Academic Programs

The Microbiology and Environmental Toxicology Department at UCSC offers undergraduate and graduate courses in microbiology and environmental toxicology, and grants Ph.D. and M.S. degrees. The curricuclum provides a strong foundation in multiple areas of microbiology, toxicology, and  pharmacology to achieve the breadth and depth of perspective required for this interdisciplinary science. 

Helpful forms can be found HERE at the division of graduate studies.

The METX Grad Handbook can be found HERE.

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Graduate Programs

Graduate training in the Department of Microbiology and Environmental Toxicology 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 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.

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.
  • A qualifying examination 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.

Ph.D. Program

Ph.D. gradutes will demonstate:

  1. Mastery of the fundamental knowledge in microbiology or environmental toxicology
  2. Ability to conduct independent research and manage a research project in either microbiology or environmental toxicology
  3. Ability to communicate scientific concepts and results in both written and oral forms.
  4. Be equipped with interdisciplinary skills needed for success in microbiology and environmental toxicology fields, where there is a great need for scientists who have broad, interdisciplinary training.
  5. Knowledge and understanding of ethical standards in proposing and executing professional scientific research.
  6. Ability to effectively teach science in a classroom environment.
  7. Ability to perform in leadership roles among peers that engage fellow students and promote the success of the departmental graduate programs. Students report annually at their advising meeting (with the Grad Advisor) how they met this requirement.

The requirements for the METX Ph.D. degree are described below.

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 238, 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).

Literature Review

Students write a literature review of the current state of the field of the proposed dissertation research, under direction of the student’s advisor. This written review will be submitted to the student’s advisor no later than the first day of fall quarter of the students second year.

Departmental Seminars

Students present a 20 minute departmental seminar each academic year, except during their third year when they present a 50 minute seminar.

Teaching Requirements

Doctoral students are required to work as teaching assistants 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.

Qualifying Examinations

The qualifying examination consists of a written description and defense of the Ph.D. thesis. This exam is taken in Spring Quarter of the 2nd year. The student’s advisor may not help in the preparation of the written or oral portion.

Advancement to Candidacy

The student advances to candidacy after completing all coursework, completing the literature review, giving a Third Year Seminar, and passing the Ph.D. Qualifying Examination Parts I and II, and forming a Dissertation Reading Committee. If all these milestones have been met, the student will be officially advanced the quarter after the QE II is passed.

Dissertation Committee (Thesis Committee)

After passing the QE II, the student forms a Dissertation Reading Committee in consultation with her/his research advisor. The Dissertation Reading Committee consists of at least three members, including two METX faculty (including the student’s advisor), and at least one member from a different department at UCSC, another UC campus, or another institution. Typically this committee contains the same members as are on the QE II Committee, although only three members are required. The committee is approved by Graduate Division by completion of this form. The student is expected to meet with their Dissertation Reading Committee at least once per year to inform them of his/her progress toward their Ph.D. The Dissertation Reading Committee remains standing until the student has completed all requirements for the doctoral degree.

Dissertation Defense

The student must submit their doctoral dissertation to the Dissertation Reading Committee for tentative approval at least one month before presenting a formal, public doctoral research seminar. All of the Dissertation Reading Committee members should be in attendance at this seminar. After the seminar, the Dissertation Reading Committee, and any other faculty wishing to do so, meet with the student to discuss her/his dissertation. The candidate must defend the work to the satisfaction of the Dissertation Reading Committee at the post-seminar session. Objections raised or deficiencies noted in this session must be met and corrected to the satisfaction of those concerned before the Chair of the Committee signs the cover sheet, signifying acceptance of the dissertation.

