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Microbiology and Environmental Toxicology

2017-18 General Catalog

430 Physical Sciences Building
Telephone (831) 459-4719
FAX (831) 459-3524
http://www.metx.ucsc.edu

Faculty | Course Descriptions

Program Description

The Microbiology and Environmental Toxicology Department (METX) offers undergraduate and graduate courses in microbiology and environmental toxicology, both within the department and through affiliated departments. The curriculum provides a strong foundation in fundamental and applied toxicology and microbiology to achieve the breadth and depth of perspective required for this interdisciplinary science. Research interests of students and faculty in METX span the fields of biology, microbiology, chemistry, Earth sciences, ocean sciences, environmental studies, and human health.

Undergraduate Programs

The METX Department only awards graduate degrees, although it does offer a select number of undergraduate courses to prepare and attract promising undergraduates for advanced studies in microbiology and environmental toxicology or health-related disciplines. Students interested in microbiology and environmental health should major in a field such as biology; marine biology; molecular, cell, and developmental biology; biochemistry; chemistry; Earth sciences; engineering; or environmental studies while taking microbiology and environmental toxicology electives.

In addition, the program provides unique opportunities for exceptional undergraduates to conduct research in microbiology and environmental toxicology. These opportunities are limited to students who have demonstrated their potential in undergraduate courses in the basic sciences and environmental health. With department approval, these undergraduates may also take graduate courses in microbiology and environmental toxicology, that coursework may be applied toward a graduate degree in microbiology and environmental toxicology if the student is accepted into the program.

Graduate Programs

Graduate training in the METX Department prepares students to solve important problems in the field of environmental health by providing stimulating coursework, extensive scientific presentation training, and for the research-oriented Ph.D. and M.S. degrees, in-depth research that culminates in a thesis. There is no other program in the world that educates students to appreciate the interplay between microbes, chemical toxins, and health and provides the training students require to work effectively in a complex world. Graduate training in the METX department prepares students to become leaders in the field, following career paths in academia, teaching, industry, and government. Doctor of Philosophy (P.D.) students typically finish in four to six years. The research-oriented Master of Science (M.S.) students typically finish in two years, while the coursework/capstone M.S. students can finish in one year.

METX Ph.D. Degree Program

Key components of our graduate training include:

  • Interdisciplinary core course that teaches critical thinking and how to approach complex problems in environmental health: METX 200, Interdisciplinary Approaches to Problems at the Interface of Microbiology and Environmental Toxicology.

  • Core course devoted to grant-writing and scientific-writing skills: METX 205, Scientific Skills, Ethics, and Writing.

  • Personalized class plan for the remaining three courses to fit the student’s background and research goals. Possible courses include METX 201, Sources and Fates of Pollutants; METX 202, Cell and Molecular Toxicology; METX 206A, Advanced Microbiology; METX 210, Molecular and Cellular Basis of Bacterial Pathogenesis; METX 238, Pathogenesis: Molecular Mechanisms of Disease; METX 250, Environmental Microbiology; and METX 270, Frontiers in Drug Action and Discovery. Courses in other departments include Ocean Sciences 220, Chemical Oceanography; and Molecular Cell and Developmental Biology 200B, Advanced Molecular Genetics.

  • Speaking presentation skills training through coursework and yearly departmental presentations. Scientific writing and literature mastery through the writing of a literature review in the first year. Weekly seminars expose students to the breadth of our fields and provide students with opportunities to interact closely with speakers and form connections and collaborations.

  • Qualifying examinations designed to perfect the student’s ability to craft and defend research plans.

  • For Ph.D. and Plan I (research thesis) M.S. students, extensive laboratory research training that starts immediately upon entering the program and culminates in the student’s Ph.D. dissertation or Master's thesis.

Sample Pathways

Pathways within the microbiology and environmental toxicology graduate program focus on interdisciplinary approaches to addressing problems in environmental and public health.  We offer several defined training pathways, and also support students who want to create their own.

Metals in the Environment

Research includes investigating the concentration, speciation, and isotopic composition of contaminant metals and metalloids in the environment, how organisms are exposed to metals as potential toxicants, and how these metals cause toxicity..

Microbiology

Microbiology provides research training on molecular genetic analysis of both non-pathogenic and pathogenic microbes. Students study host-pathogen interactions, ecology and evolution of pathogenic microorganisms, adaptation of pathogenic and non-pathogenic microorganisms to environmental stresses, and mechanisms of microbial biotransformation of pollutants and toxic metals.

