Microbiology and Environmental Toxicology
2012-13 General Catalog
430 Physical Sciences Building
Telephone (831) 459-4719
FAX (831) 459-3524
http://www.metx.ucsc.edu
Lower-Division Courses
80E. Aquatic Toxicology. *
An introduction to the sources, cycling, and impacts of toxicants in aquatic systems, including acid rain, ground water, fresh water rivers and lakes, estuaries, and the ocean. Emphasis is on the properties of toxic chemicals that influence their biogeochemical cycles and factors that influence their toxicity to aquatic organisms and humans. (General Education Code(s): SI, T-2 Natural Sciences.) A. Flegal
Upper-Division Courses
101. Sources and Fates of Pollutants. F
Presents in-depth important principles of environmental toxicology related to the introduction, transport, and fate of toxicants in aquatic and terrestrial environments, including environmental chemistry and biogeochemical cycles as well as exposure to pathways and uptake by organisms. Additional emphasis placed on susceptibility and effects of toxicants across organ systems, toxicokinetic and biomarkers of exposure, and effects at the ecosystem level. Students cannot receive credit for this course and course 201. A. Flegal
102. Cell and Molecular Toxicology. F
Emphases of biochemical, cellular, and organ system basis of intoxication, including dose-response relationships, biotransformation of toxicants, biochemical mechanisms underlying toxicity, factors influencing toxic action, and biomarkers of exposure. Emphasizes effects of various classes of toxins, including heavy metals and persistent synthetic organics, with a focus on susceptible biochemical/cellular processes of the central nervous, immune, hepatic, and renal target organ systems. Designed for advanced undergraduates. Students cannot receive credit for this course and course 202. (Formerly Cellular and Organismal Toxicology.) Prerequisite(s): Biology 20A and 20B or equivalent; Biology 100, Biochemistry, and 110, Cell Biology, are recommended. Enrollment restricted to juniors and seniors. D. Smith
119. Microbiology. F,W
Cell and molecular biology of bacteria and their viruses, including applications in medicine, public health, agriculture, and biotechnology. Prerequisite(s): BIOL 100 or BIOC 100A. V. Stone, F. Yildiz
119L. Microbiology Laboratory. F,W,S
An introduction to the principles and practices of laboratory microbiology, with a substantial presentation of optical microscopy. Students are billed a materials fee. Prerequisite(s): previous or concurrent enrollment in course 119 is required;satisfaction of Entry Level Writing and Composition requirements. Enrollment restricted to biological sciences and affiliated majors; biology minors; other majors by permission. (General Education Code(s): W.) C. Saltikov, K. Ottemann
125. Practicing Safe Science (2 credits). W
Introduces research safety principles and practices. Instructors and guest experts discuss research hazards and control measures. Students explore the safe use of research methods and materials via hands-on and outside exercises. Issues include compliance with hazardous waste and other environmental safety regulations. J. Schoonover
138. Pathogenesis: Molecular Mechanisms of Disease. *
Overview of the pathogenic mechanisms underlying human disease at the physiological and molecular levels, with their implications for epidemiology, diagnosis, and treatment. Includes discussion of clinical cases and of emerging areas of research. Geared toward students interested in future research or clinical careers in the area of human or animal health. Students cannot receive credit for this course and Microbiology and Environmental Toxicology 238. (Also offered as Biology: Molecular Cell & Dev 118. Students cannot receive credit for both courses.) Prerequisite(s): Biology 130. Enrollment restricted to students majoring in biology; health sciences; molecular, cell, and developmental biology; biochemistry and molecular biology; or neuroscience and behavior. Offered in alternate academic years. M. Camps
140. Molecular Biology of Prokaryotes. *
Focuses on several aspects of prokaryotic molecular biology. Covers transcriptional regulation, translational regulation, DNA replication and segregation, protein secretion, transport of small molecules, control of metabolism, stress response, bacterial differentiation, signal transduction, biofilm formation, and motility. Strong focus on experimental techniques and approaches used in prokaryotic molecular biology. Focus on model bacteria such as Escherichia coli and Bacillus subtilis.Students cannot receive credit for this course and course 240. Prerequisite(s): Biology 119. K. Ottemann
144. Groundwater Contamination. S
Analyses of contemporary problems in groundwater contamination, based on current scientific understanding of contaminant transport in aquifers. Topics include both theoretical concepts and case studies. To be offered in alternate academic years. Prerequisite(s): Earth Science 110B. Offered in alternate academic years. A. Flegal
