The poly-omics of ageing through individual-based metabolic modelling

Abstract Background Ageing can be classified in two different ways, chronological ageing and biological ageing. While chronological age is a measure of the time that has passed since birth, biological (also known as transcriptomic) ageing is defined by how time and the environment affect an individual in comparison to other individuals of the same chronological age. Recent research studies have shown that transcriptomic age is associated with certain genes, and that each of those genes has an effect size. Using these effect sizes we can calculate the transcriptomic age of an individual from their age-associated gene expression levels. The limitation of this approach is that it does not consider how these changes in gene expression affect the metabolism of individuals and hence their observable cellular phenotype. Results We propose a method based on poly-omic constraint-based models and machine learning in order to further the understanding of transcriptomic ageing. We use normalised CD4 T-cell gene expression data from peripheral blood mononuclear cells in 499 healthy individuals to create individual metabolic models. These models are then combined with a transcriptomic age predictor and chronological age to provide new insights into the differences between transcriptomic and chronological ageing. As a result, we propose a novel metabolic age predictor. Conclusions We show that our poly-omic predictors provide a more detailed analysis of transcriptomic ageing compared to gene-based approaches, and represent a basis for furthering our knowledge of the ageing mechanisms in human cells

A geographical model for the altitudinal zonation of mire types in the uplands of western Europe: the example of Les Monts du Forez in eastern France

The geographical distribution of mires in the oceanic mountain ranges of western Europe cannot be explained without bringing together a number of physical and human factors. In Les Monts du Forez, which are granitic and metamorphic mountains covering an area of 1800 km2 and rising to an altitude of 1634 m in the east of the French Massif Central, a series of mires on long slopes reflects the effects of changing combinations of these factors with altitude. The scale of variation falls within the limits of bioclimatic levels and is manifest as: the absence of mires at foothill levels below 900 m; small mires of anthropogenic origin and remnant peat at lower mountain levels between 900 m and 1100 m; peat systems where evolution has been more or less affected by human intervention at median mountain levels between 1100 m and 1250 m; large ombrotrophic mires, often naturally convex and dating from the first half of the Holocene epoch, at upper mountain levels between 1250 m and 1450 m; and small established mires that are more or less directly linked to human intervention at sub-alpine levels above 1450 m. The role of human societies appears to dominate, with exceptions in the upper mountain levels. Human influence presents in two forms, both of which are related to the old traditional farming methods of the region: the first is destruction of mires, mostly by drainage, and the second is mire creation through modifications of the hydrology of the valley floor and the vegetation cover. This spatial and multi-factor distribution of mires is a component that should be taken into account in relation to their conservation management

Assessing the potential impact of climate change on mire habitats in Central France: a multi-scale eco-hydroogical approach

International audienc

Assessing the potential impact of climate change on mire habitats in Central France: a multi-scale eco-hydroogical approach

International audienc

Evaluation of the use of PVC to estimate water table depth frequency curves and characterise the eco-hydrological niche of plant species in wetlands

International audienc

Evaluation of the use of PVC to estimate water table depth frequency curves and characterise the eco-hydrological niche of plant species in wetlands

International audienc

Modelling the impacts of catchment afforestation on the hydrological condition of groundwater-dependent acidic valley mires

International audienc

Origins of European biodiversity: palaeo-geographic signification of peat inception during the Holocene in the granitic eastern Massif Central (France)

International audienceMires are rare, unique environments that greatly contribute to biodiversity and occupy key functions in the hydrological cycle, but today many of these ecosystems are menaced, making conservation measures necessary. The efficiency of these measures is partly related to our knowledge of their origins and their development, a question rarely addressed. In this paper we examine the development of mires during the 10.000 last years (Holocene) in the eastern Massif Central, France, focusing on the contributions of climate change and human activities. Radiocarbon dates of the basal layers of 63 sites show that many mires formed around 7500 BP. During the Holocene, many mires were formed in the Atlantic period, characterised by warmer and wetter climatic conditions. At shorter time scales of 103–102 years, several other factors are related to peat inception, including topography, geomorphology and superficial geology, vegetation successions and human-induced changes. There is evidence that the building of small dams in headwater streams during the Iron age induced local water logging which then lead to the initiation and growth of mires. The influence of Bronze age communities is further demonstrated by new pollen analysis results. Forest clearing and grazing also favoured soil water logging, enabling peat inception. We consider human societies to be responsible for the formation of some mires. Human activities can be considered to having taken part in the development of the European biodiversity at least during the last 5 millennium

