The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection

<p>Abstract</p> <p>Background</p> <p>Oomycetes of the genus <it>Phytophthora </it>are pathogens that infect a wide range of plant species. For dicot hosts such as tomato, potato and soybean, <it>Phytophthora </it>is even the most important pathogen. Previous analyses of <it>Phytophthora </it>genomes uncovered many genes, large gene families and large genome sizes that can partially be explained by significant repeat expansion patterns.</p> <p>Results</p> <p>Analysis of the complete genomes of three different <it>Phytophthora </it>species, using a newly developed approach, unveiled a large number of small duplicated blocks, mainly consisting of two or three consecutive genes. Further analysis of these duplicated genes and comparison with the known gene and genome duplication history of ten other eukaryotes including parasites, algae, plants, fungi, vertebrates and invertebrates, suggests that the ancestor of <it>P. infestans</it>, <it>P. sojae </it>and <it>P. ramorum </it>most likely underwent a whole genome duplication (WGD). Genes that have survived in duplicate are mainly genes that are known to be preferentially retained following WGDs, but also genes important for pathogenicity and infection of the different hosts seem to have been retained in excess. As a result, the WGD might have contributed to the evolutionary and pathogenic success of <it>Phytophthora</it>.</p> <p>Conclusions</p> <p>The fact that we find many small blocks of duplicated genes indicates that the genomes of <it>Phytophthora </it>species have been heavily rearranged following the WGD. Most likely, the high repeat content in these genomes have played an important role in this rearrangement process. As a consequence, the paucity of retained larger duplicated blocks has greatly complicated previous attempts to detect remnants of a large-scale duplication event in <it>Phytophthora</it>. However, as we show here, our newly developed strategy to identify very small duplicated blocks might be a useful approach to uncover ancient polyploidy events, in particular for heavily rearranged genomes.</p

Acute and critically ill peripartum cardiomyopathy and 'bridge to' therapeutic options: a single center experience with intra-aortic balloon pump, extra corporeal membrane oxygenation and continuous-flow left ventricular assist devices

Introduction: Peripartum cardiomyopathy (PPCM) patients refractory to medical therapy and intra-aortic balloon pump (IABP) counterpulsation or in whom weaning from these therapies is impossible, are candidates for a left ventricular assist device (LVAD) as a bridge to recovery or transplant. Continuous-flow LVADs are smaller, have a better long-term durability and are associated with better outcomes. Extra corporeal membrane oxygenation (ECMO) can be used as a temporary support in patients with refractory cardiogenic shock. The aim of this study was to evaluate the efficacy and safety of mechanical support in acute and critically ill PPCM patients. Methods: This was a retrospective search of the patient database of the Ghent University hospital (2000 to 2010). Results: Six PPCM-patients were treated with mechanical support. Three patients presented in the postpartum period and three patients at the end of pregnancy. All were treated with IABP, the duration of IABP support ranged from 1 to 13 days. An ECMO was inserted in one patient who presented with cardiogenic shock, multiple organ dysfunction syndrome and a stillborn baby. Two patients showed partial recovery and could be weaned off the IABP. Four patients were implanted with a continuous-flow LVAD (HeartMate II(R), Thoratec Inc.), including the ECMO-patient. Three LVAD patients were successfully transplanted 78, 126 and 360 days after LVAD implant; one patient is still on the transplant waiting list. We observed one peripheral thrombotic complication due to IABP and five early bleeding complications in three LVAD patients. One patient died suddenly two years after transplantation. Conclusions: In PPCM with refractory heart failure IABP was safe and efficient as a bridge to recovery or as a bridge to LVAD. ECMO provided temporary support as a bridge to LVAD, while the newer continuous-flow LVADs offered a safe bridge to transplant

Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling

Genes controlling the cell cycle in two diatoms have been identified and functionally characterized, revealing environmental regulation of the cell cycle

Managing understory light conditions in boreal mixedwoods through variation in the intensity and spatial pattern of harvest: A modelling approach

