Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study. Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.https://doi.org/10.1186/1471-2164-15-110

Towards the new Thematic Core Service Tsunami within the EPOS Research Infrastructure

Tsunamis constitute a significant hazard for European coastal populations, and the impact of tsunami events worldwide can extend well beyond the coastal regions directly affected. Understanding the complex mechanisms of tsunami generation, propagation, and inundation, as well as managing the tsunami risk, requires multidisciplinary research and infrastructures that cross national boundaries. Recent decades have seen both great advances in tsunami science and consolidation of the European tsunami research community. A recurring theme has been the need for a sustainable platform for coordinated tsunami community activities and a hub for tsunami services. Following about three years of preparation, in July 2021, the European tsunami community attained the status of Candidate Thematic Core Service (cTCS) within the European Plate Observing System (EPOS) Research Infrastructure. Within a transition period of three years, the Tsunami candidate TCS is anticipated to develop into a fully operational EPOS TCS. We here outline the path taken to reach this point, and the envisaged form of the future EPOS TCS Tsunami. Our cTCS is planned to be organised within four thematic pillars: (1) Support to Tsunami Service Providers, (2) Tsunami Data, (3) Numerical Models, and (4) Hazard and Risk Products. We outline how identified needs in tsunami science and tsunami risk mitigation will be addressed within this structure and how participation within EPOS will become an integration point for community development

Towards the new Thematic Core Service Tsunami within the EPOS Research Infrastructure

Tsunamis constitute a significant hazard for European coastal populations, and the impact of tsunami events worldwide can extend well beyond the coastal regions directly affected. Understanding the complex mechanisms of tsunami generation, propagation, and inundation, as well as managing the tsunami risk, requires multidisciplinary research and infrastructures that cross national boundaries. Recent decades have seen both great advances in tsunami science and consolidation of the European tsunami research community. A recurring theme has been the need for a sustainable platform for coordinated tsunami community activities and a hub for tsunami services. Following about three years of preparation, in July 2021, the European tsunami community attained the status of Candidate Thematic Core Service (cTCS) within the European Plate Observing System (EPOS) Research Infrastructure. Within a transition period of three years, the Tsunami candidate TCS is anticipated to develop into a fully operational EPOS TCS. We here outline the path taken to reach this point, and the envisaged form of the future EPOS TCS Tsunami. Our cTCS is planned to be organised within four thematic pillars: (1) Support to Tsunami Service Providers, (2) Tsunami Data, (3) Numerical Models, and (4) Hazard and Risk Products. We outline how identified needs in tsunami science and tsunami risk mitigation will be addressed within this structure and how participation within EPOS will become an integration point for community development.publishedVersio

Towards the new Thematic Core Service Tsunami within the EPOS Research Infrastructure

publishedVersio

The classification of glomerulonephritis in systemic lupus erythematosus revisited

The classification of glomerulonephritis in systemic lupus erythematosus revisited.The currently used classification reflects our understanding of the pathogenesis of the various forms of lupus nephritis, but clinicopathologic studies have revealed the need for improved categorization and terminology. Based on the 1982 classification published under the auspices of the World Health Organization (WHO) and subsequent clinicopathologic data, we propose that class I and II be used for purely mesangial involvement (I, mesangial immune deposits without mesangial hypercellularity; II, mesangial immune deposits with mesangial hypercellularity); class III for focal glomerulonephritis (involvin

Mechanisms of progression of chronic kidney disease

Chronic kidney disease (CKD) occurs in all age groups, including children. Regardless of the underlying cause, CKD is characterized by progressive scarring that ultimately affects all structures of the kidney. The relentless progression of CKD is postulated to result from a self-perpetuating vicious cycle of fibrosis activated after initial injury. We will review possible mechanisms of progressive renal damage, including systemic and glomerular hypertension, various cytokines and growth factors, with special emphasis on the renin–angiotensin–aldosterone system (RAAS), podocyte loss, dyslipidemia and proteinuria. We will also discuss possible specific mechanisms of tubulointerstitial fibrosis that are not dependent on glomerulosclerosis, and possible underlying predispositions for CKD, such as genetic factors and low nephron number

Sulfur metabolism in hemiascomycetes yeast

Sulfur metabolism is a central function of the cell. It has been extensively studied in the model yeast Saccharomyces cerevisiae. A comparative genomic study carried out across the hemiascomycetes clade has shown that S. cerevisiae displayed specificities not shared by the other yeast species. For instance, an O-acetylserine pathway was shown to be present in many yeast species. The complex regulatory pathways seem also to be conserved, with the exception of MET28, whose presence seems to be restricted to S. cerevisiae and related species. In order to explore this pathway in two distant yeast species, Kluyveromyces lactis and Yarrowia lipolytica, transcriptomic and metabolomic studies have been carried out in different conditions of sulfur supply. These high-throughput techniques allowed confirmation of the data of the comparative genomics but also the investigation of new components and new functions linked to sulfur metabolism, for instance, the role of the O-acetylserine pathway in cysteine biogenesis and the role of the aminotransferases in the degradation of methionine were confirmed. The screening of the pools of metabolic intermediates affected by the sulfur supply allowed the identification of new components of the pathway in Y. lipolytica such as taurine and hypotaurine, which seemed to play a role of sulfur storage. These methods also allowed the identification of the set of transporters involved in sulfur metabolism. Eventually, the comparison of these results with the data accumulated in the model S. cerevisiae highlighted the large-scale conservation of this pathway but also the large diversity in the regulated steps inside the pathway

