The Bullet cluster at its best: weighing stars, gas and dark matter

We present a new strong lensing mass reconstruction of the Bullet cluster (1E 0657-56) at z=0.296, based on WFC3 and ACS HST imaging and VLT/FORS2 spectroscopy. The strong lensing constraints underwent substantial revision compared to previously published analysis, there are now 14 (six new and eight previously known) multiply-imaged systems, of which three have spectroscopically confirmed redshifts (including one newly measured from this work). The reconstructed mass distribution explicitly included the combination of three mass components: i) the intra-cluster gas mass derived from X-ray observation, ii) the cluster galaxies modeled by their fundamental plane scaling relations and iii) dark matter. The model that includes the intra-cluster gas is the one with the best Bayesian evidence. This model has a total RMS value of 0.158" between the predicted and measured image positions for the 14 multiple images considered. The proximity of the total RMS to resolution of HST/WFC3 and ACS (0.07-0.15" FWHM) demonstrates the excellent precision of our mass model. The derived mass model confirms the spatial offset between the X-ray gas and dark matter peaks. The fraction of the galaxy halos mass to total mass is found to be f_s=11+/-5% for a total mass of 2.5+/-0.1 x 10^14 solar mass within a 250 kpc radial aperture.Comment: Accepted by A&A 15 pages, 12 figure

HIFLUGCS: Galaxy cluster scaling relations between X-ray luminosity, gas mass, cluster radius, and velocity dispersion

We present relations between X-ray luminosity and velocity dispersion (L-sigma), X-ray luminosity and gas mass (L-Mgas), and cluster radius and velocity dispersion (r500-sigma) for 62 galaxy clusters in the HIFLUGCS, an X-ray flux-limited sample minimizing bias toward any cluster morphology. Our analysis in total is based on ~1.3Ms of clean X-ray XMM-Newton data and 13439 cluster member galaxies with redshifts. Cool cores are among the major contributors to the scatter in the L-sigma relation. When the cool-core-corrected X-ray luminosity is used the intrinsic scatter decreases to 0.27 dex. Even after the X-ray luminosity is corrected for the cool core, the scatter caused by the presence of cool cores dominates for the low-mass systems. The scatter caused by the non-cool-core clusters does not strongly depend on the mass range, and becomes dominant in the high-mass regime. The observed L-sigma relation agrees with the self-similar prediction, matches that of a simulated sample with AGN feedback disregarding six clusters with <45 cluster members with spectroscopic redshifts, and shows a common trend of increasing scatter toward the low-mass end, i.e., systems with sigma<500km/s. A comparison of observations with simulations indicates an AGN-feedback-driven impact in the low-mass regime. The best fits to the $L-M_{\rm gas}$ relations for the disturbed clusters and undisturbed clusters in the observational sample closely match those of the simulated samples with and without AGN feedback, respectively. This suggests that one main cause of the scatter is AGN activity providing feedback in different phases, e.g., during a feedback cycle. The slope and scatter in the observed r500-sigma relation is similar to that of the simulated sample with AGN feedback except for a small offset but still within the scatter.Comment: 45 pages, 28 figures, A&A proof-version, high-resolution figures in Appendix F can be found in the electronic version on the A&A we

Selection at a single locus leads to widespread expansion of toxoplasma gondii lineages that are virulent in mice

The determinants of virulence are rarely defined for eukaryotic parasites such as T. gondii, a widespread parasite of mammals that also infects humans, sometimes with serious consequences. Recent laboratory studies have established that variation in a single secreted protein, a serine/threonine kinase known as ROPO18, controls whether or not mice survive infection. Here, we establish the extent and nature of variation in ROP18among a collection of parasite strains from geographically diverse regions. Compared to other genes, ROP18 showed extremely high levels of diversification and changes in expression level, which correlated with severity of infection in mice. Comparison with an out-group demonstrated that changes in the upstream region that regulates expression of ROP18 led to an historical increase in the expression and exposed the protein to diversifying selective pressure. Surprisingly, only three atypically distinct protein variants exist despite marked genetic divergence elsewhere in the genome. These three forms of ROP18 are likely adaptations for different niches in nature, and they confer markedly different virulence to mice. The widespread distribution of a single mouse-virulent allele among geographically and genetically disparate parasites may have consequences for transmission and disease in other hosts, including humans

The bowfin genome illuminates the developmental evolution of ray-finned fishes.

