genetics graduate group advising highlights

Table of Contents

Genetics Graduate Group Advising Highlights

Course list

Seminar List

Expanded Guidelines for Qualifying Exam

Focus Groups

Animal Genomics

Chromosome Biology

Human Genetics

Model Plants

General Genetics

Plant Breeding and Biodiversity

Requirement Spreadsheet

Executive Committees

Advisor Information

Faculty Roster

Student Roster

Forms

Genetics Graduate Group Advising Highlights

New Student Orientation- Fall 2006

Advising-You have two official faculty mentors recognized by Office of Graduate Studies-

1. Academic Adviser

2. Major Professor (also known as your Dissertation Adviser or Thesis Adviser)

The two above must be different people! Others can serve as “mentors” as well.

Ellen Picht is also a resource (Graduate Group Complex, 310 Life Sciences)

1. Academic Adviser-nominated by Genetics Graduate Group and appointed by Graduate

Studies

Initially assigned an adviser based on research interests and your application. You may change

your adviser after consultation with the Master Adviser.

The Master Adviser is a faculty member whose job is to coordinate advising activities. The

Master Adviser as well as advisers not assigned specifically to you can also advise you if your

academic adviser is not available (for example, out of town).

Meet (academic) adviser to plan coursework to:

Ensure that deficiencies are dealt with and that remedial courses are taken

Ensue that required coursework is taken

Monitor finding research home

Help with dealing with university bureaucracy

Help solve problems with GGG program or major professor

Approve/sign petitions for late drop/PELP/Advancement to Candidacy

Get career advice

Receive periodic review of progress

Important notes:

1. If you are a full-time student: Enroll in 12 units every quarter

continuously. If you are taking classes, then schedule your 299 units to bring you up to

at least 12 units. Don’t let your registration lapse (you do not have to register for the

Summer). You must be either registered or on filing fee the quarter you submit

thesis/dissertation. Once you stop taking classes, enroll in 12 units of 299 Research units.

2. You must receive a B or better in the required GGG courses and maintain an overall B

average.

3. Do not sign up S/U for core courses or elective courses, or any courses related to GGG

and your program-these must be taken for a grade.

Times you need to see your academic adviser: You are responsible for organizing and arranging these meetings- if you are having problems,

see your Academic Adviser first.

A. First Quarter Guiding Committee Meeting-

Meet with Guiding Committee sometime during the first quarter (two other members are

assigned). If you are a member of a lab already, your future major professor should also be a

member.

Identify any prerequisites/deficiencies that need to be taken.

Discuss Winter/Spring course possibilities- discuss electives

Discuss research interest/rotations

Discuss focus group interest-decide if should switch advisers, guiding membership

Form submitted to GGG by you after meeting is held and signatures obtained.

B. Third Quarter Guiding Committee Meeting Before this meeting, Major Adviser will reconstitute committee with Adviser, future Major

Professor and one other interested faculty (can be some of the same members as above).

Suggestions from the student and major professor are advised as to composition.

Check on progress –completing prerequisites, requirements? Maintaining a B average?

Are elective courses appropriate?


C. Fifth Quarter Guiding Committee Meeting Same committee as in (B).

Verify that have completed/or will complete ALL coursework by end of 6th

quarter

Suggest Qualifying Examination Committee Members

Verify that have dissertation proposal- submit abstract


Advisers then assign QE members using suggestions from students as guide.

Official request for QE membership submitted to Graduate Studies for approval.

D. Annual Dissertation Committee Reports- After passing your QE, you are required to meet

with the Dissertation committee at least one time per year. A form must be completed with

signatures, submitted to your adviser for signature, and then submitted to GGG office.

E. Graduate Studies Annual Progress Reports- Currently required to be submitted by GGG

to Graduate Studies by July 1. Requires adviser signature, submit to GGG office.

Milestones

A. Qualifying Examination- should be taken by end of Winter Quarter of third year. Students

typically take it Summer/Fall/Winter Quarter (7th

, 8th

quarter). Students must take the QE by the

9th

quarter to remain eligible for RAs, TAs.

B. Advancement to Candidacy- After passing the QE, you form a dissertation committee.

This step requires a form submitted to Graduate Studies and the Registrar. This committee has

three members, one of which is your Major Professor. The other two are chosen by you after

consultation with your Major Professor.

Genetics Graduate Group Course List

A. GGG Required Courses

1. Core Courses:

GGG201A (Fall Quarter) Advanced Genetic Analysis/Model Systems (5 units)

(CRN 27053 or 27054 depending on which discussion section you sign up for)

Lecture: TR 0900-1020 AM 101 Bowley Center Room

Discussion: Tuesday 12:10-2 PM 3 Wellman or

Wednesday 1:10-3 PM 101 Bowley Center Room

GGG 201B (Fall Quarter) Genomics (5 units) (CRN 27055)

Lecture: TR 10:30-11:50 AM 1344 Storer

Discussion: TR 6:10-8 PM 1137 PES (Plant and Env. Sciences)

GGG 201D (Winter Quarter) Quantitative and Population Genetics

GGG201C/ MCB 221C (Spring Quarter) Molecular Biology

2. Seminar Course:

GGG 291 (Winter) History of Genetics-

GGG Seminar Courses

GGG293 (Spring quarter 2007) Seminar in Animal Genetics

GGG294 (Winter quarter 2008) Seminar in Human Genetics

GGG295 (Fall Quarter 2006) Seminar in Chromosome Biology

Wolf Heyer, Professor, Instructor-in-Charge

GGG297 (Winter quarter 2007) Seminar in Plant Genetics (Model Plants)

GGG297 (Fall quarter 2007) Seminar in Plant Genetics (Plant Biology)

B. GGG Rotation Laboratory Courses

GGG Laboratory courses:

GGG205-(Fall) Molecular Genetics Laboratory (Rotations)-Lyons (CRN 27056)

GGG205-(Winter) Molecular Genetics Laboratory (Rotations)-Syvanen

GGG207L-(Fall, Winter, Spring) Research Methods in Plant Genetics Laboratory-

C. Other GGG courses:

GGG210 (Fall 2006) Horizontal Gene Transfer-Cal Kado, Mike Syvanen (3 units)

(CRN 27059)

GGG211 (Winter) Concepts in Human Genetics and Genomics

GGG220/VCR 220 (Winter) Genomics & Biotechnology of Plant Improvement Michelmore

GGG296 (Fall 2005) Science Professionalism and Integrity- Yoder (2 units) (CRN

27062)

GGG298 (Fall, Winter, Spring) Group Study

GGG299 (Fall, Winter, Spring) Research

GGG300 (Fall, Winter, Spring) Teaching in Genetics

Additional Courses with a Genetic Component

General Genetics:

Upper Division Undergraduate

ANG 107 (Fall) Genetics and Animal Breeding

ANT 151 (Spring) Primate Evolution

ANT 152 (Winter) Human Evolution

AVS 103 (Spring) Avian Development and Genetics

BIS 101 (Fall, Winter, Spring) Genes and Gene Expression

MCB 121 (Winter, Spring) Molecular Biology of Eukaryotic Cells

MCB 162 (Fall) Human Genetics

MCB 163 (Winter) Developmental Genetics

MCB 164 (Winter) Advanced Eukaryotic Genetics

MIC 150 (Winter) Bacterial Genetics

MIC 170 (Spring) Yeast Molecular Genetics

Molecular Genetics

Graduate

ANG 211 (Spring) Genetic Engineering of Animals

ANG 212 (Winter) Sequence Analysis in Molecular Genetics

MCB 255 Molecular Mechanisms in Animal Development

MCB 256 (Fall ) Cell and Molecular Biology of Cancer

MCB 257 (Fall ) Cell Proliferation and cancer genes

MCB 262 (Winter ) Transgenic Expression Systems

MCB 263 (Winter) Biotechnology Fundamentals & Applications

MIC 200A (Fall) Biology of Prokaryotes

MIC 215 (Fall) Recombinant DNA

MIC 250 (Winter) Biology of Yeasts

MIC 263 (Spring) Principles of Protein-Nucleic Acid Interactions

MIC 298- maybe an official number come winter quarter (Winter 2005) Recombination

