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Excessive agricultural nitrogen use causes environmental problems globally1, to an extent that it has been suggested that a safe planetary boundary has been exceeded2. Earlier estimates for the planetary nitrogen boundary3,4, however, did not account for the spatial variability in both ecosystems’ sensitivity to nitrogen pollution and agricultural nitrogen losses. Here we use a spatially explicit model to establish regional boundaries for agricultural nitrogen surplus from thresholds for eutrophication of terrestrial and aquatic ecosystems and nitrate in groundwater. We estimate regional boundaries for agricultural nitrogen pollution and find both overuse and room for intensification of agricultural nitrogen. The aggregated global surplus boundary with respect to all thresholds is 43 megatonnes of nitrogen per year, which is 64 per cent lower than the current (2010) nitrogen surplus (119 megatonnes of nitrogen per year). Allowing the nitrogen surplus to increase to close yield gaps in regions where environmental thresholds are not exceeded lifts the planetary nitrogen boundary to 57 megatonnes of nitrogen per year. Feeding the world without trespassing regional and planetary nitrogen boundaries requires large increases in nitrogen use efficiencies accompanied by mitigation of non-agricultural nitrogen sources such as sewage water. This asks for coordinated action that recognizes the heterogeneity of agricultural systems, non-agricultural nitrogen losses and environmental vulnerabilities.

Excessive agricultural nitrogen use causes environmental problems globally

Protoplanetary disks, the clouds of interstellar gas and dust thought to be the precursors of solar systems, ours included, consist largely of amorphous grains of silicate. Yet the grains found in comets and meteorites (representing the early Solar System), and traced in the spectra of young stars, include large crystalline grains that must have undergone annealing or condensation at temperatures above 1,000 K, despite being surrounded by material that has never experienced such heating. This apparent anomaly has been the subject of much discussion and theorizing. Two papers published in this issue add to the discussion. Abraham et al. report mid-infrared features in the outburst spectrum of the young solar-like star EX Lupi that they attribute to crystalline forsterite. These features were not present before EX Lupi's recent outbust, so this may be the first direct observation of the crystal formation process in a celestial object. Annealing by heat from a stellar outburst is a crystal source not previously considered for protoplanetary disks. Dejan Vinkovic suggests another new mechanism that might produce crystals: infrared light arising from a protoplanetary disk can in theory lift grains bigger than 1 μm out of the inner disk, where they are pushed outwards by stellar radiation pressure while gliding above the disk. Grains re-enter the disk at radii where it is too cold to produce sufficient infrared radiation-pressure support for a given grain size and solid density. Our Solar System originated in a cloud of interstellar gas and amorphous dust, but cometary dust is mainly crystalline—and it is not clear how this crystallization occurred. The outburst spectrum of the young solar-like star EX Lupi shows mid-infrared features, attributed to crystalline forsterite, that were not present in quiescence, suggesting that crystals were produced via thermal annealing by heat from the outburst. This represents a new mechanism of crystal formation in protoplanetary disks. The Solar System originated in a cloud of interstellar gas and dust. The dust is in the form of amorphous silicate particles1,2 and carbonaceous dust. The composition of cometary material, however, shows that a significant fraction of the amorphous silicate dust was transformed into crystalline form during the early evolution of the protosolar nebula3. How and when this transformation happened has been a question of debate, with the main options being heating by the young Sun4,5 and shock heating6. Here we report mid-infrared features in the outburst spectrum of the young Sun-like star EX Lupi that were not present in quiescence. We attribute them to crystalline forsterite. We conclude that the crystals were produced through thermal annealing in the surface layer of the inner disk by heat from the outburst, a process that has hitherto not been considered. The observed lack of cold crystals excludes shock heating at larger radii.

The Red Rectangle(1) is the prototype of a class of carbon-rich reflection nebulae surrounding low-mass stars in the final stages of evolution. The central star of this nebula has ejected most of its layers (during the red-giant phase), which now form the surrounding cloud, and is rapidly evolving to a white dwarf. This star is also a member of a wide binary system(2), which is surrounded by a thick, dusty disk of material(3,4). Here we report infrared observations of the Red Rectangle that reveal the presence of oxygen-rich material: prominent emission bands from crystalline silicates, and absorption lines arising from carbon dioxide. The oxygen-rich material is located in the circumbinary disk, in contrast to the previously known carbon-rich dust, which is found mainly in the extended nebula(5'6). The properties of the oxygen-rich dust are similar to those of dusty disks surrounding young stars(7), which are believed to be the sites of planet formation. Grain processing, and perhaps even planet formation, may therefore also be occurring in the circumbinary disk of this evolved star.

