Architecture and assembly of the Gram-positive cell wall

The bacterial cell wall is a mesh polymer of peptidoglycan – linear glycan strands cross-linked by flexible peptides – that determines cell shape and provides physical protection. While the glycan strands in thin ‘Gram-negative’ peptidoglycan are known to run circumferentially around the cell, the architecture of the thicker ‘Gram-positive’ form remains unclear. Using electron cryotomography, here we show that Bacillus subtilis peptidoglycan is a uniformly dense layer with a textured surface. We further show it rips circumferentially, curls and thickens at free edges, and extends longitudinally when denatured. Molecular dynamics simulations show that only atomic models based on the circumferential topology recapitulate the observed curling and thickening, in support of an ‘inside-to-outside’ assembly process. We conclude that instead of being perpendicular to the cell surface or wrapped in coiled cables (two alternative models), the glycan strands in Gram-positive cell walls run circumferentially around the cell just as they do in Gram-negative cells. Together with providing insights into the architecture of the ultimate determinant of cell shape, this study is important because Gram-positive peptidoglycan is an antibiotic target crucial to the viability of several important rod-shaped pathogens including Bacillus anthracis, Listeria monocytogenes, and Clostridium difficile

<i>Escherichia coli</i> Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations

Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes.</p

Convergence to equilibrium for a second-order time semi-discretization ofthe Cahn-Hilliard equation

International audienceWe consider a second-order two-step time semi-discretization of the Cahn-Hilliard equation with an analytic nonlinearity. The time-step is chosen small enough so that the pseudo-energy associated with the discretization is nonin-creasing at every time iteration. We prove that the sequence generated by the scheme converges to a steady state as time tends to infinity. We also obtain convergence rates in the energy norm. The proof is based on the Lojasiewicz-Simon inequality

Diversity and P-solubilizing ability of mycorrhizosphere bacteria associated with Pinus pinaster in the Landes forest ecosystem

Ectomycorrhizal fungi (ECM) and their associated mycorrhizosphere bacteria (MB) play a major role in phosphorous (P) nutrition of maritime pine, particularly in the Landes forest ecosystem considering the low bioavailability of P in its sandy-acidic soils. In order to characterize the MB associated to ECM, three collection campaigns of ECM root tips were performed from autumn 2005 to autumn 2006 throughout three forest stations. Five MB and nine ECM genera were identified overall through sequencing of 16S rDNA and mitochondrial large subunit rDNA fragment respectively. Dramatic seasonal changes were observed in the different MB-ECM associations especially in Burkholderia-Lactarius and Bacillus-Russula that were the most abundant ones. P-solubilizing ability of MB was shown to be taxon-dependent with a large majority of P-solubilizing isolates among Burkholderia, Pseudomonas and Paenibacillus contrary to Bacillus. Relationships between functional diversity of the MB-ECM associations and bioavailability of soil P remain to be investigated. (Résumé d'auteur)

Diel Variations in Survey Catch Rates and Survey Catchability of Spiny Dogfish and their Pelagic Prey in the Northeast US Continental Shelf Large Marine Ecosystem

This study examines the potential uncertainty in survey biomass estimates of Spiny Dogfish Squalus acanthias in the Northeast U.S. Continental Shelf Large Marine Ecosystem (NES LME). Diel catch-per-unit-effort (CPUE) estimates are examined from the Northeast Fisheries Science Center bottom trawl surveys conducted during autumn (1963-2009) and spring (1968-2009). Influential environmental variables on survey catchability are identified for Spiny Dogfish life history stages and five pelagic prey species: Butterfish Peprilus triacanthus, Atlantic Herring Clupea harengus, shortfin squid Illex spp., longfin squid Doryteuthis spp., and Atlantic Mackerel Scomber scombrus. Daytime survey catchability was significantly higher than nighttime catchability for most species during autumn and for mature male Spiny Dogfish, shortfin squid, and longfin squid during spring in the NES LME. For most stages and species examined, breakpoint analyses identified significant increases in CPUE in the morning, peak CPUE during the day, and significant declines in CPUE in the late afternoon. Seasonal probabilities of daytime catch were largely driven by solar zenith angle for most species, with stronger trends identified during autumn. Unadjusted CPUE estimates appear to overestimate absolute abundance, with adjustments resulting in reductions in absolute abundance ranging from 41% for Spiny Dogfish to 91% for shortfin and longfin squids. These findings have important implications for Spiny Dogfish regarding estimates of population consumption of key pelagic prey species and their ecological footprint within the NES LME

