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 HighlightsNew Student Orientation- Fall 2006

Advising-You have two official faculty mentors recognized by Office of Graduate Studies-1. Academic Adviser2. 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 StudiesInitially 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 takenEnsue that required coursework is takenMonitor finding research homeHelp with dealing with university bureaucracyHelp solve problems with GGG program or major professorApprove/sign petitions for late drop/PELP/Advancement to CandidacyGet career adviceReceive 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 electivesDiscuss research interest/rotationsDiscuss focus group interest-decide if should switch advisers, guiding membershipForm submitted to GGG by you after meeting is held and signatures obtained.

B. Third Quarter Guiding Committee MeetingBefore 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?Form submitted to GGG by you after meeting is held and signatures obtained.

C. Fifth Quarter Guiding Committee Meeting Same committee as in (B). Verify that have completed/or will complete ALL coursework by end of 6th quarterSuggest Qualifying Examination Committee MembersVerify that have dissertation proposal- submit abstractForm submitted to GGG by you after meeting is held and signatures obtained.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 BiologyWolf 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 CoursesGGG 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 MichelmoreGGG296 (Fall 2005) Science Professionalism and Integrity- Yoder (2 units) (CRN

27062)

GGG298 (Fall, Winter, Spring) Group StudyGGG299 (Fall, Winter, Spring) ResearchGGG300 (Fall, Winter, Spring) Teaching in Genetics

Additional Courses with a Genetic Component

General Genetics:Upper Division Undergraduate

ANG 107 (Fall) Genetics and Animal BreedingANT 151 (Spring) Primate EvolutionANT 152 (Winter) Human Evolution

AVS 103 (Spring) Avian Development and GeneticsBIS 101 (Fall, Winter, Spring) Genes and Gene Expression

MCB 121 (Winter, Spring) Molecular Biology of Eukaryotic CellsMCB 162 (Fall) Human GeneticsMCB 163 (Winter) Developmental GeneticsMCB 164 (Winter) Advanced Eukaryotic GeneticsMIC 150 (Winter) Bacterial Genetics MIC 170 (Spring) Yeast Molecular Genetics

Molecular GeneticsGraduate

ANG 211 (Spring) Genetic Engineering of AnimalsANG 212 (Winter) Sequence Analysis in Molecular GeneticsMCB 255 Molecular Mechanisms in Animal DevelopmentMCB 256 (Fall ) Cell and Molecular Biology of CancerMCB 257 (Fall ) Cell Proliferation and cancer genes MCB 262 (Winter ) Transgenic Expression SystemsMCB 263 (Winter) Biotechnology Fundamentals & ApplicationsMIC 200A (Fall) Biology of Prokaryotes

MIC 215 (Fall) Recombinant DNA MIC 250 (Winter) Biology of Yeasts

MIC 263 (Spring) Principles of Protein-Nucleic Acid InteractionsMIC 298- maybe an official number come winter quarter (Winter 2005) Recombination

PBI 227 (Winter) Plant Molecular Biology

Upper Division UndergraduateANG111 (Winter) Molecular Biology Laboratory Techniques

BIS 102 (Fall, Winter, Spring) Structure and Function of BiomoleculesMCB 121(Winter, Spring) Molecular Biology of Eukaryotic Cells

MCB 161 (Winter) Molecular GeneticsMCB 160L (Fall, Winter, Spring) Principles of Genetics LaboratoryMCB163 (Winter) Developmental GeneticsMIC 170 (Spring) Yeast Molecular Genetics

CytogeneticsGraduate VCR 221 Vegetable Genomics

Upper Division UndergraduateANG101 (Spring) Animal Cytogenetics

Population GeneticsGraduate

AGR 221 (Spring) Advanced Plant BreedingEVE 210 (Spring) Molecular Phylogenetic Analysis

PBG 200A (Fall) Principles of Population BiologyPGB 200B (Winter) Principles of Population BiologyPGB 200C (Spring) Principles of Population BiologyPBG 207 (Winter) Plant Population Biology

PBG 231 (Fall) Mathmatical Methods in Population Biology PBG 270 (Fall) Evolutionary Biology

