UCR

Center for Plant Cell Biology



Training


Overview

Students will have two major professors from two disciplines and attend lab meetings from both research groups, participate in an annual retreat, and monthly ChemGen IGERT colloquia for research presentations by students and invited speakers.

First year students will perform two to three one-quarter rotations. One of the rotations will be in discipline distinct from the main discipline of the student’s graduate training (i.e. a chemistry student may perform a rotation with a biologist, engineer or computer scientist). This will facilitate the identification of two faculty Participants as co-major professors, representing two distinct disciplines.

Students will complete the coursework recommended by their graduate program, including at least one of two new courses on chemical genomics and systems biology, as well as the Chemical Genomics Design Project Studio developed specifically for the ChemGen IGERT Program.

Year 2 students will attend a professional conference that is outside of their main discipline accompanied by a faculty Participant (i.e. biologists can attend an American Chemical Society, Intelligent Systems for Molecular Biology, IEEE Computational Systems Biology, or Society of Biochemical Engineering meeting; chemists, computational scientists or engineers can attend an American Association of Cell Biologists or American Society of Plant Biologists meeting).

Students will be strongly encouraged to perform a two to four month internship at a foreign university, at a premier US research institute (i.e. Salk or Carnegie), or in industry in Year 2 or Year 3.

In the summer of Year 1, students will assist in the Copernicus project during one week of the summer. This will involve a commitment of six to eight hours of service to improve the knowledge of high school teachers.

Year 3/Year 4 students will supervise an undergraduate student researcher, for eight or nine weeks. It is anticipated that these students will be participants in CEPCEB’s NSF-Research Experiences for Undergraduates (REU) Program.

Required Coursework, Colloquia and Conference

All IGERT students will be provided extensive opportunities for interdisciplinary interactions and training. This will involve coursework, a design studio, frequent colloquia, research retreats, interactions with undergraduates and biology teachers, research conferences and internship opportunities.

ChemGen IGERT Coursework

Each student will complete the specified training in his or her graduate program. The graduate coursework required by the participating graduate programs provides sufficient elective options so that ChemGen students will not be significantly burdened with additional course requirements.

All students must take two courses to ensure cross-disciplinary training. Students must consider that there may be prerequisites to these courses. For example, IGERT students who do not have a bachelors degree in Chemistry are required to officially audit Chem 112C for in the first quarter of their graduate studies before taking Combinatorial Chemistry (CHEM242).  Chemistry students are required to pass the American Chemical Society organic chemistry qualifier exam, according to the Chemistry Department graduate program requirements, to enroll in this class. Course programs are to be discussed with the ChemGen IGERT Director or Assistant Director before students begin their first quarter of classes.

  • Combinatorial Chemistry (CHEM242)
    3-units; taught Winter Quarter
    This course will cover combinatorial chemistry principles and processes, including solid-phase synthesis and compound library production, and exemplary literature on chemical genomics.
  • ChemGen Design Studio (CMDB/BIEN 220)
    3-units; taught Fall Quarter Co-taught with faculty representing each of the program disciplines with Professor S. Cutler as lead instructor. Course activities include lectures by faculty, student presentations of literature, formulation of a design project and proposal. The course provides students with the challenge of developing interdisciplinary research projects based on chemical genomics approaches. Critical thinking in advance of testing experimental hypotheses is a hallmark of successful science. The course is taught in a case-study approach with selected students from biology, computational sciences, and chemical backgrounds on a given team. Students will enroll in this course in the Fall quarter of Year 2.

