Volume 500 Issue 7462


In addition p.253

Conflicts of interest and gaps in data contaminate US oversight of food additives.

doi: 10.1038/500253b

Beyond headscarf symbolism p.253

Turkey’s scientists show they no longer want to expend their energy on political confrontation, but political volatility is threatening their efforts to work in peace.

doi: 10.1038/500253a


News Features

Corrupted memory p.268

Elizabeth Loftus has spent decades exposing flaws in eyewitness testimony. Her ideas are gaining fresh traction in the US legal system.

doi: 10.1038/500268a

News & Views

Composite for smarter windows p.278

Glass has been prepared that selectively absorbs visible and near-infrared light when an electrochemical voltage is applied. This opens the way to 'smart' windows that block heat on demand, with or without optical transparency. See Letter p.323

doi: 10.1038/500278a

RNA exerts self-control p.279

A crystal structure of two bound RNA molecules not only provides insight into how regulatory riboswitch sequences affect messenger RNA expression, but also expands our understanding of RNA structure and architecture. See Letter p.363

doi: 10.1038/nature12460

Primed for take-off p.280

Gene therapy is finally getting a bumper crop of data that show clinical efficacy after fine-tuning of key parameters that control safety and potency. Supporting evidence comes from treatment of two life-threatening human diseases.

doi: 10.1038/500280a

Reliable teleportation p.282

Two complementary experiments have demonstrated deterministic quantum teleportation of quantum bits. The results could find applications in quantum communications and computing. See Letters p.315 & p.319

doi: 10.1038/500282a

Metabolite turns master regulator p.283

The phenomenon of catabolite repression enables microorganisms to use their favourite carbon source first. New work reveals α-ketoacids as key effectors of this process, with their levels regulating gene expression. See Article p.301

doi: 10.1038/nature12544

A weapon for bacterial warfare p.284

The finding that bacteria use a sharp spike to deliver toxins into competing microorganisms, and that this mechanism co-evolved with a bacteriophage structure, presents a new vision of bacterial secretion systems. See Letter p.350

doi: 10.1038/nature12545


Climate extremes and the carbon cycle p.287

The terrestrial biosphere is a key component of the global carbon cycle and its carbon balance is strongly influenced by climate. Continuing environmental changes are thought to increase global terrestrial carbon uptake. But evidence is mounting that climate extremes such as droughts or storms can lead to a decrease in regional ecosystem carbon stocks and therefore have the potential to negate an expected increase in terrestrial carbon uptake. Here we explore the mechanisms and impacts of climate extremes on the terrestrial carbon cycle, and propose a pathway to improve our understanding of present and future impacts of climate extremes on the terrestrial carbon budget.

doi: 10.1038/nature12350


Translating dosage compensation to trisomy 21 p.296

This study uses zinc-finger nucleases to target an inducible XIST transgene into chromosome 21 from trisomic Down’s syndrome pluripotent stem cells; the XIST RNA coats one copy of chromosome 21 and triggers whole chromosome silencing, suggesting the potential of this approach for studying chromosomal disorders such as Down’s syndrome and for research into gene therapies.

doi: 10.1038/nature12394

Coordination of bacterial proteome with metabolism by cyclic AMP signalling p.301

Cyclic AMP, one of the earliest discovered and most intensely studied signalling molecules in molecular biology, is widely believed to signal the carbon status in mediating catabolite repression in bacteria; here a quantitative approach reveals a much broader physiological role for cAMP signalling, whereby it coordinates the allocation of proteomic resources with the global metabolic needs of the cell, including, for example, nitrogen or sulphur.

doi: 10.1038/nature12446

The initiation of mammalian protein synthesis and mRNA scanning mechanism p.307

Three structures of the eukaryotic small ribosomal subunit in complex with initiator tRNA, mRNA and the initiation factors eIF1 and eIF1A have been solved; these structures offer insight into the contributions of the initiation factors, the mechanism by which mRNA is scanned, and the interactions that occur in the ribosome’s P site.