PBG 290 (Fall, Winter, Spring) Seminar

Upper Division UndergraduateANT 153 (Winter) Human Biological Variation

EVE 102 (Fall) Population and Quantitative genetics

Quantitative Genetics Graduate

AGR 221 (Spring, not offered 2004-2005) Advanced Plant BreedingANG 204 (Spring) Theory of Quantitative GeneticsANG 206 (Spring) Advanced Domestic Animal Breeding

Upper Division UndergraduateANG120 (Spring) Introduction to Statistical Genomics

EVE 102 (Fall) Population and Quantitative genetics

EvolutionGraduate

EVE 210 (Spring offered in alternate years) Molecular Phylogenetic AnalysisPBG 203 (Winter) Advanced Evolution

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

Upper Division UndergraduateANT 151 (Spring) Primate EvolutionANT 152 (Winter) Human Evolution

EVE 100 (Fall, Winter, Spring) Introduction to EvolutionEVE 103 (Winter) Phylogeny and Macroevolution

Physiological GeneticsGraduate

MCB221D (Winter) Cellular Biochemistry

Upper Division UndergraduateNPB 131 (Fall) Physiological Genomics

BreedingGraduate

AGR 221 (Spring) Advanced Plant BreedingANG 206 (Spring) Advanced Domestic Animal BreedingGGG 220/VCR 220 (Winter) Genomics & Biotechnology of Plant Improvement

VCR 221 (Spring) Genomics and Breeding of Vegetable Crops

Upper Division UndergraduateANG 107 (Fall) Genetics and Animal BreedingPLB 154 (Winter) Introduction to Plant BreedingPLB 160 (Winter) Principles of Plant Biotechnology

Biotic Stresses in PlantsGraduate

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

Upper Division UndergraduatePLP123/PLB123/ENT123 (Fall-not offered 2004-2005 ) Plant-Virus Interaction

Human/Primate GeneticsGraduate

ANT 252 (Winter) Human Evolution Seminar

Upper Division UndergraduateANT 151 (Spring) Primate EvolutionANT 152 (Winter) Human EvolutionANT 153 (Fall) Human Biological VariationANT 157 (Winter) Anthropological GeneticsANT 157L (Fall) Laboratory in Anthropological GeneticsMCB 162 (Winter) Human Genetics

Graduate Seminar CoursesANT 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 RecombinationMIC 275 (Fall, Winter, Spring) Journal Club in Recombination GeneticsECL 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 Exam1. 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 Exam1. 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- 2005Genetics Graduate Group

Interested Potential FocusFocus Group Members Address Group Leader

Animal Genomics Danika BannaschVM: Pop. Health & Repro. Anita Oberbauer

Mary Delany Animal ScienceHolly Ernest Vet Genetics LabTom Famula Animal ScienceSree Kanthaswamy Vet Genetics LabDietmar Kueltz Animal Science

Leslie LyonsVM: Pop. Health & Repro.

Marta Marthas CRPRCBernie May Animal ScienceJuan Medrano Animal ScienceJim Murray Animal ScienceAnita Oberbauer Animal ScienceAlison Van Eenennaam Animal Science

Chromosome Biology Sean Burgess MCB Wolf-Dietrich Heyer

Ken Burtis MCBAnne Britt Plant BiologyRoger Chetelat Plant SciencesWolf-Dietrich Heyer MicrobiologyNeil Hunter MicrobiologyS. Kowalczykowski MicrobiologyKen Kaplan MCBJanine LaSalle Microbiology

Human Genetics Gino CortopassiVM: Molecular Bioscience Mike Seldin

Paul Gumerlock Hematology/UCDMC

Nobuko HagiwaraMed: Cardiovascular Med.

John HersheyMed. Biological Chem.

Liping Huang NutritionHsing-Jien Kung UCD Cancer CenterJanine LaSalle Microbiology

Marta Marthas CRPRC

Maria MudrjiMed. Micro. & Immuno.

Mike SeldinMed. Biological Chem.