145. Medical Geology. *
An interdisciplinary analysis of natural geochemical processes that impact human health and of anthropogenic processes that exacerbate those impacts. Prerequisite(s): Chemistry 1A, 1B, 1C, 1M, and 1N. A. Flegal
150. Introduction to Research and Experimental Design. *
Lecture-based course for advanced undergraduates actively engaged in undergraduate research (e.g., independent study or senior thesis). Emphasizes basic lab skills, including laboratory safety and handling of laboratory equipment; experimental design; scientific record keeping; and literature searching, review, and management. K. Ottemann, (FWS) The Staff
151. Scientific Writing and Presentation. *
For advanced undergraduates who are actively engaged in undergraduate research (e.g., independent study or senior thesis). Emphasizes the collection, reduction, analysis, management, and interpretation of scientific data; the presentation of scientific data in written and oral formats; and further development of critical thinking. Prerequisite(s): satisfaction of the Entry Level Writing and Composition requirements. (General Education Code(s): W.) The Staff
160. Coastal Environmental Toxicology and Policy (3 credits). *
Interdisciplinary analysis of the scientific basis and policy development to regulate and manage environmental pollutants in coastal waters. Focuses on case studies involving aspects of environmental toxicology and policy including environmental monitoring and regulatory programs; ecosystem restoration; and regulating the environmental impacts of coastal development. Enrollment restricted to sophomores, juniors, seniors, and graduate students. M. Connor, G. Griggs, A. Flegal
170. Frontiers in Drug Action and Discovery. *
Lectures and case studies explore principles and approaches in drug discovery and development, emphasizing concepts in pharmacology; medicinal chemistry; and genomics- and bioinformatics-based approaches to drug discovery to illustrate pathways from discovery through development for clinical use. Cannot receive credit for this course and course 270. (Also offered as Biomolecular Engineering 170. Students cannot receive credit for both courses.) Prerequisite(s): Biology 100 or Chemistry 103 or Biochemistry 100A. Biology 110 and 130/L or 131/L are recommended. Enrollment restricted to juniors and seniors. D. Smith, T. Holman, M. Camps, R. Linington, P. Berman
195. Senior Thesis. F,W,S
An individually supervised course, with emphasis on independent research culminating in a senior thesis. May be repeated for credit. The Staff
195F. Senior Thesis (2 credits). F,W,S
An individually supervised course with emphasis on independent research culminating in a senior thesis. May be repeated for credit. The Staff
198. Independent Study. F,W,S
Provides for individual programs of study (a) by means other than the usual supervision in person or (b) when the student is doing all or most of the course work off campus. With permission of the department, two or three courses may be taken concurrently, or the course repeated for credit. May be repeated for credit. The Staff
198F. Independent Study (2 credits). F,W,S
Provides for individual programs of study (a) by means other than the usual supervision in person or (b) when the student is doing all or most of the coursework off campus. With permission of the department, two or three courses may be taken concurrently, or the course repeated for credit. May be repeated for credit. The Staff
199. Tutorial. F,W,S
Reading, discussion, written reports, and laboratory research on selected topics. May be repeated for credit. The Staff
199F. Tutorial (2 credits). F,W,S
Reading, discussion, written reports, and laboratory research on selected topics. Enrollment limited to 4. May be repeated for credit. The Staff
Graduate Courses
200. Interdisciplinary Approaches in Environmental Toxicology. F
Introduction to interdisciplinary, case-based approaches to problem-solving. Course demonstrates how important, current problems in environmental and human health have been addressed and solved. Assigned problems that integrate the different organization levels (environmental, molecular/cellular, organismal/public health) inherent to environmental and human health are presented. Students work in collaborative teams to analyze each problem and create a proposal for a research plan/solution. Enrollment restricted to graduate students. D. Smith, M. Camps, K. Ottemann
201. Sources and Fates of Pollutants. *
Presents in-depth important principles of environmental toxicology related to the introduction, transport, and fate of toxicants in aquatic and terrestrial environments including environmental chemistry and biogeochemical cycles as well as exposure pathways and uptake by organisms. Additional emphasis will be placed on the susceptibility and effects of toxicants across organ systems, toxicokinetics and biomarkers of exposure, and effects at the ecosystem level. Students cannot receive credit for this course and course 101. Enrollment restricted to graduate students; qualified undergraduate science majors may enroll with permission of instructor. A. Flegal
