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PGEC 20 Year Symposium
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Plant Gene Expression Center

 

20 Year Symposium

 

Clark Kerr Campus

Berkeley

June 4-6, 2007


 

Table of Contents

 

 

Program... 3

History of the Plant Gene Expression Center.. 4

Scientific Research Contributions. 5

Productivity and Recognition.. 14

FORMER POSTDOCS AND GRADUATE STUDENTS. 17

POSTER TITLES. 22

POSTER ABSTRACTS. 24

LIST OF PARTICIPANTS. 35

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Acknowledgements

 

We wish to thank the USDA Agricultural Research Service and the University of California for a very effective collaboration that led to the creation of the PGEC. We are indebted to Gerry Still for making the PGEC dream come true more than 20 years ago. Thanks to present and former Area Office directors and the National Program Staff for their support of our research. Thanks to PGEC lab managers, past, Karen Suslow and Julie Mathern, and present, Rebecca Haussmann, for keeping the PGEC running. Thanks to Anne Spelletich for getting our greenhouses off the ground, and the present greenhouse staff, David Hantz, Julie Calfas and Paloma Cuarto for keeping our plants healthy. Thanks to our office staff, especially Rona Kagawa and Kathy Robinson, for their hard work and loyalty.

 

The symposium is supported by grants from NSF and NRI.

 

 

 

Program

 

Monday, June 4th, 2007

                  7:00 - 8:00 pm             Registration

                  7:00 - 9:00 pm             Reception

 

Tuesday, June 5th, 2007

                  7:30 - 9:00 am              Breakfast

                  7:30 - 9:00 am             Registration

                  8:45 - 9:10 am              Welcoming Remarks:

                                                      Ed Knipling, Administrator, ARS

,                                                     Gerry Still, Former Center Director, PGEC                       

               9:10 -   9:50  am             Natasha Raikhel, UC Riverside,

                                                            Vesicle trafficking in plant cells

                9:50 -  10:30 am            Joe Ecker, Salk Institute,

                                                            Mapping Genotype into Phenotype: Induced, Natural and

Epigenetic Variation in Arabidopsis genomes

              10:30 - 11:00 am         Coffee break

              11:00 - 11:40 am              Sheila McCormick, PGEC,

                                                            Receptor kinase signaling during pollen tube growth

              11:40 - 12:20 am              Steve Kay, Scripps Institute,

                                                            Systems Approaches to Understanding Circadian Clocks

              12:20 -   2:00 pm             Lunch (entry closes at 1:30)

                2:00 -   2:40 pm           David Ow, PGEC,

                                                            Another decade of biotech research, what next?

                2:40 -   3:20 pm            S. Dinesh-Kumar, Yale University,

                                                            Life after death: Role for autophagy during innate immunity

                3:30 -   5:30 pm            Poster Session

                6:00 -   7:30 pm            Dinner (entry closes at 7:00)

                7:30 -   8:30 pm            Chris Somerville, Energy Bioinstitute,

Development of Biofuels

 

    Wednesday, June 6th, 2007

                7:30 -    9:00 am           Breakfast

                9:00 -    9:40 am           Xing Wang Deng, Yale University,

                                                      Light regulation and rice genomics, 16 years after PGEC

                9:40 -  10:20 am        David Jackson, Cold Spring Harbor, NY,

                                                      Genetic control of meristems late in maize

               10:20 - 11:00 am           Jenn Fletcher, PGEC,

Regulation of Shoot Apical Meristem Function in Arabidopsis

               11:00          am             Closing remarks

 

 

 


History of the Plant Gene Expression Center

 

           Recombinant DNA technology was established in the 1970’s. A report published by the National Academy of Science (NAS) in the early 1980’s indicated that the USDA-Agricultural Research Service (ARS) was lacking research facilities that used such technology and wanted to encourage their establishment. The NAS report was the catalyst for the genesis of the PGEC. The architect of the center was Dr. Gerald Still, a scientist and senior executive of ARS, who was greatly supported by Dr. Terry Kinney, the ARS administrator in the early 80’s. Both discussed the possibility of establishing a new research unit within the ARS that would use molecular genetic approaches to advance American agriculture. They decided in 1983 to establish a research institute adjacent to the Western Regional Research Center (WRRC) in Albany, California, near the University of California, Berkeley campus. The mission of the Center was and still is the development of new knowledge using recombinant DNA technology to advance plant biology and by extension American and world agriculture. They also decided that the Center should be linked with the University of California, Berkeley (UCB) campus for intellectual and administrative support. It was this marriage between ARS and UCB that constitutes one of the major cornerstones of its subsequent success. According to this plan, the newly hired PGEC Principal Investigators (PIs) would be selected by a joint ARS-UCB search committee and would serve as adjunct faculty at the Department of Plant Biology. In addition, the UCB campus would be represented at the Center by a UCB faculty member from the same department who would serve as the research director of the Center. The administrative director would be an ARS senior scientist. Dr. Gerald Still, the architect of the PGEC, would be the first Center director and would work closely with the chosen research director to advance the goals of the center.       

 

            A cooperative agreement was signed between ARS and UCB in 1986 that officially established the PGEC as a joint venture between the two institutions. UCB recruited Dr. Peter Quail (molecular biologist/biochemist) as the research director of the Center. Concomitantly, ARS hired six young investigators selected by a joint ARS-UCB search committee together with Drs. Still and Quail. Drs. Barbara Baker (molecular geneticist), Sarah Hake (developmental geneticist), Sheila McCormick (molecular biologist/cell biologist), Michael Fromm (molecular biologist), David Ow (molecular geneticist) and Athanasios Theologis (molecular biologist/biochemist) were chosen as PIs. In 1987, all seven moved into a newly renovated space at the Albany location that was very well equipped with all the necessary instrumentation for molecular genetic work and had ample greenhouse space. The PGEC was funded at about $3 million per year for PI salaries, support personnel, and indirect costs associated with the operation of the Center.  

 

            The PIs’ UCB adjunct appointments allowed them to teach at UCB, have access to graduate students and to submit competitive grants to federal agencies such as NIH, NSF, DOE, and USDA for additional funds. The submission of competitive grants was the key to the PGEC success because it not only provided additional funds but allowed for the constant evaluation of PGEC research by the American scientific infrastructure peer review system. All the PIs established highly successful research programs and received competitive research grants and training fellowships. Their scientific research has been seminal and has greatly enhanced our knowledge of how plants work. Dr. Gerald Still, the founder, retired in 1994 and was replaced by one of the PIs, Dr. Sarah Hake.  Dr. Michael Fromm, one of the original PIs, left the center in 1989. Since then, two PIs have joined the Center, Drs. Jennifer Fletcher (developmental geneticist-1999) and Frank Harmon (molecular biologist/biochemist-2005).

 

Scientific Research Contributions

 

            The PGEC mission has been to provide the means to develop plant germplasm with inherent increased productivity and quality characteristics by identifying the genetic and molecular basis of plant traits. Research at the PGEC has focused on how plants respond to their environment, including abiotic and biotic factors, and how plants develop, differentiate and grow. Some of the major discoveries include ACC synthase, the limiting enzyme in ethylene production and thus ripening; phytochrome signaling which allows plants to track incoming light; meristem-expressed genes that regulate the architecture of plants; recombination tools to improve gene transfer; pollen-expressed genes that are essential for fertilization and the N gene that provides disease resistance to plants. These discoveries could not have been possible without the outstanding contributions of postdoctoral fellows, graduate students, undergraduates and technicians. These young scientists are by far our most outstanding product (please see Table 3 and 4).

 

The Baker Lab

 

            The research in this lab seeks to understand the mechanisms of plant-pathogen interaction that lead to either a resistant or susceptible host response. Their experimental system for studying the biochemical, molecular-genetic, and evolutionary properties of pathogen recognition, (induced local and systemic signaling and inhibition of pathogen spread) consists of viral, bacterial, and fungal and oomycete plant pathogens in Solanaceae and Arabidopsis plant hosts.  The ultimate goal of the research is to contribute to the design of environmentally benign strategies for durable, broad-spectrum disease resistant crops.

 

            Using a novel insertional mutagenesis approach, the lab was one of the first to successfully isolate an R-gene, N (necrosis), encoding resistance to tobacco mosaic virus. Their findings were among the first to describe the conserved motifs that have subsequently been found encoded in most R-genes throughout the plant kingdom, and, in the case of the Toll-Interleukin-1 receptor (TIR) motif, in genes involved in immunity in animals, fungi, and bacteria (trans-kingdom innate immunity). Genetic and genomic studies in the Baker lab have revealed several components of the N-mediated signaling pathway that are shared with other R-gene mediated and innate immunity resistance systems including MAP kinases (MAPKKK MAPKK and MAPK), and a predicted lipase-domain containing product of the tomato EDS1 gene, also identified in Arabidopsis as essential for TIR-NBS-LRR R gene mediated resistance.

 

            The PI currently leads the Potato Genome Project, an international consortium of seven laboratories and several other collaborating laboratories that have produced extensive structural and functional genomic resources for analysis of growth, development, metabolism and responses to biotic and abiotic stress in potato and other Solanaceae. The Baker lab has focused on understanding the structural, functional and evolutionary properties of three resistance hotspots, comprised of closely linked pathogen resistance loci and tandemly arrayed R genes, of the wild Solanum species S. demissum, the primary source of resistance loci introduced into cultivated potato against specific races of the devastating late-blight oomycete, Phytophthora infestans. It has been hypothesized that R-gene clusters of chromosomal hotspots provide a structural environment that facilitate sequence exchange and rapid evolution of novel pathogen specificities. The Baker lab’s recent findings show that an unusually large number of known race-specific R-loci localized at a major late blight resistance hotspot are correlated to an even larger number (>135) of functionally uncharacterized, highly chimeric homologues, raising the possibility that the locus harbors additional specificities that will be triggered by unique P. infestans effectors. The lab is also investigating the biochemical signaling component of the resistance response (the concerted activation of multiple defense proteins via nitrosylation modification). Her future research will continue to seek understanding of evolutionary mechanisms, including transposable element insertions and sequence exchange within R-gene clusters, which generate structural and functional diversity in ongoing plant-pathogen interplay and build on and extend studies to understand the biochemical and molecular-genetic mechanisms of plant host-microbe interactions.

 

            The PI continues to integrate outreach activities with her research, including training programs for underrepresented Native American and Hispanic students in hands-on, computer-based approaches to explore the fundamental concepts of gene structure-function and the genetic basis of diversity.

 

The Fletcher Lab

 

            The focus of research in this laboratory is the regulation of stem cell activity and lateral organ formation in Arabidopsis thaliana. Plant development occurs via a continuous, lifelong process of reiterative organ formation and differentiation. This growth pattern requires a constant supply of new cells from stem cell reservoirs at the growing tips of the plant, which then assume leaf, stem or flower fates. The lab has shown that maintenance of Arabidopsis stem cell reservoirs occurs via an intercellular negative feedback loop mediated by the CLAVATA-WUSCHEL signal transduction pathway. We demonstrated that the polypeptide signaling molecule CLV3 is secreted by the stem cell reservoir and perceived by a receptor kinase complex in the underlying cells to negatively regulate the expression domain of the stem cell-promoting transcription factor gene WUS. This feedback loop remains the best-characterized polypeptide signaling pathway in plants. CLV3 is one of a large family of related putative polypeptide ligands called the CLE family, members of which are expressed in many different domains throughout the Arabidopsis plant. A collaborative effort is underway to determine the functions of these genes during development.

 

            We have identified several additional pathways that regulate the WUS-expressing stem cell niche. The related ULTRAPETALA1 (ULT1) and ULT2 putative transcriptional regulators act through a CLV-independent pathway to restrict the size of the WUS stem cell niche. ULT1 is also a key component of a temporal feedback loop that controls the timing of WUS repression to terminate stem cell activity in developing flowers. Conversely, the novel, essential gene UMBEL acts upstream of the CLV pathway and is required for the maintenance of the WUS domain. Our current studies aim to characterize additional members of these key stem cell regulatory pathways and the biochemical mechanisms of their activity.  

 

            Several lab projects are investigating the reciprocal interaction between the stem cell reservoir in the shoot meristem and the development of lateral organs such as leaves. We have shown that both stem cell activity and lateral organ polarity are controlled by a small RNA regulatory pathway. The microRNA miR166 cleaves the transcripts of three of its HD-ZIP transcription factor target genes in the shoot meristem, which in turn negatively regulate the level of WUS transcription within the niche cells. Present work in this area focuses on the molecular mechanisms that regulate miR166 expression and function. In a related study, the lab used a database analysis approach to identify a novel small RNA species called tasiR-ARF, one of the first representatives of a recently defined class of small RNAs called trans-acting siRNAs. tasiR-ARF negatively regulates three auxin response genes that are required for shoot maturation and the specification of lateral organ polarity, and indirectly down-regulates miR166 activity. Finally, we have determined that the BTB/POZ domain putative transcriptional regulators BLADE-ON-PETIOLE1 (BOP1) and BOP2 negatively regulate stem cell fate and promote lateral organ differentiation. The BOP pathway converges with the ARF and miR166 pathways to establish lateral organ polarity, with BOP promoting adaxial identity by up-regulating HD-ZIP gene expression on the top side of the organs and miR166 promoting abaxial identity by cleaving HD-ZIP gene transcripts on the bottom side. Together, these studies are building an integrated picture of how stem cell maintenance and lateral organ formation are coordinated throughout plant development.

 

 

 

The Hake Lab

 

            Research in the Hake lab began with the dominant Knotted1 (Kn1) mutation in maize. Cloning by transposon tagging showed that it encodes a homeobox gene expressed in the meristem and that the gain of function phenotype was due to misexpression in leaves. The gene is a member of a gene family and many other members were found to also be associated with dominant leaf phenotypes. A recessive phenotype was discovered that depends on inbred background. In some backgrounds, the shoot meristem quits and only one or two leaves form. In other backgrounds, the only vegetative phenotype is extra leaves in the axils of upper leaves, a phenotype that suggests a role for KN1 in polarity in the meristem. A clear role for KN1 in maintaining inflorescence meristems is seen in both the ear and tassel. Related genes were soon identified in Arabidopsis, which allowed for further dissection of the function of kn1 related homeobox (knox) genes. The loss of function and gain of function phenotypes have allowed former postdocs and students to connect knox genes directly to hormone biosynthesis and cell wall synthesis.

 

            KNOX proteins function as heterodimers with BELL proteins. Work in the Hake lab led to the characterization of this interaction and binding of the complex to DNA. Protein partners were also identified in Arabidopsis and their phenotypes described. Double mutants of duplicated BELL proteins showed a striking phenotype in which the plants never flowered. In summary, KN1 and interacting proteins have proven essential for a myriad of plant events, from meristem maintenance, transition to flowering, stem elongation, and leaf initiation. Recent efforts are aimed at identifying the direct targets of KN1 in maize.

