Volume 493 Number 7430



Safety catch p.5

International laboratory survey offers comfort — and caution.

doi: 10.1038/493005b


In search of credit p.5

Explicit recognition of researchers’ contributions to science is becoming more comprehensive. Not before time — especially as a means of crediting referees.

doi: 10.1038/493005a



Safety survey reveals lab risks p.9

Questionnaire suggests researchers not as safe as they feel.

doi: 10.1038/493009a


New year, new science p.11

Nature looks ahead to the key findings and events that may emerge in 2013.

doi: 10.1038/493011a


Methane leaks erode green credentials of natural gas p.12

Losses of up to 9% show need for broader data on US gas industry’s environmental impact.

doi: 10.1038/493012a

訃報:Maxine Clarke(Nature publishing executive editor)

Obituary: Maxine Clarke p.13

doi: 10.1038/493013b


US fiscal deal leaves science vulnerable p.13

Congress delays mandatory cuts to agencies.

doi: 10.1038/493013a

News Features


TB's revenge p.14


doi: 10.1038/493014a

News & Views


Palaeontology: Fossils come in to land p.28


doi: 10.1038/nature11765


Computational materials science: Soft heaps and clumpy crystals p.30


doi: 10.1038/493030a


Astronomy: Andromeda's extended disk of dwarfs p.31


doi: 10.1038/493031a


Developmental biology: Segmentation within scale p.32


doi: 10.1038/nature11849


Structural biology: Membrane enzyme cuts a fine figure p.34


doi: 10.1038/nature11768


Climate change: All in the timing p.35


doi: 10.1038/493035a


Microbiology: Break down the walls p.36


doi: 10.1038/493036a



Non-Fermi-liquid d-wave metal phase of strongly interacting electrons p.39

Developing a theoretical framework for conducting electronic fluids qualitatively distinct from those described by Landau’s Fermi-liquid theory is of central importance to many outstanding problems in condensed matter physics. One such problem is that, above the transition temperature and near optimal doping, high-transition-temperature copper-oxide superconductors exhibit ‘strange metal’ behaviour that is inconsistent with being a traditional Landau Fermi liquid. Indeed, a microscopic theory of a strange-metal quantum phase could shed new light on the interesting low-temperature behaviour in the pseudogap regime and on the d-wave superconductor itself. Here we present a theory for a specific example of a strange metal—the ‘d-wave metal’. Using variational wavefunctions, gauge theoretic arguments, and ultimately large-scale density matrix renormalization group calculations, we show that this remarkable quantum phase is the ground state of a reasonable microscopic Hamiltonian—the usual t–J model with electron kinetic energy t and two-spin exchange J supplemented with a frustrated electron ‘ring-exchange’ term, which we here examine extensively on the square lattice two-leg ladder. These findings constitute an explicit theoretical example of a genuine non-Fermi-liquid metal existing as the ground state of a realistic model.

doi: 10.1038/nature11732


Genomic variation landscape of the human gut microbiome p.45

Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.

doi: 10.1038/nature11711


CCR5 is a receptor for Staphylococcus aureus leukotoxin ED p.51

Pore-forming toxins are critical virulence factors for many bacterial pathogens and are central to Staphylococcus aureus-mediated killing of host cells. S. aureus encodes pore-forming bi-component leukotoxins that are toxic towards neutrophils, but also specifically target other immune cells. Despite decades since the first description of staphylococcal leukocidal activity, the host factors responsible for the selectivity of leukotoxins towards different immune cells remain unknown. Here we identify the human immunodeficiency virus (HIV) co-receptor CCR5 as a cellular determinant required for cytotoxic targeting of subsets of myeloid cells and T lymphocytes by the S. aureus leukotoxin ED (LukED). We further demonstrate that LukED-dependent cell killing is blocked by CCR5 receptor antagonists, including the HIV drug maraviroc. Remarkably, CCR5-deficient mice are largely resistant to lethal S. aureus infection, highlighting the importance of CCR5 targeting in S. aureus pathogenesis. Thus, depletion of CCR5+ leukocytes by LukED suggests a new immune evasion mechanism of S. aureus that can be therapeutically targeted.

doi: 10.1038/nature11724


Structure of a presenilin family intramembrane aspartate protease p.56

Presenilin and signal peptide peptidase (SPP) are intramembrane aspartyl proteases that regulate important biological functions in eukaryotes. Mechanistic understanding of presenilin and SPP has been hampered by lack of relevant structural information. Here we report the crystal structure of a presenilin/SPP homologue (PSH) from the archaeon Methanoculleus marisnigri JR1. The protease, comprising nine transmembrane segments (TMs), adopts a previously unreported protein fold. The amino-terminal domain, consisting of TM1–6, forms a horseshoe-shaped structure, surrounding TM7–9 of the carboxy-terminal domain. The two catalytic aspartate residues are located on the cytoplasmic side of TM6 and TM7, spatially close to each other and approximately 8 Å into the lipid membrane surface. Water molecules gain constant access to the catalytic aspartates through a large cavity between the amino- and carboxy-terminal domains. Structural analysis reveals insights into the presenilin/SPP family of intramembrane proteases.