Peatland Contribution to Stream Organic Carbon Exports From a Montane Watershed

International audienceMountains contain many small and fragmented peatlands within watersheds. As they are difficult to monitor, their role in the water and carbon cycle is often disregarded. This study aims to assess the stream organic carbon exports from a montane peatland and characterizes its contribution to the water chemistry in a headstream watershed. High frequency in situ monitoring of turbidity and fDOM were used to quantify respectively particulate organic carbon (POC) and dissolved organic carbon (DOC) exports at the inlet and outlet of a peatland over three years in a French Pyrenean watershed (1,343 m.a.s.l.). The DOC and POC signals are both highly dynamic, characterized by numerous short peaks lasting from a few hours to a few days. Forty-six percent of the exports occurred during 9% of the time corresponding to the highest flows monitored at the outlet. Despite its small area (3%) within the watershed, the peatland contributes at least 63% of the DOC export at the outlet. The specific DOC flux ranges from 16.1 ± 0.4 to 34.6 ± 1.5 g m 2 year −1. POC contributes 17% of the total stream organic carbon exports from the watershed. As the frequency of extreme climatic events is expected to increase in the context of climate change, further studies should be conducted to understand the evolution of underestimated mountainous peatland carbon fluxes and their implication in the carbon cycle of headwaters. Plain Language Summary Since the last glacial period, peatlands have accumulated large stocks of organic carbon. Despite representing only 3% of global continental surfaces, they store about 22% of the continental soil carbon stock. In the context of global change, peatland carbon sequestration capacity needs to be carefully monitored. In addition to greenhouse gas exchanges with the atmosphere, determining this capacity requires the quantification of aquatic organic carbon exports. Aquatic organic carbon exports have rarely been investigated at mountainous peatlands. Moreover, global change is expected to drastically modify mountain hydrology, influencing aquatic carbon exports and carbon balance of mountainous peatlands. Using high frequency in situ instrumentation, this study shows the annual quantity of aquatic organic carbon exported from a montane peatland in the French Pyrenees is in the same range as Northern lowland peatlands. These highly variable exports mainly occur during high discharge events due to snowmelt or rainfalls. Despite its restricted area, this montane peatland is the main contributor of aquatic organic carbon in the watershed. Peatlands influence headwater chemistry and further study must be conducted to monitor the evolution of these mountainous carbon stocks

An expert system model for mapping tropical wetlands and peatlands reveals South America as the largest contributor

Wetlands are important providers of ecosystem services and key regulators of climate change. They positively contribute to global warming through their greenhouse gas emissions, and negatively through the accumulation of organic material in histosols, particularly in peatlands. Our understanding of wetlands’ services is currently constrained by limited knowledge on their distribution, extent, volume, interannual flood variability and disturbance levels. We present an expert system approach to estimate wetland and peatland areas, depths and volumes, which relies on three biophysical indices related to wetland and peat formation: (1) long-term water supply exceeding atmospheric water demand; (2) annually or seasonally water-logged soils; and (3) a geomorphological position where water is supplied and retained. Tropical and subtropical wetlands estimates reach 4.7 million km2 (Mkm2). In line with current understanding, the American continent is the major contributor (45%), and Brazil, with its Amazonian interfluvial region, contains the largest tropical wetland area (800,720 km2). Our model suggests, however, unprecedented extents and volumes of peatland in the tropics (1.7 Mkm2 and 7,268 (6,076–7,368) km3), which more than threefold current estimates. Unlike current understanding, our estimates suggest that South America and not Asia contributes the most to tropical peatland area and volume (ca. 44% for both) partly related to some yet unaccounted extended deep deposits but mainly to extended but shallow peat in the Amazon Basin. Brazil leads the peatland area and volume contribution. Asia hosts 38% of both tropical peat area and volume with Indonesia as the main regional contributor and still the holder of the deepest and most extended peat areas in the tropics. Africa hosts more peat than previously reported but climatic and topographic contexts leave it as the least peat-forming continent. Our results suggest large biases in our current understanding of the distribution, area and volumes of tropical peat and their continental contributions.<br/