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Opposite latitudinal patterns for bird and arthropod predation revealed in experiments with differently colored artificial prey
No full textAt a former wood preservation site contaminated with Cu, various phytomanagement options have been assessed in the last decade through physicochemical, ecotoxicological and biological assays. In a field trial at this site, phytomanagement with a crop rotation based on tobacco and sunflower, combined with the incorporation of compost and dolomitic limestone, has proved to be efficient in Cu-associated risk mitigation, ecological soil functions recovery and net gain of economic and social benefits. To demonstrate the long-term effectiveness and sustainability of phytomanagement, we assessed here the influence of this remediation option on the diversity, composition and structure of microbial communities over time, through a metabarcoding approach. After 9 years of phytomanagement, no overall effect was identified on microbial diversity; the soil amendments, notably the repeated compost application, led to shifts in soil microbial populations. This phytomanagement option induced changes in the composition of soil microbial communities, promoting the growth of microbial groups belonging to Alphaproteobacteria, many being involved in N cycling. Populations of Nitrososphaeria, which are crucial in nitrification, as well as taxa from phyla Planctomycetacia, Chloroflexi and Gemmatimonadetes, which are tolerant to metal contamination and adapted to oligotrophic soil conditions, decreased in amended phytomanaged plots. Our study provides an insight into population dynamics within soil microbial communities under long-term phytomanagement, in line with the assessment of soil ecological functions and their recovery
Identification of lipid A deacylase as a novel, highly conserved and protective antigen against enterohemorrhagic Escherichia coli
No full textEnterohemorrhagic E. coli (EHEC) is a major cause of large outbreaks worldwide associated with hemorrhagic colitis and hemolytic uremic syndrome. While vaccine development is warranted, a licensed vaccine, specific for human use, against EHEC is not yet available. In this study, the reverse vaccinology approach combined with genomic, transcriptional and molecular epidemiology data was applied on the EHEC O157:H7 genome to select new potential vaccine candidates. Twenty-four potential protein antigens were identified and one of them (MC001) was successfully expressed onto Generalized Modules for Membrane Antigens (GMMA) delivery system. GMMA expressing this vaccine candidate was immunogenic, raising a specific antibody response. Immunization with the MC001 candidate was able to reduce the bacterial load of EHEC O157:H7 strain in feces, colon and caecum tissues after murine infection. MC001 is homologue to lipid A deacylase enzyme (LpxR), and to our knowledge, this is the first study describing it as a potential vaccine candidate. Gene distribution and sequence variability analysis showed that MC001 is present and conserved in EHEC and in enteropathogenic E. coli (EPEC) strains. Given the high genetic variability among and within E. coli pathotypes, the identification of such conserved antigen suggests that its inclusion in a vaccine might represent a solution against major intestinal pathogenic strains
Spatial and temporal patterns of a pulsed resource dynamically drive the distribution of specialist herbivores
No full textPatterns and drivers of the spatio-temporal distribution of herbivores are key elements of their ecological and evolutionary impacts on plant populations. Herbivore spatial distributions may be influenced by increased (RCH: resource concentration hypothesis) or decreased (RDH: resource dilution hypothesis) resource densities, but the effect of temporal variations in resource densities on such distributions remains poorly documented. We used a survey of a masting tree species and its seed predators in Southeastern France to address the effect of a host’s pulsed resource on the spatio-temporal distributions of highly specialized insect herbivores feeding on seeds. Variations in both resource and seed predator densities were assessed by estimating seed production and seed
infestation rates in focus trees during 10 consecutive years. We found increasing seed infestation rates with decreasing host tree densities in years of low seed production, indicating a RDH pattern of seed predators. However, such pattern was not persistent in years of high seed production during which seed infestation rates did not depend on host tree densities. We showed that temporal variations in resource density can lead to transience of seed predator spatial distribution. This study highlights how predictions of plant-herbivore interactions in natural ecosystems may rely on temporal components underlying RCH and RDH hypotheses
Geographic distribution and evolution of Cucurbitaceae and Solanaceae viruses in the French Mediterranean basin
No full textElevation of trimethylamine-n-oxide in chronic kidney disease: contribution of decreased glomerular filtration rate.
