Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of ...bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.
To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, ...which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
Measuring social networks in primates Gelardi, Valeria; Godard, Jeanne; Paleressompoulle, Dany ...
Proceedings - Royal Society. Mathematical, physical and engineering sciences,
04/2020, Volume:
476, Issue:
2236
Journal Article
Peer reviewed
Open access
Network analysis represents a valuable and flexible framework to understand the structure of individual interactions at the population level in animal societies. The versatility of network ...representations is moreover suited to different types of datasets describing these interactions. However, depending on the data collection method, different pictures of the social bonds between individuals could a priori emerge. Understanding how the data collection method influences the description of the social structure of a group is thus essential to assess the reliability of social studies based on different types of data. This is however rarely feasible, especially for animal groups, where data collection is often challenging. Here, we address this issue by comparing datasets of interactions between primates collected through two different methods: behavioural observations and wearable proximity sensors. We show that, although many directly observed interactions are not detected by the sensors, the global pictures obtained when aggregating the data to build interaction networks turn out to be remarkably similar. Moreover, sensor data yield a reliable social network over short time scales and can be used for long-term studies, showing their important potential for detailed studies of the evolution of animal social groups.
Tigers are critically endangered due to deforestation and persecution. Yet in places, Sumatran tigers (Panthera tigris sumatrae) continue to coexist with people, offering insights for managing ...wildlife elsewhere. Here, we couple spatial models of encounter risk with information on tolerance from 2386 Sumatrans to reveal drivers of human-tiger conflict. Risk of encountering tigers was greater around populated villages that neighboured forest or rivers connecting tiger habitat; geographic profiles refined these predictions to three core areas. People's tolerance for tigers was related to underlying attitudes, emotions, norms and spiritual beliefs. Combining this information into socio-ecological models yielded predictions of tolerance that were 32 times better than models based on social predictors alone. Pre-emptive intervention based on these socio-ecological predictions could have averted up to 51% of attacks on livestock and people, saving 15 tigers. Our work provides further evidence of the benefits of interdisciplinary research on conservation conflicts.
Context. Extracting the multiphase structure of the neutral interstellar medium is key to understanding star formation in galaxies. The radiative condensation of the diffuse warm neutral medium ...producing a thermally unstable lukewarm medium and a dense cold medium is closely related to the initial step leading the atomic-to-molecular (HI-to-H2) transition and the formation of molecular clouds. Up to now, the mapping of these phases out of 21 cm emission hyper-spectral cubes has remained elusive mostly due to the velocity blending of individual cold structures present on a given line of sight. As a result, most of the current knowledge about the HI phases rests on a small number of absorption measurements on lines of sight crossing radio sources. Aims. The goal of this work is to develop a new algorithm to perform separation of diffuse sources in hyper-spectral data. Specifically the algorithm was designed in order to address the velocity blending problem by taking advantage of the spatial coherence of the individual sources. The main scientific driver of this effort was to extract the multiphase structure of the HI from 21 cm line emission only, providing a means to map each phase separately, but the algorithm developed here should be generic enough to extract diffuse structures in any hyper-spectral cube. Methods. We developed a new Gaussian decomposition algorithm named ROHSA based on a multi-resolution process from coarse to fine grid. ROHSA uses a regularized nonlinear least-square criterion to take into account the spatial coherence of the emission and the multiphase nature of the gas simultaneously. In order to obtain a solution with spatially smooth parameters, the optimization is performed on the whole data cube at once. The performances of ROHSA were tested on a synthetic observation computed from numerical simulations of thermally bi-stable turbulence. We apply ROHSA to a 21 cm observation of a region of high Galactic latitude from the GHIGLS survey and present our findings. Results. The evaluation of ROHSA on synthetic 21 cm observations shows that it is able to recover the multiphase nature of the HI. For each phase, the power spectra of the column density and centroid velocity are well recovered. More generally, this test reveals that a Gaussian decomposition of HI emission is able to recover physically meaningful information about the underlying three-dimensional fields (density, velocity, and temperature). The application on a real 21 cm observation of a field of high Galactic latitude produces a picture of the multiphase HI, with isolated, filamentary, and narrow (σ ~ 1−2 km s−1) structures, and broader (σ ~ 4−10 km s−1), diffuse, and space-filling components. The test-case field used here contains significant intermediate-velocity clouds that were well mapped out by the algorithm. As ROHSA is designed to extract spatially coherent components, it performs well at projecting out the noise. Conclusions. In this paper we introduce ROHSA, a new algorithm that performs a separation of diffuse sources in hyper-spectral data on the basis of a Gaussian decomposition. The algorithm makes no assumption about the nature of the sources, except that each one has a similar line width. The tests we made shows that ROHSA is well suited to decomposing complex 21 cm line emission of regions of high Galactic latitude, but its design is general enough that it could be applied to any hyper-spectral data type for which a Gaussian model is relevant.