Craig Warden Rowe Program

Reen WuResearch Bio. & Medicine

Model Plants Steffen Abel Plant Sciences Chuck GasserJohn Bowman Plant BiologyAnne Britt Plant BiologyJudy Callis MCBChuck Gasser MCBJohn Harada Plant BiologyStacey Harmer Plant BiologyDan Kliebenstein Plant SciencesJulin Maloof Plant BiologyRichard Michelmore Plant Sciences/ MCBNeelima Sinha Plant BiologyVenkatesan Sundaresan Plant BiologyThea Wilkins Plant SciencesJohn Yoder Plant Sciences

General Genetics All faculty

Plant Breeding and Biodiversity Roger Chetelat Plant Sciences Paul Gepts

Jorge Dubcovsky Plant SciencesPaul Gepts Plant SciencesJulin Maloof Plant BiologyDavid Neale Plant SciencesDan Parfitt Plant SciencesPamela Ronald Plant PathologyDoug Shaw Plant SciencesDina St. Clair Plant SciencesLarry Teuber Plant SciencesAndy Walker Viticulture

OPERATING PROCEDURES FOR THE ANIMAL GENOMICS FOCUS GROUP

REVISED September 2003OBJECTIVESThe 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.

ACTIVITIESThe 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.

ADMINISTRATIONThe 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 LEADERThe 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.

MEMBERSHIPMembership 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 MEMBERSHIP1) 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 CURRICULUMCourses: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 PROCEDURESThese 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 GeneticsANG206 Advanced Domestic Animal BreedingANG 208 Estimation of Genetic ParametersANG 212 Sequence Analysis in Molecular Genetics [Added 9/03]AVS 220/MCB257 Cellular Proliferation of OncogenesBCM 222 Mechanisms of Translational ControlECL 208 Conservation BiologyENT 212 Molecular Biology of Insects and Insect VirusesEPI 205A Principles of EpidemiologyEVE 210 Molecular Phylogenetic AnalysisEVE 211 Applied PhylogeneticsGGG 210 Horizontal Gene TransferMCB 255 Molecular Mechanisms of Animal DevelopmentMCB 262 Transgenic Expression SystemsMIC 215 Recombinant DNAMIC215L Recombinant DNA LaboratoryMIC 263 Principles of Protein-Nucleic Acid InteractionsPBG 200A, B, C Principles of Population BiologyPBG 203 Advanced EvolutionPGG 200L Animal Cell Culture LaboratorySTA 226/BST 226 Statistical Genomics [Added 11/06]

Initial faculty membership in the Animal Genetics Focus Group

1. Danika Bannasch VM:Population Health and Reproduction2. Mary Delany Animal Science3. Thomas Famula Animal Science4. Dennis Hedgecock Animal Science5. Dietmar Kueltz Animal Science6. Leslie Lyons VM:Population Health and Reproduction7. Marta Marthas CRPRC8. Bernie May Animal Science9. Juan Medrano Animal Science10. Jim Murray Animal Science11. Anita Oberbauer Animal Science12. 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:

provide visibility for recruiting students interested in this area, develop and maintain a webpage focused on the group, allow coordination of research and training in ChromBio FG, set the specialist curricula as below, organize a GGG seminar once every two years focused on ChromBio FG, assist in the function and administration of the GGG by providing representatives to serve

on GGG standing committees, conduct a journal club focused on ChromBio FG, provide the framework for training grants.

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.

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

Qualifying Examinations: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 proceduresThese 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 BiologyKen C. Burtis, Professor of GeneticsAnne B. Britt, Associate Professor of Plant BiologyRoger Chetelat, Assistant GeneticistWolf-Dietrich Heyer, Professor of MicrobiologyStephen C. Kowalczykowski, Professor of MicrobiologyKen B. Kaplan, Assistant Professor of Molecular and Cellular BiologyJanine 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: provide visibility for recruiting students interested in this area, 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, set the specialist curricula as below, conduct a biweekly journal club/seminar series focused on Animal Genomics, organize a GGG participatory seminar course offered each years focused on Human

Genetics, 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 HGG 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.

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.

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,

Sustained activity in at least one of these four activities is required unless there are significant mitigating administrative circumstances (such as being department chair).

Course Requirements

1. GGG core courses2. 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 GeneticsANG 208 Estimation of Genetic ParametersAVS 220/MCB257 Cellular Proliferation of OncogenesBCM 222 Mechanisms of Translational Control

EPI 205A Principles of EpidemiologyEVE 210 Molecular Phylogenetic AnalysisEVE 211 Applied PhylogeneticsMCB 255 Molecular Mechanisms of Animal DevelopmentMCB 262 Transgenic Expression SystemsMIC 215 Recombinant DNAMIC215L Recombinant DNA LaboratoryMIC 263 Principles of Protein-Nucleic Acid InteractionsPBG 200A, B, C Principles of Population BiologyPBG 203 Advanced EvolutionPGG 200L Animal Cell Culture LaboratoryNPB 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.