PBI 227 (Winter) Plant Molecular Biology


ANG111 (Winter) Molecular Biology Laboratory Techniques

BIS 102 (Fall, Winter, Spring) Structure and Function of Biomolecules

MCB 121(Winter, Spring) Molecular Biology of Eukaryotic Cells

MCB 161 (Winter) Molecular Genetics

MCB 160L (Fall, Winter, Spring) Principles of Genetics Laboratory

MCB163 (Winter) Developmental Genetics

MIC 170 (Spring) Yeast Molecular Genetics

Cytogenetics

Graduate

VCR 221 Vegetable Genomics


ANG101 (Spring) Animal Cytogenetics

Population Genetics

Graduate

AGR 221 (Spring) Advanced Plant Breeding

EVE 210 (Spring) Molecular Phylogenetic Analysis

PBG 200A (Fall) Principles of Population Biology

PGB 200B (Winter) Principles of Population Biology

PGB 200C (Spring) Principles of Population Biology

PBG 207 (Winter) Plant Population Biology

PBG 231 (Fall) Mathmatical Methods in Population Biology

PBG 270 (Fall) Evolutionary Biology

PBG 290 (Fall, Winter, Spring) Seminar


ANT 153 (Winter) Human Biological Variation

EVE 102 (Fall) Population and Quantitative genetics

Quantitative Genetics

Graduate

AGR 221 (Spring, not offered 2004-2005) Advanced Plant Breeding

ANG 204 (Spring) Theory of Quantitative Genetics

ANG 206 (Spring) Advanced Domestic Animal Breeding


ANG120 (Spring) Introduction to Statistical Genomics

EVE 102 (Fall) Population and Quantitative genetics

Evolution

Graduate

EVE 210 (Spring offered in alternate years) Molecular Phylogenetic Analysis

PBG 203 (Winter) Advanced Evolution

PBG 270 (Fall, Winter, Spring) Research Conference in Evolutionary Biology




EVE 100 (Fall, Winter, Spring) Introduction to Evolution

EVE 103 (Winter) Phylogeny and Macroevolution

Physiological Genetics

Graduate

MCB221D (Winter) Cellular Biochemistry


NPB 131 (Fall) Physiological Genomics

Breeding

Graduate

AGR 221 (Spring) Advanced Plant Breeding

ANG 206 (Spring) Advanced Domestic Animal Breeding

GGG 220/VCR 220 (Winter) Genomics & Biotechnology of Plant Improvement

VCR 221 (Spring) Genomics and Breeding of Vegetable Crops


ANG 107 (Fall) Genetics and Animal Breeding

PLB 154 (Winter) Introduction to Plant Breeding

PLB 160 (Winter) Principles of Plant Biotechnology

Biotic Stresses in Plants

Graduate

PLP 210 (Fall) Biochemistry & Molecular Biology of Plant-Microbe Interaction


PLP123/PLB123/ENT123 (Fall-not offered 2004-2005 ) Plant-Virus Interaction

Human/Primate Genetics

Graduate

ANT 252 (Winter) Human Evolution Seminar




ANT 153 (Fall) Human Biological Variation

ANT 157 (Winter) Anthropological Genetics

ANT 157L (Fall) Laboratory in Anthropological Genetics

MCB 162 (Winter) Human Genetics

Graduate Seminar Courses

ANT 252 (Winter) Human evolution Seminar

AVS 290 (Fall, Winter, Spring) Seminar in Avian Genetics, Physiology, etc.

BCM 291 (Fall, etc) Human Genetics Seminar

MIC 274 (Fall, Winter, Spring) Seminar in Genetics Recombination

MIC 275 (Fall, Winter, Spring) Journal Club in Recombination Genetics

ECL 208 (Winter) Issues in Conservation Biology

Genetics Graduate Group

Expanded Guidelines for Qualifying Exam Procedures

This is a document for all: students, major professors and Qualifying examination chairs

and QE committee members. All please read.

EXAM FORMAT AND PHILOSOPHY

All focus groups require preparation of a dissertation proposal and its defense at an oral

examination. In addition, all focus groups require examination in the four areas of Genetics as

represented by the 4 core courses at the same meeting. The Chromosome Biology Focus Group

additionally requires preparation and defense of a secondary proposal.

During the examinations, the emphasis of the exam should focus on determining whether the

student has acquired the intellectual research skills and the genetic knowledge base necessary to

successfully conduct independent research in the future. In this context it is important to view the

proposals as an intellectual exercise that provides one way to measure these skills. Rather than

emphasizing the quantity of work already accomplished or the quality of the data that have been

generated, the proposal should be used to measure the potential research skills of the student. By

preparing a proposal the student should demonstrate mastery of the following skills: (1) ability to

identify and clearly define a research topic that makes a substantial and novel contribution to

genetic knowledge; (2) ability to focus the proposed research around one or more testable

scientific hypotheses; (3) ability to design and interpret scientifically feasible experiments that

will specifically test these hypotheses; (4) ability to review the scientific literature in the proposal

field to clearly define the relationship of the proposed research to existing knowledge; (5) ability

to integrate, where appropriate and feasible, various genetic approaches (e.g. transmission,

cytogenetic, quantitative genetics); and (6) ability to relate proposed experiments to the biology

of the organism.

It is critical for students, major professors and examining faculty to remember that the proposal

evaluation should not be viewed as an evaluation of the work of the major professor, or as a

contract for the work that will be ultimately completed for the dissertation. The dissertation

committee will be formally constituted after completion of the qualifying exam. Definition of the

work that constitutes the dissertation is by joint agreement of the student, the major professor and

the other members of the dissertation committee. The major professor may be involved in

guiding the student during design of the overall focus of the dissertation research topic, but the

student will ultimately have the responsibility for discussing the dissertation topic proposal in the

examination and therefore should also have the responsibility for crafting a proposal of the

highest possible scientific quality. The content of the proposal should therefore not be unduly

influenced by grant or contract constraints of the major professor that would prove detrimental to

the ability of the student to defend the scientific soundness and rigor of the proposed approaches.

In other words, the role of the proposal as a mechanism to demonstrate conceptual understanding

and the ability to think and work independently in the field of genetics should be emphasized

over its role as a measure of specific accomplishments in the lab.

It is particularly important to maintain a focus on this role of the proposal(s) for students using

that exam format, as a demonstration of intellectual ability in the field of genetics when

conducting examinations on the alternate proposals. It is not appropriate to judge proposals using

criteria that would apply for extramural grant review panels, for example. The absolute

feasibility of experimental details is less important in this context than demonstration of a

breadth in understanding of the field, ability to analyze the important scientific questions in the

field, and ability to propose reasonable approaches to address those questions.

In conducting research proposal sections of the examination, committees should try to emphasize

two areas: (1) general and specific knowledge related to the proposal area, and (2) intellectual

research skills of the student (e.g. methodological rationale, hypothesis testing and evaluation,

etc.). All areas of general genetic knowledge may not be adequately covered during the proposal

segment(s) of the examination, so it is advisable to reserve some time specifically for this task.

PREPARATION OF PROPOSAL(S)

CHOICE OF TOPICS. For students that will be preparing a dissertation proposal and an

secondary (also called alternate) proposal (where applicable) it is important to remember that the

emphasis of the two proposals must be clearly distinct and demonstrate mastery of a different set

of genetic concepts and tools. One purpose of the secondary proposal is to demonstrate breadth

of knowledge in genetics and additionally to allow the student the opportunity to formulate a

completely independent proposal, not related to or guided by the research occurring in the major

professor's lab.

Students are asked to submit a one-page abstract of their dissertation proposal, and a title or brief

description of their alternate proposal along with their 5th quarter report forms. While this

provides guidance for the assignment of examination committee members, the topic should be

discussed with and approved by the Chair of the examination committee. The one-page abstract

and alternate proposal topics (where required) will be forwarded to the appointed chair of the

qualifying exam committee. If the student subsequently changes these proposal topics

significantly, the student should again consult with their examination chair as to the acceptability

of the revised topic(s). Chairs may consult with other committee members to reach a decision on

the proposal topic suitability.

Examination committee members should not provide detailed comments on the specific content

of qualifying exam proposal(s) to the student prior to the examination itself. Exam committee

members should, however, review the proposal as soon as possible after receiving it from the

student and communicate any serious concerns about the overall structure and focus of the

proposal(s) to the chair of the committee. Appropriate concerns would include general issues

such as absence of definition of an appropriate scientific problem, defects in structuring proposal

around testable hypotheses, failure to analyze interpretation of possible experimental outcomes,

etc. These general concerns should be passed on to the student by the chair, providing a chance

to correct these structural errors in the proposal prior to potentially disastrous consequences in

the exam itself. The exam date may need to be readjusted if the corrected proposal will not be

completed prior to two weeks before the exam is scheduled. It is therefore extremely important

that the students pay close attention to these aspects of their proposals during preparation and

that they distribute their proposals prior to the two-week deadline so that this evaluation can be

made in a timely fashion.

FORMAT FOR Ph.D. QUALIFYING EXAM RESEARCH PROPOSALS

The goal of each research proposal is to provide a substantial and original contribution to the

field of genetics. The scope should be similar to that of a two-year postdoctoral grant proposal.

If an alternate proposal is required, it should be in an area outside of those normally considered

by the student's research group. The topic and approaches of the alternate proposal must be

distinct from those of the thesis proposal. The student is to develop the alternate proposal

independently, without input from the major professor. The student should discuss the alternate

topic with the qualifying exam committee chair.