Stronger together: midwifery twinning between Tanzania and Canada

Abstract This article describes a twinning relationship between the Canadian Association of Midwives (CAM) and the Tanzania Midwives Association (TAMA). It argues that the twinning relationship strengthened both associations. The article briefly reviews the existing literature on professional associations and association strengthening to demonstrate that professional associations are a vital tool for improving the performance of healthcare workers and increasing their capacity to contribute to national and international policy-making. It then suggests that midwifery associations are particularly significant given the frequent professional marginalization of midwives. The article then describes in depth the relationship between CAM and TAMA, highlighting the accomplishments of the twinned partners, and analyzing the factors that contributed to the success of the relationship. The findings demonstrate that twinning can successfully strengthen associations, increasing their ability to support their membership, care for the public, and shape national policy-making. The article therefore proposes twinning as a successful and cost-effective model for encouraging the growth of the midwifery profession

Structural and Functional Analysis of Calcium Ion Mediated Binding of 5-Lipoxygenase to Nanodiscs.

An important step in the production of inflammatory mediators of the leukotriene family is the Ca2+ mediated recruitment of 5 Lipoxygenase (5LO) to nuclear membranes. To study this reaction in vitro, the natural membrane mimicking environment of nanodiscs was used. Nanodiscs with 10.5 nm inner diameter were made with the lipid POPC and membrane scaffolding protein MSP1E3D1. Monomeric and dimeric 5LO were investigated. Monomeric 5LO mixed with Ca2+ and nanodiscs are shown to form stable complexes that 1) produce the expected leukotriene products from arachidonic acid and 2) can be, for the first time, visualised by native gel electrophoresis and negative stain transmission electron microscopy and 3) show a highest ratio of two 5LO per nanodisc. We interpret this as one 5LO on each side of the disc. The dimer of 5LO is visualised by negative stain transmission electron microscopy and is shown to not bind to nanodiscs. This study shows the advantages of nanodiscs to obtain basic structural information as well as functional information of a complex between a monotopic membrane protein and the membrane

Effects of Pregnancy on Plasma Sphingolipids Using a Metabolomic and Quantitative Analysis Approach

Changes in the maternal metabolome, and specifically the maternal lipidome, that occur during pregnancy are relatively unknown. The objective of this investigation was to evaluate the effects of pregnancy on sphingolipid levels using metabolomics analysis followed by confirmational, targeted quantitative analysis. We focused on three subclasses of sphingolipids: ceramides, sphingomyelins, and sphingosines. Forty-seven pregnant women aged 18 to 50 years old participated in this study. Blood samples were collected on two study days for metabolomics analysis. The pregnancy samples were collected between 25 and 28 weeks of gestation and the postpartum study day samples were collected ≥3 months postpartum. Each participant served as their own control. These samples were analyzed using a Ultra-performance liquid chromatography/mass spectroscopy/mass spectroscopy (UPLC/MS/MS) assay that yielded semi-quantitative peak area values that were used to compare sphingolipid levels between pregnancy and postpartum. Following this lipidomic analysis, quantitative LC/MS/MS targeted/confirmatory analysis was performed on the same study samples. In the metabolomic analysis, 43 sphingolipid metabolites were identified and their levels were assessed using relative peak area values. These profiled sphingolipids fell into three categories: ceramides, sphingomyelins, and sphingosines. Of the 43 analytes measured, 35 were significantly different during pregnancy (p < 0.05) (including seven ceramides, 26 sphingomyelins, and two sphingosines) and 32 were significantly higher during pregnancy compared to postpartum. Following metabolomics, a separate quantitative analysis was performed and yielded quantified concentration values for 23 different sphingolipids, four of which were also detected in the metabolomics study. Quantitative analysis supported the metabolomics results with 17 of the 23 analytes measured found to be significantly different during pregnancy including 11 ceramides, four sphingomyelins, and two sphingosines. Fourteen of these were significantly higher during pregnancy. Our data suggest an overall increase in plasma sphingolipid concentrations with possible implications in endothelial function, gestational diabetes mellitus (GDM), intrahepatic cholestasis of pregnancy, and fetal development. This study provides evidence for alterations in maternal sphingolipid metabolism during pregnancy