Multi-Pluridisciplinary approach of the evolution of the agro-pastural activities in the surroundings of the " narse d'Espinasse " (French Massif Central, Puy de Dôme).

The ldquonarserdquo or peat marsh of Espinasse (Saulzet-le-Froid district) situated in the southern part of the Chaîne des Puys has been the subject of a new pollen analysis concentrating on the anthropogenic impact on vegetation evolution since the Sub-Boreal. Human occupation of the surroundings of the narse is dated as early as the Neolithic, which is usual for the region. There is nevertheless an isolated record of Fagopyrum related to the Neolithic. This is a unique occurrence in the Massif Central. For successive periods and up to the recent past, a dynamic of various anthropization phases has been reconstructed. The combination of palynological data with archaeological and historical sources has for certain periods, mainly from the 11th to 13th centuries, provided new insights on the social and technical management of the territory. Furthermore, geochemical and micromorphological characterisation of sedimentary organic matter has led to the identification of erosive crises and silting which would have followed massive tree cutting in the region. On the local scale, the highly degraded organic matter at the top of the peat profile is the consequence of the current drainage of the marsh

Modeling the effects of litter stoichiometry and soil mineral N availability on soil organic matter formation using CENTURY-CUE (v1.0)

Microbial decomposition of plant litter is a crucial process for the land carbon (C) cycle, as it directly controls the partitioning of litter C between CO2 released to the atmosphere versus the formation of new soil organic matter (SOM). Land surface models used to study the C cycle rarely considered flexibility in the decomposer C use efficiency (CUEd) defined by the fraction of decomposed litter C that is retained as SOM (as opposed to be respired). In this study, we adapted a conceptual formulation of CUEd based on assumption that litter decomposers optimally adjust their CUEd as a function of litter substrate C to nitrogen (N) stoichiometry to maximize their growth rates. This formulation was incorporated into the widely used CENTURY soil biogeochemical model and evaluated based on data from laboratory litter incubation experiments. Results indicated that the CENTURY model with new CUEd formulation was able to reproduce differences in respiration rate of litter with contrasting C&thinsp;:&thinsp;N ratios and under different levels of mineral N availability, whereas the default model with fixed CUEd could not. Using the model with flexible CUEd, we also illustrated that litter quality affected the long-term SOM formation. Litter with a small C&thinsp;:&thinsp;N ratio tended to form a larger SOM pool than litter with larger C&thinsp;:&thinsp;N ratios, as it could be more efficiently incorporated into SOM by microorganisms. This study provided a simple but effective formulation to quantify the effect of varying litter quality (N content) on SOM formation across temporal scales. Optimality theory appears to be suitable to predict complex processes of litter decomposition into soil C and to quantify how plant residues and manure can be harnessed to improve soil C sequestration for climate mitigation.</p

Spatial biases reduce the ability of Earth system models to simulate soil heterotrophic respiration fluxes

Heterotrophic respiration (Rh) is, at a global scale, one of the largest CO2 fluxes between the Earth's surface and atmosphere and may increase in the future. The previous generation of Earth system models (ESMs) was able to reproduce global fluxes relatively well, but at that, time no gridded products were available to perform an in-depth evaluation. The capacity of the new generation of ESMs used within the Coupled Model Intercomparison Project Phase 6 (CMIP6) to reproduce this flux has not been evaluated, meaning that the realism of resulting CO2 flux estimates is unclear. In this study, we combine recently released observational data on Rh and ESM simulations to evaluate the ability of 13 ESMs from CMIP6 to reproduce Rh. Only 4 of the 13 tested ESMs were able to reproduce the total Rh flux, but spatial analysis underlined important bias compensation for most of the ESMs, which generally showed an overestimation in tropical regions and an underestimation in arid regions. To identify the main drivers of the bias, we performed an analysis of the residuals and found that mean annual precipitation was the most important driver explaining the difference between ESM simulations and observation-derived products of Rh, with a higher bias between ESM simulations and Rh products where precipitation was high. Based on our results, next-generation ESMs should focus on improving the response of Rh to soil moisture.</p

