Volume 496 Number 7443
A record made to be broken p.5
Japan’s major science-funding agency has a clean record when it comes to research fraud. Now is the time for it to step up and resolve a long-running case of alleged scientific misconduct.
Against the law p.5
Behaviours proposed for black holes conflict with the laws of physics.
Crick’s medal goes under the hammer p.13
Pending auction raises eyebrows but few objections.
Sizing up a slow assault on cancer p.14
Rise of immunotherapies spurs search for markers of response.
Detectors zero in on Earth’s heat p.17
Geoneutrinos paint picture of deep-mantle processes.
Detective work uncovers under-reported overfishing p.18
Excessive catches by Chinese vessels threaten livelihoods and ecosystems in West Africa.
Astrophysics: Fire in the hole! p.20
News & Views
Biochemistry: Positive and radical p.34
Earth science: Western North America's jigsaw p.35
Techniques: 3D imaging of crystal defects p.37
Cancer: A metabolic metamorphosis p.38
Materials science: The same, but better p.40
Biochemistry: Sirtuin on a high-fat diet p.41
Patterns and mechanisms of early Pliocene warmth p.43
A synthesis of geochemical proxy records of sea surface temperature shows that the early Pliocene climate was little different from today in terms of maximum ocean temperatures but had substantially lower meridional and zonal temperature gradients.
Intra-oceanic subduction shaped the assembly of Cordilleran North America p.50
A new explanation for the origin of the accreted terranes that form the mountainous Cordillera of western North America is proposed and tested: stationary, intra-oceanic subduction deposited massive slab walls in the mantle and grew volcanic archipelagos at the surface, which were overridden by and accreted to North America during Cretaceous times.
The genomes of four tapeworm species reveal adaptations to parasitism p.57
Genome sequences of human-infective tapeworm species reveal extreme losses of genes and pathways that are ubiquitous in other animals, species-specific expansions of non-canonical heat shock proteins and families of known antigens, specialized detoxification pathways, and metabolism that relies on host nutrients; this information is used to identify new potential drug targets.
SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket p.64
Crystal structures of mammalian CRY2, one of the cryptochrome flavoproteins that have light-independent functions at the core of the circadian clock, show that it binds FAD dynamically and that the F-box protein FBXL3 captures CRY2 by occupying its FAD-binding pocket and burying its PER-binding interface.
Femtosecond switching of magnetism via strongly correlated spin–charge quantum excitations p.69
The technological demand to push the gigahertz (109 hertz) switching speed limit of today’s magnetic memory and logic devices into the terahertz (1012 hertz) regime underlies the entire field of spin-electronics and integrated multi-functional devices. This challenge is met by all-optical magnetic switching based on coherent spin manipulation. By analogy to femtosecond chemistry and photosynthetic dynamics—in which photoproducts of chemical and biochemical reactions can be influenced by creating suitable superpositions of molecular states—femtosecond-laser-excited coherence between electronic states can switch magnetic order by ‘suddenly’ breaking the delicate balance between competing phases of correlated materials: for example, manganites exhibiting colossal magneto-resistance suitable for applications. Here we show femtosecond (10−15 seconds) photo-induced switching from antiferromagnetic to ferromagnetic ordering in Pr0.7Ca0.3MnO3, by observing the establishment (within about 120 femtoseconds) of a huge temperature-dependent magnetization with photo-excitation threshold behaviour absent in the optical reflectivity. The development of ferromagnetic correlations during the femtosecond laser pulse reveals an initial quantum coherent regime of magnetism, distinguished from the picosecond (10−12 seconds) lattice-heating regime characterized by phase separation without threshold behaviour. Our simulations reproduce the nonlinear femtosecond spin generation and underpin fast quantum spin-flip fluctuations correlated with coherent superpositions of electronic states to initiate local ferromagnetic correlations. These results merge two fields, femtosecond magnetism in metals and band insulators, and non-equilibrium phase transitions of strongly correlated electrons, in which local interactions exceeding the kinetic energy produce a complex balance of competing orders.
Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution p.74
Dislocations and their interactions strongly influence many material properties, ranging from the strength of metals and alloys to the efficiency of light-emitting diodes and laser diodes. Several experimental methods can be used to visualize dislocations. Transmission electron microscopy (TEM) has long been used to image dislocations in materials, and high-resolution electron microscopy can reveal dislocation core structures in high detail, particularly in annular dark-field mode. A TEM image, however, represents a two-dimensional projection of a three-dimensional (3D) object (although stereo TEM provides limited information about 3D dislocations). X-ray topography can image dislocations in three dimensions, but with reduced resolution. Using weak-beam dark-field TEM and scanning TEM, electron tomography has been used to image 3D dislocations at a resolution of about five nanometres (refs 15, 16). Atom probe tomography can offer higher-resolution 3D characterization of dislocations, but requires needle-shaped samples and can detect only about 60 per cent of the atoms in a sample. Here we report 3D imaging of dislocations in materials at atomic resolution by electron tomography. By applying 3D Fourier filtering together with equal-slope tomographic reconstruction, we observe nearly all the atoms in a multiply twinned platinum nanoparticle. We observed atomic steps at 3D twin boundaries and imaged the 3D core structure of edge and screw dislocations at atomic resolution. These dislocations and the atomic steps at the twin boundaries, which appear to be stress-relief mechanisms, are not visible in conventional two-dimensional projections. The ability to image 3D disordered structures such as dislocations at atomic resolution is expected to find applications in materials science, nanoscience, solid-state physics and chemistry.
Colossal injection of catalyst atoms into silicon nanowires p.78
The incorporation of impurities during the growth of nanowires from the vapour phase alters their basic properties substantially, and this process is critical in an extended range of emerging nanometre-scale technologies. In particular, achieving precise control of the behaviour of group III and group V dopants has been a crucial step in the development of silicon (Si) nanowire-based devices. Recently it has been demonstrated that the use of aluminium (Al) as a growth catalyst, instead of the usual gold, also yields an effective p-type doping, thereby enabling a novel and efficient route to functionalizing Si nanowires. Besides the technological implications, this self-doping implies the detachment of Al from the catalyst and its injection into the growing nanowire, involving atomic-scale processes that are crucial for the fundamental understanding of the catalytic assembly of nanowires. Here we present an atomic-level, quantitative study of this phenomenon of catalyst dissolution by three-dimensional atom-by-atom mapping of individual Al-catalysed Si nanowires using highly focused ultraviolet-laser-assisted atom-probe tomography. Although the observed incorporation of the catalyst atoms into nanowires exceeds by orders of magnitude the equilibrium solid solubility and solid-solution concentrations in known non-equilibrium processes, the Al impurities are found to be homogeneously distributed in the nanowire and do not form precipitates or clusters. As well as the anticipated effect on the electrical properties, this kinetics-driven colossal injection also has direct implications for nanowire morphology. We discuss the observed strong deviation from equilibrium using a model of solute trapping at step edges, and identify the key growth parameters behind this phenomenon on the basis of a kinetic model of step-flow growth of nanowires. The control of this phenomenon provides opportunities to create a new class of nanoscale devices by precisely tailoring the shape and composition of metal-catalysed nanowires.
July 2012 Greenland melt extent enhanced by low-level liquid clouds p.83
Melting of the world’s major ice sheets can affect human and environmental conditions by contributing to sea-level rise. In July 2012, an historically rare period of extended surface melting was observed across almost the entire Greenland ice sheet, raising questions about the frequency and spatial extent of such events. Here we show that low-level clouds consisting of liquid water droplets (‘liquid clouds’), via their radiative effects, played a key part in this melt event by increasing near-surface temperatures. We used a suite of surface-based observations, remote sensing data, and a surface energy-balance model. At the critical surface melt time, the clouds were optically thick enough and low enough to enhance the downwelling infrared flux at the surface. At the same time they were optically thin enough to allow sufficient solar radiation to penetrate through them and raise surface temperatures above the melting point. Outside this narrow range in cloud optical thickness, the radiative contribution to the surface energy budget would have been diminished, and the spatial extent of this melting event would have been smaller. We further show that these thin, low-level liquid clouds occur frequently, both over Greenland and across the Arctic, being present around 30–50 per cent of the time. Our results may help to explain the difficulties that global climate models have in simulating the Arctic surface energy budget, particularly as models tend to under-predict the formation of optically thin liquid clouds at supercooled temperatures—a process potentially necessary to account fully for temperature feedbacks in a warming Arctic climate.