No full textGut microbiota-dependent Trimethylamine-N-oxide (TMAO) has been reported to be strongly linked to renal function and to increased cardiovascular events in the general population and in Chronic Kidney Disease (CKD) patients. Considering the lack of data assessing renal handling of TMAO, we conducted this study to explore renal excretion and mechanisms of accumulation of TMAO during CKD. We prospectively measured glomerular filtration rate (mGFR) with gold standard methods and plasma concentrations of trimethylamine (TMA), TMAO, choline, betaine, and carnitine by LC-MS/MS in 124 controls, CKD, and hemodialysis (HD) patients. Renal clearance of each metabolite was assessed in a sub-group of 32 patients. Plasma TMAO was inversely correlated with mGFR (r2 = 0.388, p < 0.001), confirming elevation of TMAO plasma levels in CKD. TMAO clearances were not significantly different from mGFR, with a mean ± SD TMAO fractional excretion of 105% ± 32%. This suggests a complete renal excretion of TMAO by glomerular filtration with a negligible participation of tubular secretion or reabsorption, during all stages of CKD. Moreover, TMAO was effectively removed within 4 h of hemodiafiltration, showing a higher fractional reduction value than that of urea (84.9% ± 6.5% vs. 79.2% ± 5.7%, p = 0.04). This study reports a strong correlation between plasma TMAO levels and mGFR, in CKD, that can be mainly related to a decrease in TMAO glomerular filtration. Clearance data did not support a significant role for tubular secretion in TMAO renal eliminatio
Advanced Proteomics as a Powerful Tool for Studying Toxins of Human Bacterial Pathogens
No full textExotoxins contribute to the infectious processes of many bacterial pathogens, mainly by causing host tissue damages. The production of exotoxins varies according to the bacterial species. Recent advances in proteomics revealed that pathogenic bacteria are capable of simultaneously producing more than a dozen exotoxins. Interestingly, these toxins may be subject to post-transcriptional modifications in response to environmental conditions. In this review, we give an outline of different bacterial exotoxins and their mechanism of action. We also report how proteomics contributed to immense progress in the study of toxinogenic potential of pathogenic bacteria over the last two decades
Short-range-order minerals as powerful factors explaining deep soil organic carbon stock distribution: the case of a coffee agroforestry plantation on Andosols in Costa Rica
No full textSoil organic carbon (SOC) constitutes the largest terrestrial C stock, particularly in the Andosols of volcanic areas. Quantitative information on distribution of SOC stocks is needed to construct a baseline for studying temporal changes in SOC. The spatial variation of soil short-range-order minerals such as allophane usually explains the variability of topsoil SOC contents, but SOC data for deeper soil layers are needed. We found that within a 1 km2 Costa Rican basin covered by coffee agroforestry, SOC stocks in the upper 200 cm of soil were highly variable (24 to 72 kg C m−2). Topsoil SOC stocks were not correlated with SOC stocks present in deeper layers. Diffuse-reflectance mid-infrared (MIR) spectroscopy made possible the analysis of a large number of samples (69 soil profiles, i.e. 598 soil samples) for ammonium-oxalate and sodium-pyrophosphate-extractable forms of Al, Fe, and Si, as well as SOC content and bulk density. Using the MIR spectra, we identified two different soil materials, which were identified as allophanic and halloysitic soil material. Allophanic soil occurred on top of the halloysitic soil. The thickness of the allophanic soil material, rich in SRO minerals and related to a young andic A horizon, explained the variability of SOC. This study illustrates that knowledge of topography and pedogenesis is needed to understand and extrapolate the distribution of SOC stocks at landscape scales
The Politics of Calculation. Towards a Sociology of Quantification in Governance
No full textA diversity of modes of quantification in contemporary societies have now been explored, following the path of scholars who inspired this field, such as Alain Desrosières. This introduction to the special issue of the Revue d'Anthropologie des Connaissances on the politics of calculation argues that there remains a gap between different strains of the sociology of quantification - one that emphasizes the governmentality it embodies and the discipline it establishes, the other that pays attention to the collective mobilization capacities it offers. It is suggested that public policy and governance is a good field of investigation, to understand how these two “regimes of quantification” are articulated together, and evaluate the extent to which actors external to the networks that control public policies can influence them by recalculating both the problems addressed and the effects of policy programs. Combining the sociology of science and technology and political sociology, this special issue thus hypothesizes that calculation is one of the ways of building coalitions in governance, and one of the objects of what is being debated in its arenas; and, conversely, that governance is one of the contexts in which contemporary forms of calculation are forged and algorithms invented
Divergent functional diversification patterns in the SEP/AGL6/AP1 MADS-box transcription factor superclade
No full textMembers of SEPALLATA (SEP) and APETALA1 (AP1)/SQUAMOSA (SQUA) MADS-box transcription factor subfamilies play key
roles in floral organ identity determination and floral meristem determinacy in the rosid species Arabidopsis (Arabidopsis
thaliana). Here, we present a functional characterization of the seven SEP/AGL6 and four AP1/SQUA genes in the distant
asterid species petunia (Petunia 3 hybrida). Based on the analysis of single and higher order mutants, we report that the
petunia SEP1/SEP2/SEP3 orthologs together with AGL6 encode classical SEP floral organ identity and floral termination
functions, with a master role for the petunia SEP3 ortholog FLORAL BINDING PROTEIN2 (FBP2). By contrast, the FBP9
subclade members FBP9 and FBP23, for which no clear ortholog is present in Arabidopsis, play a major role in determining
floral meristem identity together with FBP4, while contributing only moderately to floral organ identity. In turn, the four
members of the petunia AP1/SQUA subfamily redundantly are required for inflorescence meristem identity and act as
B-function repressors in the first floral whorl, together with BEN/ROB genes. Overall, these data together with studies in other
species suggest major differences in the functional diversification of the SEP/AGL6 and AP1/SQUA MADS-box subfamilies
during angiosperm evolution
Identification of telomerase RNAs in species of the Yarrowia Clade provides insights into the co-evolution of telomerase, telomeric repeats and telomere-binding proteins
No full textTelomeric repeats in fungi of the subphylum Saccharomycotina exhibit great inter- and intra-species variability in length and sequence. Such variations challenged telomeric DNA-binding proteins that co-evolved to maintain their functions at telomeres. Here, we compare the extent of co-variations in telomeric repeats, encoded in the telomerase RNAs (TERs), and the repeat-binding proteins from 13 species belonging to the Yarrowia Glade. We identified putative TER loci, analyzed their sequence and secondary structure conservation, and predicted functional elements. Moreover, in vivo complementation assays with mutant TERs showed the functional importance of four novel TER substructures. The TER-derived telomeric repeat unit of all species, except for one, is 10 bp long and can be represented as 5'-TTNNNNAGGG-3', with repeat sequence variations occuring primarily outside the vertebrate telomeric motif 5'-TTAGGG-3'. All species possess a homologue of the Yarrowia lipolytica Tay1 protein, YlTay1p. In vitro, YlTay1p displays comparable DNA-binding affinity to all repeat variants, suggesting a conserved role among these species. Taken together, these results add significant insights into the co-evolution of TERs, telomeric repeats and telomere-binding proteins in yeasts