Written versions of both the dissertation research proposal and the alternate research proposal are

to be prepared by the student and distributed to the committee at least two weeks prior to the

examination.

The format is that of a NIH postdoctoral fellowship proposal. Organize sections the research

proposal to answer these questions: (1) What do you intend to do? (2) Why is the work

important? (3) What have you already done? (4) How are you going to do the work? (5)

References. DO NOT EXCEED 5 PAGES FOR SECTIONS 1-4.

(1) Specific Aims: What do you intend to do? (one-half page.)

Start with a paragraph containing a synopsis of the general problem addressed and clearly stating

the hypothesis to be tested. This is necessary for the specific aims to make sense. Then, list the

specific aims.

(2) Background and Significance: Why is the work important? (one page)

Briefly sketch the background to the proposal. Critically evaluate existing knowledge, and

identify the gaps that the project is intended to fill. State concisely the importance of the

proposed research by relating the specific aims to the broad, long-term objectives.

(3) Preliminary Studies: What has already been done? (one page).

Thesis research: describe the work you have already accomplished that is relevant to the proposal

or the work in your lab that forms the rationale for your proposal. Alternate proposal: describe

the work done by others that forms the rationale for the proposal.

(4) Experimental Design: How are you going to do the work? (2.5 pages).

List the aims again. Under each aim, explain the rationale for each experiment necessary to

accomplish the aim, the experimental design, the interpretation of different types of results, and

necessary methods (without intricate details). Include the means by which data will be collected,

analyzed and interpreted. Describe any new methodology and its advantage over existing

methodologies. Discuss the potential difficulties and limitations of the proposed procedures

along with alternative approaches to achieve the aims. Provide a tentative sequence for the

investigation. At the end, summarize how your experimental results will test your hypothesis.

(5) References: quote references in the text (Author[s], date) and then collect them in

alphabetical order at the end. Each citation must include the names of all authors, title of the

article, name of the book or journal, volume number, page numbers and year of publication.

PRESENTATION OF THE PROPOSAL DURING THE EXAMINATION

In order to reduce the emphasis on data already collected and to increase the emphasis on the

scholarly and general knowledge aspects of the exam, the student will not be allowed to use

computer slides or overhead projectors during their short presentation of the dissertation

proposal. Students are allowed and encouraged to use a brief outline on the blackboard to focus

and direct their presentation.

THE ROLE AND RESPONSIBILITY OF THE EXAM CHAIR:

For the Chair- Prior to exam:

1. Confirm topics of dissertation proposal (and alternate where applicable) with student.

2. Communicate general concerns about the design of proposals from exam committee to the

student.

3. Discuss exam format with student.

4. Remind committee members of the time and place of the exam if student has not already done

so; make sure committee members understand exam format and exam areas.

5. Make sure that you have appropriate paperwork.

6. Obtain from Ellen two things: student file to have present at the exam and the Graduate

Studies (GS) paperwork.

For the Chair- During the Exam

1. Assure a fair examination of the student. Make sure examination has a break.

2. Bring appropriate student records relating to past academic work to the examination for

consideration by the committee.

3. Assure that all required areas in the examination are adequately covered, by monitoring the

time spent in questioning in each area and initiating movement to the remaining topics if

necessary during the exam. For all focus groups, make sure there is sufficient time for

examination in the four core areas and that approximately 1-1 1/2 hr is spent on the

dissertation proposal. .For Chromosome Biology Focus Group: sufficient time for

examination of the secondary proposal.

4. Moderate discussion of evaluation of student performance after examination is completed.

Allow all committee members to express their evaluation of the student and vote.

For the Chair- After the Exam

1. Immediately after the final vote, communicate the outcome of the exam to the student.

2. Complete paperwork and submit to Ellen Picht in GGG office. She will forward to GS.

3. In the event of a "not pass", clearly communicate to the student verbally and in writing the

opinion of the committee and the requirements for converting a "not pass" to a "pass". A

letter should be written to Graduate Studies explaining in detail what needs to be done and

this letter and the information within must be discussed with the student. Please submit to

Ellen Picht in GGG office and she will forward to GS.

THE ROLE AND RESPONSIBILITY OF THE OTHER EXAM COMMITTEE

MEMBERS

1. Set aside time to meet with the student prior to the examination to provide general

suggestions about preparing for the exam, useful material to review during exam study, etc.

2. Review the proposal(s) soon after receipt to evaluate general proposal design. Communicate

concerns to chair of committee as soon as possible.

3. Read proposal carefully prior to the exam date.

4. Conduct a fair and thorough examination of the student, covering intellectual skills necessary

for independent scientific research as well as specific knowledge in the areas related to the

proposed dissertation work and general knowledge in genetics. It is unreasonable to expect

extensive knowledge in your own particular area of expertise, unless it is closely related to

the student’s exam topics.

5. Remember that you are examining the student, not the major professor. The student's ability

should be evaluated independently of any particular characteristics of the major professor.

6. Use evaluation criteria appropriate for the academic "stage" of the student. Do not expect that

a large portion of research for the dissertation will have already been completed at the time of

the exam.

THE ROLE AND RESPONSIBILITY OF THE STUDENT

1. Arrange for a meeting of your guiding committee to complete the fifth quarter report form

during winter quarter of your second year. For this meeting, prepare a one-page abstract of

your planned dissertation proposal, emphasizing the scientific hypotheses/questions that your

work will address and the planned approaches to test those hypotheses. Define the general

focus of your alternate proposal/area, if appropriate. If an alternate proposal is required,

provide a classification of the main areas of emphasis of the dissertation proposal and the

alternate proposal to demonstrate their distinctiveness.

2. Contact the chair and each committee member to arrange for a time to hold the examination.

Arrange, or request the chair to help you arrange, a room reservation for the examination. In

general, exams do not extend beyond 3 hours but is useful to reserve the room for 1/2 hour

preceding and following the projected exam period.

3. Meet with the chair to verify your choice of proposal topic (and alternate topic, if

applicable). Notify chair if there is a significant change in these topics.

4. Make appointments as needed with each committee member to update them on your

dissertation proposal and alternate proposal topics and to discuss with them suggestions for

study areas or resources. But do not expect committee members to provide you with detailed

lists of exact topics or questions to study.

5. Provide committee members with your proposal(s) well in advance of the exam date and

certainly no later than 2 weeks prior to your exam, to allow communication about any

general concerns regarding the design and scientific soundness of your proposal(s). Do not

expect your committee members to give you detailed feedback on the specifics of your

proposals.

Prepared by Educational Policy Committee (April/May 1996)

Jeanette Natzle (Chair), Abhaya Dandekar, Kathryn Radke, Marta Marthas, Thea Wilkins, Doug

Shaw, Anita Oberbauer, Ken Shaw

Updated by Judy Callis (April 2003) to reflect new focus group organization.

Updated by Judy Callis (Summer 2006) to remove affinity group requirements and change

procedure such that paperwork for QE is received by Ellen Picht and the chair must get the

paperwork from GGG office.

Focus Groups- 2005

Genetics Graduate Group

Interested Potential Focus

Focus Group Members Address Group Leader

Animal Genomics Danika Bannasch

VM: Pop. Health &

Repro. Anita Oberbauer

Mary Delany Animal Science

Holly Ernest Vet Genetics Lab

Tom Famula Animal Science

Sree Kanthaswamy Vet Genetics Lab

Dietmar Kueltz Animal Science

Leslie Lyons

VM: Pop. Health &

Repro.

Marta Marthas CRPRC

Bernie May Animal Science

Juan Medrano Animal Science

Jim Murray Animal Science

Anita Oberbauer Animal Science

Alison Van

Eenennaam Animal Science

Chromosome

Biology Sean Burgess MCB Wolf-Dietrich Heyer

Ken Burtis MCB

Anne Britt Plant Biology

Roger Chetelat Plant Sciences

Wolf-Dietrich

Heyer Microbiology

Neil Hunter Microbiology

S. Kowalczykowski Microbiology

Ken Kaplan MCB

Janine LaSalle Microbiology

Human Genetics Gino Cortopassi

VM: Molecular

Bioscience Mike Seldin

Paul Gumerlock Hematology/UCDMC

Nobuko Hagiwara

Med: Cardiovascular

Med.

John Hershey

Med. Biological

Chem.

Liping Huang Nutrition

Hsing-Jien Kung UCD Cancer Center

Janine LaSalle Microbiology

Marta Marthas CRPRC

Maria Mudrji

Med. Micro. &

Immuno.

Mike Seldin

Med. Biological

Chem.