Draft genome of the wheat A-genome progenitor Triticum urartu p.87
Bread wheat (Triticum aestivum, AABBDD) is one of the most widely cultivated and consumed food crops in the world. However, the complex polyploid nature of its genome makes genetic and functional analyses extremely challenging. The A genome, as a basic genome of bread wheat and other polyploid wheats, for example, T. turgidum (AABB), T. timopheevii (AAGG) and T. zhukovskyi (AAGGAmAm), is central to wheat evolution, domestication and genetic improvement. The progenitor species of the A genome is the diploid wild einkorn wheat T. urartu, which resembles cultivated wheat more extensively than do Aegilops speltoides (the ancestor of the B genome) and Ae. tauschii (the donor of the D genome), especially in the morphology and development of spike and seed. Here we present the generation, assembly and analysis of a whole-genome shotgun draft sequence of the T. urartu genome. We identified protein-coding gene models, performed genome structure analyses and assessed its utility for analysing agronomically important genes and for developing molecular markers. Our T. urartu genome assembly provides a diploid reference for analysis of polyploid wheat genomes and is a valuable resource for the genetic improvement of wheat.
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation p.91
About 8,000 years ago in the Fertile Crescent, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n = 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n = 4x = 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n = 6x = 42; AABBDD). Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker’s flour. Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae. tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.
The emergence of functional microcircuits in visual cortex p.96
Sensory processing occurs in neocortical microcircuits in which synaptic connectivity is highly structured and excitatory neurons form subnetworks that process related sensory information. However, the developmental mechanisms underlying the formation of functionally organized connectivity in cortical microcircuits remain unknown. Here we directly relate patterns of excitatory synaptic connectivity to visual response properties of neighbouring layer 2/3 pyramidal neurons in mouse visual cortex at different postnatal ages, using two-photon calcium imaging in vivo and multiple whole-cell recordings in vitro. Although neural responses were already highly selective for visual stimuli at eye opening, neurons responding to similar visual features were not yet preferentially connected, indicating that the emergence of feature selectivity does not depend on the precise arrangement of local synaptic connections. After eye opening, local connectivity reorganized extensively: more connections formed selectively between neurons with similar visual responses and connections were eliminated between visually unresponsive neurons, but the overall connectivity rate did not change. We propose a sequential model of cortical microcircuit development based on activity-dependent mechanisms of plasticity whereby neurons first acquire feature preference by selecting feedforward inputs before the onset of sensory experience—a process that may be facilitated by early electrical coupling between neuronal subsets—and then patterned input drives the formation of functional subnetworks through a redistribution of recurrent synaptic connections.
Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway p.101
Cancer cells have metabolic dependencies that distinguish them from their normal counterparts. Among these dependencies is an increased use of the amino acid glutamine to fuel anabolic processes. Indeed, the spectrum of glutamine-dependent tumours and the mechanisms whereby glutamine supports cancer metabolism remain areas of active investigation. Here we report the identification of a non-canonical pathway of glutamine use in human pancreatic ductal adenocarcinoma (PDAC) cells that is required for tumour growth. Whereas most cells use glutamate dehydrogenase (GLUD1) to convert glutamine-derived glutamate into α-ketoglutarate in the mitochondria to fuel the tricarboxylic acid cycle, PDAC relies on a distinct pathway in which glutamine-derived aspartate is transported into the cytoplasm where it can be converted into oxaloacetate by aspartate transaminase (GOT1). Subsequently, this oxaloacetate is converted into malate and then pyruvate, ostensibly increasing the NADPH/NADP+ ratio which can potentially maintain the cellular redox state. Importantly, PDAC cells are strongly dependent on this series of reactions, as glutamine deprivation or genetic inhibition of any enzyme in this pathway leads to an increase in reactive oxygen species and a reduction in reduced glutathione. Moreover, knockdown of any component enzyme in this series of reactions also results in a pronounced suppression of PDAC growth in vitro and in vivo. Furthermore, we establish that the reprogramming of glutamine metabolism is mediated by oncogenic KRAS, the signature genetic alteration in PDAC, through the transcriptional upregulation and repression of key metabolic enzymes in this pathway. The essentiality of this pathway in PDAC and the fact that it is dispensable in normal cells may provide novel therapeutic approaches to treat these refractory tumours.
