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Quantification of soil organic carbon stock in urban soils using visible and near infrared reflectance spectroscopy (VNIRS) in situ or in laboratory conditions
No full textUrban soils, like other soils, can be sink or source for atmospheric carbon dioxide, and due to urban expansion, are receiving increasing attention. Studying their highly variable attributes requires high-density sampling, which can hardly be achieved using conventional approaches. The objective of this work was to determine the ability of visible and near infrared reflectance spectroscopy (VNIRS) to quantify soil organic carbon (SOC) concentration (gC kg−1) and stock (gC dm−3, or MgC ha−1 for a given depth layer) in parks and sealed soils of two French cities, Marseille and Nantes, using spectra collected on pit walls or in laboratory conditions (air dried, 2 mm sieved samples).
Better VNIRS predictions were achieved using laboratory than in situ spectra (R2 ≈ 0.8–0.9 vs. 0.7–0.8 in validation), and for sample SOC concentration than stock (R2val up to 0.83 in situ and 0.95 in the laboratory vs. 0.78 and 0.89, respectively). Stock was conventionally calculated according to four methods that variably account for coarse particles (>2 mm); and it was better predicted when coarse particles were not taken into account. This was logical using laboratory spectra, collected on 2 mm sieved samples; but concerning in situ spectra, this suggested the operator tended to put the spectrometer beside the coarsest particles during spectrum acquisition. This point is worth considering for urban soils, often rich in coarse particles.
Stocks were then aggregated at the profile level: SOC stock prediction was more accurate at profile than sample level when using laboratory spectra (R2val = 0.94 vs. 0.89, respectively), probably due to uncertainty compensation; but this was not the case when using in situ spectra, possibly because samples collected for SOC analysis and corresponding VNIRS scans were not at the exact same location.
This work demonstrates VNIRS usefulness for quantifying SOC stock time- and cost-effectively, in urban soils especially
Resource recovery and wastewater treatment modelling
No full textTraditional wastewater treatment plants (WWTPs) are increasingly regarded as water resource recovery facilities (WRRFs), reflecting the value of water, nutrients, energy and other resources, besides ensuring the required effluent quality. Resource recovery techniques involve biochemical, physical and physicochemical processes, and even previously unexploited biological conversions. Biopolymer and bioplastic production also reveal the remarkable potential present in our microbial cultures. Models have demonstrated their usefulness to optimize WWTP operation to achieve better effluent quality at lower costs; they also constitute a useful tool to support the transition of WWTPs into WRRFs that maximize the valorization of products recovered from wastewater. In this paper, the extent to which the new techniques and unit processes applied for resource recovery could be modelled with conventional activated sludge models (ASMs) and additional modelling challenges being faced are discussed while providing recommendations of potential approaches to address current modelling research gaps
CD146 deficiency promotes plaque formation in a mouse model of atherosclerosis by enhancing RANTES secretion and leukocyte recruitment.
No full textAims The progression of atherosclerosis is based on the continued recruitment of leukocytes in the vessel wall. The previously described role of CD146 in leukocyte infiltration suggests an involvement for this adhesion molecule in the inflammatory response. In this study, we investigated the role of CD146 in leukocyte recruitment by using an experimental model of atherogenesis. Methods and results
The role of CD146 was explored in atherosclerosis by crossing CD146−/− mice with ApoE−/− mice. CD146 −/−/ApoE −/− and ApoE −/− mice were fed a Western diet for 24 weeks and were monitored for aortic wall thickness using high frequency ultrasound. The arterial wall was significantly thicker in CD146-deficient mice. After 24 weeks of Western diet, a significant increase of atheroma in both total aortic lesion and aortic sinus of CD146-null mice was observed. In addition, atherosclerotic lesions were more inflammatory since plaques from CD146-deficient mice contained more neutrophils and macrophages. This was due to up-regulation of RANTES secretion by macrophages in CD146-deficient atherosclerotic arteries. This prompted us to further address the function of CD146 in leukocyte recruitment during acute inflammation by using a second experimental model of peritonitis induced by thioglycollate. Neutrophil recruitment was significantly increased in CD146-deficient mice 12 h after peritonitis induction and associated with higher RANTES levels in the peritoneal cavity. In CD146-null macrophages, we also showed that increased RANTES production was dependent on constitutive inhibition of the p38-MAPK signaling pathway. Finally, Maraviroc, a RANTES receptor antagonist, was able to reduce atherosclerotic lesions and neutrophilia in CD146-deficient mice to the same level as that found in ApoE −/− mice. Conclusions Our data indicate that CD146 deficiency is associated with the upregulation of RANTES production and increased inflammation of atheroma, which could influence the atherosclerotic plaque fate. Thus, these data identify CD146 agonists as potential new therapeutic candidates for atherosclerosis treatment
Trends in agri-food choices for health since the 1960s: the case of fatty acids