Craig Warden Rowe Program

Reen Wu

Research Bio. &

Medicine

Model Plants Steffen Abel Plant Sciences Chuck Gasser

John Bowman Plant Biology

Anne Britt Plant Biology

Judy Callis MCB

Chuck Gasser MCB

John Harada Plant Biology

Stacey Harmer Plant Biology

Dan Kliebenstein Plant Sciences

Julin Maloof Plant Biology

Richard

Michelmore Plant Sciences/ MCB

Neelima Sinha Plant Biology

Venkatesan

Sundaresan Plant Biology

Thea Wilkins Plant Sciences

John Yoder Plant Sciences

General Genetics All faculty

Plant Breeding

and Biodiversity Roger Chetelat Plant Sciences Paul Gepts

Jorge Dubcovsky Plant Sciences

Paul Gepts Plant Sciences

Julin Maloof Plant Biology

David Neale Plant Sciences

Dan Parfitt Plant Sciences

Pamela Ronald Plant Pathology

Doug Shaw Plant Sciences

Dina St. Clair Plant Sciences

Larry Teuber Plant Sciences

Andy Walker Viticulture

OPERATING PROCEDURES FOR THE ANIMAL GENOMICS FOCUS GROUP REVISED September 2003

OBJECTIVES

The Animal Genomics (AG) focus group within the Genetics Graduate Group (GGG) will bring

together faculty who are active in this area of research to enhance the training opportunities in

this area.

Animal Genomics is defined as research that either utilizes global, genome-wide approaches or

information derived from such approaches to address questions about the causes of individual

differences in fitness in natural or agricultural environments, genome organization, evolution, or

gene function in animals.

ACTIVITIES

The AG focus group will:

provide visibility for recruiting students interested in this area,

develop and maintain a webpage focused on the faculty and research programs within the

Animal Genomics focus group,

allow coordination of research and training in Animal Genomics,

set the specialist curricula as below,

conduct a biweekly journal club/seminar series focused on Animal Genomics,

organize a GGG seminar once every two years focused on Animal Genomics,

assist in the function and administration of the GGG by providing representatives to serve

on GGG standing committees,

provide the framework for training grants.

ADMINISTRATION

The AG focus group will be administered by a group leader in consultation with the whole

membership. There will be no standing committees. Administration (recruiting, advising, etc.)

will be through representation on GGG standing committees. Focus group policy will be

decided by the whole focus group membership.

ELECTION OF FOCUS GROUP LEADER

The membership will elect a leader by an e-mail ballot of the whole membership. A simple

majority of those voting will decide the leadership. The leadership will usually be for a term of

three years. A majority vote of the membership can request an earlier election.

MEMBERSHIP

Membership is open to anyone who wishes to actively participate in the AG focus group for the

first year. At the end of the first year, the membership will self assess itself according to the

criteria below. Membership will be reviewed every three years subsequently by the whole

membership. A majority of those voting will be required for continued membership.

CRITERIA FOR CONTINUED MEMBERSHIP

1) Maintenance of an active research program in the area of animal genomics as evidenced by:

a) publications in the area of comparative and/or functional animal genomics in each of the

previous three years.

b) sufficient funding to support genomics research.

2) Activity in the AG focus group as evidenced by:

a) representing the AG focus group on a GGG standing committee,

b) teaching in a GGG core course or the AG focus group GGG seminar,

c) teaching a course directly relevant to the AG focus group,

d) sustained participation in the AG journal club, seminar and colloquium.

Sustained activity in at least one of these four activities is required unless there are significant

mitigating administrative circumstances (such as being department chair).

MEMBERSHIP APPLICATION [Added 9/03]

Once the Executive Committee of the GGG approves admission of a faculty member to GGG, the

application packet for faculty interested in the AG focus group will be forwarded to the AG focus

group membership for voting. Potential members will be evaluated on the above criteria for

membership in 1) above and the potential and willingness to be active within the focus group as

noted in 2) above. Membership acceptance requires a majority of approval by current members.

STUDENT CURRICULUM

Courses:

All students will take the GGG core courses and other courses required of all GGG students. In

addition, students will take at least two courses from the course list in their area of specialization

from the restricted electives list and at least one additional graduate course to provide breadth of

education. The required GGG courses and two restricted elective courses will be taken for a

letter grade. Students will also take the AG focus group sponsored seminar plus one other GGG

approved seminar in addition to GGG291. All students will TA a genetics course prior to

advancing to candidacy and will be encouraged to enroll in GGG300.

Rotations:

In-coming students will not be required to rotate. If needed, rotations will be organized on an

individual basis.

Qualifying Examinations:

The format of the qualifying examinations will be the presentation and defense of a research

proposal plus a specific defense of each of the four areas covered by the core courses. The chair

of the qualifying examination will be from the membership of the AG focus group. [Added 9/03]

REVISION OF OPERATING PROCEDURES

These operating procedures may be revised at anytime by a majority vote of the membership and

subject to ratification by the GGG executive committee.

GGG Animal Genomics Focus Group course list

In addition to taking all of the required GGG core courses and seminars, each student will

complete a minimum of two courses from the following list, plus one additional graduate level

course as approved by the Guiding Committee. (Substitutions for one course can be made for a

course approved by the Guiding Committee).

ANG 204 Theory of Quantitative Genetics

ANG206 Advanced Domestic Animal Breeding

ANG 208 Estimation of Genetic Parameters

ANG 212 Sequence Analysis in Molecular Genetics [Added 9/03]

AVS 220/MCB257 Cellular Proliferation of Oncogenes

BCM 222 Mechanisms of Translational Control

ECL 208 Conservation Biology

ENT 212 Molecular Biology of Insects and Insect Viruses

EPI 205A Principles of Epidemiology

EVE 210 Molecular Phylogenetic Analysis

EVE 211 Applied Phylogenetics

GGG 210 Horizontal Gene Transfer

MCB 255 Molecular Mechanisms of Animal Development

MCB 262 Transgenic Expression Systems

MIC 215 Recombinant DNA

MIC215L Recombinant DNA Laboratory

MIC 263 Principles of Protein-Nucleic Acid Interactions

PBG 200A, B, C Principles of Population Biology

PBG 203 Advanced Evolution

PGG 200L Animal Cell Culture Laboratory

STA 226/BST 226 Statistical Genomics [Added 11/06]

Initial faculty membership in the Animal Genetics Focus Group

1. Danika Bannasch VM:Population Health and Reproduction

2. Mary Delany Animal Science

3. Thomas Famula Animal Science

4. Dennis Hedgecock Animal Science

5. Dietmar Kueltz Animal Science

6. Leslie Lyons VM:Population Health and Reproduction

7. Marta Marthas CRPRC

8. Bernie May Animal Science

9. Juan Medrano Animal Science

10. Jim Murray Animal Science

11. Anita Oberbauer Animal Science

12. Alison Van Eenennaam Animal Science

Operating Procedures for the Chromosome Biology Focus Group

of the Genetics Graduate Group

Objectives:

The Chromosome Biology Focus Group (ChromBio FG) constitutes itself within the Genetics

Graduate Group as a group of faculty with a common interest in all aspects of chromosome

biology, particularly in DNA repair, DNA recombination, DNA replication, chromosome

segregation and chromosome dynamics using a variety of scientific approaches and experimental

model systems.

Activities:

The ChromBio FG will:


develop and maintain a webpage focused on the group,

allow coordination of research and training in ChromBio FG,


organize a GGG seminar once every two years focused on ChromBio FG,



conduct a journal club focused on ChromBio FG,


Administration:

The ChromBio FG focus group will be administered by a group leader in consultation with the

whole membership. There will be no standing committees. Administration (recruiting, advising,

etc.) will be through representation on GGG standing committees. Focus group policy will be

decided by the whole membership. The Operating Procedures can be changed or amended by a

simple majority of its members.

Election of Focus Group Leader:

The membership will elect a leader by an e-mail ballot of the whole membership. A simple

majority of those voting will decide the leadership. The leadership will usually be for a term of

three years. A majority vote of the membership can request an earlier election.

Membership:

Membership is open to anyone who wishes to actively participate in ChromBio FG for the first

year. At the end of the first year, the membership will self assess itself according to the criteria

below. Membership will be reviewed every three years subsequently by the whole membership.

A majority of those voting will be required for continued membership.

Criteria for Membership:

1) Maintenance of an active research program in the above mentioned areas of chromosome

biology, as evidenced by:

a) peer-reviewed publications and

b) extramural funding.

These criteria are suspended for new faculty members that need time to publish and to attract

funding and will not be applied until publications and funding can reasonably be expected.

2) Activity in the ChromBio FG as evidenced by:

a) representing the ChromBio FG on a GGG standing committee,

b) teaching a GGG core course or the ChromBio GGG seminar,

c) teaching a course directly relevant to the ChromBio FG,

d) sustained participation in the ChromBio journal club MIC275.


mitigating circumstances.