doi: 10.1038/nature12355


A variable absorption feature in the X-ray spectrum of a magnetar p.312

Soft-γ-ray repeaters (SGRs) and anomalous X-ray pulsars (AXPs) are slowly rotating, isolated neutron stars that sporadically undergo episodes of long-term flux enhancement (outbursts) generally accompanied by the emission of short bursts of hard X-rays. This behaviour can be understood in the magnetar model, according to which these sources are mainly powered by their own magnetic energy. This is supported by the fact that the magnetic fields inferred from several observed properties of SGRs and AXPs are greater than—or at the high end of the range of—those of radio pulsars. In the peculiar case of SGR 0418+5729, a weak dipole magnetic moment is derived from its timing parameters, whereas a strong field has been proposed to reside in the stellar interior and in multipole components on the surface. Here we show that the X-ray spectrum of SGR 0418+5729 has an absorption line, the properties of which depend strongly on the star’s rotational phase. This line is interpreted as a proton cyclotron feature and its energy implies a magnetic field ranging from 2 × 1014 gauss to more than 1015 gauss.

doi: 10.1038/nature12386

Deterministic quantum teleportation of photonic quantum bits by a hybrid technique p.315

Quantum teleportation allows for the transfer of arbitrary unknown quantum states from a sender to a spatially distant receiver, provided that the two parties share an entangled state and can communicate classically. It is the essence of many sophisticated protocols for quantum communication and computation. Photons are an optimal choice for carrying information in the form of ‘flying qubits’, but the teleportation of photonic quantum bits (qubits) has been limited by experimental inefficiencies and restrictions. Main disadvantages include the fundamentally probabilistic nature of linear-optics Bell measurements, as well as the need either to destroy the teleported qubit or attenuate the input qubit when the detectors do not resolve photon numbers. Here we experimentally realize fully deterministic quantum teleportation of photonic qubits without post-selection. The key step is to make use of a hybrid technique involving continuous-variable teleportation of a discrete-variable, photonic qubit. When the receiver’s feedforward gain is optimally tuned, the continuous-variable teleporter acts as a pure loss channel, and the input dual-rail-encoded qubit, based on a single photon, represents a quantum error detection code against photon loss and hence remains completely intact for most teleportation events. This allows for a faithful qubit transfer even with imperfect continuous-variable entangled states: for four qubits the overall transfer fidelities range from 0.79 to 0.82 and all of them exceed the classical limit of teleportation. Furthermore, even for a relatively low level of the entanglement, qubits are teleported much more efficiently than in previous experiments, albeit post-selectively (taking into account only the qubit subspaces), and with a fidelity comparable to the previously reported values.

doi: 10.1038/nature12366

Deterministic quantum teleportation with feed-forward in a solid state system p.319

Engineered macroscopic quantum systems based on superconducting electronic circuits are attractive for experimentally exploring diverse questions in quantum information science. At the current state of the art, quantum bits (qubits) are fabricated, initialized, controlled, read out and coupled to each other in simple circuits. This enables the realization of basic logic gates, the creation of complex entangled states and the demonstration of algorithms or error correction. Using different variants of low-noise parametric amplifiers, dispersive quantum non-demolition single-shot readout of single-qubit states with high fidelity has enabled continuous and discrete feedback control of single qubits. Here we realize full deterministic quantum teleportation with feed-forward in a chip-based superconducting circuit architecture. We use a set of two parametric amplifiers for both joint two-qubit and individual qubit single-shot readout, combined with flexible real-time digital electronics. Our device uses a crossed quantum bus technology that allows us to create complex networks with arbitrary connecting topology in a planar architecture. The deterministic teleportation process succeeds with order unit probability for any input state, as we prepare maximally entangled two-qubit states as a resource and distinguish all Bell states in a single two-qubit measurement with high efficiency and high fidelity. We teleport quantum states between two macroscopic systems separated by 6 mm at a rate of 104 s−1, exceeding other reported implementations. The low transmission loss of superconducting waveguides is likely to enable the range of this and other schemes to be extended to significantly larger distances, enabling tests of non-locality and the realization of elements for quantum communication at microwave frequencies. The demonstrated feed-forward may also find application in error correction schemes.

