bold: The Barcode of Life Data System (http://www.barcodinglife.org)

The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.     

The treatable intellectual disability APP www.treatable-id.org: A digital tool to enhance diagnosis & care for rare diseases

ABSTRACT: BACKGROUND: Intellectual disability (ID) is a devastating and frequent condition, affecting 2-3% of the population worldwide. Early recognition of treatable underlying conditions drastically improves health outcomes and decreases burdens to patients, families and society. Our systematic literature review identified 81 such inborn errors of metabolism, which present with ID as a prominent feature and are amenable to causal therapy. The WebApp translates this knowledge of rare diseases into a diagnostic tool and information portal. Methods & Results: Freely available as a WebApp via www.treatable-id.org and mid 2012 via the App store, this diagnostic tool is designed for all specialists evaluating children with global delay / ID and laboratory scientists. Information on the 81 diseases is presented in different ways with search functions: 18 biochemical categories, neurologic and non-neurologic signs & symptoms, diagnostic investigations (metabolic screening tests in blood and urine identify 60% of all IEMs), therapies & effects on primary (IQ/developmental quotient) and secondary outcomes, and available evidence For each rare condition a 'disease page' serves as an information portal with online access to specific genetics, biochemistry, phenotype, diagnostic tests and therapeutic options. As new knowledge and evidence is gained from expert input and pubmed searches this tool will be continually updated. The WebApp is an integral part of a protocol prioritizing treatability in the work-up of every child with global delay / ID. A 3-year funded study will enable an evaluation of its effectiveness. CONCLUSIONS: For rare diseases, a field for which financial and scientific resources are particularly scarce, knowledge translation challenges are abundant. With this WebApp technology is capitalized to raise awareness for rare treatable diseases and their common presenting clinical feature of ID, with the potential to improve health outcomes. This innovative digital tool is designed to motivate health care providers to search actively for treatable causes of ID, and support an evidence-based approach to rare metabolic diseases. In our current -omics world with continuous information flow, the effective synthesis of data into accessible, clinical knowledge has become ever more essential to bridge the gap between research and care.     

Using caching and optimization techniques to improve performance of the Ensembl website

Background  

The Ensembl web site has provided access to genomic information for almost 10 years. During this time the amount of data available through Ensembl has grown dramatically. At the same time, the World Wide Web itself has become a dramatically more important component of the scientific workflow and the way that scientists share and access data and scientific information.     

The nuclear lamina. Both a structural framework and a platform for genome organization

The inner face of the nuclear envelope of metazoan cells is covered by a thin lamina consisting of a one-layered network of intermediate filaments interconnecting with a complex set of transmembrane proteins and chromatin associating factors. The constituent proteins, the lamins, have recently gained tremendous recognition, because mutations in the lamin A gene, LMNA, are the cause of a complex group of at least 10 different diseases in human, including the Hutchinson-Gilford progeria syndrome. The analysis of these disease entities has made it clear that besides cytoskeletal functions, the lamina has an important role in the "behaviour" of the genome and is, probably as a consequence of this function, intimately involved in cell fate decisions. Furthermore, these functions are related to the involvement of lamins in organizing the position and functional state of interphase chromosomes as well as to the occurrence of lamins and lamina-associated proteins within the nucleoplasm. However, the structural features of these lamins and the nature of the factors that assist them in genome organization present an exciting challenge to modern biochemistry and cell biology.     

Autopoiesis: The organization of living systems,its characterization and a model

We formulate the organization of living organisms through the characterization of the class of autopoietic systems to which living things belong. This general characterization is seen at work in a computer simulated model of a minimal case satisfying the conditions for autopoietic organization.     

The identity of Ctenophrynium K. Schum. (Marantaceae)

Ctenophrynium unilaterale (Baker) K. Schum. was described from cultivated material reported to have been brought from Madagascar. It has recently been recollected in the state of Bahía, SE Brazil. A reexamination shows good agreement with the Brazilian genus Saranthe (Regel & Koern.) Eichl. The recombination Saranthe unilateralis (Baker) L. Anderss. is made and the genus Ctenophrynium is reduced to a synonym of Saranthe . The plant is redescribed and illustrated.     

The identity of Maerua macrocarpa Chiov. (Capparaceae)

It is argued that the original material of Maerua macrocarpa consists of elements from three different species: M. denhardtiorum, Thilachium thomasii and Capparis tornentosa . A lectotypification is proposed that makes M. macrocarpa a synonym of M. denhardtiorum .     

The identity of Rumicicarpus ramosissimus Chiov. (Tiliaceae)

Rumicicarpus ramosissimus Chiov. is found to be conspecific with Triumfetta trigona Sprague & Hutch. The latter name is to be used for the combined taxon, which belongs to the T. flavescens group of sect. Triumfetta. The distribution of T. trigona is mapped.     

The typification and identity of Salix eriocephala Michx. (Salicaceae)

The lectotype ofS. eriocephala was selected from the vegetative specimens collected by Michaux in the Mississippi River valley in the fall of 1795. Its identity is the same as that which recently has been known asS. missouriensis orS. rigida var.vestita. Since these taxa are not specifically distinct fromS. rigida the nameS. eriocephala takes priority as the correct name for this wide-ranging North American species.     

The identity of the African genus Oncostemma K. Schurn. (Asclepiadaceae)

Oncostemma cuspidatum K. Schum., described from the West African island of S˜o Tomé, is recognized as being synonymous with Tylophora oblonga N.E. Br., a widespread and variable species of mainland African rainforests. The monotypic genus Oncostemma K. Schum. is reduced to synonymy with Tylophora R. Br. (Asclepiadaceae-Asclepiadeae-Astephaninae).     

棒花羊蹄甲和薯叶藤的学名订正

分布于云南西双版纳的棒花羊蹄甲Bauhinia claviflora L. Chen和海南的薯叶藤B. dioscoreifolia L. Chen长期被认为是国产特有种植物,实际上分别是广泛分布的缅甸羊蹄甲B. nervosa (Wall. ex Benth.) Baker和牛蹄麻B. khasiana Baker。作者依命名法予以归并。     

多脉暗罗（番荔枝科）名实考

经过对多脉暗罗Polyalthia pingpienensis P. T. Li主模式和等模式的详细研究,发现其主模式是混杂标本。该标本上的枝和花以及等模式是斜脉暗罗P. plagioneura,而叶属于另一种尚不能鉴定出学名的植物。为多脉暗罗指定了后选模式,并将其处理为斜脉暗罗的异名。