Self-testable components: from pragmatic tests to design-for-testability methodology

International audienceTesting is a key aspect of software development, because of its cost and impact on final product reliability. Classical views on testing and their associated testing models, based on the waterfall model, are not well-suited to an OO development process. The standardization of semi-formal modeling methods, such as UML, reveals this trend: testing can no longer be separated from specification/design/code stages. A test approach integrated with the OO process must be defined with an associated testing philosophy. The approach presented in this paper aims at providing a consistent framework for building trust into components. By measuring the quality of test cases, we seek to build trust in a component passing those test cases. We present a pragmatic approach for linking design and test of classes, seen as basic unit test components. Components are self-testable by enhancing them with embedded test sequences and test oracles. Self-testable components serve as building blocks for performing systematic integration and non-regression testing. The main contribution presented in this paper consists of using component self-tests to systematically exercise main system structural dependencies. This approach has been implemented in the Eiffel, Java, Perl and C++ languages. Since it is simpler, due to the direct support for Design-by-Contract TM in the language, the Eiffel implementation is detailed here

Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis

Background: The Wuschel related homeobox (WOX) family proteins are key regulators implicated in the determination of cell fate in plants by preventing cell differentiation. A recent WOX phylogeny, based on WOX homeodomains, showed that all of the Physcomitrella patens and Selaginella moellendorffii WOX proteins clustered into a single orthologous group. We hypothesized that members of this group might preferentially share a significant part of their function in phylogenetically distant organisms. Hence, we first validated the limits of the WOX13 orthologous group (WOX13 OG) using the occurrence of other clade specific signatures and conserved intron insertion sites. Secondly, a functional analysis using expression data and mutants was undertaken. Results: The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. A large expansion of the WOX family was observed after the separation of mosses from other land plants and before monocots and dicots have arisen. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. AtWOX13 appeared to affect the floral transition. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. Conclusion: Our data provide evidence in favor of the WOX13 OG as the clade containing the most conserved WOX genes and established a functional link to organ initiation and development in Arabidopsis, most likely by preventing premature differentiation. The future use of Ostreococcus tauri and Physcomitrella patens as biological models should allow us to obtain a better insight into the functional importance of WOX13 OG genes

Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae

Proteaceae are a basal eudicot family with a highly conserved floral groundplan but which displays considerable variation in other aspects of floral and inflorescence morphology. Their morphological diversity and phylogenetic position make them good candidates for understanding the evolution of floral architecture, in particular the question of the homology of the undifferentiated perianth with the differentiated perianth of core eudicots, and the mechanisms underlying the repeated evolution of zygomorphy. In this paper, we combine a morphological approach to explore floral ontogenesis and a transcriptomic approach to access the genes involved in floral organ identity and development, focusing on Grevillea juniperina, a species from subfamily Grevilleoideae. We present developmental data for Grevillea juniperina and three additional species that differ in their floral symmetry using stereomicroscopy, SEM and High Resolution X-Ray Computed Tomography. We find that the adnation of stamens to tepals takes place at early developmental stages, and that the establishment of bilateral symmetry coincides with the asymmetrical growth of the single carpel. To set a framework for understanding the genetic basis of floral development in Proteaceae, we generated and annotated de novo a reference leaf/flower transcriptome from Grevillea juniperina. We found Grevillea homologs of all lineages of MADS-box genes involved in floral organ identity. Using Arabidopsis thaliana gene expression data as a reference, we found homologs of other genes involved in floral development in the transcriptome of G. juniperina. We also found at least 21 class I and class II TCP genes, a gene family involved in the regulation of growth processes, including floral symmetry. The expression patterns of a set of floral genes obtained from the transcriptome were characterized during floral development to assess their organ specificity and asymmetry of expression