Proteolytic elimination of N-myristoyl modifications by the Shigella virulence factor IpaJ p.106
Protein N-myristoylation is a 14-carbon fatty-acid modification that is conserved across eukaryotic species and occurs on nearly 1% of the cellular proteome. The ability of the myristoyl group to facilitate dynamic protein–protein and protein–membrane interactions (known as the myristoyl switch) makes it an essential feature of many signal transduction systems. Thus pathogenic strategies that facilitate protein demyristoylation would markedly alter the signalling landscape of infected host cells. Here we describe an irreversible mechanism of protein demyristoylation catalysed by invasion plasmid antigen J (IpaJ), a previously uncharacterized Shigella flexneri type III effector protein with cysteine protease activity. A yeast genetic screen for IpaJ substrates identified ADP-ribosylation factor (ARF)1p and ARF2p, small molecular mass GTPases that regulate cargo transport through the Golgi apparatus. Mass spectrometry showed that IpaJ cleaved the peptide bond between N-myristoylated glycine-2 and asparagine-3 of human ARF1, thereby providing a new mechanism for host secretory inhibition by a bacterial pathogen. We further demonstrate that IpaJ cleaves an array of N-myristoylated proteins involved in cellular growth, signal transduction, autophagasome maturation and organelle function. Taken together, these findings show a previously unrecognized pathogenic mechanism for the site-specific elimination of N-myristoyl protein modification.
SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine p.110
The Sir2 family of enzymes or sirtuins are known as nicotinamide adenine dinucleotide (NAD)-dependent deacetylases and have been implicated in the regulation of transcription, genome stability, metabolism and lifespan. However, four of the seven mammalian sirtuins have very weak deacetylase activity in vitro. Here we show that human SIRT6 efficiently removes long-chain fatty acyl groups, such as myristoyl, from lysine residues. The crystal structure of SIRT6 reveals a large hydrophobic pocket that can accommodate long-chain fatty acyl groups. We demonstrate further that SIRT6 promotes the secretion of tumour necrosis factor-α (TNF-α) by removing the fatty acyl modification on K19 and K20 of TNF-α. Protein lysine fatty acylation has been known to occur in mammalian cells, but the function and regulatory mechanisms of this modification were unknown. Our data indicate that protein lysine fatty acylation is a novel mechanism that regulates protein secretion. The discovery of SIRT6 as an enzyme that controls protein lysine fatty acylation provides new opportunities to investigate the physiological function of a protein post-translational modification that has been little studied until now.
Mechanistic studies of an unprecedented enzyme-catalysed 1,2-phosphono-migration reaction p.114
(S)-2-hydroxypropylphosphonate ((S)-2-HPP) epoxidase (HppE) is a mononuclear non-haem-iron-dependent enzyme responsible for the final step in the biosynthesis of the clinically useful antibiotic fosfomycin. Enzymes of this class typically catalyse oxygenation reactions that proceed via the formation of substrate radical intermediates. By contrast, HppE catalyses an unusual dehydrogenation reaction while converting the secondary alcohol of (S)-2-HPP to the epoxide ring of fosfomycin. Here we show that HppE also catalyses a biologically unprecedented 1,2-phosphono migration with the alternative substrate (R)-1-HPP. This transformation probably involves an intermediary carbocation, based on observations with additional substrate analogues, such as (1R)-1-hydroxyl-2-aminopropylphosphonate, and model reactions for both radical- and carbocation-mediated migration. The ability of HppE to catalyse distinct reactions depending on the regio- and stereochemical properties of the substrate is given a structural basis using X-ray crystallography. These results provide compelling evidence for the formation of a substrate-derived cation intermediate in the catalytic cycle of a mononuclear non-haem-iron-dependent enzyme. The underlying chemistry of this unusual phosphono migration may represent a new paradigm for the in vivo construction of phosphonate-containing natural products that can be exploited for the preparation of new phosphonate derivatives.
