ALBERT

Description: After the death of a runaway massive star, its supernova shock wave interacts with the bow shocks produced by its defunct progenitor, and may lose energy, momentum and its spherical symmetry before expanding into the local interstellar medium (ISM). We investigate whether the initial mass and space velocity of these progenitors can be associated with asymmetric supernova remnants. We run hydrodynamical models of supernovae exploding in the pre-shaped medium of moving Galactic core-collapse progenitors. We find that bow shocks that accumulate more than about 1.5 M generate asymmetric remnants. The shock wave first collides with these bow shocks 160-750 yr after the supernova, and the collision lasts until 830-4900 yr. The shock wave is then located 1.35-5 pc from the centre of the explosion, and it expands freely into the ISM, whereas in the opposite direction it is channelled into the region of undisturbed wind material. This applies to an initially 20 M progenitor moving with velocity 20 km s -1 and to our initially 40 M progenitor. These remnants generate mixing of ISM gas, stellar wind and supernova ejecta that is particularly important upstream from the centre of the explosion. Their light curves are dominated by emission from optically thin cooling and by X-ray emission of the shocked ISM gas. We find that these remnants are likely to be observed in the [O iii ] 5007 spectral line emission or in the soft energy-band of X-rays. Finally, we discuss our results in the context of observed Galactic supernova remnants such as 3C 391 and the Cygnus Loop.

Description: Balancing selection maintains advantageous genetic and phenotypic diversity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo–Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees, and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 My of independent evolution. Although the majority of these trSNPs were found in three genes of the major histocompatibility locus cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1 . All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic diversity. Here, we focus on the trSNP in LAD1 , a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction; the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1 .

Description: We explore trends in galaxy properties with Mpc-scale structures using catalogues of environment and large-scale structure from the Galaxy And Mass Assembly (GAMA) survey. Existing GAMA catalogues of large-scale structure, group, and pair membership allow us to construct galaxy stellar mass functions for different environmental types. To avoid simply extracting the known underlying correlations between galaxy properties and stellar mass, we create a mass matched sample of galaxies with stellar masses within 9.5 ≤ log M * / h –2 M  ≤ 11 for each environmental population. Using these samples, we show that mass normalized galaxies in different large-scale environments have similar energy outputs, u – r colours, luminosities, and morphologies. Extending our analysis to group and pair environments, we show that galaxies that are not in groups or pairs exhibit similar characteristics to each other regardless of broader environment. For our mass controlled sample, we fail to see a strong dependence of Sérsic index or galaxy luminosity on halo mass, but do find that it correlates very strongly with colour. Repeating our analysis for galaxies that have not been mass controlled introduces and amplifies trends in the properties of galaxies in pairs, groups, and large-scale structure, indicating that stellar mass is the most important predictor of the galaxy properties we examine, as opposed to environmental classifications.

Description: In pancreatic β-cells, mitochondria play a central role in coupling glucose metabolism to insulin secretion. Chronic exposure of β-cells to metabolic stresses impairs their function and potentially induces apoptosis. Little is known on mitochondrial adaptation to metabolic stresses, i.e. high glucose, fatty acids or oxidative stress; being all highlighted in the pathogenesis of type 2 diabetes. Here, human islets were exposed for 3 days to 25 m m glucose, 0.4 m m palmitate, 0.4 m m oleate and transiently to H 2 O 2 . Culture at physiological 5.6 m m glucose served as no-stress control. Expression of mitochondrion-associated genes was quantified, including the transcriptome of mitochondrial inner membrane carriers. Targets of interest were further evaluated at the protein level. Three days after acute oxidative stress, no significant alteration in β-cell function or apoptosis was detected in human islets. Palmitate specifically increased expression of the pyruvate carriers MPC1 and MPC2, whereas the glutamate carrier GC1 and the aspartate/glutamate carrier AGC1 were down-regulated by palmitate and oleate, respectively. High glucose decreased mRNA levels of key transcription factors (HNF4A, IPF1, PPARA and TFAM) and energy-sensor SIRT1. High glucose also reduced expression of 11 mtDNA-encoded respiratory chain subunits. Interestingly, transcript levels of the carriers for aspartate/glutamate AGC2, malate DIC and malate/oxaloacetate/aspartate UCP2 were increased by high glucose, a profile suggesting important mitochondrial anaplerotic/cataplerotic activities and NADPH-generating shuttles. Chronic exposure to high glucose impaired glucose-stimulated insulin secretion, decreased insulin content, promoted caspase-3 cleavage and cell death, revealing glucotoxicity. Overall, expression profile of mitochondrion-associated genes was selectively modified by glucose, delineating a glucotoxic-specific signature.