The safety of the European Society of Cardiology (ESC) 0/1-h algorithm for rapid rule-out and rule-in of non–ST-segment elevation myocardial infarction (NSTEMI) using high-sensitivity cardiac ...troponin (hs-cTn) has been questioned.
This study aimed to validate the diagnostic performance of the 0/1-h algorithm in a large multicenter study.
The authors prospectively enrolled unselected patients in 6 countries presenting to the emergency department with symptoms suggestive of NSTEMI. Final diagnosis was centrally adjudicated by 2 independent cardiologists. Hs-cTnT and hs-cTnI blood concentrations were measured at presentation and after 1 h. Safety of rule-out was quantified by the negative predictive value (NPV) for NSTEMI, accuracy of rule-in by the positive predictive value (PPV), and overall efficacy by the proportion of patients triaged towards rule-out or rule-in within 1 h.
Prevalence of NSTEMI was 17%. Among 4,368 patients with serial hs-cTnT measurements available, safety of rule-out (NPV 99.8%, 2,488 of 2,493), accuracy of rule-in (PPV 74.5%, 572 of 768), and overall efficacy were high by assigning three-fourths of patients either to rule-out (57%, 2,493 to 4,368) or rule-in (18%, 768 to 4,368). Similarly, among 3,500 patients with serial hs-cTnI measurements, safety of rule-out (NPV 99.7%, 1,528 of 1,533), accuracy of rule-in (PPV 62.3%, 498 of 800), and overall efficacy were high by assigning more than two-thirds of patients either to rule-out (44%, 1,533 of 3,500) or rule-in (23%, 800 of 3,500). Excellent safety was confirmed in multiple subgroup analyses including patients presenting early (≤3 h) after chest pain onset.
The ESC 0/1-h algorithm using hs-cTnT and hs-cTnI is very safe and effective in triaging patients with suspected NSTEMI. (Advantageous Predictors of Acute Coronary Syndromes Evaluation APACE; NCT00470587; and Biomarkers in Acute Cardiac Care BACC; NCT02355457)
Display omitted
RNA-protein interactions (RPIs) are promising targets for developing new molecules of therapeutic interest. Nevertheless, challenges arise from the lack of methods and feedback between computational ...and experimental techniques during the drug discovery process. Here, we tackle these challenges by developing a drug screening approach that integrates chemical, structural and cellular data from both advanced computational techniques and a method to score RPIs in cells for the development of small RPI inhibitors; and we demonstrate its robustness by targeting Y-box binding protein 1 (YB-1), a messenger RNA-binding protein involved in cancer progression and resistance to chemotherapy. This approach led to the identification of 22 hits validated by molecular dynamics (MD) simulations and nuclear magnetic resonance (NMR) spectroscopy of which 11 were found to significantly interfere with the binding of messenger RNA (mRNA) to YB-1 in cells. One of our leads is an FDA-approved poly(ADP-ribose) polymerase 1 (PARP-1) inhibitor. This work shows the potential of our integrative approach and paves the way for the rational development of RPI inhibitors.
PDF