doi: 10.1038/nature12422

Tunable near-infrared and visible-light transmittance in nanocrystal-in-glass composites p.323

Amorphous metal oxides are useful in optical, electronic and electrochemical devices. The bonding arrangement within these glasses largely determines their properties, yet it remains a challenge to manipulate their structures in a controlled manner. Recently, we developed synthetic protocols for incorporating nanocrystals that are covalently bonded into amorphous materials. This ‘nanocrystal-in-glass’ approach not only combines two functional components in one material, but also the covalent link enables us to manipulate the glass structure to change its properties. Here we illustrate the power of this approach by introducing tin-doped indium oxide nanocrystals into niobium oxide glass (NbOx), and realize a new amorphous structure as a consequence of linking it to the nanocrystals. The resulting material demonstrates a previously unrealized optical switching behaviour that will enable the dynamic control of solar radiation transmittance through windows. These transparent films can block near-infrared and visible light selectively and independently by varying the applied electrochemical voltage over a range of 2.5 volts. We also show that the reconstructed NbOx glass has superior properties—its optical contrast is enhanced fivefold and it has excellent electrochemical stability, with 96 per cent of charge capacity retained after 2,000 cycles.

doi: 10.1038/nature12398

No increase in global temperature variability despite changing regional patterns p.327

Evidence from Greenland ice cores shows that year-to-year temperature variability was probably higher in some past cold periods, but there is considerable interest in determining whether global warming is increasing climate variability at present. This interest is motivated by an understanding that increased variability and resulting extreme weather conditions may be more difficult for society to adapt to than altered mean conditions. So far, however, in spite of suggestions of increased variability, there is considerable uncertainty as to whether it is occurring. Here we show that although fluctuations in annual temperature have indeed shown substantial geographical variation over the past few decades, the time-evolving standard deviation of globally averaged temperature anomalies has been stable. A feature of the changes has been a tendency for many regions of low variability to experience increases, which might contribute to the perception of increased climate volatility. The normalization of temperature anomalies creates the impression of larger relative overall increases, but our use of absolute values, which we argue is a more appropriate approach, reveals little change. Regionally, greater year-to-year changes recently occurred in much of North America and Europe. Many climate models predict that total variability will ultimately decrease under high greenhouse gas concentrations, possibly associated with reductions in sea-ice cover. Our findings contradict the view that a warming world will automatically be one of more overall climatic variation.

doi: 10.1038/nature12310

The role of behaviour in adaptive morphological evolution of African proboscideans p.331

The fossil record richly illustrates the origin of morphological adaptation through time. However, our understanding of the selective forces responsible in a given case, and the role of behaviour in the process, is hindered by assumptions of synchrony between environmental change, behavioural innovation and morphological response. Here I show, from independent proxy data through a 20-million-year sequence of fossil proboscideans in East Africa, that changes in environment, diet and morphology are often significantly offset chronologically, allowing dissection of the roles of behaviour and different selective drivers. These findings point the way to hypothesis-driven testing of the interplay between habitat change, behaviour and morphological adaptation with the use of independent proxies in the fossil record.

doi: 10.1038/nature12275

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds OPEN p.335

Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.

doi: 10.1038/nature12309

The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK p.340

A key event in the domestication and breeding of the oil palm Elaeis guineensis was loss of the thick coconut-like shell surrounding the kernel. Modern E. guineensis has three fruit forms, dura (thick-shelled), pisifera (shell-less) and tenera (thin-shelled), a hybrid between dura and pisifera. The pisifera palm is usually female-sterile. The tenera palm yields far more oil than dura, and is the basis for commercial palm oil production in all of southeast Asia. Here we describe the mapping and identification of the SHELL gene responsible for the different fruit forms. Using homozygosity mapping by sequencing, we found two independent mutations in the DNA-binding domain of a homologue of the MADS-box gene SEEDSTICK (STK, also known as AGAMOUS-LIKE 11), which controls ovule identity and seed development in Arabidopsis. The SHELL gene is responsible for the tenera phenotype in both cultivated and wild palms from sub-Saharan Africa, and our findings provide a genetic explanation for the single gene hybrid vigour (or heterosis) attributed to SHELL, via heterodimerization. This gene mutation explains the single most important economic trait in oil palm, and has implications for the competing interests of global edible oil production, biofuels and rainforest conservation.

