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Microbiology

Faculty E-mails

Professors
Michael Allen, Ph.D. Biology and Ecology Microbial-Plant-Soil Interactions (Plant Pathology)
Nancy E. Beckage, Ph.D. Molecular Host-Parasite/Pathogen Interactions (Entomology/Cell Biology and Neuroscience)
Wilfred Chen, Ph.D. Microbial Engineering (Chemical and Environmental Engineering)
Michael D. Coffey, Ph.D. Phytophthora Taxonomy and Genetics (Plant Pathology)
Donald A. Cooksey, Ph.D. Bacterial Copper Resistance (Plant Pathology)
David E. Crowley, Ph.D. Rhizosphere Microbiology; Bioremediation (Environmental Sciences)
J. Allen Dodds, Ph.D. Molecular Virus-Host Interactions (Plant Pathology)
Brian A. Federici, Ph.D. Molecular Biology of Insect Pathogens (Entomology)
Dennis D. Focht, Ph.D. Bacterial Metabolism of Xenobiotics (Plant Pathology)
William T. Frankenberger, Ph.D. Microbial Transformation of Metals and Metalloids (Environmental Sciences)
Sarjeet S. Gill, Ph.D. Bacterial Toxic Action (Cell Biology and Neuroscience)
Bradley C. Hyman, Ph.D. Mitochondrial DNA of Yeast and Nematodes (Biology)
John A. Menge, Ph.D. Mycology, Rhizosphere Biology (Plant Pathology)
Ashok Mulchandani, Ph.D. Microbial Engineering, Biosensors, and Biodetoxification (Chemical and Environmental Engineering)
Edward G. Platzer, Ph.D. Host-Parasite Interactions (Nematology/Biology)
Neal L. Schiller, Ph.D. Human Host-Bacterial Pathogen Interactions (Biomedical Sciences)
Michael Stanghellini, Ph.D. Ecology, Epidemiology, and Control of Soil-borne Pathogens (Plant Pathology)
Marylynn V. Yates, Ph.D. Water and Wastewater Microbiology (Environmental Sciences)
Professors Emeriti
Salomon Bartnicki-Garcia, Ph.D. (Plant Pathology)
Irwin W. Sherman, Ph.D. Host-Parasite Interactions in Malaria (Biology)
Associate Professors
James E. Adaskaveg, Ph.D. Biology, Epidemiology, and Ecology of Plant Pathogenic Fungi (Plant Pathology)
Katherine A. Borkovich, Ph.D. Fungal Cell and Molecular Biology (Plant Pathology)
James G. Borneman, Ph.D. Microbial Ecology of Soil-borne Plant Pathogens (Plant Pathology)
Shou-Wei Ding, Ph.D. Molecular Biology of Plant Viruses and Gene Silencing (Plant Pathology)
Howard S. Judelson, Ph.D. Molecular Genetics of Fungi (Plant Pathology)
A.L.N. Rao, Ph.D. Molecular Plant-Virus Interactions (Plant Pathology)
Assistant Professors
Marc Deshusses, Ph.D. Biodegradation, Biofiltration and Bioremediation of Pollutants (Chemical and Environmental Engineering)
Brian Lanoil, Ph.D. Environmental Microbiology, Extreme Environments, Marine Systems (Environmental Sciences)
Lisa Stein, Ph.D. Environmental Microbiology, Anaerobic Microbiology, Biogeochemistry (Environmental Sciences)

MAJOR

The Microbiology program participates in the Biological Sciences major. See separate listing under Biological Sciences, Microbiology Track.

GRADUATE PROGRAM

The Graduate Program in Microbiology is an interdisciplinary program with participating faculty from the departments of Biology, Botany and Plant Sciences, Cell Biology and Neuroscience, Entomology, Nematology, Plant Pathology, Environmental Sciences, Division of Biomedical Sciences, and the Bourns College of Engineering. Faculty research interests are concentrated in several disciplines in the areas of basic and applied microbiology. These disciplines include the following:

• The biology, physiology, pathogenesis and genetics of bacterial, fungal, parasite and viral pathogens of animals, humans, insects, and plants, with special emphasis on molecular host–pathogen interactions

• Microbial ecology, soil microbiology and rhizosphere microbiology

• Bacterial transformation/detoxification of metals and xenobiotic chemicals

• Characterization of microbial toxins of insects

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 microbiology: MCBL 201 (Microbial Physiology), BIOL 221/MCBL 221 (Microbial Genetics), and MCBL 211/SWSC 211 (Microbial Ecology)
2. A selection of elective courses in microbiology 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 innovative and independent laboratory research as the major component of the student's education.

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 112A, CHEM 112B, CHEM 112C (Organic Chemistry)
BCH 110A, BCH 110B (Biochemistry)
MATH 009A, MATH 009B (Calculus)
STAT 100A 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.