 

Analysis of kn1 led to an interest in all meristems, in particular, meristems in the tassel and ear that are unique to grasses.  Genes were identified that affect the floral meristem, the spikelet meristem and the spikelet pair meristem in addition to overall meristem size. Other genes were identified that affect number of leaves and extent of branch length. These genes provide tools to study natural variation and evolutionary relationships among the grasses. The present goal is to understand the networks within which these genes function.

 

            The analysis of kn1 also led to an interest in how positional information is transmitted to develop patterns in nature. Maize leaves have unique tissue types that allow a dissection of this process. The blade is most distal and carries out photosynthesis, the sheath is proximal and holds the leaf to the stem, and the ligule and auricle mark the boundary between these two tissues. The dominant Knox mutants affect this patterning in a non-cell-autonomous fashion suggesting that the patterns may be established through hormones.  The liguleless1 and liguleless2 genes are required to produce the ligule and auricle in young leaves but not to establish the blade/sheath boundary. Two dominant mutants are likely to provide additional key components to this signaling pathway. Wab1 enhances the lg1 and lg2 mutant phenotypes. Lgn also enhances these recessive phenotypes in the heterozygous condition. As a homozygote, Lgn plants show a striking phenotype in which only small juvenile leaves are made with no transition to flowering. Positional cloning of Lgn and Wab1 will provide more tools to investigate the establishment of positional information in the maize leaf.

 

The Harmon Lab

 

            Prior to joining the PGEC faculty in September of 2005, Dr. Harmon did his postdoctoral work with Dr. Steve A. Kay at The Scripps Research Institute (TSRI) as a DOE-Energy Biosciences Fellow of the Life Science Research Foundation. At TSRI he contributed to work that defined a central negative feedback loop that lies at the core of the Arabidopsis oscillator by demonstrating the functional relationships between three key circadian clock genes. This work provided the first testable model for the plant circadian oscillator and this model continues to serve as the molecular framework for the plant clock. In a separate project, Dr. Harmon’s postdoctoral work revealed a novel component of phytochrome A (phyA)-mediated light signaling pathway, the F-box protein ATTENUATED FAR-RED RESPONSE (AFR). The absence of this E3 ubiquitin ligase component leads to defects in light signaling initiated by phyA, and subsequent study raised the possibility that circadian expression of AFR plays an important role in circadian gating of far-red light signals. The likely role of this pathway is to ensure maximal response to light cues in the morning.

 

            Dr. Harmon’s lab at the PGEC is continuing [m1]  work on the plant circadian system in Arabidopsis, as well as branching out to include Zea mays. The Arabidopsis project is an outgrowth of his interest in circadian gating of light signals and its goal is to define the functional relationships between the proteins involved in signaling into the circadian clock. The entry point for this project is the EARLY FLOWERING 3 (ELF3) protein. ELF3 is a highly conserved plant-specific, nuclear protein lacking readily identifiable functional motifs. ELF3 mutants are impaired in photoperception and measurement of day length. The clock in elf3 arrests in the late afternoon because light signals, which are normally blocked by ELF3, are allowed to reach the core oscillator. The current model for ELF3 action is that it abrogates light input to the clock through a direct physical interaction with phytochrome B (phyB). The immediate interest of the lab is to investigate the functional importance of an ELF3-phyB complex in appropriate clock progression and to identify any additional proteins needed for ELF3 function. This effort will lay the groundwork needed for future systems-based approaches aimed at defining the molecular basis of signaling to the clock.

 

            The lab is also interested in utilizing the wealth of molecular information for the Arabidopsis circadian oscillator along with the substantial genetic and burgeoning genomic resources for maize to investigate the impact of the circadian clock on important agronomic traits in maize. For example, domestication of maize from its ancestor teosinte converted a plant that flowers in response to short days to one that lacks strong photoperiodic behavior. An interest of the lab is to determine the genetic and molecular basis for this shift in the environmental requirement for flowering. The Molecular and Functional Diversity of the Maize Genome project has sequenced a large number of genes in diverse maize inbreds and accessions of teosinte. Genes contributing to important domestication traits, which include flowering time, are expected to be “fixed” in sequence and, therefore, these genes in maize should have significantly less sequence diversity than their teosinte counterparts. Several of the least diverse maize genes in a collection of ~30 orthologs of Arabidopsis flowering time genes represent putative clock genes. The goal of the lab is to apply reverse genetic and molecular approaches to investigate the contribution of these low diversity genes to maize flowering time and define their relationship to the circadian oscillator. In parallel, forward genetic screens of recombinant inbred line populations are anticipated to yield additional loci contributing to circadian clock function in maize.

 

 

 

 

The McCormick Lab

 

            The lab has studied various aspects of pollen development. Early on, it identified several genes that were pollen-specific, and characterized the promoter regions of these genes in some detail, as well as other aspects of transcriptional and post-transcriptional control of pollen gene expression. These promoters are widely used by the research community to express genes in a pollen-specific manner. The lab also identified the biochemical functions for some of the proteins encoded by these pollen-specific genes; using antisense experiments they showed that the cysteine-rich protein LAT52 is important for pollen germination. More recently, the lab became interested in pollen-pistil signaling, so it initiated a project to identify and characterize receptor kinases that might play signaling roles. The lab used yeast two hybrid screens to identify putative ligands and downstream interacting partners for these kinases. Coincidentally, one such identified ligand was LAT52, shown previously to be important for pollen tube growth. They further showed that different ligands interact with these kinases at different stages of pollen tube growth. The lab characterized a cytoplasmic protein, KPP, which interacts with these receptor kinases; KPP was shown to be a member of a newly-identified class of Rop-GEFs. This finding provided a link between receptor kinases and the downstream cytoplasmic remodeling (mediated by Rops) that is necessary for pollen tip growth; because Rop-GEFS are a gene family, this work further suggests that receptor kinases in other tissues will also provide links from extracellular signals to Rops, via Rop-GEFs.

 

            In 2000, a new project was initiated to characterize gene expression in plant gametes. cDNA libraries were constructed from maize sperm, eggs, and embryo sacs and >20,000 ESTs were sequenced from these rare tissue sources. The lab identified promoter elements that will direct cell-specific expression in gametes, and have provided them to the research community.  Using these EST resources and reverse genetics, genes have been identified that are important for pollen tube guidance to the embryo sac, and possibly that are important for gamete fusion.

 

            The lab has identified and characterized several mutants that disrupt pollen development in Arabidopsis. In a collaborative bioinformatics project, the lab identified a large family of proteins that were similar to the small peptide CLAVATA3, thought to be a ligand for the receptor kinase CLAVATA1, and predicted that the 14 amino acid CLE motif might be cleaved from the peptide and be the active moiety. Numerous groups are now studying this CLE protein family and others have shown that indeed the CLE motif alone is sufficient for function.  The lab also has devoted some effort in developing useful technology for the research community, including particle bombardment of pollen, a facile tomato transformation method and detailed protocols for characterizing pollen mutants in Arabidopsis. These technologies have been used in the lab as well as by many other groups.

 

The Ow Lab

 

            The Ow laboratory has been active in several areas of research.  Much of the effort has been directed to developing recombinase-based tools for the manipulation of the plant genome.  Over the years, the laboratory has shown that site-specific recombination can be used to generate chromosome deletions, inversions, insertions and translocations.

 

            An application that has been adopted by industry is the method to selectively remove antibiotics resistance genes after plant transformation, which the laboratory first demonstrated in tobacco and then also in other crop plants such as wheat and corn.  Gene transfer has relied on the use of selectable markers to detect successful DNA uptake.  However, these genes are often not needed in the commercial product, and the presence of antibiotics resistance genes in transgenic crop plants has raised environmental safety concerns.  By showing that a site-specific recombination system can be used to delete away the antibiotics resistance marker, the Ow laboratory provided a solution for industry to address a consumer and regulatory issue, as well as the option to re-use the same selection scheme for subsequent gene transfers.  The first commercial product using this technology to remove a selectable marker, a high lysine corn line developed by Monsanto and Cargill, received regulatory approval in 2006 and is heading to market.

 

            Site-specific recombination for targeting DNA into defined locations in the plant genome, as shown in tobacco and rice, also has commercial interest.  Structurally precise single copy insertions with reproducible expression of the transgene can be obtained in a sixth of the selected events, making site-specific integration a practical approach to generating transgenic crop plants.

 

            Aside from developing methods based on the site-specific recombination system known as Cre-lox, the Ow laboratory has also been active in developing new recombination systems.  The first of these new systems is known as phiC31, which differs from the Cre-lox system in that its recombination reaction is not reversible.  This means that a DNA molecule inserted into the genome will remain in place.  Several developers have licensed this recombination system, and it has since been described by other laboratories to be efficient for targeting DNA into the chloroplast genome, and for reconstructing viral expression systems in planta.  More recently, six new recombination systems have been found and are currently being adapted for plant use.

 

            Plant stress caused by heavy metals pollution has also been a topic of study in the Ow laboratory.  Using a fission yeast model system, which makes the same peptide-metal-sulfide complex as in higher plants, genes involved in the generation of this vacuolar metal complex has been described.  Most notable of these genes is HMT1, which encodes an ABC-type vacuolar membrane transporter.  It sequesters the phytochelatin peptide-cadmium complex in the vacuole, facilitating its maturation to a more stable sulfide-containing complex.  As heavy metals also cause oxidative stress, this avenue of study has also led to uncovering genes in oxidative stress tolerance.  Several of these genes have been found to encode proteins that shuttle to the nucleus during oxidative stress.  An example is the OXS2 protein, which encodes a transcription factor that responds to stress by activating a stress escape pathway to flower early.

 

            Cotton biotechnology has also been a side interest in the Ow lab.  A collaborative effort with the ARS Plant Stress laboratory at Lubbock, Texas, led to the engineering of cotton that resists drift damage from 2,4-D, an herbicide used for grasses.  The cotton lines were transferred United Ag Products (then a ConAgra subsidiary) which bred this trait into commercial cultivars.  Field trials were successful, but due to licensing issues, the 2,4-D resistant lines were not commercialized.  The Ow laboratory has since moved into another area of investigation.   Gossypol is a toxic polyphenolic compound found throughout the cotton plant and plays an important role in deterring insect infestation.  Its presence in seed, however, hampers its widespread use as food and feed.  The Ow laboratory has been exploring the possibility of engineering seed-specific breakdown of gossypol.  Cotton plants with a reduced number of gossypol glands have been obtained, but further work is needed to obtain stable transmission of the trait.

 

 

 

 

 

 

 

 

The Quail Lab

 

            The overall research goal is to understand the molecular mechanism(s) by which the five-member phytochrome (phy) family of regulatory photoreceptors (phyA through phyE) controls gene expression, and thereby plant growth and development, in response to light-signals from the environment.

 

      Using Affymetrix microarrays for global expression profiling in Arabidopsis, we have identified the full complement of genes on these arrays that are regulated by phyA and phyB in response to light signals during seedling deetiolation (the molecular phenotype). Exploitation of this molecular phenotype to monitor the photoresponsiveness of phy-null mutants has revealed differential channeling of the light signal through individual phy family members to early-response genes during initial exposure of seedlings to light. The most significant discovery from this work has been the identification of a core “master set” of transcription-factor-encoding genes that respond rapidly to the light signal, and are therefore candidates for being early, if not direct, targets of phytochrome regulation. These genes have the potential, therefore, to function as regulators of multiple downstream target genes in the phy-regulated transcriptional network that drives photomorphogenesis.

 

      To begin to dissect the role of identified signaling intermediates in phy signaling to the transcriptional network, we have initiated microarray-based expression profiling of mutants at some of these loci, beginning with the bHLH transcription factor, PIF3. The data show that PIF3 is necessary for the rapid, phy-induced expression of a subset of nuclear genes encoding chloroplast components, indicating an important function in generating a functional photosynthetic apparatus.

 

      Using conventional forward genetic screens of chemically- and insertionally-mutagenized Arabidopsis populations for mutants aberrant in light responsiveness, we have identified and molecularly cloned a considerable number of components potentially active in phytochrome signaling pathways.

 

      The single most important contribution we have made during this period was the discovery that the phy molecule interacts, specifically in its light-activated, Pfr form, with the bHLH transcription factor, PIF3 (phytochrome-interacting factor 3) which we initially identified using a yeast two-hybrid screen. Together with evidence from other researchers that the phy molecules are triggered by light to translocate from the cytoplasm into the nucleus, our data suggested that the phys might signal directly to target genes by physical interaction with the promoter-bound PIF3 transcription factor.  This represented a paradigm shift in the field, as the prevailing dogma prior to that time was that the phys were constitutively cytoplasmic and signaled to nuclear genes via second messenger pathways. Most excitingly for us, we have recently shown that light-triggered binding of phyA or phyB to PIF3 in the nucleus induces rapid phosphorylation of PIF3 prior to degradation via the ubiquitin proteosome system, and that this may be the biochemical mechanism of signal transfer from the activated photoreceptor to its target protein(s) in regulating gene expression.

 

      Our research program has led to the development of molecular-genetic tools with potential biotechnological applications. We cloned the maize ubiquitin gene, Ubi1, determined that its promoter activity is very high in monocots, and made a series of vector constructs in various configurations. These vectors have been distributed to hundreds of researchers world-wide, and are being used widely for bioengineering of a broad spectrum of important grain crops, including corn, wheat, barley, oats, sorghum and sugarcane. In collaboration with a former post-doc, Dr. Christianne Gatz, we have shown that transgenic overexpression of Arabidopsis phyB in potato increases tuber yields. This strategy has the potential to provide an environmentally friendly method of enhancing crop yields without the need for additional agrochemical or fertilizer inputs. Based on the knowledge that phy interacts specifically, rapidly and reversibly, only in its light-activated Pfr form, with PIF3, we developed a yeast two-hybrid based promoter system that is reversibly activatible by light. This system has a potentially very broad spectrum of biomedical, as well as agricultural applications, in a variety of eukaryotic cells (US Patent 6,858,429).

 

 

 

 

 

 

The Theologis Lab

 

      The laboratory has been involved during the past 20+ years in understanding the molecular aspects of auxin perception (“the auxin project”), and ethylene biosynthesis (“the ethylene project”). More recently (since 1994), the laboratory was involved in Arabidopsis structural genomics as a member of the SSP consortium (Stanford - Ron Davis / Salk - Joe Ecker / PGEC - A. Theologis). Our involvement with Arabidopsis genomics was due to the realization that the two non-genomic projects, “auxin” and “ethylene”, respectively, were not advancing rapidly enough because of the absence of basic molecular resources. With the advent of genomic technology in the early nineties, we decided to participate as part of a consortium in the international effort (AGI) to sequence the Arabidopsis genome. This allowed the development of new molecular tools for advancing our “auxin” and “ethylene” projects. More importantly, however, it provided new resources for the entire plant biology community. The PI believes that TECHNOLOGY advances BIOLOGY and vice versa.

