Volume 495 Issue 7442


Disciplinary action p.409

How scientists share and reuse information is driven by technology but shaped by discipline.

doi: 10.1038/495409b

Under the gun p.409

A ban on advocacy and promotion of gun control is keeping US agencies from conducting research that is sorely needed to inform policy on firearms and prevent shootings.

doi: 10.1038/495409a

Push the boat out p.410

The latest private research vessel to be launched could open up the world of marine science.

doi: 10.1038/495410a


News Features

A new page p.425

A special issue of Nature looks at the transformation taking place in scientific publishing.

doi: 10.1038/495425a

The library reboot p.430

As scientific publishing moves to embrace open data, libraries and researchers are trying to keep up.

doi: 10.1038/495430a

News & Views

Persuasive evidence on HIV policy p.452

Antiretroviral therapy has revolutionized the fight against the HIV/AIDS pandemic. Surveillance analyses of a large population in rural South Africa make a compelling case that sustained support for this therapy is essential.

doi: 10.1038/495452a

Nanoparticle structures served up on a tray p.453

A neat approach that involves laying an array of nanoparticles on a graphene sheet supported on an iridium substrate has allowed accurate measurement of the nanoparticles' atomic structure.

doi: 10.1038/495453a

How the ocean exhales p.454

A record of biogenic opal production in the subtropical Atlantic Ocean fuels the theory that ocean circulation, rather than winds, drove the release of carbon dioxide from deep marine waters at the end of the last ice age. See Letter p.495

doi: 10.1038/495454a

One size fits most p.456

Crystalline 'sponges' offer a way to impose order on small molecules so that their structures can be solved by X-ray crystallography. This enables nanogram quantities of material to be analysed using the technique. See Article p.461

doi: 10.1038/495456a

Receptor signals come in waves p.457

The activity of G-protein-coupled receptors is not limited to the cell surface. Evidence from microscopy points to three temporally, spatially and perhaps functionally distinct waves of signalling by these receptors. See Letter p.534

doi: 10.1038/nature12086

Tubular worms from the Burgess Shale p.458

The discovery, in 500-million-year-old rocks, of fossil acorn worms that lived in tubes illuminates the debate about whether the ancestor of vertebrates was a mobile worm-like animal or a sessile colony dweller. See Letter p.503

doi: 10.1038/nature11963



Carbon monoxide in clouds at low metallicity in the dwarf irregular galaxy WLM p.487

Carbon monoxide (CO) is the primary tracer for interstellar clouds where stars form, but it has never been detected in galaxies in which the oxygen abundance relative to hydrogen is less than 20 per cent of that of the Sun, even though such ‘low-metallicity’ galaxies often form stars. This raises the question of whether stars can form in dense gas without molecules, cooling to the required near-zero temperatures by atomic transitions and dust radiation rather than by molecular line emission; and it highlights uncertainties about star formation in the early Universe, when the metallicity was generally low. Here we report the detection of CO in two regions of a local dwarf irregular galaxy, WLM, where the metallicity is 13 per cent of the solar value. We use new submillimetre observations and archival far-infrared observations to estimate the cloud masses, which are both slightly greater than 100,000 solar masses. The clouds have produced stars at a rate per molecule equal to 10 per cent of that in the local Orion nebula cloud. The CO fraction of the molecular gas is also low, about 3 per cent of the Milky Way value. These results suggest that in small galaxies both star-forming cores and CO molecules become increasingly rare in molecular hydrogen clouds as the metallicity decreases.

doi: 10.1038/nature11933

Evidence for sympathetic vibrational cooling of translationally cold molecules p.490