Teaching molecular genetics: chapter 4—positional cloning of genetic disorders

Positional cloning is the approach of choice for the identification of genetic mutations underlying the pathological development of diseases with simple Mendelian inheritance. It consists of different consecutive steps, starting with recruitment of patients and DNA collection, that are critical to the overall process. A genetic analysis of the enrolled patients and their families is performed, based on genetic recombination frequencies generated by meiotic cross-overs and on genome-wide molecular studies, to define a critical DNA region of interest. This analysis culminates in a statistical estimate of the probability that disease features may segregate in the families independently or in association with specific molecular markers located in known regions. In this latter case, a marker can be defined as being linked to the disease manifestations. The genetic markers define an interval that is a function of their recombination frequencies with the disease, in which the disease gene is localised. The identification and characterisation of chromosome abnormalities as translocations, deletions and duplications by classical cytogenetic methods or by the newly developed microarray-based comparative genomic hybridisation (array CGH) technique may define extensions and borders of the genomic regions involved. The step following the definition of a critical genomic region is the identification of candidate genes that is based on the analysis of available databases from genome browsers. Positional cloning culminates in the identification of the causative gene mutation, and the definition of its functional role in the pathogenesis of the disorder, by the use of cell-based or animal-based experiments. More often, positional cloning ends with the generation of mice with homologous mutations reproducing the human clinical phenotype. Altogether, positional cloning has represented a fundamental step in the research on genetic renal disorders, leading to the definition of several disease mechanisms and allowing a proper diagnostic approach to many conditions

Representation of dissolved organic carbon in the JULES land surface model (vn4.4_JULES-DOCM)

Current global models of the carbon (C) cycle consider only vertical gas exchanges between terrestrial or oceanic reservoirs and the atmosphere, thus not considering the lateral transport of carbon from the continents to the oceans. Therefore, those models implicitly consider all of the C which is not respired to the atmosphere to be stored on land and hence overestimate the land C sink capability. A model that represents the whole continuum from atmosphere to land and into the ocean would provide a better understanding of the Earth's C cycle and hence more reliable historical or future projections. A first and critical step in that direction is to include processes representing the production and export of dissolved organic carbon in soils. Here we present an original representation of dissolved organic C (DOC) processes in the Joint UK Land Environment Simulator (JULES-DOCM) that integrates a representation of DOC production in terrestrial ecosystems based on the incomplete decomposition of organic matter, DOC decomposition within the soil column, and DOC export to the river network via leaching. The model performance is evaluated in five specific sites for which observations of soil DOC concentration are available. Results show that the model is able to reproduce the DOC concentration and controlling processes, including leaching to the riverine system, which is fundamental for integrating terrestrial and aquatic ecosystems. Future work should include the fate of exported DOC in the river system as well as DIC and POC export from soil

Migration of chemotactic bacteria in soft agar: role of gel concentration

We study the migration of chemotactic wild-type Escherichia coli populations in semisolid (soft) agar in the concentration range C = 0.15-0.5% (w/v). For C < 0.35%, expanding bacterial colonies display characteristic chemotactic rings. At C = 0.35%, however, bacteria migrate as broad circular bands rather than sharp rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally to our knowledge. For C = 0.4-0.5%, expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The migration front speed is weakly dependent on agar concentration at C < 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel transport parameter expressions accounting for perturbations of the chemotactic response by collisions with the agar. The model makes it possible to fit the observed front speed decay in the range C = 0.15-0.35%, and its solutions qualitatively reproduce the observed transition from chemotactic to growth/diffusion bands. We discuss the implications of our results for the study of bacteria in porous media and for the design of improved bacteriological chemotaxis assays.Comment: 28 pages, 5 figures. Published online at http://www.sciencedirect.com/science/article/pii/S000634951100721

Evolution of major milk proteins in Mus musculus and Mus spretus mouse species: a genoproteomic analysis

