Dark matter maps reveal cosmic scaffolding

Ordinary baryonic particles (such as protons and neutrons) account for only one-sixth of the total matter in the Universe. The remainder is a mysterious 'dark matter' component, which does not interact via electromagnetism and thus neither emits nor reflects light. As dark matter cannot be seen directly using traditional observations, very little is currently known about its properties. It does interact via gravity, and is most effectively probed through gravitational lensing: the deflection of light from distant galaxies by the gravitational attraction of foreground mass concentrations. This is a purely geometrical effect that is free of astrophysical assumptions and sensitive to all matter--whether baryonic or dark. Here we show high-fidelity maps of the large-scale distribution of dark matter, resolved in both angle and depth. We find a loose network of filaments, growing over time, which intersect in massive structures at the locations of clusters of galaxies. Our results are consistent with predictions of gravitationally induced structure formation, in which the initial, smooth distribution of dark matter collapses into filaments then into clusters, forming a gravitational scaffold into which gas can accumulate, and stars can be built.     

HVEM signalling at mucosal barriers provides host defence against pathogenic bacteria

The herpes virus entry mediator (HVEM), a member of the tumour-necrosis factor receptor family, has diverse functions, augmenting or inhibiting the immune response. HVEM was recently reported as a colitis risk locus in patients, and in a mouse model of colitis we demonstrated an anti-inflammatory role for HVEM, but its mechanism of action in the mucosal immune system was unknown. Here we report an important role for epithelial HVEM in innate mucosal defence against pathogenic bacteria. HVEM enhances immune responses by NF-κB-inducing kinase-dependent Stat3 activation, which promotes the epithelial expression of genes important for immunity. During intestinal Citrobacter rodentium infection, a mouse model for enteropathogenic Escherichia coli infection, Hvem?/? mice showed decreased Stat3 activation, impaired responses in the colon, higher bacterial burdens and increased mortality. We identified the immunoglobulin superfamily molecule CD160 (refs 7 and 8), expressed predominantly by innate-like intraepithelial lymphocytes, as the ligand engaging epithelial HVEM for host protection. Likewise, in pulmonary Streptococcus pneumoniae infection, HVEM is also required for host defence. Our results pinpoint HVEM as an important orchestrator of mucosal immunity, integrating signals from innate lymphocytes to induce optimal epithelial Stat3 activation, which indicates that targeting HVEM with agonists could improve host defence.     

Kemp elimination catalysts by computational enzyme design

The design of new enzymes for reactions not catalysed by naturally occurring biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination-a model reaction for proton transfer from carbon-with measured rate enhancements of up to 10(5) and multiple turnovers. Mutational analysis confirms that catalysis depends on the computationally designed active sites, and a high-resolution crystal structure suggests that the designs have close to atomic accuracy. Application of in vitro evolution to enhance the computational designs produced a >200-fold increase in k(cat)/K(m) (k(cat)/K(m) of 2,600 M(-1)s(-1) and k(cat)/k(uncat) of >10(6)). These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future.     

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.     

Fruit bats as reservoirs of Ebola virus

The first recorded human outbreak of Ebola virus was in 1976, but the wild reservoir of this virus is still unknown. Here we test for Ebola in more than a thousand small vertebrates that were collected during Ebola outbreaks in humans and great apes between 2001 and 2003 in Gabon and the Republic of the Congo. We find evidence of asymptomatic infection by Ebola virus in three species of fruit bat, indicating that these animals may be acting as a reservoir for this deadly virus.     

Preface

The second international workshop on the Statistical Physics and Mathematics for Complex Systems (SPMCS) was held in the Center for Complexity Science at Central China Normal University in Wuhan, China, from 23–27 October 2010; the first workshop, held in 2008 in Le Mans, France, was convened by the Laboratoire de Physique Statistique et Systèmes Complex-es of ISMANS, an engineering college in France. As announced in the Aims and Scope, this conference series is intended to bring together senior and junior scientists, as well as Ph.D. students, to present the state of the art, to exchange recent results, new ideas, and different points of view on     

A partial elucidation of the gauge principle

The elucidation of the gauge principle “is the most pressing problem in current philosophy of physics” said Michael Redhead in 2003. This paper argues for two points that contribute to this elucidation in the context of Yang–Mills theories. (1) Yang–Mills theories, including quantum electrodynamics, form a class. They should be interpreted together. To focus on electrodynamics is potentially misleading. (2) The essential role of gauge and BRST symmetries is to provide a local field theory that can be quantized and would be equivalent to the quantization of the non-local reduced theory. If this is correct, the gauge symmetry is significant, not so much because it implies ontological consequences, but because it allows us to quantize theories that we would not be able to quantize otherwise. Thus, in the context of Yang–Mills theories, it is essentially a pragmatic principle. This does not seem to be the case for the gauge symmetry in general relativity.     

A Comparison of SuperDARN-Derived Plasma Convection and DMSP Ion Drift Measurements

Recently several studies indicated possible deterioration of accuracy in the SuperDARN convection measurements at large distances （〉2 500 km）. In this study, the SuperDARN-derived convection was compared with ion drift measurements given by the DMSP satellites, focused on SuperDARN far-range measurements, to investigate the above-mentioned problem. Two different procedures of SuperDARN convection estimation were applied. An overall reasonable agreement between two observation systems were found though individual points in some passes show significant differences. Besides, a tendency is also clear that the SuperDARN-derived velocities were slightly smaller than those of DMSP ion drift measurements. Potential factors contributing to the velocity differences were explained.