It is becoming increasingly clear that the shape of the genome importantly influences transcription regulation. Pluripotent stem cells such as embryonic stem cells were recently shown to organize their chromosomes into topological domains that are largely invariant between cell types(1,2). Here we combine chromatin conformation capture technologies with chromatin factor binding data to demonstrate that inactive chromatin is unusually disorganized in pluripotent stem-cell nuclei. We show that gene promoters engage in contacts between topological domains in a largely tissue-independent manner, whereas enhancers have a more tissue-restricted interaction profile. Notably, genomic clusters of pluripotency factor binding sites find each other very efficiently, in a manner that is strictly pluripotent-stem-cell-specific, dependent on the presence of Oct4 and Nanog protein and inducible after artificial recruitment of Nanog to a selected chromosomal site. We conclude that pluripotent stem cells have a unique higher-order genome structure shaped by pluripotency factors. We speculate that this interactome enhances the robustness of the pluripotent state.

Detection of molecules using infrared spectroscopy probes the conditions and compositions of exoplanet atmospheres. Water (H2O), methane (CH4), carbon dioxide (CO2), and carbon monoxide (CO) have been detected in two hot Jupiters. These previous results relied on space-based telescopes that do not provide spectroscopic capability in the 2.4 - 5.2 micron spectral region. Here we report ground-based observations of the dayside emission spectrum for HD 189733b between 2.0-2.4 micron and 3.1-4.1 micron, where we find a bright emission feature. Where overlap with space-based instruments exists, our results are in excellent agreement with previous measurements. A feature at ~3.25 micron is unexpected and difficult to explain with models that assume local thermodynamic equilibrium (LTE) conditions at the 1 bar to 1 x 10-6 bar pressures typically sampled by infrared measurements. The most likely explanation for this feature is that it arises from non-LTE emission from CH4, similar to what is seen in the atmospheres of planets in our own Solar System. These results suggest that non-LTE effects may need to be considered when interpreting measurements of strongly irradiated exoplanets., Comment: 12 pages, 2 figures, published in Nature

Error-free repair of DNA double-strand breaks (DSBs) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway(1). In the absence of BRCA1-mediated HR, the administration of PARP inhibitors induces synthetic lethality of tumour cells of patients with breast or ovarian cancers(2,3). Despite the benefit of this tailored therapy, drug resistance can occur by HR restoration(4). Genetic reversion of BRCA1-inactivating mutations can be the underlying mechanism of drug resistance, but this does not explain resistance in all cases(5). In particular, little is known about BRCA1-independent restoration of HR. Here we show that loss of REV7 (also known as MAD2L2) in mouse and human cell lines re-establishes CTIP-dependent endresection of DSBs in BRCA1 deficient cells, leading to HR restoration and PARP inhibitor resistance, which is reversed by ATM kinase inhibition. REV7 is recruited to DSBs in a manner dependent on the H2AX-MDC1-RNF8-RNF168-53BP1 chromatin pathway, and seems to block HR and promote end joining in addition to its regulatory role in DNA damage tolerance(6). Finally, we establish that REV7 blocks DSB resection to promote non-homologous end-joining during immunoglobulin class switch recombination. Our results reveal an unexpected crucial function of REV7 downstream of 53BP1 in coordinating pathological DSB repair pathway choices in BRCA1-deficient cells.

Sulphur is depleted in cold dense molecular clouds with embedded young stellar objects, indicating that most of it probably resides in solid grains. Iron sulphide grains are the main sulphur species in cometary dust particles, but there has been no direct evidence for FeS in astronomical sources, which poses a considerable problem, because sulphur is a cosmically abundant element. Here we report laboratory infrared spectra of FeS grains from primitive meteorites, as well as from pyrrhotite ([Fe, Ni](1-x)S) grains in interplanetary dust, which show a broad FeS feature centred at approximately 23.5 micrometres. A similar broad feature is seen in the infrared spectra of young stellar objects, implying that FeS grains are an important but previously unrecognized component of circumstellar dust. The feature had previously been attributed to FeO. The observed astronomical line strengths are generally consistent with the depletion of sulphur from the gas phase, and with the average Galactic sulphur/silicon abundance ratio. We conclude that the missing sulphur has been found.

From research on agricultural systems in temperate regions, it is known that use of nitrogen fertilizers and animal manure results in release of nitrous (N2O) and nitric (NO) oxides to the atmosphere. The reason for caring about this phenomenon is the effect these gases may have on both global warming and atmospheric chemistry. From studies in the tropics, it now seems that releases of (N2O) and NO are much higher from tropical agricultural systems. Given the projected large increase in use of nitrogen fertilizer in such areas in the coming years, that conclusion warrants further attention.