Catalog Rights

Students matriculating in a given graduate program, including those in Microbiology and Environmental Toxicology, will select the UCSC General Catalog they will follow to meet their requirements to be either the one published the year they enter the program, or any subsequent catalog published prior to the year they are awarded the degree sought. Students who seek readmission after a break in attendance of greater than two years (six regular quarters) must adhere to the graduation requirements in effect at the time of readmission or to those subsequently established for all portions of the degree requirements not already fulfilled. The readmitting program will determine which degree requirements remain to be fulfilled, and will communicate this information in the letter offering readmission. This determination constitutes a formal requirement for readmission to the program, and the student’s acceptance of readmission implies acceptance of the program’s written stipulation of remaining degree requirements. Should any student choose to follow catalog requirements for a year in which the catalog is not printed in hard copy, the requirements will include any online catalog update for that year. A student must follow the chosen catalog in its entirety, including both the individual degree program and general university requirements. General university requirements may be found in the Graduate Student Handbook.
Ref:  http://registrar.ucsc.edu/navigator/section1/catalog-rights.html

PBSE METX Track

The Department of Microbiology and Environmental Toxicology also participates in a rotation-based Ph.D. umbrealla program in Biomedical Sciences & Engineering with the PBSE METX Track. Students interested in the broad areas of chemical biology or molecular biology should consider this interdisciplinary graduate program that brings together the expertise from the departments of Microbiology and Environmental Toxicology, Chemistry and Biochemistry, Molecular, Cell and Developmental Biology, and Biomolecular Engineering. Highlights of PBSE include research laboratory rotations, journal clubs, and targeted seminar series--all in a collaborative environment. Find more information here.

M.S. 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.
M.S. graduates will demonstrate: 
  1. Proficiency with the fundamental knowledge in either microbiology or environmental toxicology.
  2. Ability to conduct independent research in either microbiology or environmental toxicology.
  3. Ability to communicate scientific concepts and results in both written and oral forms.
  4. Be equipped with interdisciplinary skills needed for success in microbiology and environmental toxicology fields, where there is a great need for scientists who have broad, interdisciplinary training.
The requirements for the METX M.S. degree are described below.

Plan I (Coursework, Research, and Thesis)

Coursework:

  • Core courses (2):
    • METX 200, Interdisciplinary Approaches to Environmental Toxicology

    • METX 205, Scientific Skills, Ethics, and Writing

 

  • Two courses from the following (2):
    • 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
    • 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 the following: Introductory Graduate Seminar (METX 292), an Independent Study (METX 297 or 299), and a topical seminar (METX 281).

Literature Review

Students write a literature review of the current state of the field of the proposed dissertation research, under direction of the student’s advisor. This written review will be submitted to the student’s advisor no later than the first day of fall quarter of the student's second year.

Departmental Seminars

Students present a 20 minute departmental seminar each academic year. Upon completion of the Masters thesis, students present the thesis research during a full-length departmental seminar.

Master's Reading Committee

The student should form a Master's Reading Committee during their first year by completing and submitting a Master's Reading Committee Nomination Form. The Master's Reading Committee consists of at least three faculty members, of which two must be from the METX faculty, including the student's advisor. The third member may be from the department or outside the department/university. The student will meet with their Master's Reading Committee at least annually throughout their tenure in the program to discuss with the committee the student's thesis plan, progress and intention to graduate. The last meeting should be approximately one quarter before the student intends to graduate.

Master's Comprehensive Exam

The Masters Comprehensive Exam is a presentation and defense of the student's Masters research proposal, including relevant background knowledge, and preliminary data, if any. The exam will not be specifically course based, but will draw on knowledge from courses.
  • Current students, please see the Faculty Graduate Representative for a detailed description of the proposal and timing of submission.
  • The written proposal should not exceed 3 text pages, excluding references, plus one page of figures.
  • Students should schedule this exam before the end of fall quarter of their second year.
  • The exam will be given by the student’s Masters Reading Committee, established by the student at least one quarter before the exam.
  • Students should submit the written proposal to their Masters Reading Committee at least 2 weeks before the exam.
  • There is a standard Rubric used for evaluating the student's performance. It includes expectations based on departmental Program Learning Outcomes as well as an opportunity for the committee to comment on the student's performance and give recommendations. This evaluation becomes part of the student's file. Rubrics can be found at the end of the hadnbook and in the METX Google Drive.

