Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development

Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning and the specification of floral organs is established. We used a novel floral induction system in Arabidopsis, which allows the isolation of a large number of synchronized floral buds, in conjunction with whole-genome microarray analysis to identify genes with differential expression at distinct stages of flower development. We found that the onset of flower formation is characterized by a massive downregulation of genes in incipient floral primordia, which is followed by a predominance of gene activation during the differentiation of floral organs. Among the genes we identified as differentially expressed in the experiment, we detected a significant enrichment of closely related members of gene families. The expression profiles of these related genes were often highly correlated, indicating similar temporal expression patterns. Moreover, we found that the majority of these genes is specifically up-regulated during certain developmental stages. Because co-expressed members of gene families in Arabidopsis frequently act in a redundant manner, these results suggest a high degree of functional redundancy during early flower development, but also that its extent may vary in a stage-specific manner

Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development in \u3cem\u3eArabidopsis thaliana\u3c/em\u3e

In flowering plants the gynoecium is the female reproductive structure. In Arabidopsis thalianaovules initiate within the developing gynoecium from meristematic tissue located along the margins of the floral carpels. When fertilized the ovules will develop into seeds. SEUSS (SEU) and AINTEGUMENTA (ANT) encode transcriptional regulators that are critical for the proper formation of ovules from the carpel margin meristem (CMM). The synergistic loss of ovule initiation observed in the seu ant double mutant suggests that SEU and ANT share overlapping functions during CMM development. However the molecular mechanism underlying this synergistic interaction is unknown. Using the ATH1 transcriptomics platform we identified transcripts that were differentially expressed in seu ant double mutant relative to wild type and single mutant gynoecia. In particular we sought to identify transcripts whose expression was dependent on the coordinated activities of the SEU and ANT gene products. Our analysis identifies a diverse set of transcripts that display altered expression in the seu ant double mutant tissues. The analysis of overrepresented Gene Ontology classifications suggests a preponderance of transcriptional regulators including multiple members of the REPRODUCTIVE MERISTEMS (REM) and GROWTH-REGULATING FACTOR (GRF) families are mis-regulated in the seu ant gynoecia. Our in situ hybridization analyses indicate that many of these genes are preferentially expressed within the developing CMM. This study is the first step toward a detailed description of the transcriptional regulatory hierarchies that control the development of the CMM and ovule initiation. Understanding the regulatory hierarchy controlled by SEU and ANT will clarify the molecular mechanism of the functional redundancy of these two genes and illuminate the developmental and molecular events required for CMM development and ovule initiation

On the complexity of designing distributed protocols.

"Reprinted from Information and Control, vol. 53, no.3, 1982."Bibliography: leaves 217-218."ONR/N00014-77-C-0532(NR041-519)

CRABS CLAW Acts as a Bifunctional Transcription Factor in Flower Development

One of the crucial steps in the life cycle of angiosperms is the development of carpels. They are the most complex plant organs, harbor the seeds, and, after fertilization, develop into fruits and are thus an important ecological and economic trait. CRABS CLAW (CRC), a YABBY protein and putative transcription factor, is one of the major carpel developmental regulators in A. thaliana that includes a C2C2 zinc finger and a domain with similarities to an HMG box. CRC is involved in the regulation of processes such as carpel fusion and growth, floral meristem termination, and nectary formation. While its genetic interactions with other carpel development regulators are well described, its biochemical properties and molecular way of action remain unclear. We combined Bimolecular Fluorescence Complementation, Yeast Two-Hybrid, and Yeast One-Hybrid analyzes to shed light on the molecular biology of CRC. Our results showed that CRC dimerizes, also with other YABBY proteins, via the YABBY domain, and that its DNA binding is mainly cooperative and is mediated by the YABBY domain. Further, we identified that CRC is involved in floral meristem termination via transcriptional repression while it acts as a transcriptional activator in nectary development and carpel fusion and growth control. This work increases our understanding on how YABBY transcription factors interact with other proteins and how they regulate their targets

ABERRANT TESTA SHAPE encodes a KANADI family member, linking polarity determination to separation and growth of Arabidopsis ovule integuments