All students are expected to take at least one graduate level coursework in plant or fungal cellular and/or molecular biology. Any one of the following courses will satisfy this requirement:

  • The Plant Genome (BPSC/BCH 232, 4 units, taught Winter Quarter)
  • Plant Cell Biology (BPSC 237, 4 units, taught Fall Quarter)
  • Signal Transduction in Microbes and Plants (CMDB205, 4 units, taught Spring Quarter)

Students in computer science and engineering that lack basic coursework in biology are expected to take undergraduate coursework to provide proficiency in molecular biology. One of the following courses will fulfill this requirement:

  • Fundamentals of Biology (BIOL5A, taught Fall and Winter Quarters)
  • Molecular Biology (BIOL107A, taught Fall, Winter and Spring Quarter or 107B, taught Spring Quarter)

Core or Elective Courses

There are a number of graduate program core or elective courses with subject matter that directly relates to the chemical genomic theme:

  • Plant Cell Biology (BPSC237)
  • Plant Genome (BPSC231)
  • Signal Transduction in Microbes and Plants (BPSC/CMDB205)
  • Methods in Arabidopsis Research (BPSC210)
  • Cell Biology (CMDB200)
  • Computational Methods for Biomolecular Data (CS234)
  • Data Mining Techniques (CS235)
  • Algorithmic Techniques in Computational Biology (CS238)
  • Biochemistry of Macromolecules (BCH210), Biosensors (CEE230)
  • Modeling Chemical, Biochemical & Environmental Processes (CEE220)
  • Synthesis of Molecules of Biological and Theoretical Interest (CHEM270)
  • Analysis of Single Cells and Subcellular Organelles (CHEM260)
  • Bioorganic Chemistry (CHEM/BCH241)
  • Nanoscale Science & Nanotechnology (ME272), and Cell Engineering (CEE210)

It is expected that most students will also take one or more of these courses to satisfy their graduate program requirements.

Informal Training

ChemGen students are encouraged to enroll in the array of workshops in new methodologies that are held by UCR faculty, CEPCEB Academic Coordinators, visiting scientists, and in conjunction with the City of Hope, a nearby research hospital.

Sample Course Programs for ChemGen IGERT Students in Four ChemGen Disciplines

PhD Programs Plant Cell Biology/CMDB/Plant Pathology/GGB Chemical Engineering Chemistry Computer Sciences
Fall Year 1 Program Core/Elective Course(s), i.e., Plant Cell Biology Program Core/Elective Course(s), i.e., Cell Engineering Program Core Course(s) Program Core/Elective Course(s), Computational Methods for Biomolecular Data
Winter Year 1 Program Core/Elective Course(s), i.e., Signal Transduction in Mocrobes and Plants Program Core/Elective Course(s), i.e., Analysis of Single Cells and Subcellular Organelles Program Core/Elective Course(s), i.e., IGERT course: Combinatorial Chemistry Program Core Course(s)
Spring Year 1 Program Core/Elective Course(s), including IGERT course: Computational & Experimental analysis of Biochem Processes Program Core/Elective Course(s), including IGERT course: Computational & Experimental Analysis of Biochem Processes Program Core Course(s) IGERT course: Computational & Experimental Analysis of Biochem Processes; Algorithmic Techniques in Computational Biology
Fall Year 2 ChemGen IGERT Design Studio ChemGen IGERT Design Studio ChemGen IGERT Design Studio ChemGen IGERT Design Studio
Course programs will be individualized based on area of specialization within the program and breadth of interdisciplinary training. In Chemistry, Chemical Engineering and Computer Science, graduate courses may continue until the end of Year 2. Students will meet minimum teaching assistance requirement for each program: typically 1 to 2 quarters, total. The funding scheme for students involves a TAship in year 4.

ChemGen IGERT Extra-Disciplinary Research Experience

All ChemGen IGERT students are required to have a one-quarter rotation research project with an IGERT Faculty Participant who works outside of their primary discipline. The research project should be one that provides experience that can be applied to enhance their main research focus. This faculty mentor is to be a co-major professor on the student’s dissertation committee.

This rotation project should take place during the first year of graduate studies. With permission from the IGERT Steering Committee, this rotation may take place during the second year of graduate training. (Under some circumstances it may be necessary or desirable for a student to complete a second rotation project in a second discipline. Students wishing to do so must have the approval of their faculty advisor, Graduate Advisor and the IGERT Steering Committee.)