In addition to the above course work, students must attend one seminar per week each quarter in programs collaborating with Microbiology. Students are also required to present one seminar each year. These seminars can be either on the student's thesis research or related topics and can be presented in any of several program student seminar series, or at the Annual Microbiology Graduate Program Retreat at Lake Arrowhead.

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 encouraged 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 summary of their research progress and plans at the beginning of each academic year.

Master's Degree

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 committee. 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 satisfy 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 advisor after consultation with the student. The committee, 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

Doctoral Degree

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.

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.

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.

Teaching Requirement One quarter 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

UPPER-DIVISION COURSES

MCBL 120. Introduction to Plant Pathology (3) F Lecture, 3 hours. Prerequisite(s): BIOL 005A, BIOL 05LA, BIOL 005B, BIOL 005C, CHEM 001C or CHEM 01HC, CHEM 112C, MATH 009B or MATH 09HB, PHYS 002C, PHYS 02LC, BCH 100 or BCH 110A, one course in statistics; or consent of instructor. An introduction to the study of plant diseases. Topics include diseases and disease-causing agents, host-pathogen interaction during disease development, and strategies for disease management. An optional, separate laboratory is offered. Cross-listed with BIOL 120 and PLPA 120. Stanghellini

MCBL 120L. Introduction to Plant Pathology Laboratory (1) F Laboratory, 4 hours. Prerequisite(s): BIOL 005A, BIOL 005B; concurrent enrollment in BIOL 120/MCBL 120/PLPA 120 or consent of instructor; BIOL 121A/MCBL 121A and BIOL 121B/MCBL 121B recommended. Fundamentals in the use of laboratory instruments and techniques for the detection, isolation and identification of representative infectious agents that cause disease in plants. Cross-listed with BIOL 120L and PLPA 120L. Stanghellini

MCBL 121A. Microbiology (4) F, W Lecture, 3 hours; discussion, 1 hour. Prerequisite(s): BIOL 005A, BIOL 05LA, BIOL 005B, BIOL 005C, CHEM 001C or CHEM 01HC, CHEM 112C, MATH 009B or MATH 09HB, PHYS 002C, PHYS 02LC, BCH 100 or BCH 110A (BCH 100 or BCH 110A may be taken concurrently); or consent of instructor. An intensive introduction to the fundamental physiology and molecular biology of bacteria and viruses. Covers evolutionary origins of metabolic diversity, bacterial and viral molecular genetics, and an introduction to microbial pathogenesis. Cross-listed with BIOL 121A. Focht

MCBL 121B. Microbiology (4) S Lecture, 3 hours; discussion, 1 hour. Prerequisite(s): BIOL 121A/MCBL 121A with a grade of "C-" or better or consent of instructor. An intensive introduction to the fundamental physiology and molecular biology of bacteria and viruses. Covers research strategies for examining microbial pathogenic mechanisms. Cross-listed with BIOL 121B. Cooksey, Gill

MCBL 121L. Microbiology Laboratory (3) F,W,S Lecture, 1 hour; laboratory, 6 hours. Prerequisite(s): BIOL 121A/MCBL 121A with a grade of "C-" or better. Laboratory exercises in diagnostic bacteriology, basic virology, and epidemiology. Includes fundamental quantitative and diagnostic microbiological procedures, basic mechanisms of microbial genetic exchange, and a project examining bacterial epidemiology. Cross-listed with BIOL 121L. Borkovich, Borneman

MCBL 122. Food Microbiology (4) S Lecture, 3 hours; discussion, 1 hour. Prerequisite(s): BIOL 121A/MCBL 121A with a grade of "C-" or better; BIOL 121L/MCBL 121L. Covers spoilage and preservation of food; food quality and indicator organisms; the role of microorganisms in the production of dairy goods and fermented beverages; food-borne pathogens and microbiological production of toxins; and classical and modern molecular methods for detection of food microorganisms. Cross-listed with BIOL 122. Focht

MCBL 123. Introduction to Comparative Virology (4) Lecture, 3 hours; discussion, 1 hour. Prerequisite(s): BIOL 005A, BIOL 05LA, BIOL 005B, BIOL 005C, CHEM 001C or CHEM 01HC, CHEM 112C, MATH 009B or MATH 09HB, PHYS 002C, PHYS 02LC, BCH 100 or BCH 110A, one course in statistics; or consent of instructor. Considers viruses as infectious agents of bacteria, plants, and animals (vertebrates and invertebrates). Compares the major groups of viruses to each other with respect to their biological and biochemical properties, molecular and genetic characteristics, and modes of replication. Cross-listed with BIOL 123 and PLPA 123. Rao

MCBL 197. Research for Undergraduates (1-4) Directed research, 3-12 hours. Prerequisite(s): consent of instructor; upper-division standing. Individual research in microbiology performed under the guidance of the staff or faculty. Letter grades are assigned to students presenting a research paper; other students are graded Satisfactory (S) or No Credit (NC). Course is repeatable to a maximum of 9 units.

