CFTR Protects against Mycobacterium abscessus Infection by Fine-Tuning Host Oxidative Defenses

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Study of involvement of ImuB and DnaE2 in stationary-phase mutagenesis in Pseudomonas putida

Several bacterial species carry in their genomes a so-called "mutagenesis" gene cluster encoding ImuB which is similar to Y-family DNA polymerases, and DnaE2 related to the catalytic subunit DnaE of Pol III. Y-family DNA polymerases are known to be involved in stationary-phase mutagenesis and DnaE2 homologues characterized so far have expressed a mutator phenotype. In this study, we raised a question about the involvement of ImuB and DnaE2 in stationary-phase mutagenesis. Here, we show that Pseudomonas putida ImuB and DnaE2 have antagonistic effects on stationary-phase mutagenesis. ImuB facilitated accumulation of stationary-phase mutants up to two-fold. In contrast to that, DnaE2 had no significant effect on emergence of 1-bp deletion mutants and moreover, it acted as an anti-mutator in accumulation of base substitution mutants in starving bacteria. Similar antagonistic effects of DnaE2 and ImuB on mutagenesis appeared also in UV-mutagenesis study. This data distinguishes the DnaE2 of P. putida from its homologues studied in other organisms.     

‘Ten Years After’—a long-term settlement and bioerosion experiment in an Arctic rhodolith bed (Mosselbukta,Svalbard)

Rhodolith beds and bioherms formed by ecosystem engineering crustose coralline algae support the northernmost centres of carbonate production, referred to as polar cold-water carbonate factories. Yet, little is known about biodiversity and recruitment of these hard-bottom communities or the bioeroders degrading them, and there is a demand for carbonate budgets to include respective rates of polar carbonate build-up and bioerosion. To address these issues, a 10-year settlement and bioerosion experiment was carried out at the Arctic Svalbard archipelago in and downslope of a rhodolith bed. The calcifiers recorded on experimental settlement tiles (56 taxa) were dominated by bryozoans, serpulids and foraminiferans. The majority of the bioerosion traces (30 ichnotaxa) were microborings, followed by attachment etchings and grazing traces. Biodiversity metrics show that calcifier diversity and bioerosion ichnodiversity are both elevated in the rhodolith bed, if compared to adjacent aphotic waters, but these differences are statistically insignificant. Accordingly, there were only low to moderate dissimilarities in the calcifier community structure and bioerosion trace assemblages between the two depth stations (46 and 127 m), substrate orientations (up- and down-facing) and substrate types (PVC and limestone), in that order of relevance. In contrast, surface coverage as well as the carbonate accretion and bioerosion rates were all significantly elevated in the rhodolith bed, reflecting higher abundance or size of calcifiers and bioerosion traces. All three measures were highest for up-facing substrates at 46 m, with a mean coverage of 78.2% (on PVC substrates), a mean accretion rate of 24.6 g m^?2  year^?1 (PVC), and a mean bioerosion rate of ?35.1 g m^?2 year^?1 (limestone). Differences in these metrics depend on the same order of factors than the community structure. Considering all limestone substrates of the two platforms, carbonate accretion and bioerosion were nearly in balance at a net rate of ?2.5 g m^?2 year^?1. A latitudinal comparison with previous settlement studies in the North Atlantic suggests that despite the harsh polar environment there is neither a depletion in the diversity of hard-bottom calcifier communities nor in the ichnodiversity of grazing traces, attachment etchings and microborings formed by organotrophs. In contrast, microborings produced by phototrophs are strongly depleted because of limitations in the availability of light (condensed photic zonation, polar night, shading by sea ice). Also, macroborings were almost absent, surprisingly. With respect to carbonate production, the Svalbard carbonate factory marks the low end of a latitudinal gradient while bioerosion rates are similar or even higher than at comparable depth or photic regime at lower latitudes, although this might not apply to shallow euphotic waters (not covered in our experiment), given the observed depletion in bioeroding microphytes and macroborers. While echinoid grazing is particularly relevant for the bioerosion in the rhodolith bed, respective rates are far lower than those reported from tropical shallow-water coral reefs. The slow pace of carbonate production but relatively high rates of bioerosion (both promoted by low carbonate supersaturation states in Arctic waters), in concert with high retention of skeletal carbonates on the seafloor and no calcite cements forming in open pore space created by microborers, suggest a low fossilisation potential for polar carbonates, such as those formed in the Mosselbukta rhodolith beds.     