<p>Abstract</p> <p>Background</p> <p>Due to their high level of genotypic and phenotypic variability, <it>Mus spretus </it>strains were introduced in laboratories to investigate the genetic determinism of complex phenotypes including quantitative trait loci. <it>Mus spretus </it>diverged from <it>Mus musculus </it>around 2.5 million years ago and exhibits on average a single nucleotide polymorphism (SNP) in every 100 base pairs when compared with any of the classical laboratory strains. A genoproteomic approach was used to assess polymorphism of the major milk proteins between SEG/Pas and C57BL/6J, two inbred strains of mice representative of <it>Mus spretus </it>and <it>Mus musculus </it>species, respectively.</p> <p>Results</p> <p>The milk protein concentration was dramatically reduced in the SEG/Pas strain by comparison with the C57BL/6J strain (34 ± 9 g/L <it>vs</it>. 125 ± 12 g/L, respectively). Nine major proteins were identified in both milks using RP-HPLC, bi-dimensional electrophoresis and MALDI-Tof mass spectrometry. Two caseins (β and α_s1) and the whey acidic protein (WAP), showed distinct chromatographic and electrophoresis behaviours. These differences were partly explained by the occurrence of amino acid substitutions and splicing variants revealed by cDNA sequencing. A total of 34 SNPs were identified in the coding and 3'untranslated regions of the SEG/Pas <it>Csn1s1 </it>(11), <it>Csn2 </it>(7) and <it>Wap </it>(8) genes. In addition, a 3 nucleotide deletion leading to the loss of a serine residue at position 93 was found in the SEG/Pas <it>Wap </it>gene.</p> <p>Conclusion</p> <p>SNP frequencies found in three milk protein-encoding genes between <it>Mus spretus </it>and <it>Mus musculus </it>is twice the values previously reported at the whole genome level. However, the protein structure and post-translational modifications seem not to be affected by SNPs characterized in our study. Splicing mechanisms (cryptic splice site usage, exon skipping, error-prone junction sequence), already identified in casein genes from other species, likely explain the existence of multiple α_s1-casein isoforms both in SEG/Pas and C57BL/6J strains. Finally, we propose a possible mechanism by which the hallmark tandem duplication of a 18-nt exon (14 copies) may have occurred in the mouse genome.</p

Lowering water table reduces carbon sink strength and carbon stocks in northern peatlands

Peatlands at high latitudes have accumulated >400 Pg carbon (C) because saturated soil and cold temperatures suppress C decomposition. This substantial amount of C in Arctic and Boreal peatlands is potentially subject to increased decomposition if the water table (WT) decreases due to climate change, including permafrost thaw-related drying. Here, we optimize a version of the Organizing Carbon and Hydrology In Dynamic Ecosystems model (ORCHIDEE-PCH4) using site-specific observations to investigate changes in CO2 and CH4 fluxes as well as C stock responses to an experimentally manipulated decrease of WT at six northern peatlands. The unmanipulated control peatlands, with the WT 2 kg C m−2 over 100 years when WT is lowered by 50 cm, while permafrost peatlands temporally switched from C sinks to sources. These results highlight that reductions in C storage capacity in response to drying of northern peatlands are offset in part by reduced CH4 emissions, thus slightly reducing the positive carbon climate feedbacks of peatlands under a warmer and drier future climate scenario

Differential Expression of Non-Coding RNAs and Continuous Evolution of the X Chromosome in Testicular Transcriptome of Two Mouse Species

BACKGROUND: Tight regulation of testicular gene expression is a prerequisite for male reproductive success, while differentiation of gene activity in spermatogenesis is important during speciation. Thus, comparison of testicular transcriptomes between closely related species can reveal unique regulatory patterns and shed light on evolutionary constraints separating the species. METHODOLOGY/PRINCIPAL FINDINGS: Here, we compared testicular transcriptomes of two closely related mouse species, Mus musculus and Mus spretus, which diverged more than one million years ago. We analyzed testicular expression using tiling arrays overlapping Chromosomes 2, X, Y and mitochondrial genome. An excess of differentially regulated non-coding RNAs was found on Chromosome 2 including the intronic antisense RNAs, intergenic RNAs and premature forms of Piwi-interacting RNAs (piRNAs). Moreover, striking difference was found in the expression of X-linked G6pdx gene, the parental gene of the autosomal retrogene G6pd2. CONCLUSIONS/SIGNIFICANCE: The prevalence of non-coding RNAs among differentially expressed transcripts indicates their role in species-specific regulation of spermatogenesis. The postmeiotic expression of G6pdx in Mus spretus points towards the continuous evolution of X-chromosome silencing and provides an example of expression change accompanying the out-of-the X-chromosomal retroposition