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51.
Pascal Hingamp Nigel Grimsley Silvia G Acinas Camille Clerissi Lucie Subirana Julie Poulain Isabel Ferrera Hugo Sarmento Emilie Villar Gipsi Lima-Mendez Karoline Faust Shinichi Sunagawa Jean-Michel Claverie Hervé Moreau Yves Desdevises Peer Bork Jeroen Raes Colomban de Vargas Eric Karsenti Stefanie Kandels-Lewis Olivier Jaillon Fabrice Not Stéphane Pesant Patrick Wincker Hiroyuki Ogata 《The ISME journal》2013,7(9):1678-1695
Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts. 相似文献
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Mihály K. de Bie Maurits S. Buiten André Gaasbeek Mark J. Boogers Cornelis J. Roos Joanne D. Schuijf M. Jacqueline Krol Ton J. Rabelink Jeroen J. Bax Martin J. Schalij J. Wouter Jukema 《PloS one》2013,8(7)
Purpose
Significant obstructive coronary artery disease (CAD) is common in asymptomatic dialysis patients. Identifying these high risk patients is warranted and may improve the prognosis of this vulnerable patient group. Routine catheterization of incident dialysis patients has been proposed, but is considered too invasive. CT-angiography may therefore be more appropriate. However, extensive coronary calcification, often present in this patient group, might hamper adequate lumen evaluation. The objective of this study was to assess the feasibility of CT-angiography in this patient group.Methods
For this analysis all patients currently participating in the ICD2 trial (ISRCTN20479861), with no history of PCI or CABG were included. The major epicardial vessels were evaluated on a segment basis (segment 1–3, 5–8, 11 and 13) by a team consisting of an interventional and an imaging specialist. Segments were scored as not significant, significant and not interpretable.Results
A total of 70 dialysis patients, with a mean age of 66±8 yrs and predominantly male (70%) were included. The median calcium score was 623 [79, 1619].Over 90% of the analyzed segments were considered interpretable. The incidence of significant CAD on CT was 43% and was associated with cardiovascular events during follow-up. The incidence of cardiovascular events after 2-years follow-up: 36% vs. 0% in patients with no significant CAD (p<0.01).Conclusion
Despite the high calcium scores CT-angiography is feasible for the evaluation of the extent of CAD in dialysis patients. Moreover the presence of significant CAD on CT was associated with events during follow-up. 相似文献53.
Hazrat Ali Marco I. Ries Jeroen G. Nijland Peter P. Lankhorst Thomas Hankemeier Roel A. L. Bovenberg Rob J. Vreeken Arnold J. M. Driessen 《PloS one》2013,8(6)
Profiling and structural elucidation of secondary metabolites produced by the filamentous fungus Penicillium chrysogenum and derived deletion strains were used to identify the various metabolites and enzymatic steps belonging to the roquefortine/meleagrin pathway. Major abundant metabolites of this pathway were identified as histidyltryptophanyldiketopiperazine (HTD), dehydrohistidyltryptophanyldi-ketopiperazine (DHTD), roquefortine D, roquefortine C, glandicoline A, glandicoline B and meleagrin. Specific genes could be assigned to each enzymatic reaction step. The nonribosomal peptide synthetase RoqA accepts L-histidine and L-tryptophan as substrates leading to the production of the diketopiperazine HTD. DHTD, previously suggested to be a degradation product of roquefortine C, was found to be derived from HTD involving the cytochrome P450 oxidoreductase RoqR. The dimethylallyltryptophan synthetase RoqD prenylates both HTD and DHTD yielding directly the products roquefortine D and roquefortine C without the synthesis of a previously suggested intermediate and the involvement of RoqM. This leads to a branch in the otherwise linear pathway. Roquefortine C is subsequently converted into glandicoline B with glandicoline A as intermediates, involving two monooxygenases (RoqM and RoqO) which were mixed up in an earlier attempt to elucidate the biosynthetic pathway. Eventually, meleagrin is produced from glandicoline B involving a methyltransferase (RoqN). It is concluded that roquefortine C and meleagrin are derived from a branched biosynthetic pathway. 相似文献
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Impact of land‐use change to Jatropha bioenergy plantations on biomass and soil carbon stocks: a field study in Mali
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Jeroen Degerickx Joana Almeida Pieter C.J. Moonen Leen Vervoort Bart Muys Wouter M.J. Achten 《Global Change Biology Bioenergy》2016,8(2):443-455
Small‐scale Jatropha cultivation and biodiesel production have the potential of contributing to local development, energy security, and greenhouse gas (GHG) mitigation. In recent years however, the GHG mitigation potential of biofuel crops is heavily disputed due to the occurrence of a carbon debt, caused by CO2 emissions from biomass and soil after land‐use change (LUC). Most published carbon footprint studies of Jatropha report modeled results based on a very limited database. In particular, little empirical data exist on the effects of Jatropha on biomass and soil C stocks. In this study, we used field data to quantify these C pools in three land uses in Mali, that is, Jatropha plantations, annual cropland, and fallow land, to estimate both the Jatropha C debt and its C sequestration potential. Four‐year‐old Jatropha plantations hold on average 2.3 Mg C ha?1 in their above‐ and belowground woody biomass, which is considerably lower compared to results from other regions. This can be explained by the adverse growing conditions and poor local management. No significant soil organic carbon (SOC) sequestration could be demonstrated after 4 years of cultivation. While the conversion of cropland to Jatropha does not entail significant C losses, the replacement of fallow land results in an average C debt of 34.7 Mg C ha?1, mainly caused by biomass removal (73%). Retaining native savannah woodland trees on the field during LUC and improved crop management focusing on SOC conservation can play an important role in reducing Jatropha's C debt. Although planting Jatropha on degraded, carbon‐poor cropland results in a limited C debt, the low biomass production, and seed yield attained on these lands reduce Jatropha's potential to sequester C and replace fossil fuels. Therefore, future research should mainly focus on increasing Jatropha's crop productivity in these degraded lands. 相似文献
56.