Forest biomass,soil and biodiversity relationships originate from biogeographic affinity and direct ecological effects

Ecosystem biomass, soil conditions and the diversity of different taxa are often interrelated. These relationships could originate from biogeographic affinity (varying species pools) or from direct ecological effects within local communities. Disentangling regional and local causes is challenging as the former might mask the latter in natural ecosystems with varying habitat conditions. However, when the species pool contribution is considered in statistics, local ecological effects might be detected. In this study we disentangle the indirect effects of the species pool and direct ecological effects on the complex relationships among wood volume, soil conditions and diversities of different plant and fungal groups in 100 old‐growth forest sites (10 × 10 m) at the border of boreal and nemoral zones in northern Europe. We recorded all species for different vegetation groups: woody and herbaceous vascular plants, terricolous and epiphytic bryophytes and lichens. Fungal communities were detected by DNA‐based analyses from soil samples. Above‐ground wood volume was used as a proxy of biomass. We measured soil pH and nutrient content and obtained modelled climate parameters for each site. Species pool effect was considered by dividing sites into boreal and nemoral groups based on community composition. In order to disentangle direct and indirect effects, we applied variation partitioning, and raw and partial correlations. We found many significant positive relationships among studied variables. Many of these relationships were associated to boreal and nemoral species pools, thus indicating that biogeographic affinity of interacting plants and fungi largely defines forest diversity and functioning. At the same time, several relationships were significant also after considering biogeography: woody plant and ectomycorrhizal fungi diversities with wood volume, many plant and fungal groups with each other, or with soil conditions. These direct ecological interactions could be considered in forestry practices to achieve both economic gain and maintenance of biodiversity.     

Retinoic acid–induced survival effects in SH-SY5Y neuroblastoma cells

Neuroblastoma is a malignant childhood cancer arising from the embryonic sympathoadrenal lineage of the neural crest. Retinoic acid (RA) is included in the multimodal therapy of patients with high-risk neuroblastoma to eliminate minimal residual disease. However, the formation of RA-resistant cells substantially lowers 5-year overall survival rates. To examine mechanisms that lead to treatment failure, we chose human SH-SY5Y cells, which are known to tolerate incubation with RA by activating the survival kinases Akt and extracellular signal-regulated kinase 1/2. Characterization of downstream pathways showed that both kinases increased the phosphorylation of the ubiquitin ligase mouse double minute homolog 2 (Mdm2) and thereby enhanced p53 degradation. When p53 signaling was sustained by blocking complex formation with Mdm2 or enhancing c-Jun N-terminal kinase (JNK) activation, cell viability was significantly reduced. In addition, Akt-mediated phosphorylation of the cell-cycle regulator p21 stimulated complex formation with caspase-3, which also contributed to cell protection. Thus, treatment with RA augmented survival signaling and attenuated basal apoptotic pathways in SH-SY5Y cells, which increased cell viability.     

Biomarker Profiling by Nuclear Magnetic Resonance Spectroscopy for the Prediction of All-Cause Mortality: An Observational Study of 17,345 Persons

Background

Early identification of ambulatory persons at high short-term risk of death could benefit targeted prevention. To identify biomarkers for all-cause mortality and enhance risk prediction, we conducted high-throughput profiling of blood specimens in two large population-based cohorts.