No full textThe FA composition of our diet affects human health: SFAs and n-6 PUFAs in excess are a risk factor for a number of chronic diseases, while n-3 PUFAs have a protective role. These FAs should be considered together, since an excessively high n-6:n-3 ratio is linked to a strong pro-inflammatory effect. We reconstructed the FA composition of the French diet from the 1960s to the present to identify the main reasons for decreases or increases due to agriculture, food processing or food choices. From the 1960s to the late 1990s, the diet increased in SFA and n-6 PUFA levels and likely decreased in n-3 PUFA level. Consequently, food behaviors did not follow dietary recommendations. For SFAs, this was due to the sharp increase in cheese and, to a smaller extent, palm oil consumption. For n-6 PUFAs, it was due to the sharp increase in oil consumption, especially linoleic sunflower oil. For n-3 PUFAs, this was due mainly to replacement of grass by maize and soybean meal to feed ruminants. This trend has reversed since the 2000s: the SFA level decreased due to decreased consumption of palm oil and genetic improvements in pigs and poultry, n-6 PUFA level decreased due to increased consumption of oleic instead of linoleic sunflower oil, and n-3 PUFA level increased due to increased consumption of rapeseed oil. These changes are consistent with the FA composition observed in breast milk. Despite these improvements, however, the average dietary composition remains far from the recommendations, especially for n-3 PUFAs. We show the potential for improvement by supplementing animal feed with flaxseed and increasing consumption of oleic sunflower and rapeseed oils, at the expense of that of other oils
A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals
No full textBackground The gut microbiome is an important determinant of human health. Its composition has been shown to be influenced by multiple environmental factors and likely by host genetic variation. In the framework of the Milieu Interieur Consortium, a total of 1000 healthy individuals of western European ancestry, with a 1:1 sex ratio and evenly stratified across five decades of life (age 20-69), were recruited. We generated 16S ribosomal RNA profiles from stool samples for 858 participants. We investigated genetic and non-genetic factors that contribute to individual differences in fecal microbiome composition. Results Among 110 demographic, clinical, and environmental factors, 11 were identified as significantly correlated with alpha-diversity, ss-diversity, or abundance of specific microbial communities in multivariable models. Age and blood alanine aminotransferase levels showed the strongest associations with microbiome diversity. In total, all non-genetic factors explained 16.4% of the variance. We then searched for associations between > 5 million single nucleotide polymorphisms and the same indicators of fecal microbiome diversity, including the significant non-genetic factors as covariates. No genome-wide significant associations were identified after correction for multiple testing. A small fraction of previously reported associations between human genetic variants and specific taxa could be replicated in our cohort, while no replication was observed for any of the diversity metrics. Conclusion In a well-characterized cohort of healthy individuals, we identified several non-genetic variables associated with fecal microbiome diversity. In contrast, host genetics only had a negligible influence. Demographic and environmental factors are thus the main contributors to fecal microbiome composition in healthy individuals
ViroBase: An ad hoc relational database for the management and traceability of biological data
No full textFrom genomic to LC-MS/MS evidence: Analysis of PfEMP1 in Benin malaria cases
No full textBackground PfEMP1 is the major protein from parasitic origin involved in the pathophysiology of severe malaria, and PfEMP1 domain subtypes are associated with the infection outcome. In addition, PfEMP1 variability is endless and current publicly available protein repositories do not reflect the high diversity of the sequences of PfEMP1 proteins. The identification of PfEMP1 protein sequences expressed with samples remains challenging. The aim of our study is to identify the different PfEMP1 proteins variants expressed within patient samples, and therefore identify PfEMP1 proteins domains expressed by patients presenting uncomplicated malaria or severe malaria in malaria endemic setting in Cotonou, Benin. Methods We performed a multi-omic approach to decipher PfEMP1 expression at the patient's level in different clinical settings. Using a combination of whole genome sequencing approach and RNA sequencing, we were able to identify new PfEMP1 sequences and created a new custom protein database. This database was used for protein identification in mass spectrometry analysis. Results The differential expression analysis of RNAsequencing data shows an increased expression of the var domains transcripts DBL alpha 1.7, DBL alpha 1.1, DBL alpha 2 and DBL beta 12 in samples from patients suffering from Cerebral Malaria compared to Uncomplicated Malaria. Our approach allowed us to attribute PfEMP1 sequences to each sample and identify new peptides associated to PfEMP1 proteins in mass spectrometry. Conclusion We highlighted the diversity of the PfEMP1 sequences from field sample compared to reference sequences repositories and confirmed the validity of our approach. These findings should contribute to further vaccine development strategies based on PfEMP1 proteins
How different anthropogenic environments have shaped the genome of S. cerevisiae ?
No full textThe yeast Saccharomyces cerevisiae plays an important role in food and beverage fermentations. In order to known how environmental constraints imposed by anthropogenic niches have shaped S. cerevisiae genomes and phenotypes, we sequenced the genome of 82 S. cerevisiae strains from various ecological origins. Using these genomic data, we found additional genetic elements acquired by introgression or by horizontal transfer. Here, we present two remarkable examples of divergent adaptation associated to yeast domestication for wine and milk fermentation. Firstly, we demonstrated the role of oligopeptide transporters encoded by FOT genes, which are recently acquired by wine yeasts from Torulaspora microellipsoides. These transporters with a broader specificity than S. cerevisiae dipeptides transporters, confer a strong competitive advantage during grape must fermentation and thus play a key role in the adaptation of wine yeasts to the nitrogen-limited wine fermentation environment. The genome of cheese strains, secondly, present some particular features. Genes of the GAL locus were replaced by their orthologues from a species apparently basal to the Saccharomyces clade. Allelic exchange of this locus in a wine strain enables improves growth speed in a media containing the two hexoses such as when released from the hydrolysis of lactose. In addition, a highly divergent high affinity transporter GAL2 and a specific allele of the regulator GAL80 were found. This work highlights the remarkable plasticity of yeast genomes as a mechanism of their adaptation to their environment
