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14 mars 2017

3D structures of individual mammalian genomes studied by single-cell Hi-C [Nature]

The folding of genomic DNA from the beads-on-a-string-like structure of nucleosomes into higher-order assemblies is crucially linked to nuclear processes. Here we calculate 3D structures of entire mammalian genomes using data from a new chromosome conformation capture procedure that allows us to first image and then process single cells. The technique enables genome folding to be examined at a scale of less than 100 kb, and chromosome structures to be validated.(...)

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14 mars 2017

Reconstructing the genome of the most recent common ancestor of flowering plants [Nature Genetics]

Keywords : genomics, plant genetics

We describe here the reconstruction of the genome of the most recent common ancestor (MRCA) of modern monocots and eudicots, accounting for 95% of extant angiosperms, with its potential repertoire of 22,899 ancestral genes conserved in present-day crops. The MRCA provides a starting point for deciphering the reticulated evolutionary plasticity between species (rapidly versus slowly evolving lineages), subgenomes (pre- versus post-duplication blocks), genomic compartments (stable versus labile loci), genes (ancestral versus species-specific genes) and functions (gained versus lost ontologies), the key mutational forces driving the success of polyploidy in crops.(...)

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14 mars 2017

Reproducibility of computational workflows is automated using continuous analysis [Nature Biotechnology]

Keywords : data publication and archiving, publishing, software

Replication, validation and extension of experiments are crucial for scientific progress. Computational experiments are scriptable and should be easy to reproduce. However, computational analyses are designed and run in a specific computing environment, which may be difficult or impossible to match using written instructions. We report the development of continuous analysis, a workflow that enables reproducible computational analyses. Continuous analysis combines Docker, a container technology akin to virtual machines, with continuous integration, a software development technique, to automatically rerun a computational analysis whenever updates or improvements are made to source code or data. This enables researchers to reproduce results without contacting the study authors. Continuous analysis allows reviewers, editors or readers to verify reproducibility without manually downloading and rerunning code and can provide an audit trail for analyses of data that cannot be shared.

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12 mars 2017

The whole-soil carbon flux in response to warming [Science / Report]

Soil organic carbon harbors three times as much carbon as Earth’s atmosphere, and its decomposition is a potentially large climate change feedback and major source of uncertainty in climate projections. The response of whole-soil profiles to warming has not been tested in situ. In this deep warming experiment in mineral soil, CO2 production from all soil depths increased significantly with 4°C warming—annual soil respiration increased by 34-37%. All depths responded to warming with similar temperature sensitivities, driven by decomposition of decadal-aged carbon. Whole-soil warming reveals a larger soil respiration response than many in situ experiments, most of which only warm the surface soil, and models.

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12 mars 2017

Many shades of gray—The context-dependent performance of organic agriculture [Science Advances / Review]

Organic agriculture is often proposed as a more sustainable alternative to current conventional agriculture. We assess the current understanding of the costs and benefits of organic agriculture across multiple production, environmental, producer, and consumer dimensions. Organic agriculture shows many potential benefits (including higher biodiversity and improved soil and water quality per unit area, enhanced profitability, and higher nutritional value) as well as many potential costs including lower yields and higher consumer prices. However, numerous important dimensions have high uncertainty, particularly the environmental performance when controlling for lower organic yields, but also yield stability, soil erosion, water use, and labor conditions. We identify conditions that influence the relative performance of organic systems, highlighting areas for increased research and policy support.

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