Compared with atoms, molecules have a rich internal structure that offers many opportunities for technological and scientific advancement. The study of this structure could yield critical insights into quantum chemistry, new methods for manipulating quantum information, and improved tests of discrete symmetry violation and fundamental constant variation. Harnessing this potential typically requires the preparation of cold molecules in their quantum rovibrational ground state. However, the molecular internal structure severely complicates efforts to produce such samples. Removal of energy stored in long-lived vibrational levels is particularly problematic because optical transitions between vibrational levels are not governed by strict selection rules, which makes laser cooling difficult. Additionally, traditional collisional, or sympathetic, cooling methods are inefficient at quenching molecular vibrational motion. Here we experimentally demonstrate that the vibrational motion of trapped BaCl+ molecules is quenched by collisions with ultracold calcium atoms at a rate comparable to the classical scattering, or Langevin, rate. This is over four orders of magnitude more efficient than traditional sympathetic cooling schemes. The high cooling rate, a consequence of a strong interaction potential (due to the high polarizability of calcium), along with the low collision energies involved, leads to molecular samples with a vibrational ground-state occupancy of at least 90 per cent. Our demonstration uses a novel thermometry technique that relies on relative photodissociation yields. Although the decrease in vibrational temperature is modest, with straightforward improvements it should be possible to produce molecular samples with a vibrational ground-state occupancy greater than 99 per cent in less than 100 milliseconds. Because sympathetic cooling of molecular rotational motion is much more efficient than vibrational cooling in traditional systems, we expect that the method also allows efficient cooling of the rotational motion of the molecules. Moreover, the technique should work for many different combinations of ultracold atoms and molecules.

doi: 10.1038/nature11937

Deglacial pulses of deep-ocean silicate into the subtropical North Atlantic Ocean p.495

Growing evidence suggests that the low atmospheric CO2 concentration of the ice ages resulted from enhanced storage of CO2 in the ocean interior, largely as a result of changes in the Southern Ocean. Early in the most recent deglaciation, a reduction in North Atlantic overturning circulation seems to have driven CO2 release from the Southern Ocean, but the mechanism connecting the North Atlantic and the Southern Ocean remains unclear. Biogenic opal export in the low-latitude ocean relies on silicate from the underlying thermocline, the concentration of which is affected by the circulation of the ocean interior. Here we report a record of biogenic opal export from a coastal upwelling system off the coast of northwest Africa that shows pronounced opal maxima during each glacial termination over the past 550,000 years. These opal peaks are consistent with a strong deglacial reduction in the formation of silicate-poor glacial North Atlantic intermediate water (GNAIW). The loss of GNAIW allowed mixing with underlying silicate-rich deep water to increase the silicate supply to the surface ocean. An increase in westerly-wind-driven upwelling in the Southern Ocean in response to the North Atlantic change has been proposed to drive the deglacial rise in atmospheric CO2 (refs 3, 4). However, such a circulation change would have accelerated the formation of Antarctic intermediate water and sub-Antarctic mode water, which today have as little silicate as North Atlantic Deep Water and would have thus maintained low silicate concentrations in the Atlantic thermocline. The deglacial opal maxima reported here suggest an alternative mechanism for the deglacial CO2 release. Just as the reduction in GNAIW led to upward silicate transport, it should also have allowed the downward mixing of warm, low-density surface water to reach into the deep ocean. The resulting decrease in the density of the deep Atlantic relative to the Southern Ocean surface promoted Antarctic overturning, which released CO2 to the atmosphere.

doi: 10.1038/nature12006

Electrical image of passive mantle upwelling beneath the northern East Pacific Rise p.499

Melt generated by mantle upwelling is fundamental to the production of new oceanic crust at mid-ocean ridges, yet the forces controlling this process are debated. Passive-flow models predict symmetric upwelling due to viscous drag from the diverging tectonic plates, but have been challenged by geophysical observations of asymmetric upwelling that suggest anomalous mantle pressure and temperature gradients, and by observations of concentrated upwelling centres consistent with active models where buoyancy forces give rise to focused convective flow. Here we use sea-floor magnetotelluric soundings at the fast-spreading northern East Pacific Rise to image mantle electrical structure to a depth of about 160 kilometres. Our data reveal a symmetric, high-conductivity region at depths of 20–90 kilometres that is consistent with partial melting of passively upwelling mantle. The triangular region of conductive partial melt matches passive-flow predictions, suggesting that melt focusing to the ridge occurs in the porous melting region rather than along the shallower base of the thermal lithosphere. A deeper conductor observed east of the ridge at a depth of more than 100 kilometres is explained by asymmetric upwelling due to viscous coupling across two nearby transform faults. Significant electrical anisotropy occurs only in the shallowest mantle east of the ridge axis, where high vertical conductivity at depths of 10–20 kilometres indicates localized porous conduits. This suggests that a coincident seismic-velocity anomaly is evidence of shallow magma transport channels rather than deeper off-axis upwelling. We interpret the mantle electrical structure as evidence that plate-driven passive upwelling dominates this ridge segment, with dynamic forces being negligible.