Cellular and Organismal Toxicology

This pathway provides training in the biochemical, molecular, cellular, and physiological processes that are impacted by exposures to contaminants such as toxic metals. Research includes exposure pathways and toxicity of contaminants and pathogens within humans, with emphasis on the molecular and cellular mechanisms underlying toxicity.

Microbial Biology and Pathogenesis track within the Program in Biomedical Sciences and Engineering (PBSE)

The METX Department also admits students through the PBSE program Microbial Biology and Pathogenesis (MICRO) Ph.D. track. The PBSE track is a rotation-based graduate umbrella program. This training program emphasizes the application of diverse approaches, including biochemistry, genetics, genomics, ecology, and imaging to address questions at the forefront of microbial biology. Interdisciplinary research is encouraged and supported by a diverse group of faculty from the METX Department as well as from the Departments of Biomolecular Engineering; Ocean Sciences; Molecular, Cell, and Developmental Biology; Evolutionary and Ecology Biology; and Chemistry and Biochemistry.

Requirements specific to the Ph.D. degree

1. Required core courses (2):

METX 200, Interdisciplinary Approaches to Environmental Toxicology

METX 205, Scientific Skills, Ethics, and Writing

Two courses from the following:

METX 201, Sources and Fates of Pollutants

METX 202, Cell and Molecular Toxicology

METX 206A, Advanced Microbiology

METX 210, Molecular and Cellular Basis of Bacterial Pathogenesis

METX 250, Environmental Microbiology

METX 270, Drug Action and Development

At least one additional approved graduate-level METX course or from another department.

Any additional courses as recommended by your first-year advising committee.

Each quarter, students must enroll in at least the following: METX 292, Introductory Graduate Seminar; METX 297, Independent Study; and a topical seminar (METX 281).

2. Literature review. Under direction of the student’s adviser, write a literature review of the current state of the field of the proposed dissertation research. The written review will be handed in to the student’s adviser at the end of the summer of the first year.

3. Department seminar. Give a 20-minute departmental seminar each academic year, and one 50-minute departmental seminar during the fall quarter of the third year.

4. Teaching assistant. Doctoral students are required to work as teaching assistants (TA) for at least one quarter. Priority for TA positions is given to first-year doctoral students, then to current doctoral students who have not yet worked as a teaching assistant.

5. Ph.D. qualifying examination (QE1—microbiology and environmental toxicology internal). Part I of the qualifying examination consists of two portions: preparation and defense of an independent research proposal prepared by the student, and knowledge of material presented in the microbiology and environmental toxicology core courses taken by the student.  The student must complete QE1 no later than spring quarter of the second year.

6. Third-year seminar and thesis proposal. The student will present a 50-minute seminar on his/her dissertation research proposal no later than the end of fall quarter in the third year.

7. Ph.D. qualifying examination (QE2). Present and defend a dissertation research proposal to the student’s Ph.D. qualifying examination (QE) committee. The student must complete QE2 no later than fall quarter of the third year.

8. Advancement to candidacy. The student advances to candidacy after completing all coursework, completing the literature review, giving the third-year seminar and passing the Ph. D. qualifying examination parts I and II.

9. Dissertation defense. The student must submit their doctoral dissertation to the dissertation committee for tentative approval at least one month before presenting a formal, public doctoral research seminar.

METX Master’s Degree Program

The Microbiology and Environmental Toxicology Department offers a Master of Science (M.S.) degree in microbiology and environmental toxicology (METX). The METX M.S. degree can be attained through Plan I thesis (coursework and thesis, minimum 40 credits) or Plan II (coursework and capstone project, minimum 40 credits). In addition, METX offers a fifth-year Plan I (thesis) M.S. degree path when earned contiguous with an appropriate Bachelor of Science (B.S.) degree at UCSC. The METX M.S. degree combines core courses and electives to provide interdisciplinary training in microbiology, toxicology, and environmental health sciences.  Graduates from the program are exceptionally prepared to take research or management positions in organizations concerned with microbial and environmental health-related sciences. Graduates may also pursue fields in education or enter doctoral programs in biological and environmental health sciences or related fields.

Requirements Specific to the Master’s Degree

Plan I (coursework, research, and thesis) M.S. degree

Prospective students who are interested in research careers, or gaining research experience prior to entering a doctoral  program, may consider the thesis M.S. degree (Plan I).