A solution to release twisted DNA during chromosome replication by coupled DNA polymerases p.119
Chromosomal replication machines contain coupled DNA polymerases that simultaneously replicate the leading and lagging strands. However, coupled replication presents a largely unrecognized topological problem. Because DNA polymerase must travel a helical path during synthesis, the physical connection between leading- and lagging-strand polymerases causes the daughter strands to entwine, or produces extensive build-up of negative supercoils in the newly synthesized DNA. How DNA polymerases maintain their connection during coupled replication despite these topological challenges is unknown. Here we examine the dynamics of the Escherichia coli replisome, using ensemble and single-molecule methods, and show that the replisome may solve the topological problem independent of topoisomerases. We find that the lagging-strand polymerase frequently releases from an Okazaki fragment before completion, leaving single-strand gaps behind. Dissociation of the polymerase does not result in loss from the replisome because of its contact with the leading-strand polymerase. This behaviour, referred to as ‘signal release’, had been thought to require a protein, possibly primase, to pry polymerase from incompletely extended DNA fragments. However, we observe that signal release is independent of primase and does not seem to require a protein trigger at all. Instead, the lagging-strand polymerase is simply less processive in the context of a replisome. Interestingly, when the lagging-strand polymerase is supplied with primed DNA in trans, uncoupling it from the fork, high processivity is restored. Hence, we propose that coupled polymerases introduce topological changes, possibly by accumulation of superhelical tension in the newly synthesized DNA, that cause lower processivity and transient lagging-strand polymerase dissociation from DNA.
Structures of protein–protein complexes involved in electron transfer p.123
Electron transfer reactions are essential for life because they underpin oxidative phosphorylation and photosynthesis, processes leading to the generation of ATP, and are involved in many reactions of intermediary metabolism. Key to these roles is the formation of transient inter-protein electron transfer complexes. The structural basis for the control of specificity between partner proteins is lacking because these weak transient complexes have remained largely intractable for crystallographic studies. Inter-protein electron transfer processes are central to all of the key steps of denitrification, an alternative form of respiration in which bacteria reduce nitrate or nitrite to N2 through the gaseous intermediates nitric oxide (NO) and nitrous oxide (N2O) when oxygen concentrations are limiting. The one-electron reduction of nitrite to NO, a precursor to N2O, is performed by either a haem- or copper-containing nitrite reductase (CuNiR) where they receive an electron from redox partner proteins a cupredoxin or a c-type cytochrome. Here we report the structures of the newly characterized three-domain haem-c-Cu nitrite reductase from Ralstonia pickettii (RpNiR) at 1.01 Å resolution and its M92A and P93A mutants. Very high resolution provides the first view of the atomic detail of the interface between the core trimeric cupredoxin structure of CuNiR and the tethered cytochrome c domain that allows the enzyme to function as an effective self-electron transfer system where the donor and acceptor proteins are fused together by genomic acquisition for functional advantage. Comparison of RpNiR with the binary complex of a CuNiR with a donor protein, AxNiR-cytc551 (ref. 6), and mutagenesis studies provide direct evidence for the importance of a hydrogen-bonded water at the interface in electron transfer. The structure also provides an explanation for the preferential binding of nitrite to the reduced copper ion at the active site in RpNiR, in contrast to other CuNiRs where reductive inactivation occurs, preventing substrate binding.