Student Curriculum:

The ChromBio FG establishes the following minimum curriculum for its students:

• The four GGG core courses and other courses required for GGG students

• GGG291 History of Genetics

• The group requires that students rotate in four laboratories before deciding which laboratory

they join. It is encouraged, but not required, that students rotate in laboratories of ChromBio FG

faculty.

• One quarter Teaching Assistantship (TA) in a course of the GGG curriculum prior to the

qualifying examination. Students are encouraged to enroll in GGG300.

• MIC275 Seminar in DNA Repair and Recombination (every quarter). This course will be

developed further and/or alternated with a GGG295 seminar (for a grade) to be offered annually

or biannually as a ChromBio FG seminar.

• MIC263 Protein:Nucleic Acids Interactions (for a grade).

• One additional graduate level course (for a grade) in a different area to encourage diversity in

the educational experience.


The purposes of the Qualifying Examination are twofold: 1) to determine that the student has

acquired sufficient knowledge of genetics, in breadth and depth, and 2) to determine that the

student has identified a dissertation research topic that asks a significant question in genetics.

The latter includes demonstration that the student has completed a literature review of that topic,

has identified a set of achievable goals and has designed appropriate experimental approaches to

accomplish those goals. The dissertation research part of the exam is meant to be a proposal, not

a research progress report. Finally, the student's previous academic record, performance on

specific parts of the examination, and overall performance/potential for scholarly research will

be evaluated in determining the outcome of the examination.

Qualifying Examination Committees will consist of five faculty members. The Chair and

preferably two other members of the committee will be members of ChromBio FG, at least one

of whom must have agreed to serve on thesis committee of the student. Two other faculty who

are not members of ChromBio FG will be appointed by the pertinent GGG standing committee.

The five members of the Qualifying Examination Committee will represent the four core areas of

GGG as covered in the core courses (Advanced Genetic Analysis, Comparative and Functional

Genomics, Molecular Genetics, Transmission, Population and Quantitative Genetics). The leader

of ChromBio FG will recommend to the Advisors committee which ChromBio FG members

serve on a qualifying examination committee. The chair of the Qualifying Examination

Committee is expected to ensure that a student receives a fair examination. Qualifying

Examination Committees may not include the major professor who will serve as chair of the

student's dissertation committee.

Students will be informed of the prospective composition of the Qualifying Examination

Committee, and will be asked to confer with their major professor to inform their graduate

advisor of any concerns with the committee composition. With this input taken into account, the

advisors formally recommend to Graduate Studies the composition of the Qualifying

Examination Committee. Committees will be appointed by the Dean of Graduate Studies. Copies

of the approved petition are sent to the student, the chair of the examining committee, and the

GGG Program Liaison. Students must notify all members of their examination committee that

they have been appointed. This is important - for example, if a faculty member will be on

sabbatical and unable to serve, the exam committee must be reconstituted through the GGG

Student Affairs Committee and Graduate Studies.

Scheduling the Qualifying Examination. All Ph.D. candidates are expected to take their

Qualifying Examination before or during their eighth quarter following admission into the

program (i. e. the Winter Quarter of the third year), unless a prior waiver is approved in writing

by ChromBio FG. It is strongly encouraged that students take the Qualifying Examination before

the onset of the seventh quarter following admission (i.e. before the Fall quarter of the third

year).

Format of the Qualifying Examination. The Qualifying Examination will consist of a

dissertation research proposal, a secondary proposal, and an examination in the four core subject

areas (Advanced Genetic Analysis, Comparative and Functional Genomics, Molecular Genetics,

Transmission, Population and Quantitative Genetics). Candidates will be expected to submit a

written dissertation proposal and an independent secondary proposal to their committee at least

one week prior to the oral examination (see below). During the qualifying examination only a

chalk/white board is to be used.

The Dissertation Proposal. The goal of the dissertation research proposal is to provide a

substantial and original contribution to the field of genetics. The scope should be similar to that

of a grant proposal. Written versions of the thesis research proposal are to be prepared by the

student and distributed to the committee at least one week prior to the examination. The format is

that of an NIH postdoctoral fellowship proposal. Organize sections 1-5 of the research proposal

to answer these questions: (1) Specific aims. What do you intend to do? (2) Background and

significance. Why is the work important? (3) Preliminary studies. What have you already done?

(4) Research design and methods. How are you going to do the work? (5) References. DO NOT

EXCEED 5 PAGES FOR SECTIONS 1-4. The following distribution for length is

recommended:

(1) Specific aims. State briefly the broad, long-term objectives of the work. Then state the

specific purposes of the proposed research. One-half page is recommended.

(2) Background and significance. Briefly sketch the background to the proposal. Critically

evaluate existing knowledge, and identify the gaps that the project is intended to fill. State

concisely the importance of the proposed research by relating the specific aims to the broad,

long-term objectives. One page is recommended.

(3) Preliminary studies - thesis research only. Describe the work you have already

accomplished that is relevant to the proposal. A maximum of one page is recommended.

(4) Research design and methods. Outline the experimental design and the procedures to be

used to accomplish the specific aims. Include the means by which data will be collected,

analyzed and interpreted. Describe any new methodology and its advantage over existing

methodologies. Discuss the potential difficulties and limitations of the proposed procedures

along with alternative approaches to achieve the aims. Provide a tentative sequence for the

investigation. Although no specific number of pages is recommended for this section, the total

for sections 1-4 should not exceed 5 pages.

(5) References. Each citation must include the names of all authors, title of the article, name of

the book or journal, volume number, page numbers and year of publication.

The Secondary Proposal. The goal of the secondary proposal is that the candidate develops an

original hypothesis and suitable experimental tests of this hypothesis in an area independent of

the dissertation proposal. The candidate is free in the choice of topic but this choice needs

approval by the chair of the Qualifying Examination Committee. The format is identical to that

of the dissertation proposal.

ChromBio FG students may meet with each committee member to discuss his or her expectations

for the examination. This meeting should not be not a pre-examination of the research proposals.

Students should not ask for, nor should the committee members provide, comments on

weaknesses, potential problems and errors in the research proposals.

Revision of operating procedures

These operating procedures may be revised at anytime by a majority vote of the membership and

subject to ratification by the GGG executive committee.

Approved by the membership on August 8, 2002.

The present membership list is:

Sean M. Burgess, Assistant Professor of Molecular and Cellular Biology

Ken C. Burtis, Professor of Genetics

Anne B. Britt, Associate Professor of Plant Biology

Roger Chetelat, Assistant Geneticist

Wolf-Dietrich Heyer, Professor of Microbiology

Stephen C. Kowalczykowski, Professor of Microbiology

Ken B. Kaplan, Assistant Professor of Molecular and Cellular Biology

Janine M. LaSalle, Assistant Professor of Microbiology and Immunology

Human Genetics Focus Group

Statement of Mission

The GGG Human Genetics Focus Group provides students the opportunity for specialized

training in human genetics and genomics. The faculty members are dedicated to developing

and applying genetic information and methods towards understanding physiologic and

pathophysiologic human biology. Investigators are using human and/or model mammalian

species for these studies. The upper level courses taught by our faculty are centered on

understanding the concepts application of genetic tools towards defining the molecular basis

of human disease susceptibility and disease progression. These include molecular and

cytogenetic techniques as well as informatics, and statistical methodology and theory.

Individual faculty members have expertise in these broad topics as well as in transcription

regulation, signaling circuits, comparative genomics and quantitative trait analysis of complex

genetic disease.

Members of this focus group are investigating a wide array of specific diseases. These include

a variety of cancers, obesity, diabetes, cardiovascular disease, autoimmune diseases, Rett

syndrome, and mitochondrial diseases. In addition to direct analysis of human disease,

applicable animal models of human disease being developed and studied include those in

nonhuman primates, cats and the mouse.

ACTIVITIES

The HG focus group will:


develop and maintain a webpage focused on the faculty and research programs within the

Human Genetics focus group,

allow coordination of research and training in Human Genetics,


conduct a biweekly journal club/seminar series focused on Animal Genomics,

organize a GGG participatory seminar course offered each years focused on Human

Genetics,




ADMINISTRATION

The HGG focus group will be administered by a group leader in consultation with the



decided by the whole membership.


The membership will elect a leader by an e-mail ballot of the whole membership. A

simple majority of those voting will decide the leadership. The leadership will usually be for a

term of three years. A majority vote of the membership can request an earlier election.

Faculty Membership

Membership in GGG and active research in human or mammalian genetic models.

During the first year membership will be open to anyone who wishes to actively participate in

the HGG focus group for the first year. At the end of the first year, the membership will self

assess itself according to the criteria below. Membership will be reviewed every three years

subsequently by the whole membership. A majority of those voting will be required for

continued membership.

