METX - Microbiology and Environmental Toxicology

METX 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.

Credits

5

General Education Code

SI

Quarter offered

Fall

METX 100 Introduction to Microbiology

Introduces the biology of microorganisms (bacteria, archaea, viruses, fungi, and unicellular eukaryotes), with an emphasis on bacteria. Topics include microbial cell structure and function, physiology, metabolism, genetics, and diversity. Also considers the role of microbes in human health, the environment, biotechnology, and food production. Students cannot receive credit for both this course and METX 119.

Credits

5

Instructor

Jacqueline Kimmey, Michael Patnode

Requirements

Prerequisite(s): BIOL 20A or ESCI 30.

Quarter offered

Fall, Spring

METX 101 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 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 METX 201.

Credits

5

Instructor

The Staff, Chad Saltikov

METX 102 Cell and Molecular Toxicology

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 METX 202. (Formerly Cellular and Organismal Toxicology.)

Credits

5

Instructor

Donald Smith, Raquel Saltikov

Requirements

Prerequisite(s): BIOL 20A and BIOE 20B or equivalent; BIOL 100 and BIOC 110 recommended. Enrollment restricted to juniors and seniors.

Quarter offered

Winter

METX 115 Environmental Health Science

Addresses challenges related to environmental health, their impact on the health of biological structures, and humans as active elements in the process of environmental degradation, and as passive elements as well. Students discuss events as case studies of environmental health that contributed to environmental protection, and disease control and prevention. Course involves collaborative endeavor in which students develop a group assignment throughout the 10 weeks of the course that is evaluated at the end of the course.

Credits

5

Instructor

Raquel Chamorro-Garcia

Requirements

Prerequisite(s): BIOL 20A or ENVS 23 or BIOL 89.

General Education Code

PR-E

METX 119 Microbiology

Cell and molecular biology of bacteria and their viruses, including applications in medicine, public health, agriculture, and biotechnology. Students cannot receive credit for both this course and METX 100.

Credits

5

Instructor

Karen Ottemann, Victoria Stone

Requirements

Prerequisite(s): BIOC 100A or BIOL 101 or BIOL 100 or CHEM 103.

METX 119L Microbiology Laboratory

An introduction to the principles and practices of laboratory microbiology, with a substantial presentation of optical microscopy.

Credits

5

Instructor

The Staff, Chad Saltikov

Requirements

Prerequisites: Satisfaction of Entry Level Writing and Composition requirements; and one course from the following: BIOL 20L, or BIOL 101L, or BIOL 102L; and previous or concurrent enrollment in METX 100 or METX 119. Enrollment is restricted to declared Biochemistry and Molecular Biology; Biology B.S.; Molecular, Cell and Developmental Biology, and Neuroscience majors. Other majors may enroll by permission of the instructor. Students cannot enroll in METX 119L after receiving credit with a 'C' or better in BIOL 100L, BIOL 103L, BIOL 105L, BIOL 106L, BIOL 108L, BIOL 109L, BIOL 115L, BIOL 120L, BIOL 121L, BIOL 129L, and BIOL 186L.

Quarter offered

Fall, Winter, Spring, Summer

METX 125 Practicing Safe Science

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.

Credits

2

Instructor

Terra Haddad

Quarter offered

Winter

METX 135 Functional Anatomy

A rigorous systems-based course in anatomy. Lectures provide an overview of functional anatomy at all levels from the systems to the tissues. Provides a mechanistic understanding of the structures of the body as a foundation for human-health oriented studies.

Credits

5

Instructor

Manel Camps, The Staff

Requirements

Prerequisite(s): BIOL 20A and BIOE 20B. Concurrent enrollment in METX 135L is required. Enrollment restricted to biological sciences majors and affiliated majors and biology minors.

Quarter offered

Spring

METX 135C Cadaver Dissection Laboratory

Dissection of a human cadaver under the direction of an anatomy instructor.

Credits

2

Instructor

Manel Camps, The Staff

Requirements

Prerequisite(s): METX 135 and METX 135L, or ANTH 102A.

Repeatable for credit

Yes

Quarter offered

Winter

METX 135L Functional Anatomy Lab

Complements lecture course 135. Emphasizes nomenclature and recognition; includes the embryology and histology of bones, muscles, and internal organs, and the interactions between the systems of the body.

Credits

3

Instructor

Manel Camps, The Staff

Requirements

Prerequisite(s): BIOL 20A and BIOE 20B. The class is geared toward students in the biological sciences majors and affiliated majors and biology minors, but open to other majors. Concurrent enrollment in METX 135 is required.

METX 140 Molecular Biology and Microbial Genetics

Introduces students to the field of molecular biology and microbial genetics. Covers the following topics: molecular mechanisms of DNA replication, transcription, translation, regulatory systems controlling replication, transcription, and translation; basic genetic principles with an emphasis on bacterial genetics; molecular biology and microbial genetics approaches used to understand the molecular mechanisms of interaction of microorganisms with their surroundings and other organisms; and experimental methods employing molecular biology and molecular genetics and biotechnology applications which have arisen from discoveries of bacterial mechanisms.