In the context of partial harvesting, adequately managing post-harvest light conditions are essential to obtain a desired composition of tree species regeneration. The objective of this study was to determine how varying the intensity and spatial pattern of harvest would affect understory light conditions in boreal mixedwood stands of northwestern Quebec using the spatially explicit SORTIE-ND light model. The model was evaluated based on comparisons of observed and predicted light levels in both mapped and un-mapped plots. In mapped plots, reasonably accurate predictions of the overall variation in light levels were obtained, but predictions tended to lack spatial precision. In un-mapped plots, SORTIE-ND accurately predicted stand-level mean GLI (Gap Light Index) under a range of harvest intensities. The model was then used to simulate nine silvicultural treatments based on combinations of three intensities of overstory removal (30%, 45% and 60% of basal area) and three harvest patterns (uniform, narrow strips, large gaps). Simulations showed that increasing overstory removal had less impact on light conditions with uniform harvests, and a more marked effect with more aggregated harvest patterns. Whatever the harvest intensity, uniform cuts almost never created high light conditions (GLI > 50%). Gap cuts, on the other hand, resulted in up to 40% of microsites receiving GLI > 50%. Our results suggest that either a 30% strip or gap cut or a 45–60% uniform partial harvest could be used to accelerate the transition from an aspen dominated composition to a mixedwood stand because both types of cut generate the greatest proportion of moderately low light levels (e.g., 15–40% GLI). These light levels tend to favour an accelerated growth response among shade-tolerant conifers, while preventing excessive recruitment of shade-intolerant species. A better understanding of how spatial patterns of harvest interact with tree removal intensity to affect understory light conditions can provide opportunities for designing silvicultural prescriptions that are tailored to species’ traits and better suited to meet a variety of management objectives

Cryptocrine Signaling in the Thymus Network and T Cell Education to Neuroendocrine Self-Antigens

peer reviewedBoth during phylogeny and ontogeny the thymus appears as a nodal point between the two major systems of cell-to-cell signaling, the neuroendocrine and immune systems. This review presents the experimental observations which support a dual role in T cell selection played by the thymic repertoire of neuroendocrine polypeptide precursors. Through the mode of cryptocrine intercellular signaling thymic neuroendocrine-related precursors synthesized in thymic epithelial cells have been shown to influence the early steps in T cell differentiation. In addition, thymic neuroendocrine-related polypeptides are a source of self-antigens which are presented by the major histocompatibility system of the thymic epithelium. Preliminary data also suggest that the intrathymic T cell education to neuroendocrine self-antigens is not strictly superimposible to the antigen presentation by dedicated presenting cells. Insulin-like growth factor-II (IGF-II) was identified as one dominant member of the insulin family expressed by thymic epithelial and nurse cells. The intrathymic presentation of IGF-II or IGF-II derived self-antigens is under current investigation. If further confirmed, the central tolerogenic properties of IGF-II could be considered in the elaboration of a strategy for an efficient and safe prevention of insulin-dependent diabetes

Molecular characterization of irinotecan (SN-38) resistant human breast cancer cell lines

Background: Studies in taxane and/or anthracycline refractory metastatic breast cancer (mBC) patients have shown approximately 30% response rates to irinotecan. Hence, a significant number of patients will experience irinotecan-induced side effects without obtaining any benefit. The aim of this study was to lay the groundwork for development of predictive biomarkers for irinotecan treatment in BC. Methods: We established BC cell lines with acquired or de novo resistance to SN-38, by exposing the human BC cell lines MCF-7 and MDA-MB-231 to either stepwise increasing concentrations over 6months or an initial high dose of SN-38 (the active metabolite of irinotecan), respectively. The resistant cell lines were analyzed for cross-resistance to other anti-cancer drugs, global gene expression, growth rates, TOP1 and TOP2A gene copy numbers and protein expression, and inhibition of the breast cancer resistance protein (ABCG2/BCRP) drug efflux pump. Results: We found that the resistant cell lines showed 7-100 fold increased resistance to SN-38 but remained sensitive to docetaxel and the non-camptothecin Top1 inhibitor LMP400. The resistant cell lines were characterized by Top1 down-regulation, changed isoelectric points of Top1 and reduced growth rates. The gene and protein expression of ABCG2/BCRP was up-regulated in the resistant sub-lines and functional assays revealed BCRP as a key mediator of SN-38 resistance. Conclusions: Based on our preclinical results, we suggest analyzing the predictive value of the BCRP in breast cancer patients scheduled for irinotecan treatment. Moreover, LMP400 should be tested in a clinical setting in breast cancer patients with resistance to irinotecan

A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology