Complete Genome Sequence of Bacteroides ovatus V975

The complete genome sequence of Bacteroides ovatus V975 was determined. The genome consists of a single circular chromosome of 6,475,296 bp containing five rRNA operons, 68 tRNA genes, and 4,959 coding genes

The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract

Background Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown. Results To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity. Conclusions This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations

Modelling the regulative role of business processes with use and misuse cases

Business processes contain value-added and abuse prevention activities. Most modelling techniques do not provide a rationale for abuse prevention activities. Such a rationale is needed when redesigning business processes. In this paper we propose to consider business processes as the main regulatory mechanism that an organization uses to survive and flourish in its environment. We propose a theoretical framework based on the concept of Homeostasis, the maintenance of identity in a changing world. The framework classifies business processes into three levels and explains the interconnections between processes at different levels and the organization’s environment. Based on this framework, we extend the “Use and Misuse Cases” technique to support modelling of value-added and abuse prevention activities and their interconnections with the organization’s environment. We thus provide the needed rationale for business process redesign

ESAM supports neutrophil extravasation, activation of Rho, and VEGF-induced vascular permeability

Endothelial cell–selective adhesion molecule (ESAM) is specifically expressed at endothelial tight junctions and on platelets. To test whether ESAM is involved in leukocyte extravasation, we have generated mice carrying a disrupted ESAM gene and analyzed them in three different inflammation models. We found that recruitment of lymphocytes into inflamed skin was unaffected by the gene disruption. However, the migration of neutrophils into chemically inflamed peritoneum was inhibited by 70% at 2 h after stimulation, recovering at later time points. Analyzing neutrophil extravasation directly by intravital microscopy in the cremaster muscle revealed that leukocyte extravasation was reduced (50%) in ESAM−/− mice without affecting leukocyte rolling and adhesion. Depletion of >98% of circulating platelets did not abolish the ESAM deficiency–related inhibitory effect on neutrophil extravasation, indicating that it is only ESAM at endothelial tight junctions that is relevant for the extravasation process. Knocking down ESAM expression in endothelial cells resulted in reduced levels of activated Rho, a GTPase implicated in the destabilization of tight junctions. Indeed, vascular permeability stimulated by vascular endothelial growth factor was reduced in ESAM−/− mice. Collectively, ESAM at endothelial tight junctions participates in the migration of neutrophils through the vessel wall, possibly by influencing endothelial cell contacts

In vivo imaging and quantitative analysis of leukocyte directional migration and polarization in inflamed tissue

Directional migration of transmigrated leukocytes to the site of injury is a central event in the inflammatory response. Here, we present an in vivo chemotaxis assay enabling the visualization and quantitative analysis of subtype-specific directional motility and polarization of leukocytes in their natural 3D microenvironment. Our technique comprises the combination of i) semi-automated in situ microinjection of chemoattractants or bacteria as local chemotactic stimulus, ii) in vivo near-infrared reflected-light oblique transillumination (RLOT) microscopy for the visualization of leukocyte motility and morphology, and iii) in vivo fluorescence microscopy for the visualization of different leukocyte subpopulations or fluorescence-labeled bacteria. Leukocyte motility parameters are quantified off-line in digitized video sequences using computer-assisted single cell tracking. Here, we show that perivenular microinjection of chemoattractants [macrophage inflammatory protein-1alpha (MIP-1alpha/Ccl3), platelet-activating factor (PAF)] or E. coli into the murine cremaster muscle induces target-oriented intravascular adhesion and transmigration as well as polarization and directional interstitial migration of leukocytes towards the locally administered stimuli. Moreover, we describe a crucial role of Rho kinase for the regulation of directional motility and polarization of transmigrated leukocytes in vivo. Finally, combining in vivo RLOT and fluorescence microscopy in Cx3CR1(gfp/gfp) mice (mice exhibiting green fluorescent protein-labeled monocytes), we are able to demonstrate differences in the migratory behavior of monocytes and neutrophils.Taken together, we propose a novel approach for investigating the mechanisms and spatiotemporal dynamics of subtype-specific motility and polarization of leukocytes during their directional interstitial migration in vivo

Multidecadal variations of the effects of the Quasi-Biennial Oscillation on the climate system

