Regional community assembly drivers and microbial environmental sources shaping bacterioplankton in an alpine lacustrine district (Pyrenees,Spain)

Microbial communities in natural ecosystems are subject to strong ecological rules. The study of local communities along a regional metacommunity can reveal patterns of community assembly, and disentangle the underlying ecological processes. In particular, we seek drivers of community assembly at the regional scale using a large lacustrine dataset (>300 lakes) along the geographical, limnological and physico-chemical gradients in the Pyrenees. By using high throughput amplicon sequencing of the 16S rRNA gene, and inferring environmental sources of bacterial immigrants, we showed that surface aquatic bacterial assemblages were strongly influenced by terrestrial populations from soil, biofilms or sediments, and primarily selected by a pH-alkalinity gradient. Indeed, source proportions explained 27% of the community variation, and chemistry 15% of the total variation, half of it shared with the sources. Major taxonomic groups such as Verrucomicrobia, Actinobacteria and Bacteroidetes showed higher aquatic affinities than Parcubacteria, Gammaproteobacteria, Alphaproteobacteria or Betaproteobacteria, which may be recruited and selected through different hydrographic habitats. A regional fingerprint was observed with lower alpha diversity and higher beta diversity in the central Pyrenees than in both ends. We suggest an ecological succession process, likely influenced by complex interactions of environmental source dispersal and environmental filtering along the mountain range geography.     

In vitro somatic embryogenesis of Texas ebony (Ebenopsis ebano [Berland.] Barneby & J.W. Grimes)

In Vitro Cellular & Developmental Biology - Plant - Texas ebony (Ebenopsis ebano [Berland.] Barneby & J.W. Grimes) is a member of the Fabaceae that is native to Mexico. Its wood has...     

Desulfurization of dibenzothiophene using the 4S enzymatic route: Influence of operational conditions on initial reaction rates

The influence of operational conditions (pH, temperature and oxygen transfer rate) on the initial reaction rates of the four reactions involved in the 4S biodesulfurization route of dibenzothiophenes (DBT) has been studied. The bioprocess was carried out using a genetically modified organism, Pseudomonas putida CECT 5279. The rates of the four reactions were calculated from the rates of production of different compounds involved in the 4S pathway, by matrix manipulation. The initial (zero time) reaction rates showed a slight dependence on oxygen transfer rate. Temperature and pH were optimal at 30°C and 9, respectively, temperature being the most important variable. This study also identifies the last reaction as the limiting step in the pathway.     

The immunogenicity to the first anti-TNF therapy determines the outcome of switching to a second anti-TNF therapy in spondyloarthritis patients

Introduction

Anti-TNF drugs have proven to be effective against spondyloarthritis (SpA), although 30% of patients fail to respond or experience adverse events leading to treatment discontinuation. In rheumatoid arthritis, the presence of anti-drug antibodies (ADA) against the first TNF inhibitor influences the outcome after switching. Our aim was to assess whether the response to a second anti-TNF drug is related to the previous development of ADA to the first anti-TNF drug SpA patients.

Methods

Forty-two SpA patients began a second anti-TNF drug after failing to respond to the first anti-TNF therapy. Clinical activity was assessed by the Ankylosing Spondylitis Disease Activity Score (ASDAS) at baseline (at the beginning of the first and second anti-TNF therapy) and at 6 months after switching. The drug and ADA levels were measured by ELISA before each administration.

Results

All patients were treated with anti-TNF drugs and mainly due to inefficacy were switched to a second anti-TNF drug. Eleven of 42 (26.2%) developed ADA during the first biologic treatment. At baseline, no differences in ASDAS were found in patients with or without ADA to the first anti-TNF drug (3.52 ± 1.03 without ADA vs. 3.14 ± 0.95 with ADA, p = 0.399) and to the second anti-TNF drug (3.36 ± 0.94 without ADA vs. 3.09 ± 0.91 with ADA, p = 0.466). At 6 months after switching, patients with previous ADA had lower disease activity (1.62 ± 0.93 with ADA vs. 2.79 ± 1.01 without ADA, p = 0.002) and most patients without ADA had high disease activity state by the ASDAS (25 out of 31 (80.6%) without ADA vs. 3 out of 11 (27.3%) with ADA, p = 0.002).

Conclusions

In SpA the failure to respond to the first anti-TNF drug due to the presence of ADA predicts a better clinical response to a second anti-TNF drug.     

Soil Loss and Runoff in Semiarid Ecosystems: A Complex Interaction Between Biological Soil Crusts, Micro-topography, and Hydrological Drivers

