International laboratory survey offers comfort — and caution.
Explicit recognition of researchers’ contributions to science is becoming more comprehensive. Not before time — especially as a means of crediting referees.
Questionnaire suggests researchers not as safe as they feel.
Nature looks ahead to the key findings and events that may emerge in 2013.
Losses of up to 9% show need for broader data on US gas industry’s environmental impact.
Congress delays mandatory cuts to agencies.
The world is starting to win the war against tuberculosis, but drug-resistant forms pose a new threat.
News & Views
Fossils found in rocks of the Ediacaran period in Australia have been previously characterized as early marine organisms. But a report suggests that these rocks are fossilized soils. So did some of these Ediacaran organisms in fact live on land, like lichens? A palaeontologist and a geologist weigh up the evidence. See Letter p.89
A detailed simulation of the packing behaviour of deformable particles settles the debate about whether soft matter can adopt an unconventional crystal structure at high densities — it can. The hunt is now on for a real-world example.
Deep-imaging observations of the Andromeda galaxy and its surroundings have revealed a wide but thin planar structure of satellite galaxies that all orbit their host in the same rotational direction. See Letter p.62
Irrespective of an organism's size, the proportional sizes of its parts remain constant. An experimental model reveals size-dependent adjustment of segment formation and gene-expression oscillations in vertebrates. See Letter p.101
Malfunction of presenilin enzymes, which cleave proteins in cell membranes, can lead to Alzheimer's disease. A crystal structure of a microbial presenilin provides insights into the workings of this enzyme family. See Article p.56
How influential are the various factors involved in curbing global warming? A study finds that the timing of emissions reduction has the largest impact on the probability of limiting temperature increases to 2 °C. See Letter p.79
Nanoscale imaging reveals that bacterial and fungal enzymes use different mechanisms to deconstruct plant cell walls. The finding may provide clues about how to enhance the efficiency of liquid-biofuel production from biomass.
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.
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.
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
Visual responses during wakefulness are dominated by inhibition, and this inhibition shapes visual selectivity by restricting the temporal and spatial extent of neural activity.
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.
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.
Calcium–lipid electrostatic interactions are shown to amplify the tyrosine phosphorylation of CD3ε and CD3ζ in T-cell antigen receptor complex.
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.
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.