Effects of the Quasi-Biennial Oscillation (QBO) on tropospheric climate are not always strong or they appear only intermittently. Studying them requires long time series of both the QBO and climate variables, which has restricted previous studies to the past 30–50 years. Here we use the benefits of an existing QBO reconstruction back to 1908. We first investigate additional, newly digitized historical observations of stratospheric winds to test the reconstruction. Then we use the QBO time series to analyse atmospheric data sets (reconstructions and reanalyses) as well as the results of coupled ocean–atmosphere-chemistry climate model simulations that were forced with the reconstructed QBO. We investigate effects related to (1) tropical-extratropical interaction in the stratosphere, wave-mean flow interaction and subsequent downward propagation, and (2) interaction between deep tropical convection and stratospheric flow. We generally find weak connections, though some are statistically significant over the 100-year period and consistent with model results. Apparent multidecadal variations in the connection between the QBO and the investigated climate responses are consistent with a small effect in the presence of large variability, with one exception: the imprint on the northern polar vortex, which is seen in recent reanalysis data, is not found in the period 1908-1957. Conversely, an imprint in Berlin surface air temperature is only found in 1908-1957 but not in the recent period. Likewise, in the model simulations both links tend to appear alternatingly, suggesting a more systematic modulation due to a shift in the circulation, for example. Over the Pacific warm pool, we find increased convection during easterly QBO, mainly in boreal winter in observation-based data as well as in the model simulations, with large variability. No QBO effects were found in the Indian monsoon strength or Atlantic hurricane frequency

Non-target species mortality and the measurement of brodifacoum rodenticide residues after a rat (Rattus rattus) eradication on Palmyra Atoll, tropical

a b s t r a c t The use of rodenticides to control or eradicate invasive rats (Rattus spp.) for conservation purposes has rapidly grown in the past decades, especially on islands. The non-target consequences and the fate of toxicant residue from such rodent eradication operations have not been well explored. In a cooperative effort, we monitored the application of a rodenticide, 'Brodifacoum 25W: Conservation', during an attempt to eradicate Rattus rattus from Palmyra Atoll. In 2011, Brodifacoum 25W: Conservation was aerially broadcasted twice over the entire atoll (2.5 km 2 ) at rates of 80 kg/ha and 75 kg/ha and a supplemental hand broadcast application (71.6 kg/ha) occurred three weeks after the second aerial application over a 10 ha area. We documented brodifacoum residues in soil, water, and biota, and documented mortality of non-target organisms. Some bait (14-19% of the target application rate) entered the marine environment to distances 7 m from the shore. After the application commenced, carcasses of 84 animals representing 15 species of birds, fish, reptiles and invertebrates were collected opportunistically as potential non-target mortalities. In addition, fish, reptiles, and invertebrates were systematically collected for residue analysis. Brodifacoum residues were detected in most (84.3%) of the animal samples analyzed. Although detection of residues in samples was anticipated, the extent and concentrations in many parts of the food web were greater than expected. Risk assessments should carefully consider application rates and entire food webs prior to operations using rodenticides. Published by Elsevier Ltd

The evolution of ecological specialization across the range of a broadly distributed marine species

Ecological specialization is an important engine of evolutionary change and adaptive radiation, but empirical evidence of local adaptation in marine environments is rare, a pattern that has been attributed to the high dispersal ability of marine taxa and limited geographic barriers to gene flow. The broad-nosed pipefish, Syngnathus typhle, is one of the most broadly distributed syngnathid species and shows pronounced variation in cranial morphology across its range, a factor that may contribute to its success in colonizing new environments. We quantified variation in cranial morphology across the species range using geometric morphometrics, and tested for evidence of trophic specialization by comparing individual-level dietary composition with the community of prey available at each site. Although the diets of juvenile pipefish from each site were qualitatively similar, ontogenetic shifts in dietary composition resulted in adult populations with distinctive diets consistent with their divergent cranial morphology. Morphological differences found in nature are maintained under common garden conditions, indicating that trophic specialization in S. typhle is a heritable trait subject to selection. Our data highlight the potential for ecological specialization in response to spatially variable selection pressures in broadly distributed marine species.Swiss Academy of SciencesSwiss National Science FoundationSwiss National Science Foundation (SNSF)European CommissionUniversity of ZurichBrooklyn CollegeCity University of New Yorkinfo:eu-repo/semantics/acceptedVersio

Dissociation of VE-PTP from VE-cadherin is required for leukocyte extravasation and for VEGF-induced vascular permeability in vivo

Artificially stabilizing contacts between VE-cadherin and VE-PTP reduce vascular permeability and leukocyte extravasation in vivo