CRITERIA FOR MEMBERSHIP

1. Maintenance of an active research program in the area of comparative and/or function plant

genomics as evidenced by:

c) evidence of significant intellectual contributions to the field, for example, an average of at

least two peer-reviewed publications in the area of comparative and/or functional genomics in

each of the previous three years.

d) sufficient funding from competitive sources to support genomics research.

These criteria are suspended for new faculty members that need time to publish and to attract

funding and will not be applied until publications and funding can reasonably be expected.

2. Activity in the HGG focus group as evidenced by:

a) representing the HGG focus group on a GGG standing committee,

b) teaching a GGG core course, an HGFG seminar,

c) teaching a course directly relevant to the C&FPG focus group,


mitigating administrative circumstances (such as being department chair).

Course Requirements

1. GGG core courses

2. 3 Credit Participatory Seminar Series:

3. Upper level Seminar courses (3 required): Students will be encouraged to enroll in at

least one seminar course that focuses on human genetics (e.g. Human Genetics Seminar BCM

291, Molecular Medicine BCM 214).

4. History of Genetics (required)

5. Two additional upper level courses are required.

Students will select from a list of courses approved by the HGG

Currently these include:

ANG 204 Theory of Quantitative Genetics

ANG 208 Estimation of Genetic Parameters

AVS 220/MCB257 Cellular Proliferation of Oncogenes

BCM 222 Mechanisms of Translational Control

EPI 205A Principles of Epidemiology

EVE 210 Molecular Phylogenetic Analysis

EVE 211 Applied Phylogenetics

MCB 255 Molecular Mechanisms of Animal Development

MCB 262 Transgenic Expression Systems

MIC 215 Recombinant DNA

MIC215L Recombinant DNA Laboratory

MIC 263 Principles of Protein-Nucleic Acid Interactions

PBG 200A, B, C Principles of Population Biology

PBG 203 Advanced Evolution

PGG 200L Animal Cell Culture Laboratory

NPB 131 Genome Biology

TA Responsibilities

Students will be expected to fulfill a single quarter of TA experience that are an integral

part of graduate school education and preparation for a career in academics. To be compatible

with NIH MSTP guidelines, PSTP students are not required but are strongly encouraged to

participate.

Rotations

Students will be strongly encouraged but not absolutely required to participate in 3 to 4

laboratory rotations (GGG205). Rotations can be either 5 or 10 weeks . A written and oral

presentation are required for credit and evaluation. In addition, they will be strongly encouraged

that one of these labs should be of a junior faculty’s (assistant professor) lab.

Qualifying Examinations

The format of the qualifying examinations will be of a single research proposal

describing the proposed thesis project followed by a specific defense of each of the four areas

covered by the core courses.


These operating procedures may be revised at anytime by a majority vote of the

membership and subject to ratification by the GGG executive committee.

OPERATING PROCEDURES FOR THE GENETICS OF MODEL PLANTS FOCUS

GROUP

OBJECTIVES

The Genetics of Model Plants (GMP) focus group within the Genetics Graduate Group

(GGG) will bring together faculty who are active in this area of research to enhance the training

opportunities in this area.

Genetics of model plants is defined as research that employs genetic approaches utilizing

Arabidopsis thaliana, maize, tomato and other plants as model organisms to answer fundamental

biological questions.

ACTIVITIES

The GMP focus group will:


develop and maintain a webpage focused on the group,

allow coordination of research and training in GMP,

set the specialized curricula as below,

organize a GGG seminar once every two years focused on GMP,



conduct a journal club focused on GMP,


ADMINISTRATION

The GMP focus group will be administered by a group leader in consultation with the



decided by the whole membership.


The membership will elect a leader by an e-mail ballot of the whole membership. A

simple majority of those voting will decide the leadership. The leadership will usually be for a

term of three years. A majority vote of the membership can request an earlier election.

MEMBERSHIP

Membership is open to anyone who wishes to actively participate in the GMP focus

group for the first year. At the end of the first year, the membership will self assess itself

according to the criteria below. Membership will be reviewed every three years subsequently by

the whole membership. A majority of those voting will be required for continued membership.


1) Maintenance of an active research program as evidenced by:

e) significant peer-reviewed publications in the area of genetics of plant model systems

f) adequate funding from competitive sources to support such research.

These criteria will be suspended for new faculty members who will be given reasonable time to

publish and to attract funding to meet the requirement.

2) Activity in the GMP focus group as evidenced by:

a) representing the GMP focus group on a GGG standing committee,

b) teaching a GGG core course or the GMP focus group GGG seminar,

c) teaching a course directly relevant to the GMP focus group,

d) sustained participation in an GMP journal club.

Sustained effort in at least one of these four activities is required unless there are significant

mitigating circumstances (such as being department chair).

STUDENT CURRICULUM

Courses:

All students will take the core courses and other courses required of all GGG students,

including GGG 291 (History of Genetics). There is a requirement for a minimum of 3 courses in

addition to the core. Two courses are to be selected from a list approved by the GMP focus

group (attached) to provide training in the study of model plants, or in topics applicable to the

study of model plants. One course should have a molecular genetic emphasis, and one should

focus on plants as the experiment systems. In some cases, a single course can satisfy both these

requirements. The student is encouraged to consider courses with computational emphases. One

additional graduate level course, designed to encourage diversity in educational experience, is

required. This course should be chosen in consultation with your major professor and academic

adviser, and requires adviser approval. These three courses will be taken for a grade.

Seminars:

Students will also take the GMP focus group sponsored seminar, plus one other seminar

in addition to GGG291. All students will TA a genetics course prior to advancing to candidacy

and will be encouraged to enroll in GGG300.

Rotations:

In-coming students will be strongly encouraged but not absolutely required to rotate

through at least three labs during their first two quarters before deciding on a home lab. In

addition, they will be strongly encouraged that one of these labs should be in a junior faculty’s

(assistant professor) lab.


The format of the qualifying examinations will consist of a single research

proposal describing the proposed thesis research followed by an oral examination which will

include each of the four areas covered by the core courses.




Genetics of Model Focus Group Restricted Elective Course List

AGR 221 Advanced Plant Breeding Teuber Spring (no 02-03)

ECS 124 Theory and Practice of Bioinformatics Gusfield Spring

EVE 103 Phylogeny and Macroevolution Sanderson Winter

EVE 210 Molecular Phylogenetic Analysis Nadler, Sanderson

EVE 240 Paleobotany and Angiosperm Evolution Doyle Winter (no- 03-04)

Deleted: t

Deleted:

GGG 220/

VCR 220

Genomics & Biotechnology of

Plant Improvement

Michelmore Winter

MIC 215 Recombinant DNA Privalsky Fall

MIC 262 Advanced General and Molecular Virology Bruening, Manning,

Luciw

Spring (no- 02-03)

MIC 263 Principles of Protein-Nucleic Acid Interactions Kowalczykowski Spring (no 02-03)

PBI/MCB

126

Plant Biochemistry Abel/Callis Spring

PBG 203 Advanced Evolution Gottlieb Winter (no 02-03)

PBI 208 Plant Hormones & Regulators Abel W-Odd 03

PBI 218A Advanced Concepts in Plant Cell Biology:

Cell Biogenesis

Lucas Winter (even yrs)

PBI 218B Advanced Concepts in Plant Cell Biology:

Transduction

Spring (odd yrs)

PBI 219 Reproductive Biology of Flowering Plants staff F-Odd

PBI 220 Plant Development Biology Bowman/Sinha Spring (odd)

PBI 227 Plant Molecular Biology Sinha, Britt W (No 02-03)

VCR 221 Genomics and Breeding of Vegetable Crops Quiros Spring

OPERATING PROCEDURES FOR THE GENERAL GENETICS FOCUS GROUP

MISSION- The General Genetics Focus Group consists of all faculty in GGG. This focus

group’s mission is to provide a broad training in genetics. The requirements and operating

procedures not outlined here can be found in the GGG bylaws document.

ADMINISTRATION- The chair of the Genetics Graduate Group is the Chair of the General

Genetics Focus Group. Admission to the Genetics Graduate Group in essence means admission

to the General Genetics Graduate Group.

PHD COURSE REQUIREMENTS

1.a. Core Courses

i. GGG 201A, Advanced Genetic Analysis

ii. GGG 201B, Comparative and Functional Genomics

iii. GGG 201C, Molecular Genetics

iv. GGG 201D, Transmission, Population and Quantitative Genetics

b. Seminar Course

i. GGG 291, History of Genetics

2. Additional requirements- to be approved by the academic adviser. These courses must be

taken for a letter grade.

a. Two GGG seminar courses, one a GGG 29X, and an additional seminar course approved by

the adviser

b. Two courses, at least one at the graduate level aim, both to provide depth in the general area

of proposed dissertation research

c. At least one additional graduate level course to encourage diversity in educational

experience.

