The purpose of the European national organic seed databases is to list the varieties for which organically produced seeds and vegetative propagation material is available on the market. The correct functioning of the ...
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The purpose of the European national organic seed databases is to list the varieties for which organically produced seeds and vegetative propagation material is available on the market. The correct functioning of the databases can facilitate the use and distribution of organic seed by improving the transparency of the organic seed market. Each EU Member State can establish its own database, resulting in different specific technical solutions among countries. This study evaluated the quality of organic seed databases in place in the EU countries (including the United Kingdom and Switzerland) through an online survey. An Information Systems Success Model was used as a framework of our evaluation. The respondents assessed the Ease of use, Comprehension and Completeness of the databases. Based on 537 responses obtained from farmers, seed suppliers and certification bodies, our analysis revealed that the Completeness of the databases was evaluated as the most critical aspect. Interactive fully computerised databases should be preferred to the provision of static files as they positively influence perceived completeness. In addition, the support provided by the database managers on how to use databases and a straightforward administrative process for the registration of seed offers or the management of derogations can increase databases comprehensibility and ease of use.
Background: The seed integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering betw...
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Background: The seed integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the seed also provides Web services based API for programmatic access to the data in the seed, allowing the development of third-party tools and mash-ups. Results: The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the seed using common bioinformatics programming languages such as Perl, Python, and Java. Conclusions: We present a novel approach to access the seed database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.
Background: COG0523 proteins are, like the nickel chaperones of the UreG family, part of the G3E family of GTPases linking them to metallocenter biosynthesis. Even though the first COG0523-encoding gene, cobW, was ide...
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Background: COG0523 proteins are, like the nickel chaperones of the UreG family, part of the G3E family of GTPases linking them to metallocenter biosynthesis. Even though the first COG0523-encoding gene, cobW, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family. Results: Based on a combination of comparative genomics, literature and phylogenetic analyses and experimental validations, the COG0523 family can be separated into at least fifteen subgroups. The CobW subgroup involved in cobalamin synthesis represents only one small sub-fraction of the family. Another, larger subgroup, is suggested to play a predominant role in the response to zinc limitation based on the presence of the corresponding COG0523-encoding genes downstream from putative Zur binding sites in many bacterial genomes. Zur binding sites in these genomes are also associated with candidate zinc-independent paralogs of zinc-dependent enzymes. Finally, the potential role of COG0523 in zinc homeostasis is not limited to Bacteria. We have predicted a link between COG0523 and regulation by zinc in Archaea and show that two COG0523 genes are induced upon zinc depletion in a eukaryotic reference organism, Chlamydomonas reinhardtii. Conclusion: This work lays the foundation for the pursuit by experimental methods of the specific role of COG0523 members in metal trafficking. Based on phylogeny and comparative genomics, both the metal specificity and the protein target(s) might vary from one COG0523 subgroup to another. Additionally, Zur-dependent expression of COG0523 and putative paralogs of zinc-dependent proteins may represent a mechanism for hierarchal zinc distribution and zinc sparing in the face of inadequate zinc nutrition.
One of the most important and most easily measurable phys-ical characteristics of plant seeds is their weight, which influ-ences and indicates crucial ecological processes. seed weight affects spatial and temporal dis...
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One of the most important and most easily measurable phys-ical characteristics of plant seeds is their weight, which influ-ences and indicates crucial ecological processes. seed weight affects spatial and temporal dispersibility, and can also in-fluence seed predation and the germination, growth and survival of seedlings. Providing trait data for species miss-ing from international databases is key to promote stud-ies that advance our understanding of the functioning of plant communities and ecosystems, which is an essential issue in the face of the global climate change and biodi-versity loss. Compared to species from Western and North-western Europe, those with an Eastern or Central European centre of distribution are underrepresented in most interna-tional trait databases. Therefore, the creation of specific trait databases is key to help regional studies. In this respect, it is
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