202. Cell and Molecular Toxicology. F
Emphasizes biochemical, cellular, and organ system basis of intoxication, including dose-response relationships, biotransformation of toxicants, biochemical mechanisms underlying toxicity, factors influencing toxic action, and biomarkers of exposure. Emphasizes effects of various classes of toxins, including heavy metals and persistent synthetic organics, with a focus on susceptible biochemical/cellular processes of the central nervous, immune, hepatic, and renal target organ systems. Students cannot receive credit for this course and Microbiology and Environmental Toxicology 102 or BIOL 122.. (Formerly "Cellular and Organismal Toxicology.") Enrollment restricted to graduate students. D. Smith
203. Cellular and Molecular Toxicology. *
Presents in-depth cellular and molecular principles of environmental toxicology. These include modes of action and cellular and molecular targets of toxicants, as well as mechanisms of cellular and molecular responses to toxicants and their detoxification. State-of-the-art biological methodologies and approaches to identify and study cellular targets of toxicants. Designed to provide students with a broad and deep understanding of the biological aspects of toxicology at both cellular and molecular levels, and the skills to approach emerging challenges in the field. Enrollment restricted to graduate students; qualified undergraduates may enroll with instructor's permission. (FWS) The Staff
205. Scientific Skills, Ethics, and Writing. *
Course provides fundamental training of graduate students in the scientific method, experimental design, ethics in science, grant proposal and scientific writing, data presentation, and scientific speaking. Students are evaluated on class participation, performance, and a written NIH/NSF style research proposal. Enrollment restricted to graduate students. The Staff
206A. Advanced Microbiology. W
Focuses on aspects of bacterial molecular biology. Covers four main areas: (1) metabolism-catabolism, anabolism, building-block precursors; (2) transcription/signal transduction; (3) replication/plasmid biology/division; (4) translation/protein processing/secretion/cell structure. Strong focus on experimental techniques and approaches used in molecular biology, and on model bacteria, such as Esherichia coli and Bacillus subtilis. Enrollment restricted to graduate students .Advanced undergraduates may enroll with permission of instructor. K. Ottemann, V. Stone, C. Saltikov
210. Molecular and Cellular Basis of Bacterial Pathogenesis. *
Focuses on the molecular basis of bacterial pathogenesis with specific emphasis on gene expression, regulation, and ecology and evolution. Advanced undergraduates with extensive background in microbiology and biology may enroll with permission of instructor. Enrollment restricted to graduate students. Advanced undergraduates with extensive background in microbiology and biology may enroll with permission of instructor. F. Yildiz
215. Seminar in Advanced Prokaryotic Molecular Biology (2 credits). *
Seminar focuses on aspects of prokaryotic molecular biology. Specific topics include transcriptional regulation, translational regulations, DNA replication, secretion of proteins, transport of small molecules, bacterial differentiation, signal transduction, biofilm formation, and motility. Discussions focus on model bacteria such as Escherichia coli and Bacillus subtilis. Enrollment restricted to graduate students. F. Yildiz, C. Saltikov, K. Ottemann
238. Pathogenesis: Molecular Mechanisms of Disease. *
Overview of the pathogenic mechanisms underlying human disease at the physiological and molecular levels, with their implications for epidemiology, diagnosis, and treatment. Includes discussion of clinical cases and of emerging areas of research. Geared toward students interested in research or clinical careers in the area of human or animal health. Students cannot receive credit for this course and course 138. Enrollment restricted to graduate students. M. Camps
240. Molecular Biology of Prokaryotes. *
Focuses on several aspects of prokaryotic molecular biology. Covers transcriptional regulation, translational regulation, DNA replication and segregation, protein secretion, transport of small molecules, control of metabolism, stress response, bacterial differentiation, signal transduction, biofilm formation, and motility. Strong focus on experimental techniques and approaches used in prokaryotic molecular biology. Focus on model bacteria such as Escherichia coli and Bacillus subtilis.Students cannot receive credit for this course and course 140. K. Ottemann