The Master's Comprehensive exam oral defense

After submitting your written proposals, you will be orally examined by the examination committee. These exams are given as chalk talks, PowerPoint is not allowed. You should plan how you will lay out your experiments on the board, to give an organized presentation. Be prepared to present your proposed studies; discuss the rationale behind your experimental choices; discuss possible data outcomes, interpretations and alternatives; provide follow up experiments to each outcomes; discuss the significance of your research question. 

Master's Thesis

Students are required to submit a thesis for fulfillment of the degree requirements. The format and contents of the thesis will be agreed upon by the student and the Masters Reading Committee. The thesis should be submitted to the Master's Reading Committee by the second week of the final quarter of work, generally spring of the second year.

 

Plan II (Coursework and Capstone)

The Plan II MS option provides qualified students the opportunity to earn a Master’s in Microbiology and Environmental Toxicology in one year.
The distinctive features are:
  • Students will be able to earn the MS degree in a single year, versus two years for the Plan I research/thesis MS students, who require two years to complete their substantial research requirement.
  • Students will receive a rich educational experience with emphasis on multidisciplinary microbiology and environmental health-related curricula. By taking the same graduate courses as the research MS and PhD students, and by having the opportunity to closely interact with those students as well as faculty in a research university, the Plan II MS students will gain both broader and deeper perspectives into the critical environmental health issues of our day.

Coursework:

  • Core course (1):
    • METX 200, Interdisciplinary Approaches to Environmental Toxicology
  • Two courses from the following (2):
    • 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
  • At least one integrative graduate course from the following (1):
    • METX 238: Molecular Mechanisms of Defense
    • BIOL 217: Influence of Environment and Experience on Brain Development

At least one additional 200-level course within METX or another department (1).
If outside the METX department, pre-approval must be obtained by the METX graduate advisor and the instructor of the course.

At least one additional 100 or 200-level course within METX or another department (1). 
If outside the METX department, pre-approval must be obtained by the METX graduate advisor and the instructor of the course.

Winter and Spring quarter Capstone courses (2)

Departmental Seminars


Attendance at Departmental seminar series: Attendance at weekly seminar speakers is required to obtain exposure to the breadth and depth of microbiology and environmental health science and careers. Each quarter, 0 credits.

Capstone Written Proposal


The Plan II MS capstone will be achieved by taking the two required capstone preparation graduate courses in winter and spring quarter, and completing a science or policy-based proposal or review-type article to pursue a problem selected by the student in consultation with the graduate advisor and assigned METX capstone advising faculty member. Instruction on science writing, geared towards a range of possible audiences, will be provided in the capstone courses. The proposal will be read for approval by the two METX faculty assigned as capstone advisors for each student.

Catalog Rights

Students matriculating in a given graduate program, including those in Microbiology and Environmental Toxicology, will select the UCSC General Catalog they will follow to meet their requirements to be either the one published the year they enter the program, or any subsequent catalog published prior to the year they are awarded the degree sought. Students who seek readmission after a break in attendance of greater than two years (six regular quarters) must adhere to the graduation requirements in effect at the time of readmission or to those subsequently established for all portions of the degree requirements not already fulfilled. The readmitting program will determine which degree requirements remain to be fulfilled, and will communicate this information in the letter offering readmission. This determination constitutes a formal requirement for readmission to the program, and the student’s acceptance of readmission implies acceptance of the program’s written stipulation of remaining degree requirements. Should any student choose to follow catalog requirements for a year in which the catalog is not printed in hard copy, the requirements will include any online catalog update for that year. A student must follow the chosen catalog in its entirety, including both the individual degree program and general university requirements. General university requirements may be found in the Graduate Student Handbook.

Please be aware that students applying to the M.S. Program are expected to be self funded. 

5th Year Research-Based MS Program

The 5th Year (4+1) Master's path is essentially an honors program, allowing qualified undergraduates to continue their undergraduate research and earn a Master’s in Microbiology and Environmental Toxicology in one year following completion of their Bachelor’s degree.  The 5th Year Master's path has the same requirements as the METX Master's program, with the only difference being the ability to accelerate earning the METX Master's by initiating Master's research and coursework as an undergraduate senior.