Mammal responses to global changes in human activity vary by trophic group and landscape

Wildlife must adapt to human presence to survive in the Anthropocene, so it is critical to understand species responses to humans in different contexts. We used camera trapping as a lens to view mammal responses to changes in human activity during the COVID-19 pandemic. Across 163 species sampled in 102 projects around the world, changes in the amount and timing of animal activity varied widely. Under higher human activity, mammals were less active in undeveloped areas but unexpectedly more active in developed areas while exhibiting greater nocturnality. Carnivores were most sensitive, showing the strongest decreases in activity and greatest increases in nocturnality. Wildlife managers must consider how habituation and uneven sensitivity across species may cause fundamental differences in human–wildlife interactions along gradients of human influence.Peer reviewe

A many-analysts approach to the relation between religiosity and well-being

The relation between religiosity and well-being is one of the most researched topics in the psychology of religion, yet the directionality and robustness of the effect remains debated. Here, we adopted a many-analysts approach to assess the robustness of this relation based on a new cross-cultural dataset (N=10,535 participants from 24 countries). We recruited 120 analysis teams to investigate (1) whether religious people self-report higher well-being, and (2) whether the relation between religiosity and self-reported well-being depends on perceived cultural norms of religion (i.e., whether it is considered normal and desirable to be religious in a given country). In a two-stage procedure, the teams first created an analysis plan and then executed their planned analysis on the data. For the first research question, all but 3 teams reported positive effect sizes with credible/confidence intervals excluding zero (median reported β=0.120). For the second research question, this was the case for 65% of the teams (median reported β=0.039). While most teams applied (multilevel) linear regression models, there was considerable variability in the choice of items used to construct the independent variables, the dependent variable, and the included covariates

A Many-analysts Approach to the Relation Between Religiosity and Well-being

The relation between religiosity and well-being is one of the most researched topics in the psychology of religion, yet the directionality and robustness of the effect remains debated. Here, we adopted a many-analysts approach to assess the robustness of this relation based on a new cross-cultural dataset (N = 10, 535 participants from 24 countries). We recruited 120 analysis teams to investigate (1) whether religious people self-report higher well-being, and (2) whether the relation between religiosity and self-reported well-being depends on perceived cultural norms of religion (i.e., whether it is considered normal and desirable to be religious in a given country). In a two-stage procedure, the teams first created an analysis plan and then executed their planned analysis on the data. For the first research question, all but 3 teams reported positive effect sizes with credible/confidence intervals excluding zero (median reported β = 0.120). For the second research question, this was the case for 65% of the teams (median reported β = 0.039). While most teams applied (multilevel) linear regression models, there was considerable variability in the choice of items used to construct the independent variables, the dependent variable, and the included covariates

Permeability and pressure measurements in Lesser Antilles submarine slides: Evidence for pressure-driven slow-slip failure

Recent studies hypothesize that some submarine slides fail via pressure-driven slow-slip deformation. To test this hypothesis, this study derives pore pressures in failed and adjacent unfailed deep marine sediments by integrating rock physics models, physical property measurements on recovered sediment core, and wireline logs. Two drill sites (U1394 and U1399) drilled through interpreted slide debris; a third (U1395) drilled into normal marine sediment. Near-hydrostatic fluid pressure exists in sediments at site U1395. In contrast, results at both sites U1394 and U1399 indicate elevated pore fluid pressures in some sediment. We suggest that high pore pressure at the base of a submarine slide deposit at site U1394 results from slide shearing. High pore pressure exists throughout much of site U1399, and Mohr circle analysis suggests that only slight changes in the stress regime will trigger motion. Consolidation tests and permeability measurements indicate moderately low (~10⁻¹⁶–10⁻¹⁷ m²) permeability and overconsolidation in fine-grained slide debris, implying that these sediments act as seals. Three mechanisms, in isolation or in combination, may produce the observed elevated pore fluid pressures at site U1399: (1) rapid sedimentation, (2) lateral fluid flow, and (3) shearing that causes sediments to contract, increasing pore pressure. Our preferred hypothesis is this third mechanism because it explains both elevated fluid pressure and sediment overconsolidation without requiring high sedimentation rates. Our combined analysis of subsurface pore pressures, drilling data, and regional seismic images indicates that slope failure offshore Martinique is perhaps an ongoing, creep-like process where small stress changes trigger motion