Cluster scaling relations from cosmological hydrodynamic simulations in dark energy dominated universe

Clusters are potentially powerful tools for cosmology provided their observed properties such as the Sunyaev-Zel'dovich (SZ) or X-ray signals can be translated into physical quantities like mass and temperature. Scaling relations are the appropriate mean to perform this translation. It is therefore, important to understand their evolution and their modifications with respect to the physics and to the underlying cosmology. In this spirit, we investigate the effect of dark energy on the X-ray and SZ scaling relations. The study is based on the first hydro-simulations of cluster formation for diferent models of dark energy. We present results for four dark energy models which differ from each other by their equations of state parameter, $w$. Namely, we use a cosmological constant model $w=-1$ (as a reference), a perfect fluid with constant equation of state parameter $w=-0.8$ and one with $w = -1.2$ and a scalar field model (or quintessence) with varying $w$. We generate N-body/hydrodynamic simulations that include radiative cooling with the public version of the Hydra code, modified to consider an arbitrary dark energy component. We produce cluster catalogues for the four models and derive the associated X-ray and SZ scaling relations. We find that dark energy has little effect on scaling laws making it safe to use the $\Lambda$CDM scalings for conversion of observed quantities into temperature and masses.Comment: 9 pages, 7 figures, submitted to A&

Simulating the impact of dust cooling on the statistical properties of the intracluster medium

From the first stages of star and galaxy formation, non-gravitational processes such as ram pressure stripping, SNs, galactic winds, AGNs, galaxy-galaxy mergers, etc... lead to the enrichment of the IGM in stars, metals as well as dust, via the ejection of galactic material into the IGM. We know now that these processes shape, side by side with gravitation, the formation and the evolution of structures. We present here hydrodynamic simulations of structure formation implementing the effect of the cooling by dust on large scale structure formation. We focus on the scale of galaxy clusters and study the statistical properties of clusters. Here we present our results on the $T_X-M$ and the $L_X-M$ scaling relations which exhibit changes on both the slope and normalization when adding cooling by dust to the standard radiative cooling model. For example, the normalization of the $T_X-M$ relation changes only by a maximum of 2% at $M=10^{14}$ M$_\odot$ whereas the normalization of the $L_X-T_X$ changes by as much as 10% at $T_X=1$ keV for models that including dust cooling. Our study shows that the dust is an added non-gravitational process that contributes shaping the thermodynamical state of the hot ICM gas.Comment: 11 pages, 4 figures, ASR in pres

Coupled Dyson-Schwinger Equations and Effects of Self-Consistency

Using the $\sigma -\omega$ model as an effective tool, the effects of self-consistency are studied in some detail. A coupled set of Dyson-Schwinger equations for the renormalized baryon and meson propagators in the $\sigma -\omega$ model is solved self-consistently according to the dressed Hartree-Fock scheme, where the hadron propagators in both the baryon and meson self-energies are required to also satisfy this coupled set of equations. It is found that the self-consistency affects the baryon spectral function noticeably, if only the interaction with $\sigma$ mesons is considered. However, there is a cancellation between the effects due to the $\sigma$ and $\omega$ mesons and the additional contribution of $\omega$ mesons makes the above effect insignificant. In both the $\sigma$ and $\sigma -\omega$ cases the effects of self-consistency on meson spectral function are perceptible, but they can nevertheless be taken account of without a self-consistent calculation. Our study indicates that to include the meson propagators in the self-consistency requirement is unnecessary and one can stop at an early step of an iteration procedure to obtain a good approximation to the fully self-consistent results of all the hadron propagators in the model, if an appropriate initial input is chosen. Vertex corrections and their effects on ghost poles are also studied.Comment: 20 pages (include 5 tables), 17 figures (PostScript file

The molecular species responsible for α₁‐antitrypsin deficiency are suppressed by a small molecule chaperone

The formation of ordered Z (Glu342Lys) α1‐antitrypsin polymers in hepatocytes is central to liver disease in α1‐antitrypsin deficiency. In vitro experiments have identified an intermediate conformational state (M*) that precedes polymer formation but this has yet to be identified in vivo. Moreover, the mechanism of polymer formation and their fate in cells have been incompletely characterised. We have used cell models of disease in conjunction with conformation‐selective monoclonal antibodies and a small molecule inhibitor of polymerization to define the dynamics of polymer formation, accumulation and secretion. Pulse‐chase experiments demonstrate that Z α1‐antitrypsin accumulates as short chain polymers that partition with soluble cellular components and are partially secreted by cells. These precede the formation of larger, insoluble polymers with a longer half‐life (10.9 +/‐ 1.7 h and 20.9 +/ 7.4 h for soluble and insoluble polymers respectively). The M* intermediate (or a byproduct thereof) was identified in the cells by a conformation‐specific monoclonal antibody. This was completely abrogated by treatment with the small molecule which also blocked the formation of intracellular polymers. These data allow us to conclude that: the M* conformation is central to polymerization of Z α1‐antitrypsin in vivo; preventing its accumulation represents a tractable approach for pharmacological treatment of this condition; polymers are partially secreted; and polymers exist as two distinct populations in cells whose different dynamics have likely consequences for the aetiology of the disease