doi: 10.1038/nature12356

Maternal imprinting at the H19–Igf2 locus maintains adult haematopoietic stem cell quiescence p.345

The epigenetic regulation of imprinted genes by monoallelic DNA methylation of either maternal or paternal alleles is critical for embryonic growth and development. Imprinted genes were recently shown to be expressed in mammalian adult stem cells to support self-renewal of neural and lung stem cells; however, a role for imprinting per se in adult stem cells remains elusive. Here we show upregulation of growth-restricting imprinted genes, including in the H19–Igf2 locus, in long-term haematopoietic stem cells and their downregulation upon haematopoietic stem cell activation and proliferation. A differentially methylated region upstream of H19 (H19-DMR), serving as the imprinting control region, determines the reciprocal expression of H19 from the maternal allele and Igf2 from the paternal allele. In addition, H19 serves as a source of miR-675, which restricts Igf1r expression. We demonstrate that conditional deletion of the maternal but not the paternal H19-DMR reduces adult haematopoietic stem cell quiescence, a state required for long-term maintenance of haematopoietic stem cells, and compromises haematopoietic stem cell function. Maternal-specific H19-DMR deletion results in activation of the Igf2–Igfr1 pathway, as shown by the translocation of phosphorylated FoxO3 (an inactive form) from nucleus to cytoplasm and the release of FoxO3-mediated cell cycle arrest, thus leading to increased activation, proliferation and eventual exhaustion of haematopoietic stem cells. Mechanistically, maternal-specific H19-DMR deletion leads to Igf2 upregulation and increased translation of Igf1r, which is normally suppressed by H19-derived miR-675. Similarly, genetic inactivation of Igf1r partly rescues the H19-DMR deletion phenotype. Our work establishes a new role for this unique form of epigenetic control at the H19–Igf2 locus in maintaining adult stem cells.

doi: 10.1038/nature12303

PAAR-repeat proteins sharpen and diversify the type VI secretion system spike p.350

The bacterial type VI secretion system (T6SS) is a large multicomponent, dynamic macromolecular machine that has an important role in the ecology of many Gram-negative bacteria. T6SS is responsible for translocation of a wide range of toxic effector molecules, allowing predatory cells to kill both prokaryotic as well as eukaryotic prey cells. The T6SS organelle is functionally analogous to contractile tails of bacteriophages and is thought to attack cells by initially penetrating them with a trimeric protein complex called the VgrG spike. Neither the exact protein composition of the T6SS organelle nor the mechanisms of effector selection and delivery are known. Here we report that proteins from the PAAR (proline-alanine-alanine-arginine) repeat superfamily form a sharp conical extension on the VgrG spike, which is further involved in attaching effector domains to the spike. The crystal structures of two PAAR-repeat proteins bound to VgrG-like partners show that these proteins sharpen the tip of the T6SS spike complex. We demonstrate that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae and Acinetobacter baylyi. Our results indicate a new model of the T6SS organelle in which the VgrG–PAAR spike complex is decorated with multiple effectors that are delivered simultaneously into target cells in a single contraction-driven translocation event.

doi: 10.1038/nature12453

An Sp1 transcription factor coordinates caspase-dependent and -independent apoptotic pathways p.354

