Tidying up international nucleotide sequence databases

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

Projets situés: 10 ans d'expérience de terrain / 10 years of field experience

Ouvrage bilingue: français / anglaisCet ouvrage retrace la mise en œuvre du programme Africa 2009, initié par le Centre du patrimoine mondial de l'UNESCO, à travers des projets dits situés visant à améliorer les conditions de la conservation du patrimoine immobilier dans la région de l'Afrique subsaharienne tout en se positionnant dans le cadre plus large du développement durable. Cette publication illustre le dynamisme d'un réseau de professionnels aux capacités renforcées et se veut également être un instrument incitatif pour les professionnels du patrimoine africain et leurs partenaires locaux, nationaux, régionaux et internationaux, vers la poursuite et la multiplication d'actions concrètes en faveur de ce riche patrimoine

Projets situés: 10 ans d'expérience de terrain / 10 years of field experience

Ouvrage bilingue: français / anglaisCet ouvrage retrace la mise en œuvre du programme Africa 2009, initié par le Centre du patrimoine mondial de l'UNESCO, à travers des projets dits situés visant à améliorer les conditions de la conservation du patrimoine immobilier dans la région de l'Afrique subsaharienne tout en se positionnant dans le cadre plus large du développement durable. Cette publication illustre le dynamisme d'un réseau de professionnels aux capacités renforcées et se veut également être un instrument incitatif pour les professionnels du patrimoine africain et leurs partenaires locaux, nationaux, régionaux et internationaux, vers la poursuite et la multiplication d'actions concrètes en faveur de ce riche patrimoine

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

Quality and metadata annotations of fungal ITS sequences by mycorrhiza types.

1<p>all sequences belonging to EcM lineages regardless of isolation source;</p>2<p>all sequences belonging to Glomeromycota, except <i>Geosiphon;</i></p>3<p>all sequences derived from roots (with or without a culturing step) of the respective host plants;</p>4<p>Chimeric sequences consist of two or more fragments of fungal sequences and are therefore not assigned below the kingdom level;</p>5<p>nd, not determined;</p>6<p>Annotated–sum of original annotations and metadata provided in the course of this study;</p>7<p>formation of coils in ErM, formation of pelotons, stimulation of germination or development in OM.</p

Screenshot of the UNITE search page (http://unite.ut.ee/).

<p>This search tool allows queries of sequences based on taxonomic information and associated metadata.</p

Contribution of different isolation sources to the number of INSD sequences in the most common ectomycorrhizal fungal lineages.

<p>Contribution of different isolation sources to the number of INSD sequences in the most common ectomycorrhizal fungal lineages.</p

Promoting universal financial protection: a case study of new management of community health insurance in Tanzania.

BACKGROUND: The National Health Insurance Fund (NHIF), a compulsory formal sector scheme took over the management of the Community Health Fund (CHF), a voluntary informal sector scheme, in 2009. This study assesses the origins of the reform, its effect on management and reporting structures, financial flow adequacy, reform communication and acceptability to key stakeholders, and initial progress towards universal coverage. METHODS: The study relied on national data sources and an in-depth collective case study of a rural and an urban district to assess awareness and acceptability of the reform, and fund availability and use relative to need in a sample of facilities. RESULTS: The reform was driven by a national desire to expand coverage and increase access to services. Despite initial delays, the CHF has been embedded within the NHIF organisational structure, bringing more intensive and qualified supervision closer to the district. National CHF membership has more than doubled. However, awareness of the reform was limited below the district level due to the reform's top-down nature. The reform was generally acceptable to key stakeholders, who expected that benefits between schemes would be harmonised.The reform was unable to institute changes to the CHF design or district management structures because it has so far been unable to change CHF legislation which also limits facility capacity to use CHF revenue. Further, revenue generated is currently insufficient to offset treatment and administration costs, and the reform did not improve the revenue to cost ratio. Administrative costs are also likely to have increased as a result of the reform. CONCLUSION: Informal sector schemes can benefit from merger with formal sector schemes through improved data systems, supervision, and management support. However, effects will be maximised if legal frameworks can be harmonised early on and a reduction in administrative costs is not guaranteed