GRADUATE COURSES

MCBL 201. Microbial Physiology (3) F Lecture, 3 hours. Prerequisite(s): BCH 110A, BCH 110B, BIOL 121A/MCBL 121A; or equivalents; or consent of instructor. An in-depth coverage of bacterial and fungal structure and function. Specific topic areas include: biosynthesis and composition of major microbial structures; functional analysis of cell surface components; growth, morphogenesis, differentiation, and reproduction; microbial adaptation to environmental influences. Stein

MCBL 205. Signal Transduction Pathways in Microbes and Plants (4) Lecture, 3 hours; discussion, 1 hour. Prerequisite(s): graduate standing in the biological sciences, BIOL 107A or BIOL 113 or BIOL 114 or CBNS 101; or consent of instructor. Advanced topics in signal transduction pathways that regulate growth and development in plants and prokaryotic and eukaryotic microbes. Areas covered include two-component regulatory systems; quorum sensing; signaling via small and heterotrimeric G proteins; mitogen-activated protein kinase cascades; cAMP signaling; photoreceptors; plant hormone signaling; responses to low-oxygen stress; calcium signaling; and plant pathogenesis. Cross-listed with CMDB 205, BCH 205, GEN 205, BPSC 205, and PLPA 205.

MCBL 211. Microbial Ecology (3) S, Odd Years Lecture, 3 hours. Prerequisite(s): graduate standing or consent of instructor. Application of ecological principles to microbial communities. Emphasizes methods for analysis of diversity and community structure and statistical methods relating genetic and biochemical fingerprints to functional properties. Case studies explore applications for agriculture, disease biocontrol, and bioremediation of environmental contaminants. Cross-listed with SWSC 211. Crowley, Lanoil

MCBL 216. Biodegradation of Xenobiotic Chemicals (3) S Lecture, 3 hours. Prerequisite(s): BCH 100, BIOL 121A/MCBL 121A, BIOL 121L/MCBL 121L; or equivalents. Explores the importance of microorganisms in metabolizing synthetic organic chemicals. Topics include ecology, physiology, growth, isolation, and identification of degradative bacteria; bioremediation processes; and environmentally related problems. Examines studies of catabolic pathways including metabolites, enzymes, genes, and environmental factors. Cross-listed with ENTX 216 and SWSC 216. Focht

MCBL 216L. Laboratory in Biodegradation of Xenobiotic Chemicals (2) S Discussion, 1 hour; laboratory, 3 hours. Prerequisite(s): BCH 100, BIOL 121A/MCBL 121A, BIOL 121L/MCBL 121L; or equivalents. Covers laboratory methods used for isolation and identification of degradative bacteria and kinetics of growth and metabolism. Examines studies of catabolic pathways, separation, and spectroscopic identification of metabolites. Cross-listed with ENTX 216L and SWSC 216L. Focht

MCBL 221. Microbial Genetics (4) W Lecture, 3 hours; discussion, 1 hour. Prerequisite(s): BCH 110C or BIOL 107A; BIOL 102. An in-depth coverage of the genetics of microbes with emphasis on the primary data and the foundation of modern techniques using Escherichia coli and other prokaryotic systems. Topics include genome organization, plasmids, restriction-modification systems, mutation, transposable elements, regulation of gene expression, viruses, recombination, repair, and responses to stress. Cross-listed with BIOL 221. Borkovich

MCBL 241. Special Topics (2) Lecture, 2 hours. Prerequisite(s): graduate standing or consent of instructor. Oral presentations and intensive small-group discussion of selected topics in each faculty member's area of specialization. Course content emphasizes recent advances in the special topic area and varies accordingly. Graded Satisfactory (S) or No Credit (NC). Course is repeatable. Cross-listed with PLPA 241.

MCBL 250. Seminar in Microbiology (1) S Seminar, 1 hour. Prerequisite(s): graduate standing. Formal seminars by graduate students, faculty, and invited scholars on selected topics in microbiology. Graded Satisfactory (S) or No Credit (NC). Course is repeatable.

MCBL 290. Directed Studies (1-6) Research, 3-18 hours. Prerequisite(s): graduate standing; consent of instructor and graduate advisor. Experimental or literature studies on specifically selected topics conducted under the direction of a faculty member. Graded Satisfactory (S) or No Credit (NC). Course is repeatable.

MCBL 297. Directed Research (1-6) Research, 3-18 hours. Prerequisite(s): graduate standing. Directed research in microbiology performed prior to advancement to candidacy in preparation for thesis or dissertation projects. Graded Satisfactory (S) or No Credit (NC). Course is repeatable.

MCBL 299. Research for Thesis or Dissertation (1-12) Research, 3-36 hours. Prerequisite(s): graduate standing. Original research in the area selected for the advanced degree. Graded Satisfactory (S) or No Credit (NC). Course is repeatable.