doi: 10.1038/nature11801



A vast, thin plane of corotating dwarf galaxies orbiting the Andromeda galaxy p.62

About half of the satellites in the Andromeda galaxy (M 31), all with the same sense of rotation about their host, form a planar subgroup that is extremely wide but also very thin.

doi: 10.1038/nature11717


Giant magnetized outflows from the centre of the Milky Way p.66

Two giant, linearly polarized radio lobes have been found emanating from the Galactic Centre, and are thought to originate in a biconical, star-formation-driven outflow from the Galaxy’s central 200 parsecs that transports a huge amount of magnetic energy, about 1055 ergs, into the Galactic halo

doi: 10.1038/nature11734


Optical-field-induced current in dielectrics p.70

Exposing a fused silica sample to a strong, waveform-controlled, few-cycle optical field increases the dielectric’s optical conductivity by more than 18 orders of magnitude in less than 1 femtosecond, allowing electric currents to be driven, directed and switched by the instantaneous light field.

doi: 10.1038/nature11567


Controlling dielectrics with the electric field of light p.75

The ultrafast reversibility of changes to the electronic structure and electric polarizability of a dielectric with the electric field of a laser pulse, demonstrated here, offers the potential for petahertz-bandwidth optical signal manipulation.

doi: 10.1038/nature11720


Probabilistic cost estimates for climate change mitigation p.79

Modelling that integrates the effects of uncertainties in relevant geophysical, technological, social and political factors on the cost of keeping transient global temperature increase to below certain limits shows that political choices have the greatest effect on the cost distribution.

doi: 10.1038/nature11787


The oxidation state of the mantle and the extraction of carbon from Earth’s interior p.84

The oxygen fugacity of the deepest rock samples from Earth’s mantle is found to be more oxidized than previously thought, with the result that carbon in the asthenospheric mantle will be hosted as graphite or diamond but will be oxidized to produce carbonate melt through the reduction of Fe3+ in silicate minerals during upwelling.

doi: 10.1038/nature11679


Ediacaran life on land p.89

A new interpretation of fossilized soils (palaeosols) suggests that at least some Ediacaran (625–542 million years ago) organisms lived on land; thus these Ediacaran fossils were not animals, but a fungus-dominated terrestrial biota that predated vascular plants by about 100 million years.

doi: 10.1038/nature11777


Convergent acoustic field of view in echolocating bats p.93

Studying six vespertilionid bat species of different sizes to investigate the reason why smaller bats have higher frequency echolocation calls, a model is put forward that the size/frequency range is modulated by the need to maintain a focused, highly directional echolocation beam.

doi: 10.1038/nature11664


Inhibition dominates sensory responses in the awake cortex p.97

Visual responses during wakefulness are dominated by inhibition, and this inhibition shapes visual selectivity by restricting the temporal and spatial extent of neural activity.

doi: 10.1038/nature11665


Scaling of embryonic patterning based on phase-gradient encoding p.101

An ex vivo primary culture assay is developed that recapitulates mouse embryonic mesodermal patterning and segment formation; using this approach, it is shown that oscillating gene activity is central to maintain stable proportions during development.

doi: 10.1038/nature11804


Restriction of intestinal stem cell expansion and the regenerative response by YAP p.106

YAP has previously been identified as an oncogene that promotes cell growth, but now it is shown to restrict stem cell expansion during regeneration in the mouse intestine, suggesting that it may function as a tumour suppressor in colon cancer.

doi: 10.1038/nature11693


Ca2+ regulates T-cell receptor activation by modulating the charge property of lipids p.111

Calcium–lipid electrostatic interactions are shown to amplify the tyrosine phosphorylation of CD3ε and CD3ζ in T-cell antigen receptor complex.

doi: 10.1038/nature11699


Coordinated control of replication and transcription by a SAPK protects genomic integrity p.116

Upregulation of gene transcription in stressed cells can lead to clashes between the transcription and repair machineries; here, a stress-activated protein kinase (SAPK), Hog1, is shown to coordinate these two processes in yeast.

doi: 10.1038/nature11675


DNA-repair scaffolds dampen checkpoint signalling by counteracting the adaptor Rad9 p.120

DNA damage or replication stress induces the activation of checkpoint kinases, pausing the cell cycle so that DNA repair can take place; checkpoint activation must be regulated to prevent the cell-cycle arrest from persisting after damage is repaired, and now the Slx4–Rtt107 complex is shown to regulate checkpoint kinase activity by directly monitoring DNA-damage signalling.

doi: 10.1038/nature11658

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