250. Environmental Microbiology.
How microbes interact with their environments. Topics include anaerobic metabolism; biotransformation of toxic metals and organic pollutants; geomicrobiology; life in extreme environments; water quality. Advanced undergraduates with extensive background in microbiology and biology may enroll with permission of instructor. Enrollment restricted to graduate students. Offered in alternate academic years. C. Saltikov
270. Frontiers in Drug Action and Discovery. *
Lectures and case studies explore principles and approaches in drug discovery and development, emphasizing concepts in pharmacology; medicinal chemistry; and genomics- and bioinformatics-based approaches to drug discovery to illustrate pathways from discovery through development for clinical use. Cannot receive credit for this course and course 170. (Also offered as Biomolecular Engineering 270. Students cannot receive credit for both courses.) Enrollment restricted to graduate students. D. Smith, T. Holman, M. Camps, R. Linington, P. Berman
281A. Topics in Environmental Toxicology. *
Selected topics in environmental toxicology. Topics vary from year to year. Enrollment restricted to graduate students; qualified upper-division science majors may enroll with instructor's permission. May be repeated for credit. The Staff
281C. Topics in Environmental Microbiology (2 credits). F,W,S
Seminar and discussion focusing on mechanism of microbial transformation of metals. Participants present results from their research projects in a seminar format. Relevant journal articles presented and discussed. Enrollment restricted to graduate students; qualifed undergraduates may enroll with instructor's permission. C. Saltikov
281F. Topics in Aquatic Toxicology (2 credits). F,W,S
Analyses of the sources and fates of aquatic pollutants. Discussions on processes at the air-water interface, within the water column, and in aquatic sediments. Topics vary from year to year. Enrollment restricted to graduate students; qualified upper-division science majors may enroll with instructor's permission. May be repeated for credit. A. Flegal
281M. Topics in Molecular Toxicology (2 credits). F,W,S
Seminar and discussion on the mechanisms of toxicity in DNA alkylating agents. Participants present results from their research, and relevant journal articles are discussed. Enrollment restricted to graduate students. Undergraduates may enroll with instructor's permission. Enrollment limited to 5. May be repeated for credit. M. Camps
281O. Topics in Bacterial Pathogenesis (2 credits). F,W,S
Intensive seminar focusing on mechanisms of bacterial pathogenesis of the ulcer-causing bacterium Helicobacter pylori. Participants are required to present results from their own research and relevant journal articles. (Also offered as Biology: Molecular Cell & Dev 280O. Students cannot receive credit for both courses.) Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. Enrollment limited to 20. May be repeated for credit. K. Ottemann
281S. Cellular and Organismal Responses to Toxicants (2 credits). F,W,S
Intensive research seminar on the concepts, theory, and techniques in deriving physiologically based pharmacokinetic models of toxin exposure, metabolism, and efficacy of therapeutic treatment in mammalian models of human metal toxicity. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. May be repeated for credit. D. Smith
281V. Topics in Bacterial Pathogenesis and Innate Immunity (2 credits). F,W,S
Focuses on the interplay between the human gut bacterial pathogen Yersinia pseudotuberculosis and the innate immune system of the host. Participants are required to present the goals, results, and conclusions from their own research. Participation in the general discussion during others' presentations is also required. Enrollment restricted to graduate students. Qualified undergraduates performing research under the supervision of the instructor may enroll with instructor's permission. May be repeated for credit. V. Stone
281Y. Biofilms: Processes and Regulation (2 credits). F,W,S
Intensive seminar series focusing on the most current work on genes and the processes that regulate biofilm development dynamics as well as on the recent developments on visualization of biofilms. Presentation and discussion based. Enrollment restricted to graduate students. Qualified undergraduate students may enroll with instructor's permission. May be repeated for credit. F. Yildiz
282. Current Approaches to Molecular Pathogenesis (2 credits). *
Graduate level seminar focusing on the mechanisms by which bacterial pathogens cause disease. Specific topics include basic concepts of virulence and virulence factors, virulence factor regulation, toxins, and interactions of pathogens with mammalian cells and organs. Discussions focus on several key pathogens, including Helicobacter pylori, Vibrio cholerae, Salmonella typhimuruim, and Listeria monocytogenes. May be repeated for credit. K. Ottemann
290. Proseminar. *
Special topics offered from time to time by faculty, visiting professors, or staff members. Enrollment restricted to graduate students; qualified undergraduates may enroll with instructor's permission. May be repeated for credit. The Staff
290A. Epidemiology and Risk Assessment. *
Approaches different techniques of biological monitoring and the exposure and effect of biomarkers related to occupational and environmental exposure to chemicals. Available methods for risk assessment and identification of protective exposure limits also considered. (Formerly Biological Impact of Chemical Exposures.) The Staff
292. Introductory Graduate Seminar (no credit). F,W,S
Weekly seminars by academic and research faculty on their areas of special interest. Students write weekly abstracts on articles covered by the seminars. Enrollment restricted to graduate students; qualified undergraduates may enroll with instructor's permission. The Staff
297. Independent Study. F,W,S
Independent study for graduate students who have not yet settled on a research area for the thesis. Students submit petition to sponsoring agency. May be repeated for credit. The Staff
299. Thesis Research. F,W,S
Students submit petition to sponsoring agency. May be repeated for credit. The Staff