3. Laboratory Rotation Programs

Rotations are encouraged but not required. Ph.D. students may enter the GGG committed to a

specific faculty member or may enter unassigned and rotate through three or four laboratories

during their first two quarters prior to deciding on a faculty sponsor. If a student enters

uncommitted, then they must enroll in two quarters of GGG205.

4. TA Requirement

Students are required to serve as a teaching assistant for at least one genetics-oriented lecture or

laboratory course prior to advancing to candidacy in order to gain experience in teaching

genetics. A list of appropriate courses that fulfill this requirement will be assembled and

approved by the Advising Committee. The Advising Committee will have the discretion to

approve particular courses for individual students on ad hoc basis.

MS DEGREE REQUIREMENTS

C. Advising:

1. Each Masters student will be assigned to an adviser by the Advising Committee and a Guiding

Committee consisting of the major professor, the graduate advisor, and a third member of the

faculty

2. The academic curriculum and progress of each M.S. student will be followed by a guiding

committee consisting of the major professor, the adviser, and a third member of the faculty

chosen by the student in consultation with their major professor. When a thesis committee is

chosen for a Plan I student, the Guiding Committee will be discontinued.

D. Rotation Programs: M.S. students will not participate in rotation programs.

E. Curriculum

The normative time for a M.S. degree is two years. Students judged by the Advising Committee of

the GGG to be making inadequate progress towards the degree will be recommended to Graduate

Division for suspension from the program. Courses and other components of the program

chosen to fulfill the M.S. requirement must form an integrated plan to meet the individual

student's objectives. This plan will be developed by the Guiding Committee. Course work will

include the following:

Plan I: Thesis Option

Course work

a) requirements:

At least 30 quarter units in residence at UC

Davis. At least 12 of the 30 units must be in

graduate level courses.

Graduate Studies

b) GGG requirements:

1) Core courses: GGG201A

Advanced Genetic Analysis

and at least two of:

GGG201B Comparative and Functional

Genomics,

GGG201C Molecular Genetics

GGG201D Transmission, Population and


All core courses must be completed with a

grade B or better.

2) Group seminar (GGG292, 293, 295 or 297),

including one of the following:

Developmental Genetics

Cytogenetics


Population, Evolutionary and Ecological

Genetics

Animal Genetics

Molecular Genetics

Plant Genetics

3) Other courses: At least 18 of the 30 unit

requirement must be fulfilled by courses (no

299 units); 15 units must be in genetics-related

courses.

c) Focus Group requirements:

At present there are no specific Focus Group

Plan II: Course Option

Course work

a) Graduate Studies requirements:

At least 36 quarter units in residence at UC

Davis. At least 18 of the 36 units must be in

graduate level courses.

b) GGG requirements:

4. Core courses: GGG201A Advanced

Genetic Analysis

5.

and at least two of:

GGG201B Comparative and Functional

Genomics,

GGG201C Molecular Genetics

GGG201D Transmission, Population and


All core courses must be completed with a

grade B or better.

2) Group seminar (GGG292, 293, 295 or 297),

including one of the following:

Developmental Genetics

Cytogenetics


Population, Evolutionary and Ecological

Genetics

Animal Genetics

Molecular Genetics

Plant Genetics

3) Other courses: At least 27 of the 36 unit

requirement must be fulfilled by courses (no

299 units); 21 units must be in genetics-related

courses.

4) 299 (Research): At least 6 units of either

Group study (GGG298) or research (GGG299)

are required. A written report of 10 pages or

longer following the style of either a review or

research paper in a scientific journal in the

field must be submitted to and approved by the

examining committee.

c) Focus Group requirements:

At present there are no specific Focus Group

Masters Thesis

The thesis committee is appointed after the

student submits an application for candidacy

to the M.S. degree, no later than the third

quarter in residence. It consists of a Chair,

who is the major professor of the candidate,

and two additional members, one of whom

must also be a member of the GGG.

Suggestions for the membership of the

committee may be made by the guiding

committee, but the Advising Committee of the

GGG will have final responsibility for

appointing the committee. The thesis

committee will meet with the candidate to

follow the progress of the thesis research as

needed.

After providing each member of the

committee with a copy of the thesis at least

two weeks in advance, the candidate will

defend the thesis at a meeting of the thesis

committee. After the thesis is approved and

filed with the Graduate Division, a signed

copy must be sent to the GGG office.

Comprehensive Examination

The comprehensive examination committee is

appointed after the student submits an

application for candidacy to the M.S. degree,

no later than the third quarter in residence. It

consists of a Chair (who must be a member of

the GGG) and two additional members, one of

whom must also be member of the GGG.

Suggestions for the membership of the

examination committee may be made by the

guiding committee, but the Advising

Committee of the GGG will have final

responsibility for selecting the committee.

The comprehensive examination will cover

those areas of General Genetics included in

the course work completed by the student. The

Chair of the comprehensive examination

committee for Plan II students shall report the

results of the examination to the GGG office

and to the Dean of the Graduate Division.

In addition to the comprehensive examination,

Plan II students will submit a 10 page

scientific paper for approval by the examining

committee. The subject of the paper will be

by mutual agreement of the Chair of the

examining committee and the student.

PhD. Requirements- Requirements for a Ph.D. include successful completion of a Qualifying

Examination, dissertation research, and completion of a written Ph.D. dissertation.

1. The procedure for the Qualifying Examination is detailed here.

The chair of the Qualifying Examination Committee, in consultation with the student, will set the

exact date and location of the examination and provide the other members of the committee with

this information. It is the responsibility of the chair to ensure that the Graduate Division's

regulations regarding qualifying examinations are followed. When possible, the Chair will

belong to the same Focus group as the student. The role of the Chair is to 1) assure a fair

examination of the student; 2) ensure a broad examination of the major areas of genetics

(particularly if the exam is also serving as the Comprehensive Exam for a Masters degree, see

below); 3) approve the topic of the alternate proposal if required by the Focus Group.

It is the responsibility of the major professor to ensure that the student is well prepared for

examination on both the proposal and the breadth of genetics.

The Qualifying Examination Committee will conduct an oral examination to evaluate the

student's knowledge of general genetics and ability to defend one or more research proposals.

The aim of the examination is 1) to determine whether the student has a broad knowledge of

genetics at a level sufficient to teach undergraduate genetics and to be able to explain genetics to

the lay public, 2) to determine whether the student understands the scientific method, particularly

in the context of genetics, 3) whether the student reviewed the literature and has the background

and knowledge to apply the scientific method specifically to the proposed dissertation project

and 4) whether the proposed dissertation project is likely to result in a significant contribution to

genetic knowledge and the timely graduation of the student.

The chair will report the decision of the committee to the Graduate Dean, and notify the student's

graduate adviser of the outcome of the examination through the GGG Administrative Assistant.

Format of Qualifying Examination

There will be a standard format for the qualifying examination for students in all Focus Groups

as specified below. Focus Groups may request a variance from the standard format. Such

variances must be reviewed by the Ed Policy Committee and approved by the Executive

Committee.

The Qualifying Examination Committee will administer the oral examination at some time after

April 30 in the Spring Quarter of the second year of enrollment and before March 1 in the Winter

Quarter of the third year of enrollment to determine if the student is qualified for advancement to

candidacy for the Ph.D. degree based on the criteria listed in C2b above. If circumstances are

such that the qualifying examination cannot be taken before March 1 in the third year, the

student must submit a written request with justification for a delay and proposed examination

date to the Advising Committee. It is the responsibility of the student and major professor to

ensure that the qualifying exam is taken in a timely fashion.

The examination shall include the following:

a. Presentation and defense of a written research proposal covering the proposed

dissertation research. This will be submitted to committee members not less than two weeks

prior to the date of the examination. The proposal should reflect the goal of dissertation projects

to provide a substantial and original contribution to the field of genetics. The format should be

that of a Federal grant proposal and should be no more than five pages long.

b. Oral examination covering the breadth of genetics as reflected by the subject matter of the core

courses

c. A Focus Group may require an additional research proposal, written on a subject area distinct

from the dissertation proposal, to be submitted two weeks prior to the examination and defended

at the oral examination. Alternatively, Focus Groups may require the defense of an area of

genetics distinct from the subject of the dissertation proposal.

2. Dissertation Committee

After advancement to candidacy the Dissertation Committee shall be appointed by the Dean of

the Graduate Division on recommendation of the adviser, after consultation with the major

professor and the student. Changes in membership of Dissertation Committees are made by the

appointment of a new committee and must be approved by the Graduate Division.

The major professor will serve as the chair of the committee. There will be two additional

members of the Dissertation Committee

The committee shall be appointed as soon as possible after the student has passed the qualifying

examination.

The Dissertation Committee shall normally include at least two members of the Graduate Group

in Genetics. The third member may have specialist knowledge pertinent to the research area and

does not necessarily have to be a member of the GGG.