The Arabidopsis aberrant testa shape (ats) mutant produces a single integument instead of the two integuments seen in wild-type ovules. Cellular anatomy and patterns of marker gene expression indicate that the single integument results from congenital fusion of the two integuments of the wild type. Isolation of the ATS locus showed it to encode a member of the KANADI (KAN) family of putative transcription factors, previously referred to as KAN4. ATS was expressed at the border between the two integuments at the time of their initiation, with expression later confined to the abaxial layer of the inner integument. In an inner no outer (ino) mutant background, where an outer integument does not form, the ats mutation led to amorphous inner integument growth. The kan1 kan2 double mutant exhibits a similar amorphous growth of the outer integument without affecting inner integument growth. We hypothesize that ATS and KAN1/KAN2 play similar roles in the specification of polarity in the inner and outer integuments, respectively, that parallel the known roles of KAN proteins in promoting abaxial identity during leaf development. INO and other members of the YABBY gene family have been hypothesized to have similar parallel roles in outer integument and leaf development. Together, these two hypotheses lead us to propose a model for normal integument growth that also explains the described mutant phenotypes

A novel allele of FILAMENTOUS FLOWER reveals new insights on the link between inflorescence and floral meristem organization and flower morphogenesis

<p>Abstract</p> <p>Background</p> <p>The <it>Arabidopsis </it><it>FILAMENTOUS FLOWER (FIL) </it>gene encodes a YABBY (YAB) family putative transcription factor that has been implicated in specifying abaxial cell identities and thus regulating organ polarity of lateral organs. In contrast to double mutants of <it>fil </it>and other <it>YAB </it>genes, <it>fil </it>single mutants display mainly floral and inflorescence morphological defects that do not reflect merely a loss of abaxial identity. Recently, <it>FIL </it>and other <it>YABs </it>have been shown to regulate meristem organization in a non-cell-autonomous manner. In a screen for new mutations affecting floral organ morphology and development, we have identified a novel allele of FIL, <it>fil-9 </it>and characterized its floral and meristem phenotypes.</p> <p>Results</p> <p>The <it>fil-9 </it>mutation results in highly variable disruptions in floral organ numbers and size, partial homeotic transformations, and in defective inflorescence organization. Examination of meristems indicates that both <it>fil-9 </it>inflorescence and floral meristems are enlarged as a result of an increase in cell number, and deformed. Furthermore, primordia emergence from these meristems is disrupted such that several primordia arise simultaneously instead of sequentially. Many of the organs produced by the inflorescence meristems are filamentous, yet they are not considered by the plant as flowers. The severity of both floral organs and meristem phenotypes is increased acropetally and in higher growth temperature.</p> <p>Conclusions</p> <p>Detailed analysis following the development of <it>fil-9 </it>inflorescence and flowers throughout flower development enabled the drawing of a causal link between multiple traits of <it>fil-9 </it>phenotypes. The study reinforces the suggested role of <it>FIL </it>in meristem organization. The loss of spatial and temporal organization of <it>fil-9 </it>inflorescence and floral meristems presumably leads to disrupted cell allocation to developing floral organs and to a blurring of organ whorl boundaries. This disruption is reflected in morphological and organ identity aberrations of <it>fil-9 </it>floral organs and in the production of filamentous organs that are not perceived as flowers. Here, we show the role of <it>FIL </it>in reproductive meristem development and emphasize the potential of using <it>fil </it>mutants to study mersitem organization and the related effects on flower morphogenesis.</p

Status report of the baseline collimation system of CLIC. Part II

Important efforts have recently been dedicated to the characterisation and improvement of the design of the post-linac collimation system of the Compact Linear Collider (CLIC). This system consists of two sections: one dedicated to the collimation of off-energy particles and another one for betatron collimation. The energy collimation system is further conceived as protection system against damage by errant beams. In this respect, special attention is paid to the optimisation of the energy collimator design. The material and the physical parameters of the energy collimators are selected to withstand the impact of an entire bunch train. Concerning the betatron collimation section, different aspects of the design have been optimised: the transverse collimation depths have been recalculated in order to reduce the collimator wakefield effects while maintaining a good efficiency in cleaning the undesired beam halo; the geometric design of the spoilers has been reviewed to minimise wakefields; in addition, the optics design has been optimised to improve the collimation efficiency. This report presents the current status of the the post-linac collimation system of CLIC. Part II is mainly dedicated to the study of the betatron collimation system and collimator wakefield effects.Comment: 25 pages, 13 figure