107A, MCBL 121/BIOL 121 or MCBL 131,

MCBL 121L/BIOL 121L or MCBL 131L, 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 125 (when repeated), MCBL 126, MCBL 127, MCBL 128, MCBL 129, MCBL/ENSC 133, MCBL 139, MCBL 1902, MCBL 1972, NEM 159/ BIOL 159, PLPA 134/BIOL 134, PLPA 134L/ BIOL 134L

• 3. Depth 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 any course not used to fulfill requirements under b) Major Electives, BCH 162, BIOL 107B, BIOL 109, BIOL 119, and MCBL 198-I3. Some lower-division courses can also be applied such as STAT 010, STAT 011, MATH 009C, MATH 010A, or CS 009A. 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 05LA or BIOL 020, BIOL 005B 5 4

CHEM 001A or CHEM 01HA, CHEM 001B or CHEM 01HB, CHEM 001C or CHEM 01HC

4 4 4

CHEM 01LA or CHEM 1HLA, CHEM 01LB or CHEM 1HLB, CHEM 01LC or CHEM 1HLC

1 1 1

ENGL 001A, ENGL 001B 4 4

Humanities/Social Sciences 4

MATH 007A or MATH 009A, MATH 007B or MATH 009B 4 4

NASC 093 2

Total Units 15 14 17

Sophomore Year Fall Winter Spring

STAT 010 5

BIOL 005C 4

CHEM 008A and CHEM 08LA or CHEM 08HA and CHEM 08HLA, CHEM 008B and CHEM 08LB or CHEM 08HB and CHEM 08HLB, CHEM 008C and CHEM 08LC or CHEM 08HC and CHEM 08HLC

4 4 4

Elective 4

Humanities/Social Sciences 4

PHYS 002A or PHYS 02HA, PHYS 002B or PHYS 02HB, PHYS 002C or PHYS 02HC

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 or BCH 100H 4

Humanities/Social Sciences 4 4 4

BIOL 102 4

BIOL 107A 4

MCBL 121 or MCBL 131 4

MCBL 121L or MCBL 131L 3 or 4

MCBL 125 4

PHIL 0094 4

Major Electives & Depth 7

Total Units 16 15 or 16 15

Senior Year Fall Winter Spring

ENGL 001C 4

Elective 4 8

Major Electives & Depth 8 8 8

MCBL 197 2 2

Total Units 14 14 16

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 Depth

Requirements unit requirement, unless approved by the Microbiology Steering Committee.

4 Students are encouraged to take a class in ethics.

The Undergraduate and Graduate Programs in Microbiology offers a combined B.S. + M.S. program in Microbiology designed to lead to a Bachelor of Science degree as well as a Master of Science degree in five years.

Applicants for this program must intend to enroll in the UCR Microbiology M.S. program, have a high school GPA above 3.6 (when applying to enroll as a freshman or during their freshman year), a 3.5 GPA in major (upper division classes only, minimum of 11 units to be completed by the end of junior year, and a 3.2 GPA overall in their undergraduate program. Interested students who intend to enter the program in their junior year should check with their academic advisor for information on eligibility, admission requirements, and other details.

During the M.S. portion of this program, students must maintain a grade-point average (both in the major and overall) of at least 3.0 for all course work, both cumulatively and for each quarter of enrollment. If the student’s GPA falls below 3.0 (for either the major or overall), the student may be dropped from the program.

Master of Science The Graduate Program in Microbiology offers the M.S. degree in Microbiology.

General university requirements are listed in the Graduate Studies section of this catalog. Students may obtain an M.S. degree in Microbiology through the Plan II (Comprehensive Examination).

Professional Development All M.S. students participate in the program’s seminar (MCBL 250) each quarter of the master’s year when offered, and they are also encouraged to take the program’s professional development course (PLPA 265).

Plan II (Comprehensive Examination)

Overall Requirements Students must complete 36 units of approved graduate work in Microbiology. At least 24 of these 36 units must be graduate level courses (200-level). A maximum of 12 units of upper-division (100-level) MCBL courses can be applied toward the 36-unit requirement.

Course Requirements • Microbiology Graduate Core Courses

(MCBL 202, 211, 221)

• 24 units graduate level MCBL courses

(200- level) minimum

• Additional 200 and 100 level courses to

complete the 36 units

Written Comprehensive Exam Students take a comprehensive exam created from relevant material from at least 3 of the 200-level microbiology courses, usually the microbiology core courses. Failure to pass the comprehensive examinations after two opportunities constitutes grounds for dismissal from the program.

Normative Time to Degree 15 quarters (B.S. + M.S.)

3 quarters (M.S.)

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