Methods and Findings

106 candidate biomarkers were quantified by nuclear magnetic resonance spectroscopy of non-fasting plasma samples from a random subset of the Estonian Biobank (n = 9,842; age range 18–103 y; 508 deaths during a median of 5.4 y of follow-up). Biomarkers for all-cause mortality were examined using stepwise proportional hazards models. Significant biomarkers were validated and incremental predictive utility assessed in a population-based cohort from Finland (n = 7,503; 176 deaths during 5 y of follow-up). Four circulating biomarkers predicted the risk of all-cause mortality among participants from the Estonian Biobank after adjusting for conventional risk factors: alpha-1-acid glycoprotein (hazard ratio [HR] 1.67 per 1–standard deviation increment, 95% CI 1.53–1.82, p = 5×10⁻³¹), albumin (HR 0.70, 95% CI 0.65–0.76, p = 2×10⁻¹⁸), very-low-density lipoprotein particle size (HR 0.69, 95% CI 0.62–0.77, p = 3×10⁻¹²), and citrate (HR 1.33, 95% CI 1.21–1.45, p = 5×10⁻¹⁰). All four biomarkers were predictive of cardiovascular mortality, as well as death from cancer and other nonvascular diseases. One in five participants in the Estonian Biobank cohort with a biomarker summary score within the highest percentile died during the first year of follow-up, indicating prominent systemic reflections of frailty. The biomarker associations all replicated in the Finnish validation cohort. Including the four biomarkers in a risk prediction score improved risk assessment for 5-y mortality (increase in C-statistics 0.031, p = 0.01; continuous reclassification improvement 26.3%, p = 0.001).

Conclusions

Biomarker associations with cardiovascular, nonvascular, and cancer mortality suggest novel systemic connectivities across seemingly disparate morbidities. The biomarker profiling improved prediction of the short-term risk of death from all causes above established risk factors. Further investigations are needed to clarify the biological mechanisms and the utility of these biomarkers for guiding screening and prevention. Please see later in the article for the Editors'' Summary     

Effect of prenatal arsenic exposure on DNA methylation and leukocyte subpopulations in cord blood

Prenatal arsenic exposure is associated with increased risk of disease in adulthood. This has led to considerable interest in arsenic’s ability to disrupt fetal programming. Many studies report that arsenic exposure alters DNA methylation in whole blood but these studies did not adjust for cell mixture. In this study, we examined the relationship between arsenic in maternal drinking water collected ≤ 16 weeks gestational age and DNA methylation in cord blood (n = 44) adjusting for leukocyte-tagged differentially methylated regions. DNA methylation was quantified using the Infinium HumanMethylation 450 BeadChip array. Recursively partitioned mixture modeling examined the relationship between arsenic and methylation at 473,844 CpG sites. Median arsenic concentration in water was 12 µg/L (range < 1- 510 µg/L). Log₁₀ arsenic was associated with altered DNA methylation across the epigenome (P = 0.002); however, adjusting for leukocyte distributions attenuated this association (P = 0.013). We also observed that arsenic had a strong effect on the distribution of leukocytes in cord blood. In adjusted models, every log₁₀ increase in maternal drinking water arsenic exposure was estimated to increase CD8+ T cells by 7.4% (P = 0.0004) and decrease in CD4+ T cells by 9.2% (P = 0.0002). These results show that prenatal exposure to arsenic had an exposure-dependent effect on specific T cell subpopulations in cord blood and altered DNA methylation in cord blood. Future research is needed to determine if these small changes in DNA methylation alter gene expression or are associated with adverse health effects.     

Topography and Land Cover of Watersheds Predicts the Distribution of the Environmental Pathogen Mycobacterium ulcerans in Aquatic Insects

Background

An understanding of the factors driving the distribution of pathogens is useful in preventing disease. Often we achieve this understanding at a local microhabitat scale; however the larger scale processes are often neglected. This can result in misleading inferences about the distribution of the pathogen, inhibiting our ability to manage the disease. One such disease is Buruli ulcer, an emerging neglected tropical disease afflicting many thousands in Africa, caused by the environmental pathogen Mycobacterium ulcerans. Herein, we aim to describe the larger scale landscape process describing the distribution of M. ulcerans.

Methodology

Following extensive sampling of the community of aquatic macroinvertebrates in Cameroon, we select the 5 dominant insect Orders, and conduct an ecological niche model to describe how the distribution of M. ulcerans positive insects changes according to land cover and topography. We then explore the generalizability of the results by testing them against an independent dataset collected in a second endemic region, French Guiana.

Principal Findings

We find that the distribution of the bacterium in Cameroon is accurately described by the land cover and topography of the watershed, that there are notable seasonal differences in distribution, and that the Cameroon model does not predict the distribution of M. ulcerans in French Guiana.

Conclusions/Significance

Future studies of M. ulcerans would benefit from consideration of local structure of the local stream network in future sampling, and further work is needed on the reasons for notable differences in the distribution of this species from one region to another. This work represents a first step in the identification of large-scale environmental drivers of this species, for the purposes of disease risk mapping.