Effects of propidium monoazide (PMA) treatment on mycobiome and bacteriome analysis of cystic fibrosis airways during exacerbation

Introduction and Purpose : Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome. Results and Discussion : We compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1%), but caused a significant difference in the intermediate community (less than 1%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our "omic" knowledge of the CF airways

Rare mutations in SQSTM1 modify susceptibility to frontotemporal lobar degeneration

Mutations in the gene coding for Sequestosome 1 (SQSTM1) have been genetically associated with amyotrophic lateral sclerosis (ALS) and Paget disease of bone. In the present study, we analyzed the SQSTM1 coding sequence for mutations in an extended cohort of 1,808 patients with frontotemporal lobar degeneration (FTLD), ascertained within the European Early-Onset Dementia consortium. As control dataset, we sequenced 1,625 European control individuals and analyzed whole-exome sequence data of 2,274 German individuals (total n = 3,899). Association of rare SQSTM1 mutations was calculated in a meta-analysis of 4,332 FTLD and 10,240 control alleles. We identified 25 coding variants in FTLD patients of which 10 have not been described. Fifteen mutations were absent in the control individuals (carrier frequency < 0.00026) whilst the others were rare in both patients and control individuals. When pooling all variants with a minor allele frequency < 0.01, an overall frequency of 3.2 % was calculated in patients. Rare variant association analysis between patients and controls showed no difference over the whole protein, but suggested that rare mutations clustering in the UBA domain of SQSTM1 may influence disease susceptibility by doubling the risk for FTLD (RR = 2.18 [95 % CI 1.24-3.85]; corrected p value = 0.042). Detailed histopathology demonstrated that mutations in SQSTM1 associate with widespread neuronal and glial phospho-TDP-43 pathology. With this study, we provide further evidence for a putative role of rare mutations in SQSTM1 in the genetic etiology of FTLD and showed that, comparable to other FTLD/ALS genes, SQSTM1 mutations are associated with TDP-43 pathology

Efeito da braquiária sobre a disponibilidade de fósforo no solo

The objective of this work was to evaluate the effectiveness of ruzigrass (Urochloa ruziziensis) in enhancing soil‑P availability in areas fertilized with soluble or reactive rock phosphates. The area had been cropped for five years under no‑till, in a system involving soybean, triticale/black‑oat, and pearl millet. Previously to the five‑year cultivation period, corrective phosphorus fertilization was applied once on soil surface, at 0.0 and 80 kg ha-1 P2O5, as triple superphosphate or Arad rock phosphate. After this five‑year period, plots received the same corrective P fertilization as before and ruzigrass was introduced to the cropping system in the stead of the other cover crops. Soil samples were taken (0–10 cm) after ruzigrass cultivation and subjected to soil‑P fractionation. Soybean was grown thereafter without P application to seed furrow. Phosphorus availability in plots with ruzigrass was compared to the ones with spontaneous vegetation for two years. Ruzigrass cultivation increased inorganic (resin‑extracted) and organic (NaHCO3) soil P, as well as P concentration in soybean leaves, regardless of the P source. However, soybean yield did not increase significantly due to ruzigrass introduction to the cropping system. Soil‑P availability did not differ between soluble and reactive P sources. Ruzigrass increases soil‑P availability, especially where corrective P fertilization is performed.O objetivo deste trabalho foi avaliar a eficácia da braquiária (Urochloa ruziziensis) em aumentar a disponibilidade de P, em solo de áreas fertilizadas com fosfatos solúveis ou reativos. A área havia sido cultivada em semeadura direta por cinco anos, em sistema de cultivo com soja, triticale/aveia‑preta e milheto. Previamente ao período de cinco anos de cultivo, aplicou-se adubação corretiva de P à superfície do solo, com 0,0 ou 80,0 kg ha-1 P2O5, nas formas de superfosfato triplo ou fosfato Arad. Após esse período de cinco anos, as parcelas receberam a mesma adubação corretiva de antes, e a braquiária foi introduzida no sistema de cultivo no lugar das outras plantas de cobertura. Após o cultivo da braquiária, foram coletadas amostras de solo, na camada 0–10 cm, e submetidas ao fracionamento de P. A soja foi cultivada em seguida, sem adubação fosfatada no sulco de plantio. A disponibilidade de P nas parcelas com a braquiária foi comparada àquelas com vegetação espontânea, por dois anos. O cultivo da braquiária aumentou os teores de P inorgânico (extraído com resina) e orgânico (NaHCO3) no solo, bem como o conteúdo de P nas folhas da soja, independentemente da fonte de P utilizada. No entanto, a produtividade da soja não aumentou significativamente pela introdução da braquiária ao sistema de cultivo. A braquiária aumenta a disponibilidade de P no solo, especialmente nas áreas com adubação fosfatada corretiva