 

      After completion of the Arabidopsis genome sequencing, the laboratory was involved with a second genome project as a member of the same consortium. This project involved the mapping of all the transcriptional units of the Arabidopsis genome. It was a logical consequence of the Arabidopsis genome sequence project. The purpose of this project was to experimentally verify the annotation of the

Arabidopsis genome experimentally by sequencing full-length cDNAs and by hybridization analysis of whole genome tiling arrays. Concomitantly with the verification of the annotation, the project allowed the construction of ~12K ORF clones for initiating Arabidopsis proteomics. The development of the whole genome arrays (WGAs) was the first for any higher eukaryotic organism and provided the community with a tool not only for mapping the transcriptional units, but also for global mapping of DNA binding sites, QTLs, mutations, and small RNAs. In addition, during this project the laboratory produced the first software for analyzing the WGA hybridization data and established a database for Arabidopsis genomic analysis in my lab.

 

      The genomic resources that were developed facilitated the two long-term biology projects of my laboratory. We have been focused on isolating loss of function mutations for a large number of the Aux/IAA and ARF gene family members. These families have 28 and 23 members, respectively. They encode global transcriptional regulators involved in numerous aspects of auxin biology. We are aiming to elucidate their biological function by constructing higher order mutations. The laboratory discovered both groups of genes and has carried out pioneering molecular work with some of them. These factors have the capacity to homo- and heterodimerize with the potential to provide ~4,000 possible homo- and heterodimers. This capacity offers an explanation for the pleiotropic effects of auxin. We are currently attempting to elucidate whether this capacity is detected in planta using bimolecular fluorescence complementation (BiFC). In addition we are constructing the Interactome among the Aux.IAAs, ARFS and TIRs/ARBs (auxin receptors binding proteins) using the yeast two hybrid system.

 

      The availability of WGAs has allowed us to carry out studies on global mapping of the DNA binding sites of one of the ARF proteins, ARF2, using CHiP: chip experiments. It is not known which type of genes each of the ARF gene family members regulate. Chip: chip experiments using WGAs have the potential to provide fundamental information for the downstream events in auxin action. Lastly, the laboratory has cloned two auxin hypersensitive mutants, age1 and age2. We isolated both mutations in 1998 by a novel screen. AGE1 encodes the equivalent of RAD3 and XPD in yeast and humans, respectively. AGE1 is one of the nine subunits of the core transcription factor TFIIH. This protein is bifunctional; it has a helicase activity and also participates in DNA repair. AGE2 is a SAM decarboxylase. We are currently characterizing both genes molecularly and genetically.

 

      The second project is the understanding of ethylene biosynthesis at the level of ACC synthase. The lab was the first to clone this gene and using antisense experiments in the early 90’s demonstrated reversible inhibition of tomato fruit ripening; one of the early demonstrations of preventing fruit aging. The completion of the Arabidopsis genome sequence revealed the presence of 9 ACS genes. Eight of them are enzymatically active, and one inactive. We are investigating why plants such as Arabidopsis encode nine isozymes for producing ethylene. This question has been raised for numerous multigene families since the Arabidopsis genome sequence revealed that many proteins are encoded by multigene families. The ACS family is relatively small enough to carry out studies with the entire family. We hypothesize that each isozyme is expressed in cells/tissue that have the appropriate biochemical environment for its optimum function. For example, low Km (high affinity) isozymes may be expressed in tissues with a low SAM concentration and vice versa. Biochemical characterization of all Arabidopsis ACS isozymes shows a high degree of biochemical diversity. ACS is a homodimer with shared active sites. We recently discovered that the 9 ACS polypeptides can heterodimerize. The analysis was carried out by intermolecular complementation experiments and showed that active heterodimers are formed only among the ACS isozymes that belong to the same phylogenetic branch. The inactivity of certain heterodimers is not due to the absence of heterodimers but rather to the inactivity of shared active sites. We found that the 9 ACS polypeptides encoded by the Arabidopsis genome have the capacity to form 25 active homo- and heterodimers. Experiments are in progress for searching the formation of ACS heterodimers in planta using BiFC. The possible formation of ACS heterodimers is also supported by our tissue-specific expression experiments that indicate overlapping expression patterns among the various ACS genes. Do the heterodimers have distinct biochemical properties? We are currently determining the biochemical properties of the ACS heterodimers. In the near future, we plan to use nano-technological approaches for determining solute concentration in individual plant cells, for example, to determine SAM concentrations in individual cells. Furthermore X-ray crystallographic studies are currently in progress for understanding the inactivity of certain heterodimers at the structural level. 

 

 

 

 

Productivity and Recognition

 

      The PGEC has consistently published in high profile, highly cited journals (Table 1) and served as reviewers for these journals. PGEC PIs have served on editorial boards for Genes and Development, Plant Journal, The Plant Cell and Plant Physiology. They have obtained numerous grants from federal agencies (Table 2) and have served on review panels for NIH, NSF, DOE, WHO/FAO and NRI.

 

      The PIs are internationally recognized for their accomplishments. Two years ago, Dr. Peter Quail was elected a member of the National Academy of Sciences. Dr. Athanasisos Theologis received the Kumho Foundation Award in 2001 together with seven other investigators for sequencing the first plant genome of Arabidopsis. Dr. David Ow was chosen as the “USDA Pacific West Senior Scientist of the Year” in 2003 and Dr. Jennifer Fletcher received the “USDA Early Career Research Scientist of the Year award” in 2005. Sarah Hake has received the 2008 Stephen Hales Award from the ASPB and the 1996 Jeanette Siron Pelton Award.

 

 

Table 1:   PUBLICATIONS

 

Type of Publication

Number

 REVIEWED

364

 CHAPTERS

74

  REVIEWS

84

  PATENTS

14

 

 

 

 

Table 2.   FUNDING

 

COMPETITIVE GRANTS

Number

Amount in $ x K1

 

NIH

-

6,350

 

NSF

-

22,048

 

USDA

-

3,698

 

DOE

-

2,856

 

BARD

-

285

 

McKnight

-

113

 

BSF

-

112

 

ROCKEFELLER

-

127

 

TOTAL

-

35,589

 

 

 

 

 

IN-HOUSE and INDUSTRY FUNDING

 

 

 

 

 

 

ARS-CRIS

-

70,000

 

 

COOPERATIVE AGREEMENTS-SYNGENTA

-

1,810

 

 

INDUSTRIAL

-

1,487

 

 

OTHER

-

1,415

 

 

TOTAL

-

74,712

 

 

 

 

 

 

 

FELLOWSHIPS

 

 

 

 

 

 

 

NIH

2

166

 

 

NSF

6

450

 

 

USDA

1

80

 

 

OTHER

23

675

 

 

TOTAL

 

1,300

 

 

 

 

 

 

 

 

 

 

1The numbers represent the total of indirect and indirect costs. The indirect cost of extramural funds is 26% to UC Berkeley or 10% to ARS. The indirect cost of the ARS-CRIS funds is 75%.

Teaching and Training

 

       Table 4 shows the number of young plant biologists trained at the center the last 20 years. In addition some of us have served as instructors at the CSHL plant biology course as well as in other plant biology courses offered abroad. The PIs have participated as invited speakers in various conferences as well as seminar speakers (see Table 3).

 

 

TABLE 3:   TEACHING AND TRAINING

 

UNDERGRADUATE STUDENTS

167

GRADUATE STUDENTS

43

POSTDOCS TRAINED

336

TECHNICIANS

53

INVITED SPEAKER

739

TEACHING COURSES LIKE CSHL

9

 

    

 

Teaching at UC Berkeley

 

       The PGEC PIs have greatly contributed to the teaching program of the Department of Plant Biology at UC Berkeley. They have participated as instructors in the following courses, giving 10 to 20 lectures per year: PB228, PB200A, PB200B, BIO11, PB200C, PB210, PB297, PB170, PB160.

 


 

 

FORMER POSTDOCS AND GRADUATE STUDENTS

 

 

Baker Lab

 

Alejandro Calderon Urrea, Professor, Fresno State University, Fresno, CA

Choon-III Cheong, Senior Scientist, Kumho Chemical Lab, Taejeon, South Korea

Hui-Hua Chiang

Doil Choi, Senior Scientist, Genetic Engineering Research Ins, KIST, South Korea

Amy deHart, Lecturer, University of California, Berkeley, CA

Marianne Dutton, Lecturer, University of California, Berkeley, CA

David Earp, Vice President, Geron Corp.

Les Erickson, Research Associate, University of California, Berkeley, CA

Sara Freuhling

Susan Gorman, Lead Scientist, Chiron, Emeryville, CA

Vanessa Handley, Assistant Professor, Holy Names University, Oakland, CA

Judith Healy, Senior Scientist, Protein Engineering Research Unit, Suita, Osaka, Japan

Reinhard Hehl, Professor, Tech University of Braunschweig, Braunschweig, West Germany

Martha Hernandez, Medical Student, Universityof California, San Francisco, CA

Steve Holzberg, Scientist, Large Scale Biology, Vacaville, CA

Mary Homma, Assistant Professor, Duke University, Durham, NC

Gongshe Hu, Geneticist, ARS, Aberdeen, ID

Shayne Huff

Hailing Jin, Assistant Professor, University of California, Riverside, CA

Igor Kardailsky, Senior Scientist, AgResearch, New Zealand

Dinesh Kumar, Associate Professor, Yale University, New Haven, CT

Bingwei Lu, Postdoc, UCSF, San Francisco, CA

KwangChul Oh, Postdoc, Ohio State University, Columbus, OH

Brian Osborn, Group Leader, Cadus Corp.

Carolyn Ustach, Postdoc, Wayne State University School of Medicine,

Candace Waddell, Professor, McGill University, Montreal, Canada

Xiaoxue Wang, Research Scientist, National Inst Biological Sciences, Beijing, China

Fusheng Wei, Specialist, University Arizona Plant Genetics Institute, Arizona

Steve Whitham, Associate Professor, Iowa State University, Ames, IA

Uwe Wirtz, Scientist, Titan Pharmaceuticals, South San Francisco, CA

Miki Yamamoto, Postdoc, Lawrence Berkeley Lab, Berkeley, CA

Zhong-Lin Zhang, Postdoc, Duke University, Durham, NC

Peifen Zhang, Bioinformaticist, TAIR, Stanford, CA

 

Fletcher Lab

 

Vibeke Alm, Postdoc, University of Oslo, Oslo, Norway

Dan Choffnes Inada, Assistant Professor, Carthage College, Kenosha, WI

Colin Leasure, Postdoc, San Francisco State University, San Francisco, CA

Karen Osmont, Postdoc, University of Lausanne, Lausanne, Switzerland

Vijay Sharma, Research Scientist, Ceres, Inc., Thousand Oaks, CA

Fromm Lab

 

Steve Goff, University of Oregon

Ted Klein, Dupon de Nemours & Co.

Fionnuala Morrish, Fred Hutchinson Cancer Center, Seattle, WA

Brad Roth, Pioneer, Ames, IA

Jutta Tuerk

 

Hake Lab

 

David Barnes, Scientist, Pfizer Global Research & Development, La Jolla, CA

Bharat Char, Scientist, Cambia, Black Mountain, Australia

Toshi Foster, Senior Scientist, HortResearch, Palmerstown, NZ

Ben Greene, Research Scientist, University of Alaska, Anchorage, AK

Angela Hay, Postdoc, Oxford University, Oxford, UK

Hans Holtan, Scientist, Mendel Biotechnology Co., Hayward, CA

Lauren Hubbard, mom

David Jackson, Professor, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

Randy Kerstetter, Assistant Professor, Waksman Institute at Rutgers Univ, New Brunswick, NJ

Kati Krolikowski, Scientist, Mendel Biotechnology Co., Hayward, CA

Debbie Laudencia, Senior Scientist, USDA ARS WRRC, Albany, CA

Cindy Lincoln, Instructor, Duke University, Durham, NC

Brenda Lowe, Scientist, Dekalb/Monsanto, Mystic, CT

Paula McSteen, Assistant Professor, Pennsylvania State University, State College, PA

Giovanni Mele, Researcher, National Research Council (CNR), Rome, Italy

Lisa Newman, Scientist, Pioneer Hi-Bred, Ames, IA

Naomi Ori, Assistant Professor, Hebrew University, Rehovet, Israel

Leonore Reiser, Outreach Coordinator, Molecular Sciences Institute, Berkeley, CA

Mark Running, Scientist, Danforth Center, St. Louis, MO

Yutaka Sato, Assistant Professor, Nagoya University, Nagoya, Japan

Kristen Shepherd, Assistant Professor, Barnard College, New York, NY

Neelima Sinha, Professor, University of California, Davis, CA

Laurie Smith, Associate Professor, University of California, San Diego, CA

Harley Smith, Assistant Professor, University of California, Riverside, CA

Bruce Veit, Scientist, AgResearch, Palmerstown, NZ

Erik Vollbrecht, Assistant Professor, Iowa State University, Ames, IA

Richard Walko, Scientist, Pharmacia Biotechnology, Piscataway, NJ

 

McCormick Lab

 

Zaure Aytasheva, Department Chair, Institute of Genetics, Almaty , Kazakhstan

Debu Basu, Senior Lecturer, Bose Institute, Calcutta, India

Yun-Chia Sophia Chen, Law/MBA Student, Northwestern University, Evanston, IL

Cathy Curie, Directeur de Recherche, CNRS University, Montpellier, France

Lori Dircks, Scientist, Biotech Company, Emeryville, CA

Peter Dodds, Scientist, CSIRO, Canberra, Australia

Michele Engel, Assistant Professor, University of Colorado, Denver, CO

Yoram Eyal, Scientist, Volcani Center, Israel

Inés Ezcurra, Associate Professor, KTH Royal Institute of Tech, Sweden

Susan Gorman, Patent Attorney, Birch Stewart Kolasch & Birch LLP, San Diego, CA

Keith Hamby, R&D Director, Bio-Rad Laboratories, Hercules, CA

Rachel Holmes-Davis, Scientist, Investigen, Hercules, CA

Sheila Johnson-Brousseau, TBA

Pulla Kaothien, Postdoc, Nara Institute Science Technology, Nara, Japan

Hyun Uk Kim, Postdoc, Washington State University, Pullman, WA

Jean-Louis Magnard, Maitre de Conferences, University St. Etienne, St. Etienne, France