Credits

5

Instructor

Fitnat Yildiz

Requirements

Prerequisite(s): BIOL 100 or BIOC 100A.

Quarter offered

Spring

METX 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.

Credits

5

Instructor

Chad Saltikov

Quarter offered

Spring

METX 195 Senior Thesis

An individually supervised course, with emphasis on independent research culminating in a senior thesis.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 195F Senior Thesis

An individually supervised course with emphasis on independent research culminating in a senior thesis.

Credits

2

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring, Summer

METX 198 Independent Study

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.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 198F Independent Study

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.

Credits

2

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring, Summer

METX 199 Tutorial

Reading, discussion, written reports, and laboratory research on selected topics.

Credits

5

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 199F Tutorial

Reading, discussion, written reports, and laboratory research on selected topics.

Credits

2

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring, Summer

METX 200 Interdisciplinary Approaches in Environmental Toxicology

Introduction to interdisciplinary, case-based approaches to problem-solving. Demonstrates how important, current problems in environmental and human health have been addressed and solved. Presents assigned problems that integrate the different organization levels (environmental, molecular/cellular, organismal/public health) inherent to environmental and human health. Students work in collaborative teams to analyze each problem and create a proposal for a research plan/solution. This course must be taken for a letter grade.

Credits

5

Instructor

Don Smith

Requirements

Enrollment is restricted to graduate students. Advanced undergraduates may enroll by permission of the instructor.

Quarter offered

Fall

METX 200B Graduate Research Project Development

Presents a framework for scientific writing related to developing a thesis research proposal in a topical area of microbiology and/or environmental toxicology.

Credits

2

Instructor

Chad Saltikov

Quarter offered

Winter

METX 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 METX 101.

Credits

5

Instructor

Chad Saltikov

Requirements

Enrollment is restricted to graduate students; qualified undergraduate science majors may enroll with permission of instructor.

METX 202 Cell and Molecular Toxicology

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 METX 102 or BIOL 122.

Credits

5

Instructor

David Smith, Chad Saltikov, Raquel Chamorro-Garcia

Requirements

Enrollment is restricted to graduate students.

Quarter offered

Winter

METX 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.

Credits

5

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with instructor's permission.

METX 205 Scientific Grant Writing

Provides fundamental training of graduate students in the scientific method; experimental design; ethics in science; grant proposal and scientific writing; and data presentation and scientific speaking. Students are evaluated on class participation, performance, and a written NIH/NSF-style research proposal. (Formerly Scientific Skills, Ethics, and Writing.)

Credits

5

Requirements

Enrollment restricted to graduate students. Advanced undergraduates may enroll with permission of the instructor.

METX 206A Advanced Microbiology

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 Escherichia coli and Bacillus subtilis.

Credits

5

Instructor

Manel Camps, Karen Ottemann, Chad Saltikov, Victoria Stone

Requirements

Enrollment is restricted to graduate students. Advanced undergraduates may enroll with permission of instructor.

Quarter offered

Winter

METX 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.

Credits

5

Instructor

Fitnat Yildiz, Victoria Auerbuch Stone, Jaqueline Kimmey, Michael Patnode

Requirements

Enrollment is restricted to graduate students.Advanced undergraduates with extensive background in microbiology and biology may enroll with permission of instructor.

Quarter offered

Spring

METX 215 Antibiotics: Actions and Resistance

Critical review of scientific literature covering genetic and physiological mechanisms conferring resistance to antibiotics and their spread in the population. Format based on structured discussion of selected topics and original research proposal.

Credits

3

Instructor

Fitnat Yildiz, Manel Camps

Requirements

Prerequisite(s): METX 206A or METX 119, or by permission of the instructor. Enrollment is restricted to graduate students.

METX 238 Pathogenesis: Molecular Mechanisms of Disease

Provides an overview of the mammalian innate immune response and the role of inflammation in disease. Also, presents how both environmental stressors and microbial pathogens impact inflammation.

Credits

5

Instructor

Donald Smith, Manel Camps, Victoria Stone

Requirements

Enrollment is restricted to graduate students.

METX 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 METX 140.

Credits

5

Instructor

Karen Ottemann

METX 245A Scientific Communication in Microbiology and Environmental Toxicology A

Introduces multiple forms of scientific presentation and communication to graduate students. Students learn to craft and deliver multiple types of written and visual communications, including formal and informal modes, on a topic developed as part of the class.

Credits

5

Instructor

Karen Ottemann, Don Smith

Requirements

Prerequisite(s): METX 200. Enrollment is restricted to graduate students.

Quarter offered

Spring

METX 245B Scientific Communication in Microbiology and Environmental Toxicology B

Continuation of METX 245A. Students develop and refine a capstone in-depth report in a written form and as an oral presentation.