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells as well as the interrogation of cell population heterogeneity. However, in many instances, computational tools to analyze the wealth of data generated by these technologies are lacking. Here, we present a computational framework for unbiased combinatorial polyfunctionality analysis of antigen-specific T-cell subsets (COMPASS). COMPASS uses a Bayesian hierarchical framework to model all observed cell subsets and select those most likely to have antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, and human subject-level responses are quantified by two summary statistics that describe the quality of an individual's polyfunctional response and can be correlated directly with clinical outcome. Using three clinical data sets of cytokine production, we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals cellular 'correlates of protection/immunity' in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software

Classification and determinants of passing difficulty in soccer: a multivariate approach

Introduction Usually, the players’ or teams’ efficiency to perform passes is measured in terms of accuracy. The degree of difficulty of this action has been overlooked in the literature. Objectives The present study aimed to classify the degree of passing difficulty in soccer matches and to identify and to discuss the variables that most explain the passing difficulty using spatiotemporal data. Results The data used corresponds to 2,856 passes and 32 independent variables. The Fisher Discriminant Analysis presented 72.0% of the original grouped cases classified correctly. The passes analyzed were classified as low (56.5%), medium (22.6%), and high difficulty (20.9%), and we identified 16 variables that best explain the degree of passing difficulty related to the passing receiver, ball trajectory, pitch position and passing player. Conclusions The merit and ability of the player to perform passes with high difficulty should be valued and can be used to rank the best players and teams.In addition, the highlighted variables should be looked carefully by coaches when analyzing profiles, strengths and weaknesses of players and teams, and talent identification context.acceptedVersio

Monitoring Testbed Experiments with MonEx

International audienceAlmost all testbed experiments deal with different kinds of metrics which are collected from and/or about various kinds of resources. Despite the importance of collecting experiment metrics in the experiment life cycle, this phase is often done via ad hoc, manual, and artisanal actions such as manually combining multiple scripts, or manipulating some missing values. A few tools (e.g. Vendetta, OML) can be used for monitoring experiments. However their work is restricted to communicating metrics towards a central server, and they do not cover different features from user perspective such as drawing and archiving experiments results.In this talk, we will firstly discuss the requirements of experiment monitoring. Having a well-defined set of requirements eliminates the potential ambiguity around what should be targeted by any Experiment Monitoring Framework (EMF). The defined requirements are not testbed dependent nor technology-dependent, so any testbed community can build their own EMF by implementing these requirements, using different software systems.We will then describe our own proposition, MonEx (for long: Monitoring Experiments), which is an EMF that satisfies all the defined requirements. MonEx is built over several off-the-shelf infrastructure monitoring tools, and supports various monitoring approaches such as pull- and push-based monitoring, agent-based and agent-less monitoring. MonEx covers all the required steps of monitoring experiments from collecting metrics to archiving experiments data and producing figures.We will then demonstrate MonEx’s usability through a set of experiments , performed on the Grid’5000 testbed and being monitored by MonEx. Each of those experiments have different requirements, and as a group they show how MonEx meets all defined requirements. We show how MonEx nicely integrates the experimental workflow and how it simplifies the monitoring task, reducing the efforts of users during experimentation and pushing towards the repeatability of experiments’ analysis and metrics comparison