doi: 10.1038/nature11932

Tubicolous enteropneusts from the Cambrian period p.503

Hemichordates are a marine group that, apart from one monospecific pelagic larval form, are represented by the vermiform enteropneusts and minute colonial tube-dwelling pterobranchs. Together with echinoderms, they comprise the clade Ambulacraria. Despite their restricted diversity, hemichordates provide important insights into early deuterostome evolution, notably because of their pharyngeal gill slits. Hemichordate phylogeny has long remained problematic, not least because the nature of any transitional form that might serve to link the anatomically disparate enteropneusts and pterobranchs is conjectural. Hence, inter-relationships have also remained controversial. For example, pterobranchs have sometimes been compared to ancestral echinoderms. Molecular data identify enteropneusts as paraphyletic, and harrimaniids as the sister group of pterobranchs. Recent molecular phylogenies suggest that enteropneusts are probably basal within hemichordates, contrary to previous views, but otherwise provide little guidance as to the nature of the primitive hemichordate. In addition, the hemichordate fossil record is almost entirely restricted to peridermal skeletons of pterobranchs, notably graptolites. Owing to their low preservational potentials, fossil enteropneusts are exceedingly rare, and throw no light on either hemichordate phylogeny or the proposed harrimaniid–pterobranch transition. Here we describe an enteropneust, Spartobranchus tenuis (Walcott, 1911), from the Middle Cambrian-period (Series 3, Stage 5) Burgess Shale. It is remarkably similar to the extant harrimaniids, but differs from all known enteropneusts in that it is associated with a fibrous tube that is sometimes branched. We suggest that this is the precursor of the pterobranch periderm, and supports the hypothesis that pterobranchs are miniaturized and derived from an enteropneust-like worm. It also shows that the periderm was acquired before size reduction and acquisition of feeding tentacles, and that coloniality emerged through aggregation of individuals, perhaps similar to the Cambrian rhabdopleurid Fasciculitubus. The presence of both enteropneusts and pterobranchs in Middle Cambrian strata, suggests that hemichordates originated at the onset of the Cambrian explosion.

doi: 10.1038/nature12017

Preservation of ovarian follicles reveals early evolution of avian reproductive behaviour p.507

The two groups of archosaurs, crocodilians and birds, form an extant phylogenetic bracket for understanding the reproductive behaviour of dinosaurs. This behaviour is inferred from preserved nests and eggs, and even gravid individuals. Data indicate that many ‘avian’ traits were already present in Paraves—the clade that includes birds and their close relatives—and that the early evolution of the modern avian form of reproduction was already well on its way. Like living neornithine birds, non-avian maniraptorans had daily oviposition and asymmetrical eggs with complex shell microstructure, and were known to protect their clutches. However, like crocodilians, non-avian maniraptorans had two active oviducts (one present in living birds), relatively smaller eggs, and may not have turned their eggs in the way that living birds do. Here we report on the first discovery of fossilized mature or nearly mature ovarian follicles, revealing a previously undocumented stage in dinosaur reproduction: reproductively active females near ovulation. Preserved in a specimen of the long bony-tailed Jeholornis and two enantiornithine birds from the Early Cretaceous period lacustrine Jehol Biota in northeastern China, these discoveries indicate that basal birds only had one functional ovary, but retained primitive morphologies as a result of their lower metabolic rate relative to living birds. They also indicate that basal birds reached sexual maturity before skeletal maturity, as in crocodiles and paravian dinosaurs. Differences in follicular morphology between Jeholornis and the enantiornithines are interpreted as forming an evolutionary gradient from the reproductive condition in paravian dinosaurs towards neornithine birds. Furthermore, differences between the two enantiornithines indicate that this lineage might also have evolved advanced reproductive traits in parallel to the neornithine lineage.