Stage 1: Undergraduate students apply for acceptance to the contiguous BS/MS program, in consultation with their undergraduate faculty advisor. Due August 15 prior to the start of the last undergrad year.

Prospective students must identify a faculty mentor, and then work with their faculty mentor to prepare an application and plan for their 5-year BS/MS. The faculty mentor can be in any department, but must approve of the student earning a METX MS degree. The METX Grad Program Director and Grad Advisor can help with this step if needed. The application should provide evidence of solid academic performance in general and in the student's undergraduate major. The plan should be completed and submitted to the METX Grad Program Advisor (metxadmn@ucsc.edu) by August 15, prior to the start of the students last undergrad year (e.g. end of the junior year). It should include the following:

  • A 1 page statement describing i) your motivation and academic preparation for entering the program, ii) your goals for the MS program, including the area of concentration, iii) the name of a faculty member willing to serve as your MS thesis advisor, and iv) future professional goals. Note, the advising faculty member does not have to be in the METX department, but must approve of the student earning a METX MS degree.
  • 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 faculty member who will supervise the MS work. If the student is new to that lab, they should include a second letter from a faculty member attesting to the student’s promise for a MS degree.
  • A coursework plan that will enable the student to complete both the requirements for the BS in their undergraduate department and MS in METX in 5-years, including demonstrating sufficient coursework capacity to complete at least two METX graduate courses in their final undergraduate year. Students in the 5th year program must take at least one graduate class in Fall Quarter of their undergraduate year. 

The METX Grad Program Advisor will submit the applications of students who meet these minimum requirements to the METX Admissions Committee for consideration for acceptance into the contiguous 5-year BS/MS program. Acceptance will be decided before the start of Fall Quarter. 

Stage 2:  Students will go through the regular METX MS application process in their senior year.

The criteria for admission to the METX MS program will be the same as for all METX MS program applicants.  Since students in the contiguous BS/MS program will take some METX graduate courses in their senior year (e.g., METX 200, and up to two additional courses from  201, 202, 206, or 210), performance in these courses will also contribute to the assessment of student progress and ability to complete the METX MS degree in one post-baccalaureate year.

 

Undergraduate Programs

The Microbiology and Environmental Toxicology Department offers a select number of undergraduate courses to prepare and attract promising undergradutes 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 sciences undergraduates to conduct research in the labs of faculty within the Microbiology and Environmental Toxicology Department. 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. Contact individual faculty for more information. 

Enrollment

Unless noted below, all courses will have an auto-enroll wait list during your Second-Pass Enrollment period.

All students enrolled, waitlisted, or seeking a seat in courses MUST attend the first class meeting.
You must meet the prerequisites and major or class-level restrictions in order to enroll.

METX 119: If course is full, please check your student portal for your Second-Pass Enrollment time and date and enroll on the wait list. In MyUCSC, click on "details" under "Enrollment Dates".

METX 119L: If course is full, please check your student portal for your Second-Pass Enrollment time and date and enroll on the wait list. In MyUCSC, click on "details" under "Enrollment Dates".

Please note that enrollment does shift after grades post for the previous quarter. Those who are enrolled but do not pass the prerequisites will be dropped.

Enrollment FAQs for Students
METX Class Schedule
Course Catalog & Prerequisites

Independent Study Request Form

Independent Study in the METX department can take many forms and offers students an opportunity to work directly with Faculty on a research project. In the UCSC catalog, the description is simply " directed reading, supervised research, and organized projects relating to METX problems".  We encourage students to propose an idea to a faculty member who teaches and does research in the area of interest.

How to enroll in Independent Study.

  1. Formulate an idea with help from METX advising; TA's; friends; mentors; METX Faculty
  2. Select a couple METX faculty members and bring your idea to them during their office hours.
  3. Once the project is decided on with a faculty member, fill out the "Petition for Undergraduate Individual Studies Course" enrollment form.  Independent study courses do not exist on the schedule of classes and are only enrollmed in through this process.
  4. Your faculty sponsor will give out the class number that is entered on the enrollment page of the MyUCSC student center.

Independent study projects will carry either 2 units or 5 units, depending on the complexity of the project and how many weekly hours are expected.

See Also