Jorge Muschietti, Professor, University of Argentina, Buenos Aires, Argentina

Sung Han OK, Postdoc, Korea University, Seoul, Korea

Mineo Senda, Associate Professor, Hirosaki University, Japan

Bin Shuai, Assistant Professor, Wichita State University, Wichita, KS

Salma Talhouk, Professor, American University, Beirut, Lebanon

Wei-hua Tang, Professor, Shanghai Inst Plant Phys & Ecol, Shanghai, China

David Twell, Professor, University Leicester, Leicester, UK

Virginia Ursin, Staff Scientist, Monsanto, Mystic, CT

Guy Vancanneyt, Staff Scientist, Bayer Crop Science, Belgium

Rod Wing, Professor, University of Arizona, Tucson, AZ

Heping Yang, Senior Scientist, Monsanto, St. Louis, MO

Ming Yang, Associate Professor, Oklahoma State University, Stillwater, OK

Bauke Ylstra, Professor, University of Amsterdam, The Netherlands

 

Ow Lab

 

Henrik Albert, Scientist, USDA, Aiea, HI

Shunong Bai, Professor, Peking University, Beijing, China

Neel Barnaby, Research Biologist, FBI Laboratory, Quantico, VA

Yinghao Cheng, Lab Director, Beijing Chemclin Biotech Co Ltd, Beijing, China

Sonya Clark, Group Lead, Pacific Biosciences, Menlo Park, CA

Emily Dale, Div Marketing Manager, Bio-Rad Laboratories, Hercules, CA

Christopher Day, Assistant Professor, University of Wisconsin, Madison, WI

John Henstrand, Senior Scientist, Biopharmaceuticals, Novato, CA

Lynn Holppa, Postdoctoral Researcher, Harvard University, Cambridge, MA

Rajiv L. Joshi, Principal Investigator, Université René Descartes, Paris, France

Rong-Huay Juang, Professor, National Taiwan University, Taipei, Taiwan

Jong-Heon Kim, Postdoc, USDA ARS WRRC, Albany, CA

Heather Koshinsky, Founder & CEO, Investigen, Hercules, CA

Kent McCue, Scientist, USDA ARS WRRC, Albany, CA

Mike Morgan, Lab Manager, Wake Community College, Cary, NC

Daniel Ortiz, Associate Professor, Tufts University Sch of Med, Boston, MA

Liangcai Peng, Principal Investigator, Huazhong Agricultural University, Wuhan, P.R. China

Minmin Qin, Senior Director, Five Prime Therapeutics, Inc., San Francisco, CA

Wen Song, Staff Scientist, Bio-Rad Laboratories, Hercules, CA

David Speiser, Division Vice President, Science Applications Intl Corp, Falls Church, VA

Vibha Srivastava, Associate Professor, University of Arkansas, Fayetteville, AR

Lynn Thomason, Postdoctoral Researcher, National Cancer Institute, Frederick, MD

Jim Thomson, Scientist, USDA ARS WRRC CIU, Albany, CA

Pei-Lan Tsou, Assistant Professor, Grand Valley State University, Allendale, MI

Yueju Wang, Postdoctoral Researcher, Cornell University, New York, NY

Todd Zankel, Co-Founder, Raptor, Novato, CA

 

Quail Lab

 

Bassem Al-Sady, Postdoc, University of California, San Francisco, CA

Debabrata Basu, Senior Lecturer, Bose Institute, Calcutta, India

Margaret Boylan

Wesley Bruce, Scientist, Pioneer Hi-Bred, Ames, IA

Maria Bucholc, Scientist, , Budapest, Hungary

Francisco Cantón, Assistant Professor, University of Malaga, Malaga, Spain

Timothy Caspar, Scientist, DuPont,

Alan Christensen, Professor, George Mason University,

Katie Dehesh, Professor, University of California, Davis, CA

Xing Wang Deng, Professor, Yale University, New Haven, CT

Jackie Dulson

Craig Fairchild

Kenneth Franke

Kerry Franklin, Postdoc, University of Leicester, England

Carlos Garcia-Ferris, Scientist, Spain

Gary Gardner, Professor, University of Minnesota, St. Paul, MN

Karen Halliday, Lecturer, University of Edinburgh, Edinburgh, Scotland

Ute Hoecher, Professor, Univ of Koeln, Koeln, Germany

Matthew Hudson, Assistant Professor, University of Illinois, Urbana , IL

Enamul Huq, Assistant Professor, University of Texas, Austin, TX

Yong-sic Hwang, Postdoc, University of California, Santa Barbara, California

Henrick Johanneson, , Scientist, Evol Biol Center, Uppsala, Sweden,

Karen Kaczorowski, ARS Research Geneticist, Purdue University, West Lafayette, IN

Rajnish Khanna, Scientist, Mendel Biotechnology Co., Hayward, CA

Elise Kikis, Postdoc, University of Chicago

Robert Kuhn

James Lissemore, Graduate Student, Prof, John Carroll University, Ohio,

Colleen Marion, Scientist, Mendel, Biotechnology Co., Hayward, CA

Jaime Martinez-Garcia, Scientist, Institut de Biologia Molecular de Barcelona (CSIC), Spain,

Elena Monte, Scientist, Institut de Biologia Molecular de Barcelona (CSIC), Spain,

Julia Montgomery

Akira Morishima, Japan

Min Ni, Associate Professor, University of Minnesota

Jorge Nieto-Sotelo, Assoc. Professor, Institute of Biotechnology-UNAM, Cuernavaca, Mexico

Brian Parks, Biocore Coordinator, University of Washington

Jennifer Pfluger, Postdoc, University of Pennsylvania

Minmin Qin, Graduate Student

Christoph Ringli, Assistant Professor, University of Zurich, Zurich, Switzerland

Irma Roig-Villanova, Visiting Student Researcher, Grad Student, Barcelona, Spain,

Francisco Ruiz-Canton, Assistant Professor, Universidad de Málaga, Málaga, Spain

Michael Schumaker, SRA I, Affymetrix

Kevin Seeley

Robert Sharrock, Professor, Montana State University, Bozeman, MT

Sae Shimizu-Sato, Scientist, Nagoya University, Japan,

Timothy Short, Professor, Queen's College of CUNY

David Somers, Associate Professor, Ohio State University

Gabriela Toledo-Ortiz, Graduate Student, Postdoc, University of Kyoto, Japan

Doris Wagner, Associate Professor, University of Pennsylvania

JoAnne Welsch

Yong-sic Xu

Yuxian Zhu, Professor, Peking University, Beijing, China

 

Theologis Lab

 

Steffen Abel, Professor, University of California, Davis, CA

Kazunari Arima, Professor, Kagoshima University, Kagoshima, Japan

Josh Armstrong, Senior Scientist, Mendel Biotechnology Co., Hayward, CA

Nurit Ballas, Research Associate Professor, Howard Hughes Medical Institute, Stony Brook, NY

Gladys Cassab, Professor, Institute of Biotechnology, Cuyernavaca, Mexico

Grace Chen, Scientist, USDA ARS WRRC, Albany, CA

Klaus Harter, Professor, Tubingen University, Tubingen, Germany

Pung Huang, Professor, National Taiwan University, Taipei, Taiwan

Kazuhito Kawakita, Professor, Nagoya University, Nagoya, Japan

Jung-Mook Kim, Professor, Kumho Life & Envir Sci Lab, Seoul, Korea

Tomokazu Koshiba, Professor, Tokyo Metropolitan University, Tokyo, Japan

Xizowu Liang, Vice President, Immport Therapeutics Inc., Irvine, CA

Yoko Okushima, Assistant Professor, Nara Institute Science Technology, Nara, Japan

Yutaka Oono, Professor, Japan Atomic Energy Res Inst, Takasaki, Japan

Francois Oulette, Assistant Professor, University of Quebec, Montreal , Canada

Paul Overoorde, Associate Professor, Macalester College, St. Paul, MN

Gary Peter, Associate Professor, University of Florida, Gainesville, FL

William Rottman, Senior Scientist, Westvaco Forest Research, Summerville, SC

Takahide Sato, Professor, Chiba University, Chiba, Japan

Lovey Taylor, Program Director, National Science Foundation, Washington, DC

Lu-Min Wong, Senior Scientist, Amgen Co., Thousand Oaks, CA

Kayoko Yamada, Senior Scientist, B-Bridget International, Inc., Mountain View, CA

Takeshi Yamakami, Assistant Professor, Kyushu University, Fukuoka, Japan

Thomas Zarembinski, Senior Scientist, Glycosan Biosystems, Salt Lake City, UT

 

 

 

 


POSTER TITLES

 

 

1.         GEX3, a sperm-specific plasma membrane-localized protein, is important for fertilization Monica Alandete-Saez, Mily Ron and Sheila McCormick

 

2.         Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation

Bassem Al-Sady, Ni Weimin and Peter H Quail.

 

3.         The Role in Disease Resistance and Mechanism of Action of XB10, a Putative WRKY-Family Transcription Factor that Interacts with the XA21 Rice Pathogen Recognition Receptor

Laura E Bartley, Ying Peng, Kihong Jung, Mawsheng Chern, Christopher Dardick, Randy Ruan and Pamela C. Ronald.

 

4.         Cereal Crop Promoters That Confer Organ-Specific Transgene Expression

        Roger Thilmony, Mara E. Guttman, Dawn Chiniquy and Ann E. Blechl

 

5.         An improved method for in vitro pollen germination facilitates functional characterization of male gametophyte mutants in Arabidopsis thaliana

        Leonor C. Boavida and Sheila McCormick

 

6.         Insight into the function of KNOTTED1 in maize meristems

        Nathalie Bolduc and Sarah Hake    

 

 

 

 

 

 

7.         Functional analysis of meristem-specific microRNAs enriched in branched silkless1 mutants

George Chuck and Sarah Hake

 

8.         The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis

        Michael F. Covington and Stacey L. Harmer

 

9.          BLADE-ON-PETIOLE1 and 2 Control Arabidopsis Lateral Organ Fate Through            Activation of LOB-Domain Genes and Regulation of Organ Polarity Genes

Chan Man Ha, Ji Hyung Jun, Hong Gil Nam1 and Jennifer C. Fletcher

 

10.     ELF3 is required for circadian rhythms in etiolated Arabidopsis seedlings after temperature entrainment

Frank Harmon

 

11.     Sequencing crop genomes using next-generation methods

        Matthew Hudson

 

12.     Mapping of the Rag1 aphid resistance locus of soybean with microarray-generated SNP markers    

        Karen Kaczorowski, Ki Seung Kim, Brian Diers, and Matthew Hudson

 

13.     Jasmonic acid controls floral organ abscission in Arabidopsis through ethylene independent pathway

Joonyup Kim, Brad Binder, and Sara E. Patterson

 

14.     PIF7, a new phytochrome-interacting bHLH transcription factor, together with PIF3 and PIF4, regulates long-term growth responses in red light by modulating phyB photoreceptor levels

Pablo Leivar, Elena Monte, Bassem Al-Sady, Christine Carle, Alyssa Storer, Jose M. Alonso, Joseph R. Ecker, and Peter H. Quail

 

15.     YUCCA genes are required for shade-induced increases in auxin signaling

Melissa L. Pytlak, Kazunari Nozue, Youfa Cheng, Michael F. Covington, Stacey L. Harmer, Yunde Zhao, and Julin N. Maloof.

 

16.     Intron-Mediated Enhancement of Gene Expression in Arabidopsis

Alan B. Rose and Ian F. Korf

 

17.     PIF5: A Possible Node For Crosstalk Between Ethylene and Early Light Signaling Pathways

Rajnish Khanna, Yu Shen, Colleen M. Marion, Christine M. Carle, Eberhard Schaefer and Peter H. Quail

 

18.     Floral integration requires the function of homeobox genes PENNYWISE and POUND-FOOLISH in Arabidopsis

Siddhartha Kanrar, Moni Bhattacharya, Blake Arthur and Harley M. S. Smith

 

19.     The Molecular Mechanism of ELF3 in Arabidopsis Circadian Rhythms

Bryan Thines, Allison Tam and Frank Harmon

 

20.     The parA resolvase performs site-specific genomic excision in Arabidopsis

James Thomson, Yuan-Yeu Yau, Robert Blanvillain, and David W. Ow

 

21.     The Arabidopsis 1-Aminocyclopropane-1-Carboxylic Acid Synthase (ACS) Gene Family

     Atsunari Tsuchisaka, Takeshi Yamagami, Jose M. Alonso, Joseph R. Ecker and Athanasios Theologis

 

22.     Maize Anther Development:  Cell Fate Acquisition and Maintenance

Virginia Walbot, Dave Skibbe, Gillian Nan, Darren Morrow, John Fernandes, Zac Cande, Lisa Harper

 

23.     AIK1 and AIK2, two Leucine-Rich Repeat Receptor Kinases, Regulate the Orientation of Cell Expansion in Arabidopsis

Shouling Xu, Hyun Sook Chae, Abidur Rahman, Tobias Baskin, and Joseph J Kieber

 

24.     Pollen receptor kinases are critical for maintaining pollen tube polarity and growth in Arabidopsis thaliana

Yan Zhang, Rajsree Mungur, Colleen Lau, and Sheila McCormick1


 

POSTER ABSTRACTS

 

1.      GEX3, a sperm-specific plasma membrane-localized protein, is important for fertilization

      Monica Alandete-Saez, Mily Ron and Sheila McCormick

      Plant Gene Expression Center/University of California, Berkeley

 

 

 

In flowering plants the male gametophyte or pollen grain contains three cells: a large vegetative cell which forms the pollen tube and two sperm cells enclosed within the vegetative cell cytoplasm. The sperm cells have plasma membranes but lack a cell wall. Unlike mammalian sperm, the two sperm cells in plant are not motile, but instead are transported within the vegetative cell cytoplasm via pollen tube growth through female tissues. The female gametophyte or embryo sac develops within the ovule and consists of seven cells, including four cell types: three antipodal cells, two synergid cells, one egg cell and one central cell. The egg and the central cell are the fusion partners for the two sperm cells during double fertilization. Upon arrival at the embryo sac, the pollen tube discharges the sperm cells and one fuses with the central cell to give rise to the primary endosperm cell while the other fuses with the egg cell to give rise to the zygote. Although double fertilization in angiosperms was discovered in 1898, the molecular details of this unique feature of the angiosperm life cycle are poorly understood. Until recently, molecules involved in gamete signaling were largely unexplored because of the inaccessibility of plant gametes, which are embedded in sporophytic tissues. Our lab previously constructed a high-quality cDNA library from sperm cells of maize as a resource for gene discovery and to identify genes exhibiting cell-specific expression patterns. Because proteins involved in sperm-egg and sperm-central cell interactions are likely to be located on the plasma membrane, we selected transcripts that were predicted to be plasma membrane–localized from the maize ESTs and then identified their best sequence match in Arabidopsis.  Here we present characterization of AtGEX3, a protein which is specifically expressed in the sperm cells of Arabidopsis and is predicted to be plasma membrane-localized. Using GFP fusion proteins, we show that AtGEX3 is localized to the plasma membrane. To determine if AtGEX3 is important for some step in the fertilization process, we generated over-expressing and down-regulating transgenic plants for GEX3. These lines have reduced seed set, which supports the idea that GEX3 is important for fertilization.