Credits

5

Instructor

Karen Ottemann, Don Smith

Requirements

Prerequisite(s): METX 245A. Enrollment is restricted to graduate students.

Quarter offered

Spring

METX 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.

Credits

5

Instructor

Chad Saltikov

Requirements

Enrollment is restricted to graduate students.

Quarter offered

Spring

METX 281A Topics in Environmental Toxicology

Selected topics in environmental toxicology. Topics vary from year to year.

Credits

5

Requirements

Enrollment is restricted to graduate students; qualified upper-division science majors may enroll with instructor's permission.

Repeatable for credit

Yes

METX 281C Topics in Environmental Microbiology

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.

Credits

2

Instructor

Chad Saltikov

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with instructor's permission.

Quarter offered

Fall, Winter, Spring

METX 281J Mechanisms of Virulence and Resistance to Infectious Disease

Research seminar focusing on the mechanisms underlying host resistance or susceptibility to infectious diseases, and virulence strategies utilized by bacterial pathogens. Participants are required to present results from their own research and relevant journal articles.

Credits

2

Requirements

Enrollment is restricted to graduate students. Qualified undergraduate students may enroll with instructor’s permission.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 281M Topics in Molecular Toxicology

Seminar and discussion on the mechanisms of toxicity in DNA alkylating agents. Participants present results from their research, and relevant journal articles are discussed.

Credits

2

Instructor

Manel Camps

Requirements

Enrollment is restricted to graduate students. Undergraduates may enroll with instructor's permission.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 281O Topics in Bacterial Pathogenesis

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.

Credits

2

Instructor

Karen Ottemann

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with permission of instructor.

Repeatable for credit

Yes

METX 281P Origins and Applications of Human Gut Microbial Symbiosis

Research seminar focusing on how beneficial and harmful bacterial species living in the human intestine compete with one another for nutrients in food, and how our immune systems influence the outcomes of these competitions. Emphasis is placed on the evolution of relationships between organisms. Discussion will include genetic, biochemical, bioinformatic, and immunological methods for advancing knowledge about the impacts of microbes on host health. Participants are required to present results from their own research, analyze current literature, and develop future aims for their studies. All lab members of the Patnode Lab are required to take this course.

Credits

2

Instructor

Michael Patnode

Requirements

Enrollment is restricted to graduate students. Qualified undergraduate students may enroll with instructor’s permission.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 281R Topics in Genome-Environment Interactions

Intensive research seminar focusing on the effects of exposure to environmental agents and multigenerational epigenetic inheritance of disease. Participants are required to present results from their own research and relevant journal articles.

Credits

2

Requirements

Enrollment is restricted to graduate students. Qualified undergraduate students may enroll with instructor’s permission.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 281S Cellular and Organismal Responses to Toxicants

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.

Credits

2

Instructor

Donald Smith

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with permission of instructor.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 281V Topics in Bacterial Pathogenesis and Innate Immunity

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.

Credits

2

Instructor

Victoria Stone

Requirements

Enrollment is restricted to graduate students. Qualified undergraduates performing research under the supervision of the instructor may enroll with instructor's permission.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 281Y Biofilms: Processes and Regulation

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.

Credits

2

Instructor

Fitnat Yildiz

Requirements

Enrollment is restricted to graduate students. Qualified undergraduate students may enroll with instructor's permission.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 282 Current Approaches to Molecular Pathogenesis

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.

Credits

2

Instructor

Karen Ottemann

Repeatable for credit

Yes

METX 290 Proseminar

Special topics offered from time to time by faculty, visiting professors, or staff members.

Credits

5

Requirements

Enrollment is restricted to graduate students; qualified undergraduates may enroll with instructor's permission.

Repeatable for credit

Yes

METX 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.

Credits

5

METX 292 Introductory Graduate Seminar

Weekly seminars by academic and research faculty on their areas of special interest. Students write weekly abstracts on articles covered by the seminars. This course can be taken for Satisfactory/Unsatisfactory credit only.

Credits

0

Requirements

Enrollment is restricted to graduate students.

Repeatable for credit

Yes

Quarter offered

Fall, Winter, Spring

METX 297A Independent Study

Independent study for graduate students who have not yet settled on a research area for the thesis. Students submit petition to sponsoring agency.

Credits

5

Repeatable for credit

Yes

METX 297B Independent Study

Independent study for graduate students who have not yet settled on a research area for the thesis. Students submit petition to sponsoring agency.

Credits

10

Repeatable for credit

Yes

METX 297C Independent Study

Independent study for graduate students who have not yet settled on a research area for the thesis. Students submit petition to sponsoring agency.

Credits

15

Repeatable for credit

Yes

METX 299A Thesis Research

Students submit petition to sponsoring agency.

Credits

5

Repeatable for credit

Yes

METX 299B Thesis Research

Students submit petition to sponsoring agency.

Credits

10

Repeatable for credit

Yes

METX 299C Thesis Research

Students submit petition to sponsoring agency.

Credits

15

Repeatable for credit

Yes