Quantitative studies of the evolution and cosmological consequences of networks of cosmic strings (or other topological defects) require a combination of numerical simulations and analytic modeling ...with the velocity-dependent one-scale (VOS) model. In previous work, we demonstrated that a GPU-accelerated code for local Abelian-Higgs string networks enables a statistical separation of key dynamical processes affecting the evolution of the string networks and thus a precise calibration of the VOS model. Here we further exploit this code in a detailed study of two important aspects connecting the simulations with the VOS model. First, we study the sensitivity of the model calibration to the presence (or absence) of thermal oscillations due to high gradients in the initial conditions. This is relevant since in some Abelian-Higgs simulations described in the literature a period of artificial (unphysical) dissipation-usually known as cooling-is introduced with the goal of suppressing these oscillations and accelerating the convergence to scaling. We show that a small amount of cooling has no statistically significant impact on the VOS model calibration, while a longer dissipation period does have a noticeable effect. Second, in doing this analysis we also introduce an improved Markov Chain Monte Carlo based pipeline for calibrating the VOS model, Comparison to our previous bootstrap based pipeline shows that the latter accurately determined the best-fit values of the VOS model parameter, but underestimated the uncertainties in some of the parameters. Overall, our analysis shows that the calibration pipeline is robust and can be applied to future much larger field theory simulations.
Meiotic progression requires exquisitely coordinated translation of maternal messenger (m)RNA that has accumulated during oocyte growth. A major regulator of this program is the cytoplasmic ...polyadenylation element binding protein 1 (CPEB1). However, the temporal pattern of translation at different meiotic stages indicates the function of additional RNA binding proteins (RBPs). Here, we report that deleted in azoospermia-like (DAZL) cooperates with CPEB1 to regulate maternal mRNA translation. Using a strategy that monitors ribosome loading onto endogenous mRNAs and a prototypic translation target, we show that ribosome loading is induced in a DAZL- and CPEB1-dependent manner, as the oocyte reenters meiosis. Depletion of the two RBPs from oocytes and mutagenesis of the 3' untranslated regions (UTRs) demonstrate that both RBPs interact with the Tex19.1 3' UTR and cooperate in translation activation of this mRNA. We observed a synergism between DAZL and cytoplasmic polyadenylation elements (CPEs) in the translation pattern of maternal mRNAs when using a genome-wide analysis. Mechanistically, the number of DAZL proteins loaded onto the mRNA and the characteristics of the CPE might define the degree of cooperation between the two RBPs in activating translation and meiotic progression.
The composition and activity of the microbiota in the human gastrointestinal tract are primarily shaped by nutrients derived from either food or the host. Bacteria colonizing the mucus layer have ...evolved to use mucin as a carbon and energy source. One of the members of the mucosa-associated microbiota is
, which is capable of producing an extensive repertoire of mucin-degrading enzymes. To further study the substrate utilization abilities of
, we constructed a genome-scale metabolic model to test amino acid auxotrophy, vitamin biosynthesis, and sugar-degrading capacities. The model-supported predictions were validated by
experiments, which showed
to be able to utilize the mucin-derived monosaccharides fucose, galactose, and
-acetylglucosamine. Growth was also observed on
-acetylgalactosamine, even though the metabolic model did not predict this. The uptake of these sugars, as well as the nonmucin sugar glucose, was enhanced in the presence of mucin, indicating that additional mucin-derived components are needed for optimal growth. An analysis of whole-transcriptome sequencing (RNA-Seq) comparing the gene expression of
grown on mucin with that of the same bacterium grown on glucose confirmed the activity of the genes involved in mucin degradation and revealed most of these to be upregulated in the presence of mucin. The transcriptional response was confirmed by a proteome analysis, altogether revealing a hierarchy in the use of sugars and reflecting the adaptation of
to the mucosal environment. In conclusion, these findings provide molecular insights into the lifestyle of
and further confirm its role as a mucin specialist in the gut.
is among the most abundant mucosal bacteria in humans and in a wide range of other animals. Recently,
has attracted considerable attention because of its capacity to protect against diet-induced obesity in mouse models. However, the physiology of
has not been studied in detail. Hence, we constructed a genome-scale model and describe its validation by transcriptomic and proteomic approaches on bacterial cells grown on mucus and glucose, a nonmucus sugar. The results provide detailed molecular insight into the mucus-degrading lifestyle of
and further confirm the role of this mucin specialist in producing propionate and acetate under conditions of the intestinal tract.