 

 

 

 

2.            Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome mediated degradation

Bassem Al-Sady, Ni Weimin and Peter H Quail.

Plant Gene Expression Center/University of California, Berkeley

 

The phytochrome (phy) family of sensory photoreceptors (phyA through phyE) monitor incident light signals and direct adaptational growth and developmental responses in plants appropriate to the prevailing environment.  Current evidence indicates that the mechanism underlying this process involves rapid light-induced translocation of the phy molecule from the cytoplasm into the nucleus, where it interacts directly with signaling partners that include the bHLH transcription factor PIF3, and induces alterations in target gene expression.  The biochemical mechanism comprising signal transfer from phy to PIF3 has remained undefined, but it leads to rapid degradation of PIF3, apparently via the ubiquitin-proteasome (UPS) system.  We provide evidence that photoactivation of phy in Arabidopsis seedlings leads, within 1 minute, to PIF3 phosphorylation, followed by proteasome-inhibitor-sensitive degradation with a half-time of about 30 minutes.  PIF3 phosphorylation and subsequent degradation both require the photoactivated form of the phy molecule, and are inhibited by concomitant site-directed mutations in two separate binding sites for phyA and phyB that we identified within the PIF3 protein.  Mutation of these binding sites also blocks the rapid light-induced intra-nuclear relocation of YFP:PIF3 fusion protein into nuclear speckles, and the ensuing disappearance of the fluorescently-labeled molecule, that is observed for the unmutated protein.  Collectively, these data suggest that phy-induced phosphorylation of PIF3 may represent the primary intermolecular signaling transaction of the activated photoreceptor, flagging the transcription factor for proteasomal degradation, possibly localized in nuclear speckles.

 

 

 

 

3.              The Role in Disease Resistance and Mechanism of Action of XB10, a Putative WRKY-Family Transcription Factor that Interacts with the XA21 Rice Pathogen Recognition Receptor

Laura E Bartley, Ying Peng, Kihong Jung, Mawsheng Chern, Christopher Dardick, Randy Ruan and Pamela C. Ronald

Department of Plant Pathology, University of California at Davis, Davis, CA

 

Xa21 confers rice with resistance to bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), and codes for a protein with an extracellular leucine-rich repeat domain and an intracellular kinase. Plants possessing Xa21 perceive bacteria that secrete a specific factor, AvrXa21, into the environment. Recognition triggers a signaling cascade leading to altered gene expression and disease resistance; however, few of the signaling molecules have yet been characterized. To identify such proteins, we conducted yeast two-hybrid screening of rice cDNA libraries for proteins that interact with XA21. One of eight XA21 binding (XB) proteins identified in this screen was XB10, a member of the WRKY zinc finger transcription factor family. Consistent with a functional interaction between XB10 and XA21, RNA microarray analysis shows that levels of Xb10 transcript increase upon inoculation of XA21-expressing plants with Xoo. Additional screening with XB10 as bait identified three other WRKY IIa members that interact with XB10, termed XB10i-1, -2, and -3. Simultaneous over expression of all four of the WRKY IIa genes leads to a partial resistance phenotype. As we do not know the native DNA sequence to which XB10 binds, we have constructed a chimeric protein in which the putative DNA binding domain of XB10 is replaced with the DNA binding domain of the yeast GAL4 transcriptional activator. We can use the chimera to determine if and under what conditions XB10 effects transcription. Under un-induced conditions, the XB10-GAL4 chimera does not induce transcription of a luciferase construct with a promoter that contains the GAL4 up-stream activating sequence; whereas, a control chimera made from the viral transcriptional activator, VP16, induces high levels of luciferase expression.

 

 

 

 

 

 

4.              Cereal Crop Promoters That Confer Organ-Specific Transgene Expression

Roger Thilmony, Mara E. Guttman, Dawn Chiniquy and Ann E. Blechl

USDA-ARS Western Regional Research Center, Albany CA

 

We are identifying and characterizing novel promoters from rice, barley and wheat that provide useful tools for control of organ-specific transgene expression. Our goal is to make these promoters useful plant biotechnology tools that increase the precision of transgenesis technology. We have utilized a 14,000 element rice cDNA microarray to examine gene expression in leaf, root, panicle, kernel, callus and anther RNA samples. We have also mined an Affymetrix Barley1 GeneChip gene expression dataset created by Druka et al. (2006), who examined 8 developmental stages and 15 tissue types. Gene candidates that exhibited distinct organ-specific expression patterns based on microarray analysis have been cloned and independently validated using RNA blot hybridization. Six rice candidate promoters were transcriptionally fused to a gusA-enhancedGFP bifunctional reporter gene in the pGPro1 binary vector and transformed into rice. Reporter gene expression in the T0 and T1 transgenic rice plants is being documented throughout development. One candidate promoter, derived from a leucine-rich repeat receptor-like kinase, drives expression in the aerial, vegetative parts of the plant, with most lines displaying little or no detectable expression in reproductive or root tissues. A second candidate promoter, derived from a putative pectinesterase gene, drives strong GUS expression only in developing anthers and pollen. Our research will develop a battery of publicly available cereal crop promoters useful for controlling organ-specific transgene expression and reducing the unintended effects transgenes may have on crop plant physiology. 

 


 

 

 

 

 

 

 

5.              An improved method for in vitro pollen germination facilitates functional  characterization of male gametophyte mutants in Arabidopsis thaliana

Leonor C. Boavida and Sheila McCormick

Plant Gene Expression Center, USDA/University of California, Berkeley

 

In vitro pollen germination is considered the best assay of pollen viability, i.e. the ability of a pollen grain to perform its function of delivering sperm cells to the embryo sac following compatible pollination. Despite much effort, no protocol for robust in vitro germination of Arabidopsis thaliana pollen exists. Here we show that controlled temperatures, a largely disregarded factor in previous studies, and a simple optimized medium, solid or liquid, yield reproducible pollen germination rates with both Columbia and Landsberg ecotypes. We also present conditions that improve pollen germination and pollen tube growth rates and help synchronize pollen germination for time course analyses. We used this method for in vitro pollen studies of insertional mutants affected in male gametophyte function, and were able to show that some mutants had alterations in germination or tube growth performance, parameters which are difficult to measure in vivo. Arabidopsis thaliana can now be considered a suitable model for physiological studies of pollen tube elongation and tip growth. 

       

6.              Insight into the function of KNOTTED1 in maize meristems

Nathalie Bolduc and Sarah Hake 

Plant and Microbial Biology Department, USDA-Plant Gene Expression Center, UC Berkeley, 800 Buchanan St, Albany, California, USA, 94710

 

The maize homeobox protein KNOTTED1 (KN1) and its orthologues (KNOX) in various monocot and dicot species are involved in the establishment and maintenance of vegetative and floral meristems. In species with simple leaves such as maize, KN1 and other KNOX genes are strictly excluded from developing leaves. Dominant mutations leading to ectopic KN1 expression in maize leaves induce cellular proliferations or knots to form on the leaf blade, while recessive mutant alleles of kn1 have severe inflorescence and floral defects. Although the implication of KNOX genes in plant development has been extensively documented, their functions at the molecular level are poorly understood. It is currently believed that KNOX proteins regulate meristem activities by simultaneously promoting cytokinins (CKs) and repressing gibberellins (GA) biosynthesis.

 

In order to get a broader understanding of KN1 function and to identify direct and indirect downstream targets, microarray analyses were undertaken using maize long oligos (70 mer) arrays. RNA of young immature leaves from the dominant gain of function allele Kn1-N as well as RNA of immature male inflorescences (tassels) from the recessive loss of function allele kn1-E1 were compared to that of their respective wild-type siblings. As previously described in Arabidopsis and Populus, genes involved in cell wall and lignin metabolism were found to be differentially expressed. Additionally, data indicate that some hormonal pathways are affected by KN1 miss-regulation. We also observed the significant modulation of a large amount of transcription factors, which are putative direct KN1 targets. Chromatin immunoprecipitation revealed that KN1 binds in vivo to regulatory elements of some of the candidates found.

 

 

 

 

 

 

 

7.              Functional analysis of meristem-specific microRNAs enriched in branched silkless1 mutants

George Chuck and Sarah Hake

Plant Gene Expression Center/University of California, Berkeley

 

Most of the world's food supply is derived from the products of spikelets, the fundamental floral units of all grass species. The branched silkess1 (bd1) gene of maize is an ERF transcription factor that specifies spikelet meristem (SM) identity. In bd1 mutants branches replace the SM and floral meristems are not made. Since bd1 mutant inflorescences consist mainly of meristem, we used them as a source to enrich for meristem-specific microRNAs that may function in the bd1 pathway. A small RNA library was made from bd1 mutant ear primordia and sequenced by 454 Life Sciences. We discovered three classes of microRNAs that were enriched in the bd1 library compared to wildtype, MIR156, MIR159 and MIR172. Through chromosome walking we discovered both loss of function and gain of function mutations for two of these microRNAs, Corngrass1 (Cg1) and tasselseed4 (ts4).

 

 

 

 

8.              The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis

          Michael F. Covington and Stacey L. Harmer

          Section of Plant Biology, University of California, Davis, CA

 

The circadian clock plays a pervasive role in the temporal regulation of plant physiology, environmental responsiveness, and development.  In contrast, the phytohormone auxin plays a similarly far-reaching role in the spatial regulation of plant growth and development.  Seventy years ago, Went and Thimann noted that plant sensitivity to auxin varied according to the time of day, an observation which they could not explain.  Here we present work that explains this puzzle, demonstrating that the circadian clock regulates auxin signal transduction.  Using genome-wide transcriptional profiling, we found many auxin-induced genes are under clock regulation.  We verified that endogenous auxin signaling is clock regulated with a luciferase-based assay.  Exogenous auxin has only modest effects on the plant clock, but the clock controls plant sensitivity to applied auxin.  Notably, we found both transcriptional and growth responses to exogenous auxin are gated by the clock.  Thus the circadian clock regulates some, and perhaps all, auxin responses.  Consequently, many aspects of plant physiology not previously thought to be under circadian control may show time-of-day specific sensitivity, with likely important consequences for plant growth and environmental responses.

 

9.            BLADE-ON-PETIOLE1 and 2 Control Arabidopsis Lateral Organ Fate Through Activation

         of LOB-Domain Genes and Regulation of Organ Polarity Genes

         Chan Man Ha, Ji Hyung Jun, Hong Gil Nam1 and Jennifer C. Fletcher

Plant Gene Expression Center/University of California, Berkeley; 1Division of Molecular Life Science and the I-BIO Graduate Program, Pohang University of Science and Technology

 

Continuous lateral organ formation is critical for higher plants to produce their characteristic architectures, but the regulatory pathways that specify organ cell fate are still poorly understood. Here, we present a novel function for the putative transcriptional regulators BLADE-ON-PETIOLE1 (BOP1) and BOP2 in the control of LATERAL ORGAN BOUNDARIES (LOB)-domain (LBD) and adaxial-abaxial polarity gene expression during Arabidopsis lateral organ development. 35S:BOP1 and 35S:BOP2 plants exhibit a very short and compact stature, hyponastic leaves, and downward-orienting siliques. We show that three LBD genes, ASYMMETRIC LEAVES2 (AS2), LOB and LBD36/ASL1, are up-regulated in 35S:BOP and down-regulated in bop mutant plants. Ectopic activation of BOP1 or BOP2 also results in repression of class I knox gene expression. In addition, some 35S:BOP phenotypes are eliminated in the as2 and as1 mutant backgrounds. We demonstrate a role for BOP1 and BOP2 in the establishment of the adaxial-abaxial polarity axis in the leaf petiole, where they regulate PHB and FIL expression and overlap in function with AS1 and AS2. Interestingly, we find that KANADI1 (KAN1) and KAN2 promote adaxial organ identity as well as abaxial organ identity.

 

Our data indicate that BOP1 and BOP2 act at the lateral organ boundary to repress genes that promote meristem cell fate and to induce genes that promote lateral organ fate and polarity, thereby restricting the developmental potential of the organ-forming cells and facilitating their differentiation.

 

10.          ELF3 is required for circadian rhythms in etiolated Arabidopsis seedlings after temperature

           entrainment

           Frank Harmon

           Plant Gene Expression Center/University of California, Berkeley

 

Circadian clocks maintain approximately 24 hour rhythms in a variety of physiological processes. These internal rhythms are coupled with environmental cycles through a process called entrainment. Changes in both light and temperature cues serve to entrain the clock in plants. In the case of temperature, cycles that differ by as little as 4°C (i.e., 22°C to 18°C) are sufficient to entrain the circadian oscillator. The mechanism by which temperature is perceived and transmitted to the clock in Arabidopsis is largely unknown. Pervious work has implicated EARLY FLOWERING 3 (ELF3) in light input to the clock, where ELF3 allows the clock to progress past a light sensitive phase in the evening. In the absence of this activity, the clock rapidly arrests in constant light conditions. Unexpectedly, ELF3 activity is also vital for proper circadian rhythms following temperature entrainment in the complete absence of light. Etiolated elf3 seedlings grown in temperature cycles lack detectable rhythms after release into constant temperature, whereas wild type seedlings exhibit robust rhythms after the same treatment. Overall, the phenotype of etiolated, temperature entrained elf3 seedlings closely matches the light-grown phenotype. Thus, ELF3 is likely to have a common function for both temperature and light signals. This study demonstrates that ELF3 represents a point of convergence for light and temperature information. Future work will be directed toward identifying the molecular mechanism of ELF3 action and defining the interplay between light and temperature entrainment.

 

11.          Sequencing crop genomes using next-generation methods

Matt Hudson

           Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL

 

Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. This survey sequence data, when combined with the informatics tools we have developed, allows the detection of copy number of repeats, detection of gene copy number polymorphisms, and discovery of repeats and higher-order structures within satellite repeats. This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. Here we demonstrate the use of this technique on the soybean genome.

