Impact of Regional Vein Thrombosis in Patients with Klebsiella pneumoniae Liver Abscess

Klebsiella liver abscess (KLA) is an emerging infection in Asia caused by hypermucoviscous strains of Klebsiella pneumoniae. It is associated with thrombophlebitis of portal and hepatic veins. The natural history and role of anticoagulation for this regional thrombophlebitis is unclear. In a retrospective study of 169 subjects with KLA over 7 years, thrombophlebitis was identified in 53/169 (31.4%). Only 1 received therapeutic anticoagulation. Despite this 30/49 (73.2%) of those with follow up scan available showed improvement or recanalization (mean duration between scans 44 days). Abscess resolution was associated with improvement in thrombophlebitis.     

Phylogeography of the temperate marine bivalve Cerastoderma edule (Linnaeus, 1758) (Bivalvia: Cardiidae) in the Subarctic: Unique diversity and strong population structuring at different spatial scales

Using mitochondrial COI sequencing, we explored the genetic diversity and population structuring of the common cockle Cerastoderma edule (Linnaeus, 1758) in the Norwegian and Barents Seas. Phylogeographic diversity and hence the evolutionary history of C. edule on the Scandinavian and Russian coastlines were found to be richer than expected for populations of temperate species in postglacially colonized seas. A major phylogeographic break at Lofoten Islands separated a group of subarctic populations dominated by a distinct star‐shaped clade of haplotypes from those to the south, extending to the North Sea and having highest gene diversities (h). At the northeastern edge of the range of C. edule, the Russian Murman coast, populations show a mosaic structure with considerable admixture of haplotypes from the south and high local‐scale variation in haplotype diversity (ranging between 0 and 0.8). To explain this mosaic we refer to the core‐satellite metapopulation model, with Norwegian populations as core, and Murman populations as satellites. Our results contradict the conventional biogeographic paradigm implying lack of metapopulation structuring in marine broadcast spawning invertebrates. Hypotheses considered to explain the origin of the unique variation in cockles from Northern Norway involve an early postglacial colonization and establishment of these populations (10–12 ka ago), a persistent oceanographic break at Lofoten, and a mitochondrial selective sweep associated with the postglacial recolonization of the subarctic seas by the boreal C. edule.     

Osmoregulatory function of large vacuoles found in notochordal cells of the intervertebral disc running title: an osmoregulatory vacuole

The nucleus pulposi of many species contain residual cells from the embryonic notochord, which exhibit a very unusual appearance (large vacuoles occupying approximately 80% of the cell volume, surrounded by an actin cytoskeleton). While the vacuoles have been qualitatively described, their composition and function has remained elusive. Given that these cells are believed to generate and experience significant osmotic pressures in both the notochord and intervertebral disc, we hypothesized that the vacuoles may serve as osmoregulatory organelles. Using both experimental and theoretical means, we demonstrated that the vacuoles contain a low-osmolality solution, generated via ion pumps on the vacuolar membrane. During hypotonic stress the vacuoles release their contents into the cytoplasm, diluting the cytoplasm and restoring the osmotic balance across the cell membrane. Thus the vacuoles function to regulate the cell volume and tonicity during rapid osmotic stress, protecting the cells from potentially damaging swelling pressures.     

Learning string similarity measures for gene/protein name dictionary look-up using logistic regression

MOTIVATION: One of the bottlenecks of biomedical data integration is variation of terms. Exact string matching often fails to associate a name with its biological concept, i.e. ID or accession number in the database, due to seemingly small differences of names. Soft string matching potentially enables us to find the relevant ID by considering the similarity between the names. However, the accuracy of soft matching highly depends on the similarity measure employed. RESULTS: We used logistic regression for learning a string similarity measure from a dictionary. Experiments using several large-scale gene/protein name dictionaries showed that the logistic regression-based similarity measure outperforms existing similarity measures in dictionary look-up tasks. AVAILABILITY: A dictionary look-up system using the similarity measures described in this article is available at http://text0.mib.man.ac.uk/software/mldic/.     

Approaches for systematic proteome exploration

With the completion of the human genome project (HUGO) during recent years, gene function, protein abundance and expression patterns in tissues and cell types have emerged as central areas for the scientific community. A mapped human proteome will extend the value of the genome sequence and large-scale efforts aiming at elucidating protein localization, abundance and function are invaluable for biomarker and drug discovery. This research area, termed proteomics, is more demanding than any genome sequencing effort and to perform this on a wide scale is a highly diverse task. Therefore, the proteomics field employs a range of methods to examine different aspects of proteomics including protein localization, protein-protein interactions, posttranslational modifications and alteration of protein composition (e.g. differential expression) in tissues and body fluids. Here, some of the most commonly used methods, including chromatographic separations together with mass spectrometry and a number of affinity proteomics concepts are discussed and exemplified.     

Artery and vein formation: a tug of war between different forces

How arterial and venous fates are established is largely unknown. In the past, circulatory dynamics were thought to be the exclusive cause of arteries and veins being structurally and functionally distinct; however, growing evidence indicates that an orderly progression of molecular signals controls arterial-venous specification in the developing vertebrate vascular system.