Analyse fonctionnelle des gènes WOX les plus conservés chez Arabidopsis thaliana

Chez les plantes supérieures, l organogénèse est principalement post-embryonnaire et assurée par les méristèmes. Les familles de gènes CLE (CLAVATA3/ENDOSPERMSURROUNDING REGION related) et WOX (WUSCHEL-LIKE HOMEOBOX) sont des régulateurs majeurs de l activité des méristèmes. Des analyses phylogénétiques des gènes WOX de différentes espèces ont identifié trois groupes d orthologie, dont le groupe WOX13OG. Ce dernier contient le seul gène WOX d Ostreococcus tauri, les trois gènes WOX de Physcomitrella patens, ainsi que trois des gènes WOX parmi les quinze que compte Arabidopsis thaliana. L objectif de ma thèse a été de caractériser la fonction des gènes du groupe WOX13 OG chez A. thaliana.Parmi les mutants nuls identifiés pour ces gènes, seul le mutant wox14 présente des phénotypes forts, à savoir un retard de transition florale et des défauts de développement vasculaire. Ces résultats sont en accord avec l induction de l expression de WOX14 à la jonction des faisceaux vasculaires lors de la transition florale. Les résultats indiquent que WOX14 est impliqué dans le contrôle du nombre de faisceaux vasculaires initiés lors de cette dernière. La restauration conjointe de la transition florale et du nombre de faisceaux vasculaires, par complémentation du mutant wox14 ou application de gibbérellines (GA),suggère un lien direct entre ces deux processus. Cette étude nous a permis d identifier le gène CLE46 comme étant dérégulé dans le mutant wox14. Son expression dans les cellules du xylème, associée à l augmentation du nombre de faisceaux vasculaires chez wox14, suggèrent que CLE46 est un élément d une voie de signalisation de contrôle du nombre de faisceaux vasculaires. L importance des interactions WOX-CLE dans le développement vasculaire est soulignée par l induction de WOX4 et WOX14 par le peptide CLE41. Les analyses du transcriptome du mutant wox14 révèlent que la signalisation des GA est déficiente. Ce qui confirme les résultats de la complémentation du phénotype wox14 par les GA. De plus, le gène GA3ox1 a été identifié comme une cible potentielle de régulation de la biosynthèse de GA par le gène WOX14.Whilst primary meristems are initiated during embryogenesis, in higher plants additionalsecondary meristems initiate post-embryonically and contribute to the plant architecture andthe vascular strand development. Differentiation of the plant vascular cambium into xylemand phloem was shown to be regulated by cell to cell communication. The large CLE(CLAVATA3/ENDOSPERM SURROUNDING REGION related) signaling peptide familyand the WOX (WUSCHEL-LIKE HOMEOBOX) transcription factor family are thought to beconserved regulators of stem cell fate. In this thesis we report the presence of supernumeraryvascular bundles in the young inflorescence stem of the wox14 mutant. Our data indicate thatWOX14 prevents additional cambium cell to differentiate into vascular bundles during floraltransition. Moreover, the data suggest that vascular differentiation and floral transition arelinked. Consistently, WOX14 expression is induced within the connecting vascular strandduring floral transition. Furthermore, the application of gibberellins (GA) fully rescued boththe floral transition and the vascular bundle phenotype of the wox14 mutants. A detail analysisof GA biosynthesis and target genes showed that WOX14 controls the amount of bioactiveGA within the vasculature. However, WOX14 is also specifically expressed in the phloem ofthe inflorescence stem indicating a function in late vascular bundle development. We alsoshowed that not only WOX4 but also WOX14 are the target of the CLE41 peptide duringvascular development. Furthermore, the data indicate that another CLE gene, namely CLE46,is misregulated in the wox14 mutant. These results suggest that CLE46 might be the firstidentified CLE signal from the xylem that impacts vascular differentiation.PARIS11-SCD-Bib. électronique (914719901) / SudocSudocFranceF

Molecular cloning and developmental expression of AtGR1, a new growth-related Arabidopsis gene strongly induced by ionizing radiation

International audienceScreening for mRNAs that accumulate after DNA damage induced by ionizing radiation, we have isolated a 2.0-kb cDNA coding for a new Arabidopsis PEST-box protein named AtGR1 (A. thaliana gamma response 1) with an expression profile similar to that observed for several plant cell cycle-related proteins. Using an anti-AtGR1 antibody, we have shown that the AtGR1 protein is expressed at basal levels in mitotically dividing cells (meristematic tissues and organ primordia) and at a strongly enhanced level in endoreduplicating cells (stipules, trichomes). Using transgenic Arabidopsis plants that express the GUS reporter gene under the control of the AtGR1 promoter, we have demonstrated that the observed AtGR1 protein distribution is due to the promoter activity. Our results suggest that basal AtGR1 levels are associated with progression through mitosis, whereas elevated intracellular levels of AtGR1 seem to induce changes between the S and M phases of the cell cycle that trigger somatic cells to enter the endoreduplication cycle. Ionizing radiation-induced rapid and dose-dependent accumulation of AtGR1 mRNA in cell cultures and plant tissues leads to tissue-specific accumulation of AtGR1 protein, best observed in ovules, which never undergo an endoreduplication cycle. It therefore appears that the radiation-induced transient AtGR1 accumulation reflects DNA damage-dependent transient cell cycle arrest before mitosis, which is necessary to accomplish DNA repair prior to chromosome segregation and cytokinesis

WOX14 promotes bioactive gibberellin synthesis and vascular cell differentiation in Arabidopsis

Procambial and cambial stem cells provide the initial cells that allow the formation of vascular tissues. WOX4 and WOX14 have been shown to act redundantly to promote procambial cell proliferation and differentiation. Gibberellins (GAs), which have an important role in wood formation, also stimulate cambial cell division. Here we show that the loss of WOX14 function phenocopies some traits of GA-deficient mutants that can be complemented by exogenous GA application, whereas WOX14 overexpression stimulates the expression of GA3ox anabolism genes and represses GA2ox catabolism genes, promoting the accumulation of bioactive GA. More importantly, our data clearly indicate that WOX14 but not WOX4 promotes vascular cell differentiation and lignification in inflorescence stems of Arabidopsis