 

12.          Mapping of the Rag1 aphid resistance locus of soybean with microarray-generated SNP markers

Karen Kaczorowski, Ki Seung Kim, Brian Diers, and Matthew Hudson

USDA-ARS/Purdue University, West Lafayette, IN

 

Affymetrix Soybean GeneChip microarrays were used to discover single nucleotide polymorphism (SNP) variation between soybean cultivars for use in fine mapping Rag1, a gene responsible for aphid resistance. Genomic DNA of the aphid susceptible cultivar Dwight and the aphid resistant cultivar Dowling was labeled and hybridized to arrays and more than 1500 putative single feature polymorphisms (SFPs) were identified genome-wide. SFPs were verified by sequencing the probe target sequences at an empirically-determined false-discovery rate of 20%. To find sequence polymorphisms useful for fine mapping the Rag1 aphid resistance locus, genomic DNA samples from two near-isogenic lines (NILs) developed through backcrossing Rag1 four times into the Dwight background were hybridized to the array. Comparison of hybridization signals between the NILs and the recurrent parent identified more than 100 SFPs in each NIL, and we focused on ~30 SFPs which were shared between the two NILs. Sequencing the targets of these probes revealed a false discovery rate of 60%. We developed molecular markers for the true SNP polymorphisms and determined that two of these markers are genetically linked to the aphid resistance region.  The technique that we describe can be used to quickly identify polymorphisms in a genetic region of interest and generate molecular markers closely linked to an agronomically important trait between any two genotypes for which sequence information is poor or unavailable.

 

13.          Jasmonic acid controls floral organ abscission in Arabidopsis through ethylene independent pathway

Joonyup Kim, Brad Binder, and Sara E. Patterson

Department of Horticulture, University of Wisconsin, Madison

 

Abscission has been recently highlighted as both evolutionary and agriculturally important trait in the history of human beings. We have been characterizing novel delayed abscission mutants in Arabidopsis to understand cell separation processes in the plant. One mutant with delayed abscission, dab4-1, has recently been map-based cloned and is being characterized for its functions in plant development. Previous studies show that DAB4/COI1 is central to jasmonic acid signaling pathway possibly through F-box mediated proteolysis. Distinctive from the coi1 mutant, dab4-1 possesses other developmental roles that have been overlooked. These include strong apical dominance and epinastic leaf growth that are unique to dab4-1. Genetic analysis revealed that this is due to WS-specific genetic modifier(s) in dab4-1. dab4-1 shows insensitivity to exogenous treatment of JA while in wild type acceleration of floral organ abscission, senescence in leaves, and meristem arrest is observed with the same treatment. When dab4-1 is ethylene-treated, however, it shows normal ethylene responses that are similar to those from JA treatment. We hypothesize that JA controls floral organ abscission in an ethylene independent manner in Arabidopsis.

 

14.          PIF7, a new phytochrome-interacting bHLH transcription factor, together with PIF3 and PIF4,

regulates long-term growth responses in red light by modulating phyB photoreceptor levels

Pablo Leivar, Elena Monte, Bassem Al-Sady, Christine Carle, Alyssa Storer, Jose M. Alonso,1 Joseph R. Ecker,1 and Peter H. Quail

Plant Gene Expression Center/University of California, Berkeley; 1Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California

 

Following photoactivation, members of the phytochrome (phy) family of photoreceptors translocate into the nucleus and induce changes in target gene expression to regulate plant development. Several members of the bHLH family of transcriptional regulators (referred to as phy-interacting factors-PIFs) interact specifically with the active Pfr form of the phy molecule, suggesting that the phy may directly modulate light-regulated gene expression. Recent evidence indicates that this process might involve rapid light-induced phosphorylation and degradation of PIF3. To better define the functional role and mechanism of action of PIF3 and other closely related PIFs in the bHLH family, we have characterized the newly identified PIF7. Our results show that PIF7 is a low abundance protein that interacts selectively with the Pfr form of phyB through a conserved domain called the Active phyB binding (APB) motif. Similar to PIF3, upon light exposure PIF7 is rapidly induced to migrate to intranuclear speckles, where it co-localizes with phyB. However, in striking contrast to PIF3, this process is not accompanied by light-induced degradation of PIF7. Despite these differences, studies of Arabidopsis PIF7-deficient mutants indicate that the role of PIF7 in prolonged red light is similar to that of PIF3 in that it acts as a weak negative regulator of phyB-mediated seedling deetiolation. We are currently examining the genetic interactions between different PIFs as well as the molecular requirements for their action. Our data suggest that the mechanism by which PIF3, PIF4 and PIF7 operate on the phyB signaling pathway under prolonged red light is through maintaining low phyB protein levels in an additive or synergistic manner.

 

15.          YUCCA genes are required for shade-induced increases in auxin signaling

Melissa L. Pytlak, Kazunari Nozue, Youfa Cheng1, Michael F. Covington, Stacey L. Harmer, Yunde Zhao1, and Julin N. Maloof.

Section of Plant Biology, University of California, Davis, CA; 1Division of Biological Sciences, University of California, San Diego, La Jolla, CA

 

Because plants depend on light for energy they have developed the ability to detect adjacent plants and alter their growth to compete for light. Neighbor detection can lead to the shade-avoidance syndrome, a suite of traits that includes increased stem and petiole elongation, early flowering, and changes in resource allocation. Work by others has established that auxin is involved in shade-induced increases in cell elongation, but how shade alters auxin signaling is unclear. One model suggests that shade increases lateral transport of auxin; other data suggests that shade increases auxin biosynthesis. To examine shade/auxin interactions in real-time, we have used the synthetic auxin responsive promoter DR5 to drive expression of firefly luciferase (LUC). We observed a strong increase in DR5:LUC bioluminescence after treating plants with end-of-day far red (EOD-FR) to induce the shade-avoidance syndrome. Auxin transport inhibitors did not prevent the shade-induced increase in DR5 expression, consistent with shade increasing auxin biosynthesis rather than changing transport. To test this idea further we examined extant microarray data and found three putative auxin biosynthesis genes, YUCCA5, 8, and 9, that are all induced by shade treatment. Analysis of a quintuple mutant that removes function of YUCCA5, 8, and 9, along with two other YUCCA genes in the same clade, shows that these genes are required for shade-induced increases in auxin signaling. In addition, we find that although inhibition of auxin transport does not prevent increased DR5:LUC bioluminescence, it does prevent increases in cell elongation. Together our data suggests that shade causes an increase in auxin biosynthesis by increasing YUCCA expression, and that auxin transport is required to bring the newly synthesized auxin to target tissues.

 

16.          Intron-Mediated Enhancement of Gene Expression in Arabidopsis

Alan B. Rose and Ian F. Korf

Molecular and Cellular Biology, University of California, Davis, CA

 

Many introns increase gene expression in diverse organisms by unknown mechanisms. In Arabidopsis, efficiently spliced introns differ widely in their ability to stimulate mRNA levels, indicating that there must be sequences that differ between introns that determine the magnitude of intron-mediated enhancement (IME). To locate these sequences, a series of deletion-containing and hybrid introns were tested in a fusion between the TRP1 gene and GUS in transgenic Arabidopsis. The results show conclusively that the sequences responsible for enhancement are redundant and distributed throughout stimulating introns. To identify enhancing sequences, an algorithm (the IMEter) was devised that determines how well a test intron matches the pentamer sequence profile of all the introns in genes whose expression is predicted to be in the top 20% of Arabidopsis genes, based on codon usage. The score generated by the IMEter is proportional to the degree to which 11 out of 12 introns elevate TRP1:GUS expression, including 5 out of 6 introns chosen solely on the basis of their IMEter scores. Of the 16 Arabidopsis introns shown by other labs to enhance expression, virtually all generate an IMEter score of 10 or more, even though less than 2.8% of all Arabidopsis introns yield a score this high. Average IMEter scores of introns separated by their ordinal number drop from first introns to sixth introns and then level off. This pattern is in striking agreement with the finding that the ability of an intron to stimulate mRNA accumulation declines with distance from the promoter until it is lost entirely around 1 Kb from the start. The IMEter is currently being refined and used to generate motifs whose role in IME will be tested.


17.          PIF5: A Possible Node For Crosstalk Between Ethylene and Early Light Signaling Pathways

Rajnish Khanna, Yu Shen, Colleen M. Marion, Christine M. Carle, Eberhard Schaefer and Peter H. Quail.

Plant Gene Expression Center/University of California, Berkeley

 

Light triggers seedling de-etiolation by suppressing hypocotyl cell elongation, along with apical hook opening, cotyledon expansion and greening. Different members of the phytochrome family (phyA-E) act with differential, and partly overlapping, photosensory and/or physiological functions in this process. Phytochrome Interacting Factor 5 (PIF5), a bHLH-class transcription factor, binds specifically to the light activated (Pfr) form of phyB through the Active Phytochrome Binding (APB) motif. Our studies with pif5-mutant and PIF5-overexpressing (OX) seedlings have revealed that PIF5 is involved in an intricate interplay between ethylene and early light signaling pathways. In seedlings grown in darkness, PIF5-(OX) enhances the expression of ACS5 and ACS8, two key enzymes for ethylene biosynthesis. PIF5-(OX) seedlings carrying functional or mutated APB (mAPB) motifs exhibit a triple response in the dark that can be rescued by treatment with Ag+ ions, a characteristic phenotype caused by elevated ethylene levels. In seedlings grown in red light (Rc) the PIF5 protein is rapidly  degraded through the 26S proteasome pathway. Strikingly, phyB protein levels are also greatly reduced in Rc-treated PIF5-(OX) seedlings with the functional APB, but not in PIF5-(OX) with a mAPB. Treatment with MG132, an inhibitor of the 26S proteasome pathway, blocks the degradation of PIF5 and phyB in these seedlings. Together, these results indicate that PIF5 may regulate ethylene levels in dark grown seedlings, and that in the light phyB (Pfr) binds PIF5 through the APB motif possibly to facilitate PIF5 degradation and/or to modulate its activity. PIF5 may play a pivotal role during the dark to light transition, providing a mechanism of crosstalk between ethylene and early light-signaling pathways.

 

18.           Floral integration requires the function of homeobox genes PENNYWISE and POUND-

           FOOLISH in Arabidopsis

Siddhartha Kanrar, Moni Bhattacharya, Blake Arthur and Harley M. S. Smith

Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA

 

Flowering is a major developmental phase change that transforms the fate of the shoot apical meristem (SAM) from a leaf bearing vegetative meristem to that of a flower producing inflorescence meristem. In Arabidopsis, floral meristems are specified on the periphery of the inflorescence meristem by the combined activities of the FLOWERING LOCUS T (FT)-FD complex and the flower meristem identity gene, LEAFY (LFY). Two redundant functioning homeobox genes, PENNYWISE (PNY) and POUND-FOOLISH (PNF), which are expressed in the vegetative and inflorescence SAM regulate inflorescence-patterning events during reproductive development. pny pnf double mutants display a non-flowering phenotype, indicating a possible link between these homeobox genes and FT, FD and LFY during inflorescence development. Results from this study demonstrate that FT and LFY expression in inflorescence apices is dependent upon PNY and PNF. Ectopic expression of LFY promotes early flowering in pny pnf plants, while the floral promoting activity of ectopic FT is severely attenuated. Genetic analysis shows that when mutations in pny and pnf genes are combined with lfy, a synergistic phenotype is displayed that disrupts floral specification and flower development. In conclusion, results from this study support a model in which PNY and PNF function up-stream of FT and LFY in the SAM. In addition, the floral promoting activity of FT is dependent upon the activity of PNY and PNF.

 


19.          The Molecular Mechanism of ELF3 in Arabidopsis Circadian Rhythms

Bryan Thines, Allison Tam and Frank Harmon

Plant Gene Expression Center/University of California, Berkeley

 

To optimize the incidence of physiological processes throughout the day, plants have evolved the ability to measure time over 24 hours.  At the core of this time-keeping ability is an endogenous molecular oscillator known as the circadian clock.  To protect the core oscillator from spurious resetting signals, the clock uses a mechanism called “gating” to buffer input cues, such as light, in a phase-dependent manner.  EARLY FLOWERING 3 (ELF3) is a critical gating factor, and loss of ELF3 function in Arabidopsis thaliana renders the core oscillator hypersensitive to light.  Based on the result that ELF3 physically interacts with the red light photoreceptor phytochrome B (phyB) in vitro, our hypothesis is that ELF3 blocks light input into the core oscillator by inhibiting the action of phyB.  Using a reverse yeast two-hybrid screening approach, we are creating elf3 interaction-defective (elf3id) mutants that either lack or have diminished capacity to interact with phyB.  A sensitive co-immunoprecipitation assay is being used to measure the interaction between phyB and the elf3di proteins.  Confirmed elf3di mutants will be introduced into elf3 plants and assayed for complementation of mutant circadian clock phenotypes to assess the importance of the phyB-ELF3 association, and to study the influence of this interaction specifically on clock function.  In addition, to further delineate the role of ELF3, we are using a yeast two-hybrid screen to identify novel interacting partners and have identified several candidates.  The ultimate goal of these approaches is to understand how the ELF3 contributes to setting the circadian clock. 

 

20.          The parA resolvase performs site-specific genomic excision in Arabidopsis

James Thomson1, Yuan-Yeu Yau, Robert Blanvillain, and David W. Ow

Plant Gene Expression Center/University of California, Berkeley and 1Western Regional Research Center, Albany, CA

 

We investigated the function of the ParA site-specific recombination system in Arabidopsis.  Using a stable expression assay we showed that the ParA recombinase is catalytically active and capable of performing site-specific excision of a chromosomally integrated target from the Arabidopsis genome.  The ParA recombinase is a novel tool for genome manipulation in transgenic plants and may provide a way to remove marker genes or other unneeded transgenic sequences.  A novel Arabidopsis promoter derived from the OXS3 gene was used to express parA in transgenic plants.  The OXS3 promoter is an alternative non-patented promoter that provides constitutive expression in Arabidopsis.

