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2000-2001 General Catalog
University of California, Riverside
David E. Crowley, Ph.D., Program Director
Program Office, 1151 Batchelor Hall
(800) 735-0717 or (909) 787-4116
http://cnas.ucr.edu/~micro/microintro.html
Professors
Nancy E. Beckage, Ph.D. Molecular Host-Parasite/Pathogen Interactions(Entomology/Cell Biology and Neuroscience)
Michael D. Coffey, Ph.D. Phytophthora Taxonomy and Genetics (Plant Pathology)
Donald A. Cooksey, Ph.D. Bacterial Copper Resistance (Plant Pathology)
J. Allen Dodds, Ph.D. Molecular Virus-Host Interactions (Plant Pathology)
Joseph W. Eckert, Ph.D. Mechanism of Fungicide Action (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)
David J. Gumpf, Ph.D. Viral and Mycoplasmal Plant Pathogens (Plant Pathology)
Bradley C. Hyman, Ph.D. Mitochondrial DNA of Yeast and Nematodes (Biology)
Noel T. Keen, Ph.D. Plant-Pathogen Interactions(Plant Pathology)
John A. Menge, Ph.D. Mycology, Rhizosphere Biology (Plant Pathology)
Edward G. Platzer, Ph.D. Host-Parasite Interactions (Nematology/Biology)
Neal L. Schiller, Ph.D. Human Host-Bacterial Pathogen Interactions (Biomedical Sciences)
Irwin W. Sherman, Ph.D. Host-Parasite Interactions in Malaria (Biology)
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)
Associate Professors
Wilfred Chen, Ph.D. Microbial Engineering(Chemical and Environmental Engineering)
Timothy J. Close, Ph.D. Plant and Microbial Genetics (Botany and Plant Sciences)
David E. Crowley, Ph.D. Rhizosphere Microbiology; Bioremediation (Environmental Sciences)
Howard S. Judelson, Ph.D. Molecular Genetics of Fungi (Plant Pathology)
A.L.N. Rao, Ph.D. Molecular Plant-Virus Interactions (Plant Pathology)
Linda L. Walling, Ph.D. Molecular Plant-Pathogen Interactions (Botany and Plant Sciences)
Assistant Professors
James E. Adaskaveg, Ph.D. Biology, Epidemiology, and Ecology of Plant Pathogenic Fungi (Plant Pathology)
James G. Borneman, Ph.D. Microbial Ecology of Soil-borne Plant Pathogens(Plant Pathology)
Marc Deshusses, Ph.D.Biodegradation, Biofiltration and Bioremediation of Pollutants(Chemical and Environmental Engineering)
Rajesh K. Mehra, Ph.D. Molecular Detoxification of Metals (Cell Biology and Neuroscience)
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, and Soil and Environmental Sciences, the 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 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
- A core sequence of classes in microbiology: MCBL 201, Microbial Physiology; BIOL 221/MCBL 221, Microbial Genetics; and MCBL 211/SWSC 211, Soil Microbial Ecology
- A selection of elective courses in microbiology and other relevant fields chosen in consultation with the student's major professor and the Student Advisory Committee in order to develop depth in particular areas of specialization
- 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. Two years is the normative time for the completion of the M.S. (Plan I -- Master's Thesis) program; five years (15 quarters) is the normative time required to complete the Ph.D. program.
For admission into the graduate program in Microbiology, a student must have a Bachelor of Arts or Sciences degree from an accredited institution and an academic record which satisfies the minimum admission standards established by the Graduate Division, University of California, Riverside. In addition, results of the Graduate Record Examination (GRE) General Test scores (verbal, quantitative and analytical) must be submitted to the program by all applicants 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 intending 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, an occasional student may be admitted into the graduate program with one or more course work deficiencies; such students must satisfy these coursework deficiencies usually within the first, and no later than within the second, year of graduate study.
In addition to the above coursework, students are required to 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 Student Advisory 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 Student 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, the student presents the Student Advisory Committee with a written summary of the student's research progress and plans at the beginning of each academic year.
Master's Degree
M.S. students must fulfill the requirements for Plan I (Master's Thesis) of the Graduate Council. They must complete the core series of courses as well as 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.
Doctoral Degree
Ph.D. students must meet all requirements of the Graduate Council. Students will satisfactorily complete the core class requirements and complete 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 do original research by preparation and submission of an acceptable dissertation.
It is expected that students enrolled in the Microbiology Ph.D. program become actively engaged in a research project no later than the end of their first year, and research progress is monitored by the Student Advisory Committee until the student advances to candidacy and a dissertation committee is appointed.
The preliminary examination consists of a written, comprehensive examination based on general microbiology and required material in the student's area of specialization. The examination is administered by the Graduate Advisory Committee. 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. After completion of the preliminary examination, the qualifying committee 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 Graduate 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 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.
One quarter of teaching experience is required for the Microbiology Ph.D. degree. The teaching requirement may be satisfied by serving as a TA in any of the microbiology courses listed.
There is no foreign language requirement for the Ph.D. degree in Microbiology.
UPPER-DIVISION COURSES
MCBL 120. Introduction to Plant Pathology. (3) F
Lecture, three hours. Prerequisite(s): BIOL 005A, BIOL 005B, BIOL 121A/MCBL 121A and BIOL 121B/MCBL 121B recommended. 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, four 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)
Lecture, three hours; discussion, one hour. Prerequisite(s): BIOL 005A, BIOL 005B, BIOL 005C, CHEM 001C or CHEM 01HC, CHEM 112C, MATH 009B or MATH 09HB; 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.
MCBL 121B. Microbiology. (4)
Lecture, three hours; discussion, one 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.
MCBL 121L. Microbiology Laboratory. (3)
Lecture, one hour; laboratory, six 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.
MCBL 122. Food Microbiology. (4) S
Lecture, three hours; discussion, one hour. Prerequisite(s): BIOL 121A/MCBL 121A with a grade of "C-" or better. 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) W
Lecture, three hours; discussion, one hour. Prerequisite(s): BCH 110A-BCH 110B (BCH 110B may be taken concurrently); BIOL 107A or BIOL 121A/MCBL 121A (BIOL 107A or BIOL 121A/MCBL 121A may be taken concurrently); 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, three to twelve 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, three 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. Schiller
MCBL 211. Microbial Ecology. (3)
Lecture, three 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.
MCBL 216. Biodegradation of Xenobiotic Chemicals. (3)
Lecture, three 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.
MCBL 216L. Laboratory in Biodegradation of Xenobiotic Chemicals. (3)
Discussion, one hour; laboratory, three 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.
MCBL 221. Microbial Genetics. (4)
Lecture, three hours; discussion, one 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.
MCBL 250. Seminar in Microbiology. (1) S
Seminar, one 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, three to eighteen 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 to 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, three to thirty-six 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.
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