RotationsStudents 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 ExaminationsThe 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.

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.

OPERATING PROCEDURES FOR THE GENETICS OF MODEL PLANTS FOCUS GROUP

OBJECTIVESThe 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.

ACTIVITIESThe GMP focus group will:

provide visibility for recruiting students interested in this area, 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, assist in the function and administration of the GGG by providing representatives to serve

on GGG standing committees, conduct a journal club focused on GMP, provide the framework for training grants.

ADMINISTRATIONThe GMP 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.

ELECTION OF FOCUS GROUP LEADERThe 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.

MEMBERSHIPMembership 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.

CRITERIA FOR MEMBERSHIP1) Maintenance of an active research program as evidenced by:

e) significant peer-reviewed publications in the area of genetics of plant model systemsf) 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 CURRICULUMCourses:

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. tTwo 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.

Qualifying Examinations: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.

REVISION OF OPERATING PROCEDURESThese operating procedures may be revised at anytime by a majority vote of the

membership and subject to ratification by the GGG executive committee.

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 WinterEVE 210 Molecular Phylogenetic Analysis Nadler, SandersonEVE 240 Paleobotany and Angiosperm Evolution Doyle Winter (no- 03-04)

GGG 220/VCR 220

Genomics & Biotechnology of Plant Improvement

Michelmore Winter

MIC 215 Recombinant DNA Privalsky FallMIC 262 Advanced General and Molecular Virology Bruening, Manning,

LuciwSpring (no- 02-03)

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

PBI/MCB126

Plant Biochemistry Abel/Callis Spring

PBG 203 Advanced Evolution Gottlieb Winter (no 02-03)PBI 208 Plant Hormones & Regulators Abel W-Odd 03PBI 218A Advanced Concepts in Plant Cell Biology:

Cell BiogenesisLucas Winter (even yrs)

PBI 218B Advanced Concepts in Plant Cell Biology: Transduction

Spring (odd yrs)

PBI 219 Reproductive Biology of Flowering Plants staff F-OddPBI 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 Coursesi. GGG 201A, Advanced Genetic Analysisii. GGG 201B, Comparative and Functional Genomicsiii. GGG 201C, Molecular Geneticsiv. GGG 201D, Transmission, Population and Quantitative Genetics

b. Seminar Coursei. 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 researchc. 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. CurriculumThe 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: GGG201AAdvanced Genetic Analysis

and at least two of:

GGG201B Comparative and Functional Genomics,GGG201C Molecular GeneticsGGG201D Transmission, Population and Quantitative Genetics

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 GeneticsCytogeneticsQuantitative GeneticsPopulation, Evolutionary and Ecological GeneticsAnimal GeneticsMolecular GeneticsPlant 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.

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 GeneticsGGG201D Transmission, Population and Quantitative Genetics

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 GeneticsCytogeneticsQuantitative GeneticsPopulation, Evolutionary and Ecological GeneticsAnimal GeneticsMolecular GeneticsPlant 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 requirements. Focus Groups may, at some time in the future, impose such requirements as are within the general guidelines imposed by the Graduate Division.

c) Focus Group requirements:

At present there are no specific Focus Group requirements. Focus Groups may, at some time in the future, impose such requirements as are within the general guidelines imposed by the Graduate Division

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

OBJECTIVESThe 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.

ACTIVITIESThe PB&B focus group will:

provide visibility for recruiting students interested in this area, 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, assist in the function and administration of the GGG by providing representatives to serve

on GGG standing committees, conduct a monthly journal club focused on PB&B, provide a framework for training grants.

ADMINISTRATIONThe 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.

ELECTION OF FOCUS 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.

MEMBERSHIPMembership 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.

CRITERIA FOR MEMBERSHIP1) 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 CURRICULUMCourses:

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.

Qualifying Examinations: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:

These operating procedures may be revised at anytime by a majority vote of the membership and subject to ratification by the GGG executive committee.

ORIGINATING FACULTYPaul GeptsDina St. ClairDavid NealeJorge 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 QuarterStatistics & 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

B PBI210 Plant ecophysiology Pearcy 3 Winter, alternate years

List Number Title Instructor Units QuarterB PBI220 Plant developmental

biologyBowman, 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 PLP215X

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