 

21.          The Arabidopsis 1-Aminocyclopropane-1-Carboxylic Acid Synthase (ACS) Gene Family

Atsunari Tsuchisaka, Takeshi Yamagami, Jose M. Alonso1, Joseph R. Ecker2 and Athanasios Theologis1

Plant Gene Expression Center/University of California, Berkeley; 1Department of Genetics, North Carolina State University, Raleigh, NC; 2Salk Institute for Biological Studies, La Jolla, CA

 

1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE (ACS) catalyzes the rate-limiting step in the ethylene biosynthetic pathway in plants. The Arabidopsis genome encodes nine ACS polypeptides that form eight functional and one non-functional homodimers. Why are there so many ACS isozymes in Arabidopsis? We hypothesize that that each member of the ACS family may have a distinct biological function. Here, we report various approaches for elucidating the role of each isozyme. Firstly, biochemical characterization of the various ACS polypeptides revealed that they are biochemically diverse. We think that the biochemical diversity defines a distinct biological function of each isozyme which in turn defines its tissue specific expression. Second, functional intermolecular complementation experiments in E.coli show that all isozymes can form heterodimers. However, functional heterodimers are detected only among members that belong to the same phylogenetic branch. We propose that functional heterodimerization enhances the biochemical diversity of the ACS gene family; non-functional heterodimers may also play a regulatory role during the plant life cycle. Thirdly, analysis of promoter-GUS fusions reveals unique and overlapping expression patterns during plant development. This raises the prospect that functional ACS heterodimers may be formed in planta. Lastly, we have identified T-DNA insertion lines for five (ACS2, ACS4, ACS5, ACS6 and ACS9) among the nine ACS genes; double and higher order mutations were constructed. The analysis reveals that ethylene produced by specific ACS isozymes play a central role in flowering time determination. The data suggest that isozyme specific ethylene production regulates the relative ratio of repressors/activators responsible for flowering time. These observations provide molecular insight into the unique and overlapping functions of the ACS gene family members in Arabidopsis.

 

22.          Maize Anther Development:  Cell Fate Acquisition and Maintenance

Virginia Walbot, Dave Skibbe, Gillian Nan, Darren Morrow, John Fernandes, Zac Cande1, Lisa Harper1

Stanford University; 1University of California, Berkeley

 

We are interested in defining the steps required for anther locule cells to differentiate appropriately in the stages preceding meiosis and at the entry into meiosis.  We are using a combination of genetic and molecular approaches to understand anther development.  Two mutants define the developmental window that interests us.  In the msca1 mutant stamen specification and filament development are normal, but all cells of the anther locule mis-differentiate.  In ameiotic1, all cell types appear to be normal, however, the central cells conduct mitosis rather than meiosis.  Using these mutants and others with defects affecting specific cell types (ms23, no tapetum; mac1, excess meiotic cells and no tapetum or middle layer) for comparison to wild-type siblings we have elucidated the following principles of anther development in maize.

 

#1 Transcriptomes are very similar in anthers from different backgrounds (compared to leaves) with  progressively fewer differences as development proceeds. Therefore, we can compare anther mutants in different backgrounds.  #2  Severity and timing of mutant phenotypes correlate with the extent of transcriptome differences compared to fertile siblings.  #3  Anthers are modified leaves, support for a classical theory.  Fertile 1.0 mm anthers express leaf developmental genes, but these disappear in the 1.5 mm anther transcriptome.  msca1 mutants fail to repress leaf transcripts and have cells with leaf-like characters.  They also express >90% of the normal anther transcriptome.   #4  Cell differentiation is "late" --evidence against cell lineage models of specification.  #5  The anther transcriptome is the most complex in maize = 24,000 genes expressed over several days prior to meiosis.  #6  There is almost no new gene expression during meiosis (a 5-7 day period) in the entire anther (90% composed of somatic cells).  #7  Regulatory genes important early in floral development are "recycled" making genetic analysis difficult.

 

Our next steps are to analyze ~400 additional male-sterile mutants at the cytological level to identify additional steps in cell fate specification and maintenance.  Approximately 500 Mu transposon lines carrying insertions into anther-expressed genes will also be evaluated to determine if "knockouts" cause male-sterility.  Anther total and nuclear proteomes are also being developed, in collaboration with Al Burlingame at UCSF.

 

23.       AIK1 and AIK2, two Leucine-Rich Repeat Receptor Kinases, Regulate the Orientation of

Cell Expansion in Arabidopsis

Shouling Xu, Hyun Sook Chae, Abidur Rahman1,2, Tobias Baskin2, and Joseph J Kieber

Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC; 1Department of Biology, University of Massachusetts, Amherst, MA; 2Current address: Cryobiosystem Research Center, Iwate University, Iwate, Japan

 

The proper regulation of cell expansion is a key parameter that determines the shape of plant organs. We identified two Arabidopsis leucine-rich repeat receptor-like kinases (LRR-RLKs), which we have called AIK1 and AIK2 (ACS interacting receptor Kinase), using a yeast two-hybrid screen with an ACS5 bait, an enzyme that catalyzes the rate-limiting step in ethylene biosynthesis. Disruption of both AIK1 and AIK2 causes conditional anisotropic growth defects in Arabidopsis root cells, resulting in short, swollen roots. These cell elongation defects can be reversed by inhibition of ethylene biosynthesis, but not by blocking the known ethylene response pathway. While AIK1 was found to be an active protein kinase in vitro, mutant versions of AIK1 or AIK2 that eliminated the kinase catalytic activity were able to fully complement aik1aik2, indicating that intrinsic kinase activity was not required for AIK function. The previously identified sos5 mutant was found to have very similar properties with aik1aik2, and genetic analysis suggests that these gene products act on a linear pathway. In contrast, another mutant affecting the orientation of root cell expansion, cob-1, was found to be additive with the aik1aik2 mutants and thus likely acts on a separate pathway. The data suggest that AIK1 and AIK2 act to mediate anisotropic cell elongation in an ACS-dependent manner.

 

24.       Pollen receptor kinases are critical for maintaining pollen tube polarity and growth in

          Arabidopsis thaliana

Yan Zhang, Rajsree Mungur, Colleen Lau, and Sheila McCormick1

Plant Gene Expression Center/University of California, Berkeley

 

Sexual reproduction of angiosperms relies on successful fertilization, a process that requires sustained maintenance and flexible reorientation of pollen tube growth in female tissues. Pollen receptor kinases (PRKs) are considered critical for this process based on their subcellular localization and reversible phosphorylation although direct evidence was scarce. Here we show that two Arabidopsis PRKs, homologs of the tomato PRKs LePRK1 and LePRK2, are critical regulators of pollen tube growth. Overexpression of either AtPRK1a or mAtPRK1a reduced pollen tube growth and induced tip swelling, whereas overexpression of AtPRK2a, but not of mAtPRK2a, resulted in isotropic tube growth. Co-overexpression of AtPRK1a and AtPRK2a showed reduced pollen tube growth, indicating that heterodimers inhibit tube growth. Overexpression of the two AtPRKs differently perturbed actin polymerization. AtPRK2a overexpression phenotypes were suppressed by overexpression of the C-terminal domain of a pollen-specific AtROPGEF, suggesting a potential signaling relay through the small GTPase Rop. We propose a model in which spatially partitioned activities of AtPRKs regulate pollen tube polarity.

 


LIST OF PARTICIPANTS

 

Jun Cheul Ahn                        PGEC - USDA/UCB                                                             510-559-5964

                                                    800 Buchanan St.                                                                 jcahn@berkeley.edu

                                                    Albany, CA 94710                                                                               

Alan Rose                                 UCD                                                                                       530/754-9892

                                                    1 Shields Avenue                                                                

                                                    Davis, CA  95616                                                                                 

Monica Alandete-Saez            PGEC - USDA/UCB                                                             510-559-5918

                                                    800 Buchanan St.                                                                 monica_alandete@berkeley.edu

                                                    Albany, CA 94710                                                                               

Barbara Baker                        PGEC - USDA/UCB                                                             510-559-5912, Fx 5929

                                                    800 Buchanan St.                                                                 bbaker@calmail.berkeley.edu

                                                    Albany, CA 94710                                                                               

Anindya Bandyopadhyay        PGEC - USDA/UCB                                                             510-559-5920

                                                    800 Buchanan St.                                                                 anindya@berkeley.edu

                                                    Albany, CA 94710                                                                               

Rebecca Bart                            UCD                                                                                       530-752-7834

                                                    1229 Carrison St                                                                   rbart@ucdavis.edu

                                                    Berkeley, Ca 94702                                                                              

Glen Bartley                             USDA ARS WRRC                                                              510-559-5845

                                                    800 Buchanan St                                                                  geb@pw.usda.gov

                                                    Albany, CA  94710                                                                              

Laura Bartley                          UCD                                                                                       530/754-6940

                                                    Ronald lab Plant Pathology                                                lebartley@ucdavis.edu

                                                    Davis, CA  95616                                                                                 

Dominique Bergmann            Stanford                                                                                 650/736-0987

                                                    371 Serra Mall                                                                       dbergmann@stanford.edu

                                                    Stanford, Ca 94305                                                                              

Ann Blechl                               USDA ARS WRRC                                                              510-559-5716

                                                    800 Buchanan St                                                                  ablechl@pw.usda.gov

                                                    Albany, CA  94710                                                                              

Leonor Boavida                        PGEC - USDA/UCB                                                             510-559-5918

                                                    800 Buchanan St.                                                                 lboavida@berkeley.edu

                                                    Albany, CA 94710                                                                               

Nathalie Bolduc                       PGEC - USDA/UCB                                                             510/559-5922

                                                    800 Buchanan St.                                                                 nathaliebolduc@berkeley.edu

                                                    Albany, CA 94710                                                                               

Esteban Bortiri                        PGEC - USDA/UCB                                                             510-559-5919

                                                    800 Buchanan St.                                                                 ebortiri@berkeley.edu

                                                    Albany, CA 94710                                                                               

Diane Burgess                         UCB                                                                                        510-643-4862

                                                    221 Koshland Hall                                                                dburgess@nature.berkeley.edu

                                                    Berkeley, CA 94720                                                                             

Christine Carle                       PGEC - USDA/UCB                                                             510-559-5896

                                                    800 Buchanan St.                                                                 carlec@berkeley.edu

                                                    Albany, CA 94710                                                                               


Gilles Cellier                           PGEC - USDA/UCB                                                             510-559-5920

                                                    800 Buchanan St.                                                                

                                                    Albany, CA 94710                                                                               

Divya Chandran                       UCB                                                                                        510-643-4862

                                                    221 Koshland Hall                                                                divya@nature.berkeley.edu

                                                    Berkeley, CA 94720                                                                             

Kwang Suk Chang                  PGEC - USDA/UCB                                                             510-559-5964

                                                    800 Buchanan St.                                                                 kschang@ucdavis.edu

                                                    Albany, CA 94710                                                                               

Grace Chen                              USDA ARS WRRC                                                              510-559-5627

                                                    800 Buchanan St                                                                  qhgc@pw.usda.gov

                                                    Albany, CA  94710                                                                              

Mawsheng Chern                    UC Davis                                                                               530/752-7834

                                                    One Shields Ave                                                                  mschern@ucdavis.edu

                                                    Davis, Ca  95616                                                                                  

Hye Sun Cho                            UCB                                                                                        510-643-1725

                                                    451 Koshland Hall                                                                hscho@nature.berkeley.edu

                                                    Berkeley, CA  94720-3102                                                                  

George Chuck                         PGEC - USDA/UCB                                                             510-559-5922

                                                    800 Buchanan St.                                                                 gchuck@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

Gitta Coaker                            UCD                                                                                       530-752-6541

                                                    254 Hutchison Hall                                                              glcoaker@ucdavis.edu

                                                    Davis, CA  95616                                                                                 

Darleen A. DeMason              UC Riverside                                                                         951 827 3580

                                                    Riverside, CA                                                                       demason@ucr.edu

Zhiping Deng                           Carnegie Institution                                                             650-325-1521 x226

                                                    260 Panama Street                                                                zdeng@stanford.edu

                                                    Stanford, CA 94305                                                                             

S. Dinesh-Kumar                    Yale University                                                                     203-432-9965

                                                    KBT826, MCDB, Yale University                                      savithramma.dinesh-kumar@yale.edu

                                                    New Haven, CT 06520-8103                                                               

Joe Ecker                                  The Salk Institute                                                                 858-453-4100 x1752

                                                    10010 N. Torrey Pines Road                                               ecker@salk.edu

                                                    La Jolla, CA 92037                                                                               

Motomu Endo                            Kyoto University                                                                 81/75-753-4139

                                                    Kitashirakawa Oiwake                                                         endo@physiol.bot.kyoto-u.ac.jp

                                                    Kyoto, Japan                                                                                       

Lewis Feldman                         UCB                                                                                        510/642-9877

                                                    111 Koshland Hall                                                                feldman@nature.berkeley.edu

                                                    Berkeley, Ca 94720                                                                              

Beat Fischer                             UCB                                                                                        510-643-5206

                                                    441 Koshland Hall                                                                bfischer@nature.berkeley.edu

                                                    Berkeley, CA  94720-3102                                                                  

Jenn Fletcher                           PGEC - USDA/UCB                                                             510-559-5917

                                                    800 Buchanan St.                                                                 fletcher@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               


Chan Man Ha                           PGEC - USDA/UCB                                                             510-559-5815

                                                    800 Buchanan St.                                                                 cmha@berkeley.edu

                                                    Albany, CA 94710                                                                               

Sarah Hake                              PGEC - USDA/UCB                                                             510-559-5907

                                                    800 Buchanan St.                                                                 maizesh@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

Andrew Hammond                   USDA ARS PWA                                                                510/559-6170

                                                    800 Buchanan St.                                                                 ahammond@pw.ars.usda.gov

                                                    Albany, Ca  94710                                                                               

David Hantz                              PGEC - USDA/UCB                                                             510-559-5902

                                                    800 Buchanan St.                                                                 dhantz@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

Frank Harmon                         PGEC - USDA/UCB                                                             510-559-5939

                                                    800 Buchanan St.                                                                 fharmon@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

Lisa Harper                              PGEC - USDA/UCB                                                             510-559-5629

                                                    800 Buchanan St.                                                                 ligule@nature.berkeley.edu

                                                    Albany, CA 94710

Rebecca Haussmann               PGEC - USDA/UCB                                                             510-559-5913

                                                    800 Buchanan St.                                                                 rebeccah@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

Laticia A. Holley                      PGEC - USDA/UCB                                                             510-559-5922

                                                    800 Buchanan St.                                                                

                                                    Albany, CA 94710

Wei Hu                                      UC Davis                                                                               530 752 7026

                                                    31 Briggs Hall - 1 Shields Ave                                           weihu@ucdavis.edu

                                                    Davis, CA  95616                                                                                 

Matthew Hudson                      U of Illinois                                                                           217-244-8096

                                                    Dept of Crop Sciences, 33NSRC                                        mhudson@uiuc.edu

                                                    Urbana, Illinois, 61801                                                                        

David Jackson                          Cold Spring Harbor                                                              516-367-8467/ 8800

                                                    One Bungtown Road                                                           jacksond@cshl.edu

                                                    Cold Spring Harbor, NY 11724                                                          

Susan Jenkins                         UCB                                                                                        510-643-1968

                                                    111 Koshland Hall MC3102                                                sjenkins@nature.berkeley.edu

                                                    Berkeley.ca 94720-3102                                                                      

Keni Jiang                                UCB                                                                                        510-642-9877

