Evaluation of the Potential for Soil Organic Carbon Content Monitoring With Farmers

Increasing soil organic carbon (SOC) content is crucial for soil quality and climate changemitigation. SOC monitoring is indispensable to the corresponding policies and shouldprovide results at farm scale to allow for incentives. In Switzerland, farmers performmandatory analyses of the SOC content of the 0–20 cm topsoil of every field, based ona composite sample, at least every 10 years. The corresponding results are stored in adatabase in canton of Geneva. These data may be relevant for topsoil SOC monitoring,in particular for carbon sequestration policies, provided that they show appropriatequality, which is analyzed in this study. The minimum detectable change (MDC) of pastresults calculated based on the observed SOC changes was 0.013% g g−1at cantonscale (2,700 fields). Based on extended sampling of three representative fields, differentsampling strategies were simulated to determine the best future sampling guidelines forfarmers. Collecting 20 aliquots with a gouge on the field diagonals was considered thebest sampling compromise with field MDC of∼0.1% g g−1and a sampling durationof 20 min. Compared to this procedure, former farmers’ sampling was not biased inaverage but showed a variance of 0.22% g g−1due to smaller number of aliquotsand varying sampling depths. Based on the best sampling results and assumptions onfarm-scale SOC variance or SOC differences, the MDCs at farm scale ranged from0.21 to 0.12% g g−1(5 fields) and 0.09 to 0.05% g g−1(30 fields), respectively.These MDCs are small compared to published monitoring networks MDCs and allowdetermining SOC change rates at farm scale, thus offering perspectives for inexpensiveand efficient monitoring in the frame of soil quality or climate mitigation incentives. Forthe latter, however, additional information with equivalent soil mass and deeper-layercarbon content would be necessary

Évaluer le stock de carbone dans les sols ::des principes à ne pas perdre de vue, une méthode simplifiée

Évaluer le stock de carbone organique du sol est devenu une activité de service à laquelle de nombreux acteurs se consacrent. Cette question est portée par les stratégies climat, depuis que la Cop21, en lançant l’initiative « 4 pour 1000 », a popularisé le potentiel de séquestration de carbone organique dans les sols comme une des technologies de séquestration du CO2 atmosphérique les plus prometteuses. Mais évaluer le stock de carbone dans les sols n’est pas si simple, rien qu’en matière de matériel utilisé, manière d’échantillonner, etc. Une équipe de recherche en Suisse a refait le point et nous livre ses conclusions

Endogenous fluctuations of OCT 4 and SOX 2 bias pluripotent cell fate decisions

SOX2 and OCT4 are pioneer transcription factors playing a key role in embryonic stem (ES) cell self‐renewal and differentiation. How temporal fluctuations in their expression levels bias lineage commitment is unknown. Here, we generated knock‐in reporter fusion ES cell lines allowing to monitor endogenous SOX2 and OCT4 protein fluctuations in living cells and to determine their impact on mesendodermal and neuroectodermal commitment. We found that small differences in SOX2 and OCT4 levels impact cell fate commitment in G1 but not in S phase. Elevated SOX2 levels modestly increased neuroectodermal commitment and decreased mesendodermal commitment upon directed differentiation. In contrast, elevated OCT4 levels strongly biased ES cells towards both neuroectodermal and mesendodermal fates in undirected differentiation. Using ATAC‐seq on ES cells gated for different endogenous SOX2 and OCT4 levels, we found that high OCT4 levels increased chromatin accessibility at differentiation‐associated enhancers. This suggests that small endogenous fluctuations of pioneer transcription factors can bias cell fate decisions by concentration‐dependent priming of differentiation‐associated enhancers

The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles

The function of membrane proteins is best understood if their structure in the lipid membrane is known. Here, we determined the structure of the mouse serotonin 5-HT3 receptor inserted in lipid bilayers to a resolution of 12 Å without stabilizing antibodies by cryo electron tomography and subtomogram averaging. The reconstruction reveals protein secondary structure elements in the transmembrane region, the extracellular pore, and the transmembrane channel pathway, showing an overall similarity to the available X-ray model of the truncated 5-HT3 receptor determined in the presence of a stabilizing nanobody. Structural analysis of the 5-HT3 receptor embedded in a lipid bilayer allowed the position of the membrane to be determined. Interactions between the densely packed receptors in lipids were visualized, revealing that the interactions were maintained by the short horizontal helices. In combination with methodological improvements, our approach enables the structural analysis of membrane proteins in response to voltage and ligand gating

Data from: Mitotic chromosome binding predicts transcription factor properties in interphase

Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding. How these properties affect their ability to occupy specific genomic sites and modify the epigenetic landscape is unclear. The association of TFs with mitotic chromosomes observed by fluorescence microscopy is largely mediated by non-specific DNA interactions and differs broadly between TFs. Here we combine quantitative measurements of mitotic chromosome binding (MCB) of 501 TFs, TF mobility measurements by fluorescence recovery after photobleaching, single molecule imaging of DNA binding, and mapping of TF binding and chromatin accessibility. TFs associating to mitotic chromosomes are enriched in DNA-rich compartments in interphase and display slower mobility in interphase and mitosis. Remarkably, MCB correlates with relative TF on-rates and genome-wide specific site occupancy, but not with TF residence times. This suggests that non-specific DNA binding properties of TFs regulate their search efficiency and occupancy of specific genomic sites

Single molecule tracking data and code of Raccaud et. al

The file contains single molecule tracks and Hoechst areas of nine transcription factors and the code to analyse lifetimes and pseudo-on-rates