Biological soil crusts (BSCs) cover non-vegetated areas in most arid and semiarid ecosystems. BSCs play a crucial role in the redistribution of water and sediments and, ultimately, in the maintenance of ecosystem function. The effects of BSCs on water infiltration are complex. BSCs increase porosity and micro-topography, thus enhancing infiltration, but, at the same time, they can increase runoff by the secretion of hydrophobic compounds and clogging of soil pores upon wetting. BSCs confer stability on soil surfaces, reducing soil detachment locally; however, they can also increase runoff, which may increase sediment yield. Although the key role of BSCs in controlling infiltration–runoff and erosion is commonly accepted, conflicting evidence has been reported concerning the influence of BSCs on runoff generation. Very little is known about the relative importance of different BSC features such as cover, composition, roughness, or water repellency, and the interactions of these attributes in runoff and erosion. Because BSC characteristics can affect water flows and erosion both directly and indirectly, we examined the direct and indirect effects of different BSC features on runoff and erosion in a semiarid ecosystem under conditions of natural rainfall. We built structural equation models to determine the relative importance of BSC cover and type and their derived surface attributes controlling runoff and soil erosion. Our results show that the hydrological response of BSCs varies depending on rainfall properties, which, in turn, determine the process governing overland flow generation. During intense rainfalls, runoff is controlled not only by rainfall intensity but also by BSC cover, which exerts a strong direct and indirect influence on infiltration and surface hydrophobicity. Surface hydrophobicity was especially high for lichen BSCs, thus masking the positive effect of lichen crust on infiltration, and explaining the lower infiltration rates recorded on lichen than on cyanobacterial BSCs. Under low intensity, rainfall volume exerts a stronger effect than rainfall intensity, and BSC features play a secondary role in runoff generation, reducing runoff through their effect on surface micro-topography. Under these conditions, lichen BSCs presented higher infiltration rates than cyanobacterial BSCs. Our results highlight the significant protective effect against erosion exerted by BSCs at the plot scale, enhancing surface stability and reducing sediment yield in both high- and low-magnitude rainfall events.     

Unimodal size scaling of phytoplankton growth and the size dependence of nutrient uptake and use

Phytoplankton size structure is key for the ecology and biogeochemistry of pelagic ecosystems, but the relationship between cell size and maximum growth rate (μ_max) is not yet well understood. We used cultures of 22 species of marine phytoplankton from five phyla, ranging from 0.1 to 10⁶ μm³ in cell volume (V_cell), to determine experimentally the size dependence of growth, metabolic rate, elemental stoichiometry and nutrient uptake. We show that both μ_max and carbon‐specific photosynthesis peak at intermediate cell sizes. Maximum nitrogen uptake rate (V_maxN) scales isometrically with V_cell, whereas nitrogen minimum quota scales as V_cell^0.84. Large cells thus possess high ability to take up nitrogen, relative to their requirements, and large storage capacity, but their growth is limited by the conversion of nutrients into biomass. Small species show similar volume‐specific V_maxN compared to their larger counterparts, but have higher nitrogen requirements. We suggest that the unimodal size scaling of phytoplankton growth arises from taxon‐independent, size‐related constraints in nutrient uptake, requirement and assimilation.     

Anti-inflammatory effects of clarithromycin in ventilator-induced lung injury

Background

Mechanical ventilation can promote lung injury by triggering a pro-inflammatory response. Macrolides may exert some immunomodulatory effects and have shown significant benefits over other antibiotics in ventilated patients. We hypothesized that macrolides could decrease ventilator-induced lung injury.

Methods

Adult mice were treated with vehicle, clarithromycin or levofloxacin, and randomized to receive mechanical ventilation with low (12 cmH₂O, PEEP 2 cmH₂O) or high (20 cmH₂O, ZEEP) inspiratory pressures for 150 minutes. Histological lung injury, neutrophil infiltration, inflammatory mediators (NFκB activation, Cxcl2, IL-10) and levels of adhesion molecules (E-selectin, ICAM) and proteases (MMP-9 and MMP-2) were analyzed.

Results

There were no differences among groups after low-pressure ventilation. Clarithromycin significantly decreased lung injury score and neutrophil count, compared to vehicle or levofloxacin, after high-pressure ventilation. Cxcl2 expression and MMP-2 and MMP-9 levels increased and IL-10 decreased after injurious ventilation, with no significant differences among treatment groups. Both clarithromycin and levofloxacin dampened the increase in NFκB activation observed in non-treated animals submitted to injurious ventilation. E-selectin levels increased after high pressure ventilation in vehicle- and levofloxacin-treated mice, but not in those receiving clarithromycin.

Conclusions

Clarithromycin ameliorates ventilator-induced lung injury and decreases neutrophil recruitment into the alveolar spaces. This could explain the advantages of macrolides in patients with acute lung injury and mechanical ventilation.     

Molecular Typing of Lung Adenocarcinoma on Cytological Samples Using a Multigene Next Generation Sequencing Panel

Identification of driver mutations in lung adenocarcinoma has led to development of targeted agents that are already approved for clinical use or are in clinical trials. Therefore, the number of biomarkers that will be needed to assess is expected to rapidly increase. This calls for the implementation of methods probing the mutational status of multiple genes for inoperable cases, for which limited cytological or bioptic material is available. Cytology specimens from 38 lung adenocarcinomas were subjected to the simultaneous assessment of 504 mutational hotspots of 22 lung cancer-associated genes using 10 nanograms of DNA and Ion Torrent PGM next-generation sequencing. Thirty-six cases were successfully sequenced (95%). In 24/36 cases (67%) at least one mutated gene was observed, including EGFR, KRAS, PIK3CA, BRAF, TP53, PTEN, MET, SMAD4, FGFR3, STK11, MAP2K1. EGFR and KRAS mutations, respectively found in 6/36 (16%) and 10/36 (28%) cases, were mutually exclusive. Nine samples (25%) showed concurrent alterations in different genes. The next-generation sequencing test used is superior to current standard methodologies, as it interrogates multiple genes and requires limited amounts of DNA. Its applicability to routine cytology samples might allow a significant increase in the fraction of lung cancer patients eligible for personalized therapy.