Land-use change and global warming are important factors driving bee decline, but it is largely unknown whether these drivers have resulted in changes in the life-history traits of bees. Recent studies have shown a stronger population decline of large- than small-bodied bee species, suggesting there may have been selective pressure on large, but not on small species to become smaller. Here we test this hypothesis by analyzing trends in bee body size of 18 Dutch species over a 147-year period using specimens from entomological collections. Large-bodied female bees shrank significantly faster than small-bodied female bees (6.5% and 0.5% respectively between 1900 and 2010). Changes in temperature during the flight period of bees did not influence the size-dependent shrinkage of female bees. Male bees did not shrink significantly over the same time period. Our results could imply that under conditions of declining habitat quantity and quality it is advantageous for individuals to be smaller. The size and sex-dependent responses of bees point towards an evolutionary response but genetic studies are required to confirm this. The declining body size of the large bee species that currently dominate flower visitation of both wild plants and insect-pollinated crops may have negative consequences for pollination service delivery. 相似文献
57.
Marijke Dekker Andreas Pasch Frank van der Sande Constantijn Konings Matthias Bachtler Mauro Dionisi Matthias Meier Jeroen Kooman Bernard Canaud 《PloS one》2016,11(4)
BackgroundCalciprotein particles (CPPs) may play an important role in the calcification process. The calcification propensity of serum (T50) is highly predictive of all-cause mortality in chronic kidney disease patients. Whether T50 is therapeutically improvable, by high-flux hemodialysis (HD) or hemodiafiltration (HDF), has not been studied yet.MethodsWe designed a cross-sectional single center study, and included stable prevalent in-center dialysis patients on HD or HDF. Patients were divided into two groups based on dialysis modality, were on a thrice-weekly schedule, had a dialysis vintage of > 3 months and vascular access providing a blood flow rate > 300 ml/min. Calcification propensity of serum was measured by the time of transformation from primary to secondary CPP (T50 test), by time-resolved nephelometry.ResultsWe included 64 patients, mean convective volume was 21.7L (SD 3.3L). In the pooled analysis, T50 levels increased in both the HD and HDF group with pre- and post-dialysis (mean (SD)) of 244(64) - 301(57) and 253(55) - 304(61) min respectively (P = 0.43(HD vs. HDF)). The mean increase in T50 was 26.29% for HD and 21.97% for HDF patients (P = 0.61 (HD vs. HDF)). The delta values (Δ) of calcium, phosphate and serum albumin were equal in both groups. Baseline T50 was negatively correlated with phosphate, and positively correlated with serum magnesium and fetuin-A. The ΔT50 was mostly influenced by Δ phosphate (r = -0.342; P = 0.002 HD and r = -0.396; P<0.001 HDF) in both groups.ConclusionsHD and HDF patients present with same baseline T50 calcification propensity values pre-dialysis. Calcification propensity is significantly improved during both HD and HDF sessions without significant differences between both modalities. 相似文献
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Jeroen Atsma Femke Maij Mathieu Koppen David E. Irwin W. Pieter Medendorp 《PLoS computational biology》2016,12(3)
Our ability to interact with the environment hinges on creating a stable visual world despite the continuous changes in retinal input. To achieve visual stability, the brain must distinguish the retinal image shifts caused by eye movements and shifts due to movements of the visual scene. This process appears not to be flawless: during saccades, we often fail to detect whether visual objects remain stable or move, which is called saccadic suppression of displacement (SSD). How does the brain evaluate the memorized information of the presaccadic scene and the actual visual feedback of the postsaccadic visual scene in the computations for visual stability? Using a SSD task, we test how participants localize the presaccadic position of the fixation target, the saccade target or a peripheral non-foveated target that was displaced parallel or orthogonal during a horizontal saccade, and subsequently viewed for three different durations. Results showed different localization errors of the three targets, depending on the viewing time of the postsaccadic stimulus and its spatial separation from the presaccadic location. We modeled the data through a Bayesian causal inference mechanism, in which at the trial level an optimal mixing of two possible strategies, integration vs. separation of the presaccadic memory and the postsaccadic sensory signals, is applied. Fits of this model generally outperformed other plausible decision strategies for producing SSD. Our findings suggest that humans exploit a Bayesian inference process with two causal structures to mediate visual stability. 相似文献