doi: 10.1038/nature11985

Accelerated gene evolution through replication–transcription conflicts p.512

Several mechanisms that increase the rate of mutagenesis across the entire genome have been identified; however, how the rate of evolution might be promoted in individual genes is unclear. Most genes in bacteria are encoded on the leading strand of replication. This presumably avoids the potentially detrimental head-on collisions that occur between the replication and transcription machineries when genes are encoded on the lagging strand. Here we identify the ubiquitous (core) genes in Bacillus subtilis and determine that 17% of them are on the lagging strand. We find a higher rate of point mutations in the core genes on the lagging strand compared with those on the leading strand, with this difference being primarily in the amino-acid-changing (nonsynonymous) mutations. We determine that, overall, the genes under strong negative selection against amino-acid-changing mutations tend to be on the leading strand, co-oriented with replication. In contrast, on the basis of the rate of convergent mutations, genes under positive selection for amino-acid-changing mutations are more commonly found on the lagging strand, indicating faster adaptive evolution in many genes in the head-on orientation. Increased gene length and gene expression amounts are positively correlated with the rate of accumulation of nonsynonymous mutations in the head-on genes, suggesting that the conflict between replication and transcription could be a driving force behind these mutations. Indeed, using reversion assays, we show that the difference in the rate of mutagenesis of genes in the two orientations is transcription dependent. Altogether, our findings indicate that head-on replication–transcription conflicts are more mutagenic than co-directional conflicts and that these encounters can significantly increase adaptive structural variation in the coded proteins. We propose that bacteria, and potentially other organisms, promote faster evolution of specific genes through orientation-dependent encounters between DNA replication and transcription.

doi: 10.1038/nature11989

A central role for TFIID in the pluripotent transcription circuitry p.516

Embryonic stem (ES) cells are pluripotent and characterized by open chromatin and high transcription levels, achieved through auto-regulatory and feed-forward transcription factor loops. ES-cell identity is maintained by a core of factors including Oct4 (also known as Pou5f1), Sox2, Klf4, c-Myc (OSKM) and Nanog, and forced expression of the OSKM factors can reprogram somatic cells into induced pluripotent stem cells (iPSCs) resembling ES cells. These gene-specific factors for RNA-polymerase-II-mediated transcription recruit transcriptional cofactors and chromatin regulators that control access to and activity of the basal transcription machinery on gene promoters. How the basal transcription machinery is involved in setting and maintaining the pluripotent state is unclear. Here we show that knockdown of the transcription factor IID (TFIID) complex affects the pluripotent circuitry in mouse ES cells and inhibits reprogramming of fibroblasts. TFIID subunits and the OSKM factors form a feed-forward loop to induce and maintain a stable transcription state. Notably, transient expression of TFIID subunits greatly enhanced reprogramming. These results show that TFIID is critical for transcription-factor-mediated reprogramming. We anticipate that, by creating plasticity in gene expression programs, transcription complexes such as TFIID assist reprogramming into different cellular states.

doi: 10.1038/nature11970

A syringe-like injection mechanism in Photorhabdus luminescens toxins p.520

Photorhabdus luminescens is an insect pathogenic bacterium that is symbiotic with entomopathogenic nematodes. On invasion of insect larvae, P. luminescens is released from the nematodes and kills the insect through the action of a variety of virulence factors including large tripartite ABC-type toxin complexes (Tcs). Tcs are typically composed of TcA, TcB and TcC proteins and are biologically active only when complete. Functioning as ADP-ribosyltransferases, TcC proteins were identified as the actual functional components that induce actin-clustering, defects in phagocytosis and cell death. However, little is known about the translocation of TcC into the cell by the TcA and TcB components. Here we show that TcA in P. luminescens (TcdA1) forms a transmembrane pore and report its structure in the prepore and pore state determined by cryoelectron microscopy. We find that the TcdA1 prepore assembles as a pentamer forming an α-helical, vuvuzela-shaped channel less than 1.5 nanometres in diameter surrounded by a large outer shell. Membrane insertion is triggered not only at low pH as expected, but also at high pH, explaining Tc action directly through the midgut of insects. Comparisons with structures of the TcdA1 pore inserted into a membrane and in complex with TcdB2 and TccC3 reveal large conformational changes during membrane insertion, suggesting a novel syringe-like mechanism of protein translocation. Our results demonstrate how ABC-type toxin complexes bridge a membrane to insert their lethal components into the cytoplasm of the host cell. We believe that the proposed mechanism is characteristic of the whole ABC-type toxin family. This explanation of toxin translocation is a step towards understanding the host–pathogen interaction and the complex life cycle of P. luminescens and other pathogens, including human pathogenic bacteria, and serves as a strong foundation for the development of biopesticides.