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•Application of fourteen biological indicators at 76 sites across Europe.•Land use intensification lowered density networks and reduced in the average number of neighbours.•Basal ...respiration, molecular microbial biomass and fungal richness describe soil carbon cycling.
Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, grass, forestry). Samples collected from across these sites ranged in soil properties; soil organic carbon (SOC), pH and texture. To assess the range in biodiversity and ecosystem function across the sites, fourteen biological methods were applied as proxy indicators for these functions. These methods measured the following: microbial diversity: DNA yields (molecular biomass), archaea, bacteria, total fungi and arbuscular mycorrhizal fungi; micro fauna diversity: nematode trophic groups; meso fauna diversity: enchytraeids and Collembola species; microbial function: nitrification, extracellular enzymes, multiple substrate induced respiration, community level physiological profiling and ammonia oxidiser/nitrification functional genes. Network analysis was used to identify the key connections between organisms under the different land use scenarios. Highest network density was found in forest soils and lowest density occurred in arable soils. Key taxomonic units (TUs) were identified in each land-use type and in relation to SOC and pH categorisations. Top-connected taxonomic units (i.e. displaying the most co-occurrence to other TUs) were identified for each land use type. In arable sites this was dominated by bacteria and fungi, while in grassland sites bacteria and fungi were most connected. In forest soils archaeal, enchytraeid and fungal TUs displayed the largest number of neighbours, reflecting the greatest connectivity. Multiple regression models were applied to assess the potential contribution of soil organisms to carbon cycling and storage and nutrient cycling of specifically nitrogen and phosphorus. Key drivers of carbon cycling were microbial biomass, basal respiration and fungal richness; these three measures have often been associated with carbon cycling in soils. Regression models of nutrient cycling were dependent on the model applied, showing variation in biological indicators.
Domain walls form at phase transitions which break discrete symmetries. In a cosmological context, they often overclose the Universe (contrary to observational evidence), although one may prevent ...this by introducing biases or forcing anisotropic evolution of the walls. In a previous work Correia et al., Phys. Rev. D 90, 023521 (2014), we numerically studied the evolution of various types of biased domain wall networks in the early Universe, confirming that anisotropic networks ultimately reach scaling while those with a biased potential or biased initial conditions decay. We also found that the analytic decay law obtained by Hindmarsh was in good agreement with simulations of biased potentials, but not of biased initial conditions, and suggested that the difference was related to the Gaussian approximation underlying the analytic law. Here, we extend our previous work in several ways. For the cases of biased potential and biased initial conditions, we study in detail the field distributions in the simulations, confirming that the validity (or not) of the Gaussian approximation is the key difference between the two cases. For anisotropic walls, we carry out a more extensive set of numerical simulations and compare them to the canonical velocity-dependent one-scale model for domain walls, finding that the model accurately predicts the linear scaling regime after isotropization. Overall, our analysis provides a quantitative description of the cosmological evolution of these networks.
Nosocomial late-onset sepsis represents a frequent cause of morbidity and mortality in preterm neonates. The Staphylococcus capitis clone NRCS-A has been previously described as an emerging cause of ...nosocomial bacteraemia in French neonatal intensive-care units (NICUs). In this study, we aimed to explore the possible unrecognized dissemination of this clone on a larger geographical scale. One hundred methicillin-resistant S. capitis strains isolated from neonates (n = 86) and adult patients (n = 14) between 2000 and 2013 in four different countries (France, Belgium, the UK, and Australia) were analysed with SmaI pulsed-field gel electrophoresis (PFGE) and dru typing. The vast majority of NICU strains showed the NRCS-A pulsotype and the dt11c type (96%). We then randomly selected 14 isolates (from neonates, n = 12, three per country; from adult patients, n = 2), considered to be a subset of representative isolates, and performed further molecular typing (SacII PFGE, SCCmec typing, and multilocus sequence typing-like analysis), confirming the clonality of the S. capitis strains isolated from neonates, despite their distant geographical origin. Whole genome single-nucleotide polymorphism-based phylogenetic analysis of five NICU isolates (from the different countries) attested to high genetic relatedness within the NRCS-A clone. Finally, all of the NRCS-A strains showed multidrug resistance (e.g. methicillin and aminoglycoside resistance, and decreased vancomycin susceptibility), with potential therapeutic implications for infected neonates. In conclusion, this study represents the first report of clonal dissemination of methicillin-resistant coagulase-negative Staphylococcus clone on a large geographical scale. Questions remain regarding the origin and means of international spread, and the reasons for this clone's apparent predilection for neonates.
