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The switch from plant vegetative growth to reproductive development (transition to flowering), is a critical stage in the life cycle of a plant. As such, flowering is tightly controlled by diverse developmental, hormonal and environmental cues, day length and temperature being the most important of these environmental signals (Posè et al. Curr Opin Plant Biol. 2012; Huijser and Schmid, Development 2011). Flowering time diversity has adaptive value in natural populations and plays a major role in agricultural production. Specifically, flowering delay in different environmental conditions is a crucial breeding trait for yield and nutritive quality of leafy crops and forages. Genetic and molecular analyses in the model plant Arabidopsis thaliana have identified regulatory pathways that control the floral transition (Turck et al. Annu. Rev. Plant Biol. 2008; Amasino Plant J. 2010; Fornara et al. Cell 2010). These pathways act in different tissues of the plant but ultimately converge at the shoot apical meristem (SAM) (Huijser and Schmid, Development 2011). Our studies aim to translate the knowledge acquired in Arabidopsis to leafy vegetables of high commercial value, endive and escarole (Cichorium endivia), whose transcriptome was recently sequenced in our lab in collaboration with the International seed breeding company Enza Zaden (R&D Italia). The final goal is to identify novel functional single nucleotide polymorphisms (SNPs), which may account for flowering time diversity as a tool for molecular breeding of leafy crops. We used a candidate gene approach and focus on well known Arabidopsis regulators of flowering transition and novel potential regulators belonging to the TALE (Three Amino acid Loop Extension, KNOX and BLH genes) family of homeobox transcription factors, which are expressed in the SAM (Hake et al. 2004; Di Giacomo et al. 2013). In silico analysis of Arabidopsis genome identified potential TALE binding sites in the regulatory regions of several flowering time genes. Sequenced genomes of A. thaliana natural accessions were screened for SNPs in the potential TALE binding sites to select Arabidopsis accessions for further studies. Characterization of the flowering time response of mutants and transgenics with altered KNOX expression is in progress. Homologous genes for known Arabidopsis regulators of flowering transition and TALEs were identified in the C. endivia transcriptome. Identification of putative functional SNPs in flowering regulatory genes and TALEs in different C. endivia varieties is in progress. Transcript profiling of adult leaves through RNAseq, in varieties which display different flowering time responses, identified possible gene expression markers of flowering time to be considered for functional validation.

Assembly and development of Cichorium endivia transcriptome to assess identity and traceability of endives and escaroles. Endives (Cichorium endivia var. crispum) and escaroles (C. e. latifolium) are widely consumed as fresh, minimally processed and cooked food. Italy is a major world consumer and producer. The project CISIA (www.ibba.mlib.cnr.it/Projects/Cisia/Project.html) has been developing markers (metabolic, transcriptional and allelic variants) used for identity, traceability and valorisation of curly- and broad- leafed cultivars in collaboration with the Enza Zaden Group. A de novo transcriptome was assembled (reference cultivar 'Domari') using RNA of several organs (from young and adult plants) and Illumina HiSeq2000 technology (100bp paired-end), which generated ca. 240M reads. The filtered reads were assembled into 91,784 contigs (77,360 unigenes) with an average length of ca. 1,202bp (N50 = 1,545bp). As for the unigenes, 68,858 (75.0%) showed significant similarity (E-value

Assessment of environmental status and integral safety requires combination of information from many sources, coming from either databases or increasingly via live model (scenario) simulations. Many of these models require input from one another, sometimes unidirectional, but more and more two-directional as well. Many protocols and frameworks are available for model coupling, often based on open standards and implementations. Previous overviews of coupling protocols have focused on data exchange volume, data complexity, invasiveness into existing models and support for specific programming languages. We extend the overview using recent developments in web-based protocols and focus on the suitability for internet-based data exchange. We also extend the focus of previous reviews by also taking the coupling with aggregated information products for end-users into account. We propose a hierarchical ordering of all standards for specific types of end-users.

The fatty acid synthetase (FAS) system in plants and bacteria consists of a type II FAS complex assembled from different monofunctional polypeptides catalysing the individual reactions involved in each cycle of the de novo synthesis of fatty acids. Enoyl-ACP reductase (EC 1.3.1.9) plays the determinant role in completing cycles of de novo fatty acid biosynthesis, by removing a trans-unsaturated double bond to give a saturated acyl-ACP. Genetic analyses revealed that the NADH-specific enoyl-ACP reductase (ENR) is encoded by a single gene in different plant species like Petunia hybrida and Arabidopsis thaliana, whereas the allotetraploid Nicotiana tabacum contains two enr encoding genes. This implies that enhanced expression of enr genes, e.g. during seed development, is due to a modification of the expression level of a housekeeping gene. Besides a high degree of homology observed within the exon and intron sequences of the analysed enr genes, the positions of the introns and exons were also found to be conserved. Other similarities are the presence of a large intron in the 5' untranslated leader sequence of the genes as well as a conserved 5' GC intron splice site. Experiments have been performed to analyse the functional importance of this 5' GC splice site with regard to the regulation of enr expression. Homology between the 5' flanking region of both tobacco enr genes, enr-T1 and enr-T2, appears to be limited to short stretches of conserved sequences which are frequently interrupted by insertions of different (retro) transposon-like elements in the promoter of enr-T2. By contrast, the arabidopsis enr promoter region does not show any significant homology when compared with similar regions of the tobacco enr genes.