                                                    421 Koshland Hall                                                                kenij@neture.berkeley.edu

                                                    Berkeley.ca 94720-3102                                                                      

Alexander Jones                      UCB                                                                                        510/207-5317

                                                    1637 Carleton St                                                                   Xanderjones@berkeley.edu

                                                    Berkeley, Ca  94703                                                                             

Ji Hyung Jun                           PGEC - USDA/UCB                                                             510-559-5815

                                                    800 Buchanan St.                                                                 jhjun@calmail.berkeley.edu

                                                    Albany, CA 94710                                                                               

Karen Kaczorowski                USDA/Purdue University                                                   765-494-8057

                                                    915 West State Street                                                          karen.kaczorowski@ars.usda.gov

                                                    West Lafayette, IN 47907                                                                  

 

Victor Kaupas                          PGEC - USDA/UCB                                                             510-559-5900

                                                    800 Buchanan St.                                                                 vkaupas@berkeley.edu

                                                    Albany, CA 94710                                                                               

Steve Kay                                  Scripps Research Institue                                                   858-784-2360

                                                    10550 N. Torrey Pines Road                                               stevek@scripps.edu

                                                    La Jolla, CA                                                                          

Nancy M. Kerk                        Yale                                                                                        203 432 8060

                                                    74 Thankful Stow Rd                                                           nancy.kerk@yale.edu

                                                    Guiford, CT  06437                                                                              

Phichaya Khamai                    UCB                                                                                        510-642-6209

                                                    111 Koshland Hall, P&MB                                                 phichayak@gmail.com

                                                    Berkeley, CA  94720-3102                                                                  

Rajnish Khanna                       Mendel Biotechnology                                                       510/259-6154

                                                    21375 Cabot Blvd                                                                 rkhanna@mendelbio.com

                                                    Hayward, Ca  94545                                                                            

Joonyup Kim                            U Wisconsin Madison                                                        608-262-8322

                                                    1575 Linden Drive                                                                joonyupkim@wisc.edu

                                                    Madison, WI  53706                                                                           

Edward Knipling                      ARS Administrator                                                              (202) 720-3656

                                                    1400 Independence Ave, SW                                            edward.knipling@ars.usda.gov

                                                    Washington, DC  20250                                                                     

Hanhui Kuang                          PGEC - USDA/UCB                                                             510-559-5919

                                                    800 Buchanan St.                                                                 kuang@berkeley.edu

                                                    Albany, CA 94710                                                                               

Debbie Laudencia                    USDA ARS WRRC                                                              510-550-6173

       -Chingcuanco                    800 Buchanan St                                                                  dlc@pw.usda.gov

                                                    Albany, CA  94710                                                                              

Pablo Leivar                             PGEC - USDA/UCB                                                             510-559-5916

                                                    800 Buchanan St.                                                                 pleivar@berkeley.edu

                                                    Albany, CA 94710                                                                               

Peggy G. Lemaux                    UCB                                                                                        642-1589

                                                    111 Koshland Hall, P&MB                                                 lemauxpg@nature

                                                    Berkeley, CA  94720-3102                                                                  

Feng Li                                      PGEC - USDA/UCB                                                             510-559-5713

                                                    800 Buchanan St.                                                                 lifeng@berkeley.edu

                                                    Albany, CA 94710                                                                               

Jianzhong Liu                          PGEC - USDA/UCB                                                             510-559-5931

                                                    800 Buchanan St.                                                                 jzliu@berkeley.edu

                                                    Albany, CA 94710                                                                               

Tie Liu                                       Stanford                                                                                 650/736-2377

                                                    371 Serra Mall                                                                       tieliu@stanford.edu

                                                    Stanford, Ca 94305                                                                              

China Lunde                             PGEC - USDA/UCB                                                             510-599-5710

                                                    800 Buchanan St.                                                                 lundec@berkeley.edu

                                                    Albany, CA 94710                                                                               

Julin N Maloof                         UC Davis                                                                               530 752 8077

                                                    1 Shields Avenue                                                                 jnmaloof@ucdavis.edu

                                                    Davis, CA  95616                                                                                 

 

Sheila McCormick                 PGEC - USDA/UCB                                                             510-559-5906

                                                    800 Buchanan St.                                                                 sheilamc@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

Tara McHugh                           USDA ARS WRRC                                                              510-559-5864

                                                    800 Buchanan St                                                                  thm@pw.usda.gov

                                                    Albany, CA  94710                                                                              

Jihyun Moon                            PGEC - USDA/UCB                                                             510-559-5922

                                                    800 Buchanan St.                                                                 moonj@berkeley.edu

                                                    Albany, CA 94710                                                                               

Rajsree Mungur                      PGEC - USDA/UCB                                                             510-559-5918

                                                    800 Buchanan St.                                                                 rajsree_mungur@berkeley.edu

                                                    Albany, CA 94710                                                                               

Hideki Nakayama                    Nara Institute                                                                        81-743-72-5453

                                                    8916-5 (B-402), Takayama                                                   nakayama@bs.naist.jp

                                                    Nara,  Japan 630-0101                                                                         

Pulla Nakayama                      Nara Institute                                                                        81-743-72-5453

                                                    8916-5 (B-402), Takayama                                                   pullamail@aol.com

                                                    Nara,  Japan 630-0101                                                                         

Jennifer L. Nemhauser          Univ Washington                                                                206 543 0753

                                                    P.O. Box 351800                                                                    jn7@u.washington.edu

                                                    Seattle, WA  98185-1800                                                                    

Weiman Ni                               PGEC - USDA/UCB                                                             510-559-5896

                                                    800 Buchanan St.                                                                 wzn1@berkeley.edu

                                                    Albany, CA 94710                                                                               

Kris Niyogi                               UCB                                                                                        510-643-6602

                                                    111 Koshland Hall, P&MB                                                 niyogi@nature.berkeley.edu

                                                    Berkeley, CA  94720-3102                                                                  

Devin O'Connor                      PGEC - USDA/UCB                                                             510/559-5922

                                                    800 Buchanan St.                                                                 devo@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

David Ow                                   PGEC - USDA/UCB                                                             510-559-5909

                                                    800 Buchanan St.                                                                 david_ow@berkeley.edu

                                                    Albany, CA 94710                                                                               

Marta Paciorek                       Stanford                                                                                 650/736-2377

                                                    371 Serra Mall                                                                       martap@stanford.edu

                                                    Stanford, Ca 94305                                                                              

Tomasz Paciorek                    Stanford                                                                                 650/736-2377

                                                    371 Serra Mall                                                                       paciorek@stanford.edu

                                                    Stanford, Ca 94305                                                                              

Sungsoon Park                        UCB                                                                                        510-642-6209

                                                    111 Koshland Hall, P&MB                                                 sungsoon@nature.berkeley.edu

                                                    Berkeley, CA 94720                                                                             

Helena Pires                            PGEC - USDA/UCB                                                             510-559-5815

                                                    800 Buchanan St.                                                                 helenarp@berkeley.edu

                                                    Albany, CA 94710                                                                               

Peter Quail                               PGEC - USDA/UCB                                                             510-559-5910

                                                    800 Buchanan St.                                                                 quail@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

 

Natasha Raikhel                      UC Riverside                                                                         951-827-6370

                                                    Institute for Integrative Genome Biology                        nraikhel@citrus.ucr.edu

                                                    Riverside, CA                                                                      

 

Peter Repetti                            Mendel Biotechnology                                                       510/259-6151

                                                    21375 Cabot Blvd                                                                 prepetti@mendelbio.com

                                                    Hayward, Ca  94545

Mily Ron                                   PGEC - USDA/UCB                                                             510-559-5918

                                                    800 Buchanan St.                                                                 milyron@berkeley.edu

                                                    Albany, CA 94710                                                                               

Pam Ronald                              UCD                                                                                       530-754-2252

                                                    1 Shields Avenue                                                                 pcronald@ucdavis.edu

                                                    Davis, CA  95616                                                                                 

Elizabeth Ruchenski              PGEC - USDA/UCB                                                             510-559-5847

                                                    800 Buchanan St.                                                                 lruchens@berkeley.edu

                                                    Albany, CA 94710                                                                               

James Seiber                           USDA ARS WRRC                                                              510-559-5600

                                                    800 Buchanan St                                                                  jseiber@pw.usda.gov

                                                    Albany, CA  94710                                                                              

Yu Shen                                     PGEC - USDA/UCB                                                             510-559-5916

                                                    800 Buchanan St.                                                                 yshen@berkeley.edu

                                                    Albany, CA 94710                                                                               

Mary Simmons                        George Washington Carver                                               301/504-5560

                                                    G. Washington Carver Room 4-2202                                 Kay.Simmons@ars.usda.gov

                                                    Beltsville, MD                                                                                      

Harley (Matthew) Smith         UC Riverside                                                                         951 827 2643

                                                    Ctr Plant Cell Bio                                                                  harleys@ucr.edu

                                                    Riverside, CA  92521                                                                          

Chris Somerville                     Carnegie Institution                                                             650-325-1521

                                                    260 Panama Street                                                                crs@stanford.edu

                                                    Stanford, CA 94305                                                                             

Brian Staskawicz                    UCB                                                                                        510-642-3721

                                                    111 Koshland Hall                                                                stask@berkeley.edu

                                                    Berkeley.ca 94720-3102                                                                      

Gerry Still                                PGEC – USDA/UCB                                                            ggstill@nature.berkeley.edu         

                                                    Walnut Creek, CA                                                               

Marcus Strawn                        UCB                                                                                        510/643-4862

                                                    2540 Le Conte Ave #4                                                         strawn@berkeley.edu

                                                    Berkeley, Ca  94709                                                                             

Ian Sussex                                Yale                                                                                        203-453-9094

                                                    74 Thankful Stow Rd                                                           ian.sussex@yale.edu

                                                    Guiford, CT  06437                                                                              

James Tepperman                   PGEC - USDA/UCB                                                             510-559-5935

                                                    800 Buchanan St.                                                                 jmtepp@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

Athanasios Theologis             PGEC - USDA/UCB                                                             510-559-5911

                                                    800 Buchanan St.                                                                 theo@nature.berkeley.edu

                                                    Albany, CA 94710                                                                               

 

Bryan Thines                           PGEC - USDA/UCB                                                             510-559-6089

                                                    800 Buchanan St.                                                                 bthines@berkeley.edu

                                                    Albany, CA 94710                                                                               

Beth Thompson                        PGEC - USDA/UCB                                                             510-559-5922

                                                    800 Buchanan St.                                                                 bethompson@berkeley.edu

                                                    Albany, CA 94710                                                                               

James G. Thomson                  PGEC - USDA/UCB                                                             510-559-5721

                                                    800 Buchanan St.                                                                 jthomson@pw.usda.gov

                                                    Albany, CA 94710                                                                               

Phoi Tran                                  UCB                                                                                        510-643-5206

                                                    441 Koshland Hall                                                                pttran@berkeley.edu

                                                    Berkeley, CA 94720                                                                             

Atsunari Tsuchisaka             PGEC - USDA/UCB                                                             510-559-5921

                                                    800 Buchanan St.                                                                 atsunari@berkeley.edu

                                                    Albany, CA 94710                                                                               

Tracie Tsukida                        PGEC - USDA/UCB                                                             510/559-5889

                                                    800 Buchanan St.                                                                 tracie28@berkeley.edu

                                                    Albany, CA 94710                                                                               

Ludmila Tyler                          PGEC - USDA/UCB                                                             510-559-5815

                                                    800 Buchanan St.                                                                 ltyler@berkeley.edu

                                                    Albany, CA 94710

John Vogel                               USDA ARS WRRC                                                              510-559-6117

                                                    800 Buchanan St                                                                  jvogel@pw.usda.gov

                                                    Albany, CA  94710                                                                              

Erik Vollbrecht                       Iowa State University                                                          515-294-9009

                                                    2206 Molecular Biology Building                                      vollbrec@iastate.edu

                                                    Ames, IA  50011-3250                                                                         

Setsuko Wakao                       UCB                                                                                        510-643-6604

                                                    441 Koshland Hall                                                               

                                                    Berkeley, CA 94720                                                                             

Virginia Walbot                      Stanford                                                                                 650 723 2227

                                                    Biological Sciences                                                              walbot@stanford.edu

                                                    Stanford, CA  94305-5020                                                                  

Dong Wang                              Stanford                                                                                 650/723-3122

                                                    Dept. of Biological Sciences                                              dw@stanford.edu

                                                    Stanford, Ca 94305                                                                              

Huanzhong Wang                   PGEC - USDA/UCB                                                             510-559-5918

                                                    800 Buchanan St.                                                                 hzwang@berkeley.edu

                                                    Albany, CA 94710                                                                               

Xing Wang Deng                    Yale University                                                                     203-432-8908/8909

                                                    165 Prospect Street                                                              xingwang.deng@yale.edu

                                                    New Haven, CT 06520-8104                                                               

Spencer Wei                            PGEC - USDA/UCB                                                             510-559-5892

                                                    800 Buchanan St.                                                                 onewei@mindspring.com

                                                    Albany, CA 94710                                                                               

Maureen Whalen                    USDA ARS WRRC                                                              510-559-5950

                                                    800 Buchanan St                                                                  mwhalen@pw.usda.gov

                                                    Albany, CA  94710                                                                              

 

Leor Williams                         PGEC - USDA/UCB                                                             510-559-5815

                                                    800 Buchanan St.                                                                 leorw@berkeley.edu

                                                    Albany, CA 94710                                                                               

Shouling Xu                             U. North Carolina                                                                 919/962-2273

                                                    CB #3280 Coker Hall                                                            SLXU@EMAIL.unc.edu

                                                    Chapel Hill, NC                                                                                    

Frank Yau                                 PGEC - USDA/UCB                                                             510-559-5920

                                                    800 Buchanan St.                                                                 yyau2000@berkeley.edu

                                                    Albany, CA 94710                                                                               

Guixia Yu                                  PGEC - USDA/UCB                                                             510-559-5924

                                                    800 Buchanan St.                                                                 gyu@berkeley.edu

                                                    Albany, CA 94710

Patricia Zambryski                UCB                                                                                        510-643-9203

                                                    PMB dept., Koshland Hall                                                  zambrysk@nature.berkeley.edu

                                                    Berkeley, CA 94720                                                                             

Yan Zhang                                PGEC - USDA/UCB                                                             510-559-5918

                                                    800 Buchanan St.                                                                 mpizyanzhang@berkeley.edu

                                                    Albany, CA 94710                                                                               

 


 [m1]Why is it in future tense, he’s been here for 2 years, it should be present tense

 [m2]Wasn’t that 2 years ago now?


Last Modified: 8/17/2007
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