doi: 10.1038/nature11987

Critical role of Trib1 in differentiation of tissue-resident M2-like macrophages p.524

Macrophages consist of at least two subgroups, M1 and M2 (refs 1, 2, 3). Whereas M1 macrophages are proinflammatory and have a central role in host defence against bacterial and viral infections, M2 macrophages are associated with responses to anti-inflammatory reactions, helminth infection, tissue remodelling, fibrosis and tumour progression. Trib1 is an adaptor protein involved in protein degradation by interacting with COP1 ubiquitin ligase. Genome-wide association studies in humans have implicated TRIB1 in lipid metabolism. Here we show that Trib1 is critical for the differentiation of F4/80+MR+ tissue-resident macrophages—that share characteristics with M2 macrophages (which we term M2-like macrophages)—and eosinophils but not for the differentiation of M1 myeloid cells. Trib1 deficiency results in a severe reduction of M2-like macrophages in various organs, including bone marrow, spleen, lung and adipose tissues. Aberrant expression of C/EBPα in Trib1-deficient bone marrow cells is responsible for the defects in macrophage differentiation. Unexpectedly, mice lacking Trib1 in haematopoietic cells show diminished adipose tissue mass accompanied by evidence of increased lipolysis, even when fed a normal diet. Supplementation of M2-like macrophages rescues the pathophysiology, indicating that a lack of these macrophages is the cause of lipolysis. In response to a high-fat diet, mice lacking Trib1 in haematopoietic cells develop hypertriglyceridaemia and insulin resistance, together with increased proinflammatory cytokine gene induction. Collectively, these results demonstrate that Trib1 is critical for adipose tissue maintenance and suppression of metabolic disorders by controlling the differentiation of tissue-resident M2-like macrophages.

doi: 10.1038/nature11930

CLASP-mediated cortical microtubule organization guides PIN polarization axis p.529

Recent evidence indicates a correlation between orientation of the plant cortical microtubule cytoskeleton and localization of polar cargoes. However, the molecules and mechanisms that create this correlation have remained unknown. Here we show that, in Arabidopsis thaliana, the microtubule orientation regulators CLASP and MAP65 (refs 3, 4) control the abundance of polarity regulator PINOID kinase at the plasma membrane. By localized upregulation of clathrin-dependent endocytosis at cortical microtubule- and clathrin-rich domains orthogonal to the axis of polarity, PINOID accelerates the removal of auxin transporter PIN proteins from those sites. This mechanism links directional microtubule organization to the polar localization of auxin transporter PIN proteins, and clarifies how microtubule-enriched cell sides are kept distinct from polar delivery domains. Our results identify the molecular machinery that connects microtubule organization to the regulation of the axis of PIN polarization.

doi: 10.1038/nature11980

Conformational biosensors reveal GPCR signalling from endosomes p.534

A long-held tenet of molecular pharmacology is that canonical signal transduction mediated by G-protein-coupled receptor (GPCR) coupling to heterotrimeric G proteins is confined to the plasma membrane. Evidence supporting this traditional view is based on analytical methods that provide limited or no subcellular resolution. It has been subsequently proposed that signalling by internalized GPCRs is restricted to G-protein-independent mechanisms such as scaffolding by arrestins, or GPCR activation elicits a discrete form of persistent G protein signalling, or that internalized GPCRs can indeed contribute to the acute G-protein-mediated response. Evidence supporting these various latter hypotheses is indirect or subject to alternative interpretation, and it remains unknown if endosome-localized GPCRs are even present in an active form. Here we describe the application of conformation-specific single-domain antibodies (nanobodies) to directly probe activation of the β2-adrenoceptor, a prototypical GPCR, and its cognate G protein, Gs (ref. 12), in living mammalian cells. We show that the adrenergic agonist isoprenaline promotes receptor and G protein activation in the plasma membrane as expected, but also in the early endosome membrane, and that internalized receptors contribute to the overall cellular cyclic AMP response within several minutes after agonist application. These findings provide direct support for the hypothesis that canonical GPCR signalling occurs from endosomes as well as the plasma membrane, and suggest a versatile strategy for probing dynamic conformational change in vivo.

doi: 10.1038/nature12000