Description: The Yellowstone–East Snake River Plain hotspot track has been intensely studied since several decades and is widely considered to result from the interaction of a mantle plume with the North American plate. An integrated conclusive geodynamic interpretation of this extensive data set is however presently still lacking, and our knowledge of the dynamical processes beneath Yellowstone is patchy. It has been argued that the Yellowstone plume has delaminated the lower part of the thick Wyoming cratonic lithosphere. We derive an original dynamic model to quantify delamination processes related to mantle plume–lithosphere interactions. We show that fast (~300 ka) lithospheric delamination is consistent with the observed timing of formation of successive volcanic centres along the Yellowstone hotspot track and requires (i) a tensile stress regime within the whole lithosphere exceeding its failure threshold, (ii) a purely plastic rheology in the lithosphere when stresses reach this yield limit, (iii) a dense lower part of the 200 km thick Wyoming lithosphere and (iv) a decoupling melt horizon inside the median part of the lithosphere. We demonstrate that all these conditions are verified and that ~150 km large and ~100 km thick lithospheric blocks delaminate within 300 ka when the Yellowstone plume ponded below the 200 km thick Wyoming cratonic lithosphere. Furthermore, we take advantage of the available extensive regional geophysical and geological observation data sets to design a numerical 3-D upper-mantle convective model. We propose a map of the ascending convective sheets contouring the Yellowstone plume. The model further evidences the development of a counter-flow within the lower part of the lithosphere centred just above the Yellowstone mantle plume axis. This counter-flow controls the local lithospheric stress field, and as a result the trajectories of feeder dykes linking the partial melting source within the core of the mantle plume with the crust by crosscutting the lithospheric mantle. This counter-flow further explains the 50 km NE shift observed between the mantle plume axis and the present-day Yellowstone Caldera as well as the peculiar shaped crustal magma chambers.

Description: The modification of star formation (SF) in galaxy interactions is a complex process, with SF observed to be both enhanced in major mergers and suppressed in minor pair interactions. Such changes likely to arise on short time-scales and be directly related to the galaxy–galaxy interaction time. Here we investigate the link between dynamical phase and direct measures of SF on different time-scales for pair galaxies, targeting numerous star- formation rate (SFR) indicators and comparing to pair separation, individual galaxy mass and pair mass ratio. We split our sample into the higher (primary) and lower (secondary) mass galaxies in each pair and find that SF is indeed enhanced in all primary galaxies but suppressed in secondaries of minor mergers. We find that changes in SF of primaries are consistent in both major and minor mergers, suggesting that SF in the more massive galaxy is agnostic to pair mass ratio. We also find that SF is enhanced/suppressed more strongly for short-duration SFR indicators (e.g. Hα), highlighting recent changes to SF in these galaxies, which are likely to be induced by the interaction. We propose a scenario where the lower mass galaxy has its SF suppressed by gas heating or stripping, while the higher mass galaxy has its SF enhanced, potentially by tidal gas turbulence and shocks. This is consistent with the seemingly contradictory observations for both SF suppression and enhancement in close pairs.

