A steady-state superradiant laser with less than one intracavity photon

The spectral purity of an oscillator is central to many applications, such as detecting gravity waves, defining the second, ground-state cooling and quantum manipulation of nanomechanical objects, and quantum computation. Recent proposals suggest that laser oscillators which use very narrow optical transitions in atoms can be orders of magnitude more spectrally pure than present lasers. Lasers of this high spectral purity are predicted to operate deep in the 'bad-cavity', or superradiant, regime, where the bare atomic linewidth is much less than the cavity linewidth. Here we demonstrate a Raman superradiant laser source in which spontaneous synchronization of more than one million rubidium-87 atomic dipoles is continuously sustained by less than 0.2 photons on average inside the optical cavity. By operating at low intracavity photon number, we demonstrate isolation of the collective atomic dipole from the environment by a factor of more than ten thousand, as characterized by cavity frequency pulling measurements. The emitted light has a frequency linewidth, measured relative to the Raman dressing laser, that is less than that of single-particle decoherence linewidths and more than ten thousand times less than the quantum linewidth limit typically applied to 'good-cavity' optical lasers, for which the cavity linewidth is much less than the atomic linewidth. These results demonstrate several key predictions for future superradiant lasers, which could be used to improve the stability of passive atomic clocks and which may lead to new searches for physics beyond the standard model.     

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes--so-called sporadic or simplex families--we sequenced all coding regions of the genome (the exome) for parent-child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected β-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.     

Possible tropical lakes on Titan from observations of dark terrain

Titan has clouds, rain and lakes--like Earth--but composed of methane rather than water. Unlike Earth, most of the condensable methane (the equivalent of 5?m depth globally averaged) lies in the atmosphere. Liquid detected on the surface (about 2?m deep) has been found by radar images only poleward of 50° latitude, while dune fields pervade the tropics. General circulation models explain this dichotomy, predicting that methane efficiently migrates to the poles from these lower latitudes. Here we report an analysis of near-infrared spectral images of the region between 20°?N and 20°?S latitude. The data reveal that the lowest fluxes in seven wavelength bands that probe Titan's surface occur in an oval region of about 60?×?40?km(2), which has been observed repeatedly since 2004. Radiative transfer analyses demonstrate that the resulting spectrum is consistent with a black surface, indicative of liquid methane on the surface. Enduring low-latitude lakes are best explained as supplied by subterranean sources (within the last 10,000 years), which may be responsible for Titan's methane, the continual photochemical depletion of which furnishes Titan's organic chemistry.     

Biodiversity and ecosystem stability in a decade-long grassland experiment

Human-driven ecosystem simplification has highlighted questions about how the number of species in an ecosystem influences its functioning. Although biodiversity is now known to affect ecosystem productivity, its effects on stability are debated. Here we present a long-term experimental field test of the diversity-stability hypothesis. During a decade of data collection in an experiment that directly controlled the number of perennial prairie species, growing-season climate varied considerably, causing year-to-year variation in abundances of plant species and in ecosystem productivity. We found that greater numbers of plant species led to greater temporal stability of ecosystem annual aboveground plant production. In particular, the decadal temporal stability of the ecosystem, whether measured with intervals of two, five or ten years, was significantly greater at higher plant diversity and tended to increase as plots matured. Ecosystem stability was also positively dependent on root mass, which is a measure of perenniating biomass. Temporal stability of the ecosystem increased with diversity, despite a lower temporal stability of individual species, because of both portfolio (statistical averaging) and overyielding effects. However, we found no evidence of a covariance effect. Our results indicate that the reliable, efficient and sustainable supply of some foods (for example, livestock fodder), biofuels and ecosystem services can be enhanced by the use of biodiversity.     