Summary
Soil nutrient availability can strongly affect root traits. In tropical forests, phosphorus (P) is often considered the main limiting nutrient for plants. However, support for the P paradigm ...is limited, and N and cations might also control tropical forests functioning.
We used a large‐scale experiment to determine how the factorial addition of nitrogen (N), P and cations affected root productivity and traits related to nutrient acquisition strategies (morphological traits, phosphatase activity, arbuscular mycorrhizal colonisation and nutrient contents) in a primary rainforest growing on low‐fertility soils in Central Amazonia after 1 yr of fertilisation.
Multiple root traits and productivity were affected. Phosphorus additions increased annual root productivity and root diameter, but decreased root phosphatase activity. Cation additions increased root productivity at certain times of year, also increasing root diameter and mycorrhizal colonisation. P and cation additions increased their element concentrations in root tissues. No responses were detected with N addition.
Here we showed that rock‐derived nutrients determined root functioning in low‐fertility Amazonian soils, demonstrating not only the hypothesised importance of P, but also highlighting the role of cations. The changes in fine root traits and productivity indicated that even slow‐growing tropical rainforests can respond rapidly to changes in resource availability.
Three experiments were conducted to examine the effects of injectable trace minerals (ITM) on measures of trace mineral status and performance in pre- and postweaned Brangus-crossbred beef calves. In ...Exp. 1, calves were assigned to treatments in alternating birth order (n = 150; 75/treatment), consisting of a 1-mL subcutaneous injection of ITM (MultiMin 90; MultiMin USA, Inc., Fort Collins, CO) or sterile saline. The ITM formulation consisted of 60, 10, 15, and 5 mg/mL of Zn, Mn, Cu, and Se. Treatments were readministered at 100 and 200 d of age. Calf BW was recorded at birth and on d 100, 150, 200, and 250 (weaning). Trace mineral status was assessed in liver biopsy samples (n = 12/treatment) collected on d 150, 200, and 250. Administration of ITM had no impact on BW gain (P ≥ 0.55) but did result in greater (P ≤ 0.02) concentrations of liver Cu and Se and lesser (P = 0.05) liver Fe concentrations compared to saline-injected calves. In Exp. 2, 24 heifers were selected from the weaned calves of Exp. 1 (n = 12/treatment) and transported 1,600 km. Remaining on their original treatments, heifers were administered 5 mL of ITM or saline following transport (d 0). Blood samples, for acute phase protein (APP) analysis, were collected on d 0, 1, 3, 6, 9, and 13 and liver biopsy samples for assessment of trace mineral status on d 13. Plasma APP concentrations increased in all calves following weaning and transport but concentrations were greatest (P < 0.05) in ITM- vs. saline-injected heifers on d 6 and 9. Liver concentrations of Cu, Se, and Zn were greater (P ≤ 0.04) but ADG lesser (P = 0.05) for heifers receiving ITM vs. saline. In Exp. 3, 34 heifers, without previous exposure to ITM, were enrolled in a 177-d development study (n = 17/treatment). Treatments consisted of 2.5-mL injections of ITM or sterile saline on d 0, 51, and 127. Humoral immune response to an injection of porcine red blood cells (PRBC) was evaluated on d 51. Trace mineral status was evaluated in liver biopsy samples collected on d 177. Overall heifer ADG, PRBC antibody titers, and liver Se concentrations were greatest (P ≤ 0.06) for ITM vs. control heifers. Collectively, these studies demonstrate an increased trace mineral status, a greater humoral response to novel antigen, and a heightened APP response to weaning and transport stress in pre- and postweaned beef calves administered ITM.
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