The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era

Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

Protein conformational changes and dynamic behavior are fundamental for such processes as catalysis, regulation, and substrate recognition. Although protein dynamics have been successfully explored in computer simulation, there is an intermediate-scale of motions that has proven difficult to simulate—the motion of individual segments or domains that move independently of the body the protein. Here, we introduce a molecular-dynamics perturbation method, the Rotamerically Induced Perturbation (RIP), which can generate large, coherent motions of structural elements in picoseconds by applying large torsional perturbations to individual sidechains. Despite the large-scale motions, secondary structure elements remain intact without the need for applying backbone positional restraints. Owing to its computational efficiency, RIP can be applied to every residue in a protein, producing a global map of deformability. This map is remarkably sparse, with the dominant sites of deformation generally found on the protein surface. The global map can be used to identify loops and helices that are less tightly bound to the protein and thus are likely sites of dynamic modulation that may have important functional consequences. Additionally, they identify individual residues that have the potential to drive large-scale coherent conformational change. Applying RIP to two well-studied proteins, Dihdydrofolate Reductase and Triosephosphate Isomerase, which possess functionally-relevant mobile loops that fluctuate on the microsecond/millisecond timescale, the RIP deformation map identifies and recapitulates the flexibility of these elements. In contrast, the RIP deformation map of α-lytic protease, a kinetically stable protein, results in a map with no significant deformations. In the N-terminal domain of HSP90, the RIP deformation map clearly identifies the ligand-binding lid as a highly flexible region capable of large conformational changes. In the Estrogen Receptor ligand-binding domain, the RIP deformation map is quite sparse except for one large conformational change involving Helix-12, which is the structural element that allosterically links ligand binding to receptor activation. RIP analysis has the potential to discover sites of functional conformational changes and the linchpin residues critical in determining these conformational states

Not just playing: The politics of designing games for impact on anticipatory climate governance

Simulation games are increasingly popular tools for opening up future imaginaries, especially in the arena of sustainability policy-making and decision support. However, there is a lack of understanding regarding the potential power of games in anticipatory governance. We argue that the utility of simulation games in support of anticipatory climate governance can be greatly increased when game processes are consciously designed to impact present day planning and action. At the same time, game designers with the intention to support or intervene in governance and policy-making inevitably enter political arenas and bear responsibility for understanding and managing their influence at the science-policy interface. We present two case studies: a game simulating a sustainable food policy council with food system actors in Kyoto, Japan, and a game focused on the exploration and imagination of the global impacts of climate tipping points aimed at participants of the global climate negotiation community. Each case study represents a specific logic for translating game play into real-world impacts at different governance scales with distinct political implications. Based on these two case studies, we develop principles for the design and evaluation of simulation games that seek to impact anticipatory climate governance, based on five lenses: (1) purpose and positionality; (2) conceptions of the future and imaginaries; (3) beneficiaries, key stakeholders and participants; (4) the politics of game features and design; and (5) evaluation

Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices

Position-specific scoring matrices (PSSMs) are useful for detecting weak homology in protein sequence analysis, and they are thought to contain some essential signatures of the protein families. In order to elucidate what kind of ingredients constitute such family-specific signatures, we apply singular value decomposition to a set of PSSMs and examine the properties of dominant right and left singular vectors. The first right singular vectors were correlated with various amino acid indices including relative mutability, amino acid composition in protein interior, hydropathy, or turn propensity, depending on proteins. A significant correlation between the first left singular vector and a measure of site conservation was observed. It is shown that the contribution of the first singular component to the PSSMs act to disfavor potentially but falsely functionally important residues at conserved sites. The second right singular vectors were highly correlated with hydrophobicity scales, and the corresponding left singular vectors with contact numbers of protein structures. It is suggested that sequence alignment with a PSSM is essentially equivalent to threading supplemented with functional information. The presented method may be used to separate functionally important sites from structurally important ones, and thus it may be a useful tool for predicting protein functions.Comment: 22 pages, 7 figures, 4 table