Palaeoceanography: methane release in the Early Jurassic period

Dramatic global warming, triggered by release of methane from clathrates, has been postulated to have occurred during the early Toarcian age in the Early Jurassic period. Kemp et al. claim that this methane was released at three points, as recorded by three sharp excursions of delta13C(org) of up to 3 per thousand magnitude. But they discount another explanation for the excursions: namely that some, perhaps all, of the rapid excursions could be a local signature of a euxinic basin caused by recycling of isotopically light carbon from the lower water column. This idea has been proposed previously (see ref. 3, for example) and is supported by the lack evidence for negative delta13C excursions in coeval belemnite rostra. Kemp et al. dismiss this alternative, claiming that each abrupt shift would have required the recycling of about double the amount of organic carbon that is currently present in the modern ocean; however, their measurements are not from an ocean but from a restricted, epicontinental seaway and so would not require whole-ocean mixing to achieve the excursions.     

Gene network shaping of inherent noise spectra

Recent work demonstrates that stochastic fluctuations in molecular populations have consequences for gene regulation. Previous experiments focused on noise sources or noise propagation through gene networks by measuring noise magnitudes. However, in theoretical analysis, we showed that noise frequency content is determined by the underlying gene circuits, leading to a mapping between gene circuit structure and the noise frequency range. An intriguing prediction from our previous studies was that negative autoregulation shifts noise to higher frequencies where it is more easily filtered out by gene networks--a property that may contribute to the prevalence of autoregulation motifs (for example, found in the regulation of approximately 40% of Escherichia coli genes). Here we measure noise frequency content in growing cultures of E. coli, and verify the link between gene circuit structure and noise spectra by demonstrating the negative autoregulation-mediated spectral shift. We further demonstrate that noise spectral measurements provide mechanistic insights into gene regulation, as perturbations of gene circuit parameters are discernible in the measured noise frequency ranges. These results suggest that noise spectral measurements could facilitate the discovery of novel regulatory relationships.     

Mechanisms of drug inhibition of signalling molecules

The emergence of tumour-specific, molecularly targeted agents signifies a paradigm shift in cancer therapy, with less reliance on drugs that non-discriminately kill tumour and host cells. Although the diversity of targets giving rise to this new generation of anticancer drugs has expanded, many challenges persist in the design of effective treatment regimens. The complex interplay of signal-transduction pathways further complicates the customization of cancer treatments to target single mechanisms. However, despite uncertainty over precise or dominant mechanisms of action, especially for compounds targeting multiple gene products, emerging agents are producing significant therapeutic advances against a broad range of human cancers.     

A single amino acid governs enhanced activity of DinB DNA polymerases on damaged templates

Translesion synthesis (TLS) by Y-family DNA polymerases is a chief mechanism of DNA damage tolerance. Such TLS can be accurate or error-prone, as it is for bypass of a cyclobutane pyrimidine dimer by DNA polymerase eta (XP-V or Rad30) or bypass of a (6-4) TT photoproduct by DNA polymerase V (UmuD'2C), respectively. Although DinB is the only Y-family DNA polymerase conserved among all domains of life, the biological rationale for this striking conservation has remained enigmatic. Here we report that the Escherichia coli dinB gene is required for resistance to some DNA-damaging agents that form adducts at the N2-position of deoxyguanosine (dG). We show that DinB (DNA polymerase IV) catalyses accurate TLS over one such N2-dG adduct (N2-furfuryl-dG), and that DinB and its mammalian orthologue, DNA polymerase kappa, insert deoxycytidine (dC) opposite N2-furfuryl-dG with 10-15-fold greater catalytic proficiency than opposite undamaged dG. We also show that mutating a single amino acid, the 'steric gate' residue of DinB (Phe13 --> Val) and that of its archaeal homologue Dbh (Phe12 --> Ala), separates the abilities of these enzymes to perform TLS over N2-dG adducts from their abilities to replicate an undamaged template. We propose that DinB and its orthologues are specialized to catalyse relatively accurate TLS over some N2-dG adducts that are ubiquitous in nature, that lesion bypass occurs more efficiently than synthesis on undamaged DNA, and that this specificity may be achieved at least in part through a lesion-induced conformational change.