The student needs to consult with their major professor in the selection of the faculty member in a second discipline. It is expected that the student will discuss the appropriateness of research collaboration with this individual.

Extra-Disciplinary Research Proposal

To provide a rewarding research experience, the student is directed to prepare a one-page proposal that includes the following:

  1. The name, department and research focus of the advisor in the second discipline.
  2. The dates of the rotation and the credit units (297 research) to be taken to fulfill the research.
  3. The goals of the research rotation, including an outline of the research plan.
  4. A summary of the expected outcome of the rotation.
  5. Signatures of the student’s major professor and the second discipline professor.

This proposal is to be submitted by email to the ChemGen IGERT Director for evaluation by the Steering Committee, at least three weeks in advance of the beginning of the rotation.

Extra-Disciplinary Research Experience Report:

Within two weeks of the completion of the rotation project, the student is to write a 500-word report that summarizes the research activities and outcome of the rotation. This report should indicate how the research experience is envisioned to enhance the graduate research project.

ChemGen IGERT Colloquia

All ChemGen IGERT students are required to attend seminars designated a ChemGen IGERT seminar. There will be one or two ChemGen IGERT seminars per month. Most of these seminars will be held on Friday at noon in the in the CEPCEB Friday Noon Seminar Series. This forum provides CEPCEB graduate students, postdoctoral researchers, NSF-REU students, special guest researchers, and faculty the opportunity to present their hypotheses and findings in an informal and interactive setting.

Both UCR speakers and invited speakers will be designated IGERT speakers. These will be designated CEPCEB/ChemGen IGERT Friday Noon Seminars. IGERT students will attend theses seminar and then to meet with the speaker and the speaker’s host for a thirty-minute discussion following the seminar. These “brainstorming” sessions will be geared towards students asking and answering questions, such as, “What next?” with respect to the research presented. The UCR ChemGen IGERT Participant who hosts the speaker will facilitate the interactive session.

The ChemGen IGERT program foresees that the more advanced ChemGen IGERT students will ultimately be the organizers of the schedule for the ChemGen IGERT seminars. The ChemGen IGERT students will be encouraged to identify prominent scientists in the field of chemical genomics, chemistry, engineering, bioinformatics/computational sciences, and cell biology. The development of the nine-speaker schedule will be overseen by several faculty Participants. It is anticipated that the students will be directly involved in inviting and hosting these speakers. This will enhance exposure to outstanding scientists and provide contacts that may be of value for many years to come.

ChemGen IGERT students will also be required to attend any presentation by a ChemGen IGERT student given in the CEPCEB Friday Noon Seminar Series. These seminars could report student research progress or could be PhD defense seminars.

In addition, this Friday-noon forum will be the venue for the program group discussions and will be attended by all ChemGen IGERT students and their faculty mentors. These sessions will be scheduled once or twice per year.

ChemGen IGERT Retreat

IGERT students and their faculty mentors will participate in an annual retreat which will convene in the fall, typically in September or October. The retreat will commence on a Friday evening with a social gathering and continue though lunch on the Sunday. The Retreat agenda will be designed to foster effective interaction and communication between students and faculty of different academic backgrounds. It will provide a setting for moderately formal presentation and informal discussions between members of the IGERT group.

The goals of the retreat will be to:

  1. facilitate the identification of participant faculty members’ laboratories for rotations of new students;
  2. sustain enthusiasm about the interdisciplinary nature of the program;
  3. provide students an opportunity to present results in a moderately formal setting; and
  4. increase familiarity and collaborative interactions between program participants. Students in their first year will have the opportunity to present the goals of their first research rotations.