1. Required core courses (2):

METX 200, Interdisciplinary Approaches to Environmental Toxicology

METX 205, Scientific Skills, Ethics, and Writing

Two courses from the following:

METX 201, Sources and Fates of Pollutants

METX 202, Cell and Molecular Toxicology

METX 206A, Advanced Microbiology

METX 210, Molecular and Cellular Basis of Bacterial Pathogenesis

METX 250, Environmental Microbiology

METX 270, Drug Action and Development

At least one additional approved graduate-level METX course or from another department.

Any additional courses as recommended by your first year Advising Committee.

Each quarter, students must enroll in at least the following: Introductory Graduate Seminar (METX 292), Independent Study (METX 297), and a topical seminar (METX 281).

2. Literature review. Under direction of the student’s adviser, write a literature review of the current state of the field of the proposed dissertation research. The written review will be handed in to the student’s adviser at the end of the summer of the first year.

3. Department seminars. Give a 20-minute departmental seminar in the first academic year and one 50-minute departmental seminar on thesis work during the spring of the second year.

4. Master’s comprehensive examination. The master’s comprehensive exam is a presentation and defense of the student’s master’s research proposal, including relevant background knowledge. The examination will not be specifically course-based, but will draw on knowledge from courses. This examination is taken in the fall quarter of the second year.

5. Thesis. Students are required to submit a thesis for fulfillment of the degree requirements. The thesis should be submitted to the student’s master’s reading committee one month before the due date.

Plan II (Coursework and Capstone) M.S. Degree

The Plan II coursework M.S. degree may be of interest to students interested in interdisciplinary graduate training in microbiology and environmental health-related fields, but with career goals other than research, such as government service, non-profit NGOs, and private sector biotech and environmental health companies.

1. Required core course:

METX 200, Interdisciplinary Approaches to Environmental Toxicology

Two courses from the following:

METX 201, Sources and Fates of Pollutants

METX 202, Cell and Molecular Toxicology

METX 206A, Advanced Microbiology

METX 210, Molecular and Cellular Basis of Bacterial Pathogenesis

One course from the following:

METX 238, Pathogenesis: Molecular Mechanisms of Disease

BIOL 217, Influence of Environment and Experience on Brain Development

At least one additional approved graduate-level METX course or from another department.

At least one additional approved general elective METX course or from another department.

Each quarter, students must enroll in Introductory Graduate Seminar (METX 292)

2, Plan II MS students will also complete a capstone writing project (METX 240A and METX 240B) to be completed under the guidance/mentorship of a faculty member in the department.  As an example, capstone projects may include a scientific research proposal or a substantial review article.

METX Fifth-Year M.S. pathway

METX offers a fifth-year Plan I (thesis) M.S. degree path when earned contiguous with an appropriate Bachelor of Science (B.S.) degree at UCSC. The fifth-year M.S. path provides highly motivated undergraduate majors the opportunity to earn separate B.S. and M.S. degrees in five years. The path provides the additional level of preparation and experience that students need to pursue careers in industry, government, or to increase their competitiveness for top Ph.D. programs. Students apply to be accepted into the fifth-year M.S. path in consultation with their faculty or undergraduate adviser, no later than the end of the spring quarter of the junior year.

To be accepted to the path, students will need to prepare an application and plan for their fifth-year BS/MS, providing evidence of solid academic performance in general and in their undergraduate major. The application should be submitted no later than end spring quarter of the junior year, and should include:

  • A one-page personal statement describing a) the student’s motivation and academic preparation for entering the path; b) the student’s goals for the fifth-year path, including the area of concentration; c) the name of a faculty member willing to serve as their thesis adviser (if appropriate); and d) future professional goals.

  • Copy of unofficial transcripts establishing the GPA requirements in the undergraduate major and overall. Applicants should possess a GPA in courses of their undergraduate major (biology, chemistry, etc.) of 3.2 or above, and an overall GPA of 3.0 or above.

  • A letter of recommendation from the METX faculty member attesting to the student’s promise for a M.S. degree in METX.

  • A coursework plan that will enable them to complete both the requirements for the B.S. in their undergraduate department and M.S. in METX in five years, including demonstrating sufficient coursework capacity to complete at least one to two METX graduate courses in their final undergraduate year.

If accepted into the fifth-year B.S./M.S. path, students will go through the regular METX M.S. application process early in their senior year. The criteria for admission to the METX M.S. program will be the same as for all METX M.S. program applicants.

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Revised: 09/01/17