The Dissertion Committee will provide the student with intellectual and technical advice on the

research project so as to allow the student to complete the research for the Ph.D in a timely

manner. It should be comprised of faculty that are capable of providing such specialized advice.

The major professor will call for a meeting of the Dissertation Committee no more than six

months after its appointment to review the status of the student's research.

Additional meetings should be held once each year and may be held more frequently at the

request of the major professor, other members of the committee, or the student. A thesis

committee report signed by all members of the thesis committee must be completed annually for

the student to be considered as making adequeate progress towards completion of their degree.

Students are encouraged to consult with all members of the committee with respect to his/her

research.

The major professor, if absent for more than two months, should so inform the student’s adviser,

and recommend a substitute to serve in his/her absence. If absent beyond the completion of the

student's research, the major professor, in consultation with the adviser, the other members of the

committee, and the student, should make all necessary arrangements for completion of the

research and review of the dissertation.

The committee shall evaluate the merits of the dissertation. The dissertation will be judged as

satisfactory on three criteria: 1) The demonstration of an in depth understanding of the specific

area of research. 2) The demonstration of the application of the scientific method in a genetic

context. 3) The generation and interpretation of data that represent significant and novel

contributions to knowledge.

3. Format and presentation of Dissertation

Students will submit a dissertation based upon original research completed as a graduate student

to their Dissertation Committee for approval at least four weeks before the student wishes to

submit the approved thesis to the Graduate Division. The committee should review the thesis

within four weeks of receipt and provide the students with written comments. Prior to final

approval the Dissertation Committee should meet with the student and reach a consensus

regarding the thesis based on the criteria listed above in section IID2f.

At some time during their final six months, and before the dissertation can be signed, students

must present their dissertation research in a public seminar which shall be advertised to the

membership of the GGG.

Draft January 24, 2005; modified April 14, 2005 with comments of the GGG Exec;

approved by GGG Exec May 17, 2005

OPERATING PROCEDURES FOR

THE PLANT BREEDING & BIODIVERSITY FOCUS GROUP

OBJECTIVES

The Plant Breeding & Biodiversity (PB&B) focus group within the Genetics Graduate

Group (GGG) will bring together faculty who are active in plant breeding and biodiversity

research to enhance the training opportunities for interested graduate students.

Plant Breeding is defined broadly as the application of genetics principles to plant

improvement for human-designated use. Research in plant breeding may involve primarily

classical breeding and genetics methodologies, or integrate them with modern molecular and

genomic techniques, to accomplish crop improvement and/or further the utilization and

development of germplasm resources. Research interests by members of this focus group span

topic areas such as varietal development, germplasm resource development and maintenance,

genetic/germplasm diversity, breeding methodology development, quantitative and qualitative

trait inheritance and expression, linkage and QTL mapping, marker-assisted selection,

bioinformatics, and gene introgression from wild species through sexual or transgenic means.

The study of Biodiversity seeks to understand the evolutionary causes of patterns of

genetic diversity. In turn, this information allows us to better maintain existing diversity, protect

threatened populations or species, and utilize it for the purpose of Plant Breeding. Biodiversity

studies have benefited significantly from the analysis of DNA and protein sequences to

understand past demographic events (such as episodes of sharp increases or decreases in

population size), ecological occurrences (such as episodes of selection), the molecular basis of

phenotypic variation, and particularly adaptation.

ACTIVITIES

The PB&B focus group will:


develop and maintain a web page focused on the group with links to lab home pages,

facilitate and coordinate training in PB&B,

set the specialist curricula as described below (and to be developed),

organize and facilitate a GGG student-participatory seminar once every two years

focused on PB&B,

organize a GGG invited speaker seminar once every two years focused on PB&B,



conduct a monthly journal club focused on PB&B,

provide a framework for training grants.

ADMINISTRATION

The PB&B focus group will be administered by a group leader in consultation with the

focus groups members. Recruiting, advising, curriculum development, etc. for this focus group

will be the responsibility of designated focus group members, and these efforts will be

coordinated with GGG standing committees. Focus group policy will be decided by the focus

group members. Regular meetings of the focus group will be the responsibility of the group

leader.


The focus group members will elect a Leader and by an e-mail ballot, and a simple

majority of those voting will decide the leadership. The Leader will usually serve a term of at

least two years. Service as Leader will rotate among all group members. A majority vote of the

membership can request an earlier election.

MEMBERSHIP

Membership is open to anyone who wishes to actively participate in the PB&B focus

group for the first year. The membership will self assess itself according to the criteria below at

the end of the first year. Thereafter, membership will be reviewed every three years by all focus

group members. A majority of the votes cast by the other group members will be required for

continued membership.


1) Maintenance of an active research program in the area of plant breeding and biodiversity as

evidenced by:

g) research activity as evidenced by peer-reviewed publications (including varietal or

germplasm releases) in the area of plant breeding and biodiversity.

h) adequate funding resources to support graduate students and to maintain a PB&B-related

research program.

2) Sustained activity in the PB&B focus group, as evidenced by active and regular participation

in at least one of the following:

a) representing the PB&B focus group on a GGG standing committee,

b) teaching or co-teaching a GGG core course or the PB&B focus group GGG seminar,

c) teaching a course directly relevant to the PB&B focus group curriculum,

d) serving the PB&B focus group as the leader or by conducting activities such as curriculum

development, journal club, student recruitment, student advising, etc.

STUDENT CURRICULUM

Courses:

All students will take the core courses and other courses required of all GGG students. In

addition, students will take at least two courses from the list A for specialization and at least one

course from list B to provide a depth of education in PB&B. These courses will be taken for a

grade. Students will also take the PB&B focus group-sponsored seminar, plus one other, in

addition to GGG291. All students will be required to TA a genetics or plant breeding-related

course and will be encouraged to enroll in GGG300 prior to advancing to candidacy.

Rotations:

In-coming students will be introduced to the breath of research of PB&B members by lab

rotations and PB&B faculty research presentations during fall quarter. In-coming students will

be required to rotate through at least two labs during their first two quarters to expose new

students to the research of PB&B members. Rotations will be coordinated by the focus group.


The format of the qualifying examinations will be of a single research proposal plus a

specific defense of each of the four areas covered by the core courses with a particular emphasis

on breeding. At least one member of the exam committee will be from the PB&B focus group.

The research proposal will focus on, or be directly relevant related to, plant breeding, genetics,

and biodiversity analysis.

REVISION OF OPERATING PROCEDURES:



ORIGINATING FACULTY

Paul Gepts

Dina St. Clair

David Neale

Jorge Dubcovsky

Course list for Plant Breeding and Biodiversity focus group: List A: depth; List B: breadth

Substitution of a course of the course list can be made with approval of the guiding committee.

List Number Title Instructor Units Quarter

Statistics & Bioinformatics

A AGR205 Experimental design

& analysis

Dubcovsky 4 Winter, every

year

A AGR206 Multivariate

systems & modeling

Laca 4 Spring, every

year

Biodiversity

A ECL207 Plant population

biology

Rice 3 Winter, alternate

year

B ECL216 Ecology and

agriculture

Jackson 3 Fall, every year

B ECL222 Human ecology of

agriculture

Brush 4 Fall, alternate

years

B EVE210 Molecular

phylogenetic

analysis

Nadler, Sanderson 3 Spring, alternate

years

B EVE211 Applied

phylogenetics

Sanderson, Shagger,

Wainwright

3 Spring, every

year

Population and quantitative genetics

A EVE102 Population and

quantitative genetics

Langley 4 Check with

instructor

Breeding

A PLB154 Introduction to plant

breeding

St. Clair 4 Winter, every

year

A GGG220 Genomics &

biotechnology of

plant improvement

Michelmore 3 Winter, alternate

years

A AGR221 Advanced plant

breeding

Teuber 4 Spring, alternate

year

Plant molecular biology, development, and physiology

List Number Title Instructor Units Quarter

B PBI210 Plant ecophysiology Pearcy 3 Winter, alternate

years

B PBI220 Plant developmental

biology

Bowman, Sinha 4 Alternate years

B PBI227 Plant molecular

biology

Britt, Sinha 4 Winter, alternate

years

B PBI229 Molecular biology

of plant

reproduction

O’Neill 3 Alternate years

B SSC208 Soil-plant

interrelationships

Richards 3 Winter, alternate

years

Plant pathology

B PLP210 Biochemistry and

molecular biology

of plant-microbe

interactions

Gilchrist, Bostock 4 Fall, alternate

years

B PLP215

X

Genetics and

molecular biology

of plant pathogens

X 4 Winter, alternate

years

Entomology

B ENT123 Plant-Virus-Vector

Interactions

Lucas, Gilbertson,

Ullman

3 Fall, alternate

years

genetics graduate group advising highlights

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