In this paper we explore the role of the river run-off, the tidal regime and the local winds in the dynamics of the Ria de Arousa estuary during the summer period, using for that purpose the numerical model Delft3D. First of all, a simulation under real hydrological and meteorological conditions is conducted in order to validate the ability of the model to reproduce measured salinity and temperature profiles. Subsequently, a series of simulations considering simplified meteorological input data and river discharge conditions are carried out in order to study the sensitivity of stratification conditions in the estuary to the various external forcings of the model. The results are analyzed using potential energy anomaly arguments, which allow quantifying and ranking the contribution of the different processes to the stratification of the estuarine system.

In 2003 various projects at Deltares and the TU-Delft merged their toolboxes for marine and coastal science and engineering into one toolbox, culminating in 2008 in an open source release, known as OpenEarthTools (OET). OpenEarth adopts the wikipedia approach to growth: web 2.0 crowd sourcing. All users are given full write access to help improve the collection. Quality is assured by version control, tracking all changes. OpenEarth started as a social experiment to investigate whether crowd sourcing was possible in our community of marine and coastal researchers. The answer is yes: over 1000 users registered, now enjoying over 5000 contributions from over 100 contributors. The most important asset is a general toolbox to plot any data type in Google Earth. With this toolbox it has become very easy for marine and coastal experts to disseminate their data via Google Earth. It enables the NCK community to make its data available to end-users and the general public with only little effort. They can now consume our data as simple as watching YouTube: DataTube. In this paper it is shown that OpenEarth has added important value by analyzing a wide range of marine and coastal data types from NCK simultaneously in Google Earth. To match the traditional gap between specialist knowledge and end users, Google Earth is shown to be a very powerful tool. The possibilities for outreach by NCK are manifold.

Research, consultancy as well as construction projects commonly spend a significant part of their budget to set-up some basic infrastructure for data and knowledge management, most of which dissipates again once the project is finished. Standing initiatives so far have not been successful in providing a proper data and knowledge management system for data, models and tools. OpenEarth (www.openearth.eu) was developed as a free and open source alternative to the current often ad-hoc approaches to deal with data, models and tools. OpenEarth as a whole (philosophy, user community, infrastructure and workflow) is the first comprehensive approach to handling data, models and tools that actually works in practice at a truly significant scale. It is implemented effectively not only at its originally founding organizations Delft University of Technology and Deltares but also in a number of sizeable research programs with multiple partners (such as the 28 million euro 4-year research program Building with Nature – 19 partners from 1 country) from multiple countries (such as the 4.6 million euro 3-year EU FP7 research program MICORE – 15 partners from 9 countries). For data, models and tools that are truly strategic and really cannot be shared, OpenEarth stimulates the setup of internal OpenEarth clones. This way the OpenEarth workflow can still be adopted, promoting collaboration within the organization, while taking care of security considerations at the same time. This paper describes the OpenEarth philosophy, its infrastructure and main workflow protocols. To illustrate the systems practical effectiveness the paper finishes with an example of OpenEarth as it is applied in Building with Nature.

The conductance of the vacuolar membrane at elevated cytosolic Ca

The NADH-specific enoyl-acyl carrier protein (ACP) reductase, which catalyses the last reducing step during the fatty acid biosynthesis cycle, is encoded in Arabidopsis thaliana encoded by a single housekeeping gene (ENRA) which is differentially expressed during plant development. To identify elements involved in its tissue-specific transcriptional control, a fragment comprising the 1470 bp region directly upstream of the ATG start codon of the ENR-A gene was fused to the uidA (GUS) reporter gene and analysed in transgenic Nicotiana tabacum plants. GUS activity found during development of the transgenic plants was similar to endogenous ENR protein levels found in both tobacco and Arabidopsis plants, except for developing flowers. In floral tissue the promoter fragment showed very little activity in contrast to the relatively high level of endogenous ENR expression. Successive deletions from the 5' and 3' regions of the promoter fragment revealed the presence of at least three elements which control GUS expression in different stages of development in the transgenic tobacco plants. First, expression in young developing leaves required both the presence of sequences between -329 to -201 relative to the transcription start and part of the untranslated leader comprising the first intron. Second, root-specific GUS expression was still observed after deletion of the 5'-upstream sequences up to 19 bp of the transcription initiation site. Further, the additional removal of the intron from the untranslated leader increased root-specific expression by ca. 4- to 5-fold. Third, high expression in seeds was still observed with the minimal upstream promoter segment of 19 bp. This seed expression level was found to be independent of the presence or absence of the intron in the untranslated leader. Finally, 3' deletion of the leader sequence up to 17 bp of the transcription start greatly impaired GUS activity during all stages of plant development, suggesting that the deleted sequence of the leader either functions as an enhancer for transcription initiation or stabilizes the mRNA.