The conference will begin with student introductions. This will be followed by media-free presentations on current and future projects by a small number of Participant Faculty. These “chats” will aim familiarize new students with the diverse research opportunities within the program. The following morning there will be a presentation by an invited speaker, who will be selected to provide a novel perspective on research that is apropos or ancillary to chemical genomics. Following the talk, there will be an open discussion moderated by two faculty Participants. This session will be followed by more traditional 15 to 20 minute presentations by student conferees. Saturday afternoon will conclude either in the form of an athletic event, such as a rope and climbing course program under professional supervision. Saturday evening and Sunday morning sessions will be reserved for more formal presentations by ChemGen students.

First year students may be asked to present the research goals of their first rotation project in a mini-talk or on a poster. Second through fifth year students may be asked to present their research in 15 to 20 minute oral presentations. All IGERT students who do not give a talk, with the exception of first year students, will give a poster presentation on their research. The retreat may also include presentations on the topic of chemical genomics by other graduate students and postdoctoral researchers from UCR. New faculty members, new participants in the program, and faculty without an IGERT student will be invited to present media-free talks, formal talks or to present posters on their laboratory research.

A vital component of the retreat will be the participation of a Keynote Speaker from another institution or from industry. This speaker will be an established investigator in the field of chemical genomics. This will provide students and faculty a unique occasion for extensive discourse. ChemGen IGERT students will be encouraged to choose, extend an invitation, and contribute to the hosting of the Keynote speaker.

The 2007 retreat will be a joint meeting of UCR’s ChemGen IGERT and UCSD’s Plant Systems Biology IGERT.

The retreat attendance of IGERT fellows will be funded by the ChemGen IGERT program. Attendance by faculty and other UCR researchers is not likely to be sponsored by program funds.

ChemGen IGERT Fellow Extension of Knowledge Opportunities

To develop the next generation of socially responsible scientists well equipped to make the transition from academia to research careers, students will participate in mentoring of potential future scientists.

Year 2 Students: ChemGen students will participate in UCR’s Department of Education-sponsored Copernicus program for high school science teacher recruitment, preparation and enrichment. This will be accomplished by contributing a total of four to eight hours to this program in their second summer by participating in the summer workshops on biology for middle and high school students. IGERT students may be asked to provide an array of assistance, from giving laboratory demonstrations to mini-lectures for the Copernicus participants.

Year 3 or Year 4 Students: ChemGen students will serve as a mentor for an undergraduate researcher in an eight to nine-week summer internship program. (CEPCEB has established this model with its NSF-sponsored REU program and has included students who have performed chemical genomics screens and worked in engineering labs in conjunction with biologists.

As an undergraduate mentor the ChemGen student will receive mentoring training, design a project with realistic goals, supervise a student for a nine-week research internship. Supervision of the student is likely to involve a CEPCEB faculty mentor as well. The ChemGen student will supervise day-to-day experimentation and notebook keeping. The undergraduates typically are required to write a research report and prepare a research presentation. Their ChemGen mentor is expected to participate in student guidance in this process.

To benefit the summer intern scientists, the ChemGen IGERT trainees will coordinate a half-day workshop dedicated to the topic of educating the public on science and biotechnology. As our REU program has done in the past, this workshop will involve UCR faculty, such as Dr. Alan McHughen (UC Cooperative Extension Biotechnologist) or Professor Norman Ellstrand (Director of UCR’s Biotechnology Impacts Center of the IIGB) both of whom are actively involved in societal issues of biotechnology.

ChemGen IGERT students are only requested to participate in these outreach programs once during their graduate training program. However, some ChemGen IGERT students will have the opportunity to supervise UCR undergraduates in research.

Student activity in this area will be recorded on the annually submitted ChemGen IGERT Student Annual Progress Form.


More Information

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

Career OpportunitiesUCR Libraries
Campus StatusDirections to UCR

Center Information

Center for Plant Cell Biology
Botany & Plant Sciences Department
2150 Batchelor Hall

Tel: (951) 827-7177
Fax: (951) 827-5155
E-mail: genomics@ucr.edu

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