Description: The visual system in the colorful cichlid fishes from the African great lakes is believed to be important for their adaptive radiations. However, few studies have attempted to compare the visual system of radiating cichlid lineages with that of cichlids that have not undergone recent radiations. One such study published in this journal (Schott RK, Refvik SP, Hauser FE, López-Fernández H, Chang BSW. 2014. Divergent positive selection in rhodopsin from lake and riverine cichlid fishes. Mol Biol Evol. 31:1149–1165) found divergent selection on rhodopsin between African lacustrine and riverine cichlid species and riverine Neotropical cichlids, concluding that ecology drives the molecular evolution of this opsin. Here, we expand this analysis by incorporating rhodopsin sequences from Neotropical lacustrine cichlids and show that both ecology and phylogeny are important drivers of the molecular evolution of rhodopsin in cichlids. We found little overlap of sites under selection between African and Neotropical lineages and a faster rate of molecular evolution in African compared with Neotropical cichlids. These results support the notion that genetic or population genetic features particular to African cichlids contributed to their radiations.

Description: We present the catalogue of blended galaxy spectra from the Galaxy And Mass Assembly (GAMA) survey. These are cases where light from two galaxies are significantly detected in a single GAMA fibre. Galaxy pairs identified from their blended spectrum fall into two principal classes: they are either strong lenses, a passive galaxy lensing an emission-line galaxy; or occulting galaxies, serendipitous overlaps of two galaxies, of any type. Blended spectra can thus be used to reliably identify strong lenses for follow-up observations (high-resolution imaging) and occulting pairs, especially those that are a late-type partly obscuring an early-type galaxy which are of interest for the study of dust content of spiral and irregular galaxies. The GAMA survey setup and its autoz automated redshift determination were used to identify candidate blended galaxy spectra from the cross-correlation peaks. We identify 280 blended spectra with a minimum velocity separation of 600 km s –1 , of which 104 are lens pair candidates, 71 emission-line-passive pairs, 78 are pairs of emission-line galaxies and 27 are pairs of galaxies with passive spectra. We have visually inspected the candidates in the Sloan Digital Sky Survey (SDSS) and Kilo Degree Survey (KiDS) images. Many blended objects are ellipticals with blue fuzz ( Ef in our classification). These latter ‘Ef’ classifications are candidates for possible strong lenses, massive ellipticals with an emission-line galaxy in one or more lensed images. The GAMA lens and occulting galaxy candidate samples are similar in size to those identified in the entire SDSS. This blended spectrum sample stands as a testament of the power of this highly complete, second-largest spectroscopic survey in existence and offers the possibility to expand e.g. strong gravitational lens surveys.

Description: Motivation : Using gene expression to infer changes in protein phosphorylation levels induced in cells by various stimuli is an outstanding problem. The intra-species protein phosphorylation challenge organized by the IMPROVER consortium provided the framework to identify the best approaches to address this issue. Results : Rat lung epithelial cells were treated with 52 stimuli, and gene expression and phosphorylation levels were measured. Competing teams used gene expression data from 26 stimuli to develop protein phosphorylation prediction models and were ranked based on prediction performance for the remaining 26 stimuli. Three teams were tied in first place in this challenge achieving a balanced accuracy of about 70%, indicating that gene expression is only moderately predictive of protein phosphorylation. In spite of the similar performance, the approaches used by these three teams, described in detail in this article, were different, with the average number of predictor genes per phosphoprotein used by the teams ranging from 3 to 124. However, a significant overlap of gene signatures between teams was observed for the majority of the proteins considered, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched in the union of the predictor genes of the three teams for multiple proteins. Availability and implementation : Gene expression and protein phosphorylation data are available from ArrayExpress (E-MTAB-2091). Software implementation of the approach of Teams 49 and 75 are available at http://bioinformaticsprb.med.wayne.edu and http://people.cs.clemson.edu/~luofeng/sbv.rar , respectively. Contact : gyanbhanot@gmail.com or luofeng@clemson.edu or atarca@med.wayne.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Contact: Julia.Hoeng@pmi.com