During animal development, the proper regulation of apoptosis requires the precise spatial and temporal execution of cell-death programs, which can include both caspase-dependent and caspase-independent pathways. Although the mechanisms of caspase-dependent and -independent cell killing have been examined extensively, how these pathways are coordinated within a single cell that is fated to die is unknown. Here we show that the Caenorhabditis elegans Sp1 transcription factor SPTF-3 specifies the programmed cell deaths of at least two cells—the sisters of the pharyngeal M4 motor neuron and the AQR sensory neuron—by transcriptionally activating both caspase-dependent and -independent apoptotic pathways. SPTF-3 directly drives the transcription of the gene egl-1, which encodes a BH3-only protein that promotes apoptosis through the activation of the CED-3 caspase. In addition, SPTF-3 directly drives the transcription of the AMP-activated protein kinase-related gene pig-1, which encodes a protein kinase and functions in apoptosis of the M4 sister and AQR sister independently of the pathway that activates CED-3 (refs 4, 5). Thus, a single transcription factor controls two distinct cell-killing programs that act in parallel to drive apoptosis. Our findings reveal a bivalent regulatory node for caspase-dependent and -independent pathways in the regulation of cell-type-specific apoptosis. We propose that such nodes might act as features of a general mechanism for regulating cell-type-specific apoptosis and could be therapeutic targets for diseases involving the dysregulation of apoptosis through multiple cell-killing mechanisms.

doi: 10.1038/nature12329

Epithelial junctions maintain tissue architecture by directing planar spindle orientation p.359

During epithelial cell proliferation, planar alignment of the mitotic spindle coordinates the local process of symmetric cell cleavage with the global maintenance of polarized tissue architecture. Although the disruption of planar spindle alignment is proposed to cause epithelial to mesenchymal transition and cancer, the in vivo mechanisms regulating mitotic spindle orientation remain elusive. Here we demonstrate that the actomyosin cortex and the junction-localized neoplastic tumour suppressors Scribbled and Discs large 1 have essential roles in planar spindle alignment and thus the control of epithelial integrity in the Drosophila imaginal disc. We show that defective alignment of the mitotic spindle correlates with cell delamination and apoptotic death, and that blocking the death of misaligned cells is sufficient to drive the formation of basally localized tumour-like masses. These findings indicate a key role for junction-mediated spindle alignment in the maintenance of epithelial integrity, and also reveal a previously unknown cell-death-mediated tumour-suppressor function inherent in the polarized architecture of epithelia.

doi: 10.1038/nature12335

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA p.363

In Gram-positive bacteria, T-box riboswitches regulate the expression of aminoacyl-tRNA synthetases and other proteins in response to fluctuating transfer RNA aminoacylation levels under various nutritional states. T-boxes reside in the 5′-untranslated regions of the messenger RNAs they regulate, and consist of two conserved domains. Stem I contains the specifier trinucleotide that base pairs with the anticodon of cognate tRNA. 3′ to stem I is the antiterminator domain, which base pairs with the tRNA acceptor end and evaluates its aminoacylation state. Despite high phylogenetic conservation and widespread occurrence in pathogens, the structural basis of tRNA recognition by this riboswitch remains ill defined. Here we demonstrate that the ∼100-nucleotide T-box stem I is necessary and sufficient for specific, high-affinity (dissociation constant (Kd) ∼150 nM) tRNA binding, and report the structure of Oceanobacillus iheyensis glyQ stem I in complex with its cognate tRNA at 3.2 Å resolution. Stem I recognizes the overall architecture of tRNA in addition to its anticodon, something accomplished by large ribonucleoproteins such as the ribosome, or proteins such as aminoacyl-tRNA synthetases, but is unprecedented for a compact mRNA domain. The C-shaped stem I cradles the L-shaped tRNA, forming an extended (1,604 Å2) intermolecular interface. In addition to the specifier–anticodon interaction, two interdigitated T-loops near the apex of stem I stack on the tRNA elbow in a manner analogous to those of the J11/12–J12/11 motif of RNase P and the L1 stalk of the ribosomal E-site. Because these ribonucleoproteins and T-boxes are unrelated, this strategy to recognize a universal tRNA feature probably evolved convergently. Mutually induced fit of stem I and the tRNA exploiting the intrinsic flexibility of tRNA and its conserved post-transcriptional modifications results in high shape complementarity, which in addition to providing specificity and affinity, globally organizes the T-box to orchestrate tRNA-dependent transcription regulation.

doi: 10.1038/nature12440