Target-distractor synchrony affects performance in a novel motor task for studying action selection

The study of action selection in humans can present challenges of task design since our actions are usually defined by many degrees of freedom and therefore occupy a large action-space. While saccadic eye-movement offers a more constrained paradigm for investigating action selection, the study of reach-and-grasp in upper limbs has often been defined by more complex scenarios, not easily interpretable in terms of such selection. Here we present a novel motor behaviour task which addresses this by limiting the action space to a single degree of freedom in which subjects have to track (using a stylus) a vertical coloured target line displayed on a tablet computer, whilst ignoring a similarly oriented distractor line in a different colour. We ran this task with 55 subjects and showed that, in agreement with previous studies, the presence of the distractor generally increases the movement latency and directional error rate. Further, we used two distractor conditions according to whether the distractor's location changes asynchronously or synchronously with the location of the target. We found that the asynchronous distractor yielded poorer performance than its synchronous counterpart, with significantly higher movement latencies and higher error rates. We interpret these results in an action selection framework with two actions (move left or right) and competing 'action requests' offered by the target and distractor. As such, the results provide insights into action selection performance in humans and supply data for directly constraining future computational models therein

Microbial community drivers of PK/NRP gene diversity in selected global soils

Background The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils. Results Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria, but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes, as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP. Conclusions The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites

Open labware: 3-D printing your own lab equipment

The introduction of affordable, consumer-oriented 3-D printers is a milestone in the current “maker movement,” which has been heralded as the next industrial revolution. Combined with free and open sharing of detailed design blueprints and accessible development tools, rapid prototypes of complex products can now be assembled in one’s own garage—a game-changer reminiscent of the early days of personal computing. At the same time, 3-D printing has also allowed the scientific and engineering community to build the “little things” that help a lab get up and running much faster and easier than ever before

ANIA:ANnotation and Integrated Analysis of the 14-3-3 interactome

The dimeric 14-3-3 proteins dock onto pairs of phosphorylated Ser and Thr residues on hundreds of proteins, and thereby regulate many events in mammalian cells. To facilitate global analyses of these interactions, we developed a web resource named ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome, which integrates multiple data sets on 14-3-3-binding phosphoproteins. ANIA also pinpoints candidate 14-3-3-binding phosphosites using predictor algorithms, assisted by our recent discovery that the human 14-3-3-interactome is highly enriched in 2R-ohnologues. 2R-ohnologues are proteins in families of two to four, generated by two rounds of whole genome duplication at the origin of the vertebrate animals. ANIA identifies candidate ‘lynchpins’, which are 14-3-3-binding phosphosites that are conserved across members of a given 2R-ohnologue protein family. Other features of ANIA include a link to the catalogue of somatic mutations in cancer database to find cancer polymorphisms that map to 14-3-3-binding phosphosites, which would be expected to interfere with 14-3-3 interactions. We used ANIA to map known and candidate 14-3-3-binding enzymes within the 2R-ohnologue complement of the human kinome. Our projections indicate that 14-3-3s dock onto many more human kinases than has been realized. Guided by ANIA, PAK4, 6 and 7 (p21-activated kinases 4, 6 and 7) were experimentally validated as a 2R-ohnologue family of 14-3-3-binding phosphoproteins. PAK4 binding to 14-3-3 is stimulated by phorbol ester, and involves the ‘lynchpin’ site phosphoSer99 and a major contribution from Ser181. In contrast, PAK6 and PAK7 display strong phorbol ester-independent binding to 14-3-3, with Ser113 critical for the interaction with PAK6. These data point to differential 14-3-3 regulation of PAKs in control of cell morphology. Database URL: https://ania-1433.lifesci.dundee.ac.uk/prediction/webserver/index.p

The impact of cooling and pre-heating on the Sunyaev-Zel'dovich effect

We use hydrodynamical simulations to assess the impact of radiative cooling and `pre-heating' on predictions for the Sunyaev--Zel'dovich (SZ) effect. Cooling significantly reduces both the mean SZ signal and its angular power spectrum, while pre-heating can give a higher mean distortion while leaving the angular power spectrum below that found in a simulation without heating or cooling. We study the relative contribution from high and low density gas, and find that in the cooling model about 60 per cent of the mean thermal distortion arises from low overdensity gas. We find that haloes dominate the thermal SZ power spectrum in all models, while in the cooling simulation the kinetic SZ power spectrum originates predominantly in lower overdensity gas.Comment: 4 pages LaTeX file with five figures incorporated. Various clarifications to the discussion. Further colour images and animations at http://astronomy.susx.ac.uk/users/antonio/sz.htm