Regulation of expression of two LY-6 family genes by intron retention and transcription induced chimerism.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Regulation of the expression of particular genes can rely on mechanisms that are different from classical transcriptional and translational control. The LY6G5B and LY6G6D genes encode LY-6 domain proteins, whose expression seems to be regulated in an original fashion, consisting of an intron retention event which generates, through an early premature stop codon, a non-coding transcript, preventing expression in most cell lines and tissues. RESULTS: The MHC LY-6 non-coding transcripts have shown to be stable and very abundant in the cell, and not subject to Nonsense Mediated Decay (NMD). This retention event appears not to be solely dependent on intron features, because in the case of LY6G5B, when the intron is inserted in the artificial context of a luciferase expression plasmid, it is fully spliced but strongly stabilises the resulting luciferase transcript. In addition, by quantitative PCR we found that the retained and spliced forms are differentially expressed in tissues indicating an active regulation of the non-coding transcript. EST database analysis revealed that these genes have an alternative expression pathway with the formation of Transcription Induced Chimeras (TIC). This data was confirmed by RT-PCR, revealing the presence of different transcripts that would encode the chimeric proteins CSNKbeta-LY6G5B and G6F-LY6G6D, in which the LY-6 domain would join to a kinase domain and an Ig-like domain, respectively. CONCLUSION: In conclusion, the LY6G5B and LY6G6D intron-retained transcripts are not subjected to NMD and are more abundant than the properly spliced forms. In addition, these genes form chimeric transcripts with their neighbouring same orientation 5' genes. Of interest is the fact that the 5' genes (CSNKbeta or G6F) undergo differential splicing only in the context of the chimera (CSNKbeta-LY6G5B or G6F-LY6G6C) and not on their own

Brightest galaxies as halo centre tracers in SDSS DR7

Determining the positions of halo centres in large-scale structure surveys is crucial for many cosmological studies. A common assumption is that halo centres correspond to the location of their brightest member galaxies. In this paper, we study the dynamics of brightest galaxies with respect to other halo members in the Sloan Digital Sky Survey DR7. Specifically, we look at the line-of-sight velocity and spatial offsets between brightest galaxies and their neighbours. We compare those to detailed mock catalogues, constructed from high-resolution, dark-matter-only $N$-body simulations, in which it is assumed that satellite galaxies trace dark matter subhaloes. This allows us to place constraints on the fraction $f_{\rm BNC}$ of haloes in which the brightest galaxy is not the central. Compared to previous studies we explicitly take into account the unrelaxed state of the host haloes, velocity offsets of halo cores and correlations between $f_{\rm BNC}$ and the satellite occupation. We find that $f_{\rm BNC}$ strongly decreases with the luminosity of the brightest galaxy and increases with the mass of the host halo. Overall, in the halo mass range $10^{13} - 10^{14.5} h^{-1} M_\odot$ we find $f_{\rm BNC} \sim 30\%$, in good agreement with a previous study by Skibba et al. We discuss the implications of these findings for studies inferring the galaxy--halo connection from satellite kinematics, models of the conditional luminosity function and galaxy formation in general.Comment: 24 pages, 15 figures. Accepted for publication in MNRA

The Galaxy Clustering Crisis in Abundance Matching

Galaxy clustering on small scales is significantly under-predicted by sub-halo abundance matching (SHAM) models that populate (sub-)haloes with galaxies based on peak halo mass, $M_{\rm peak}$. SHAM models based on the peak maximum circular velocity, $V_{\rm peak}$, have had much better success. The primary reason $M_{\rm peak}$ based models fail is the relatively low abundance of satellite galaxies produced in these models compared to those based on $V_{\rm peak}$. Despite success in predicting clustering, a simple $V_{\rm peak}$ based SHAM model results in predictions for galaxy growth that are at odds with observations. We evaluate three possible remedies that could "save" mass-based SHAM: (1) SHAM models require a significant population of "orphan" galaxies as a result of artificial disruption/merging of sub-haloes in modern high resolution dark matter simulations; (2) satellites must grow significantly after their accretion; and (3) stellar mass is significantly affected by halo assembly history. No solution is entirely satisfactory. However, regardless of the particulars, we show that popular SHAM models based on $M_{\rm peak}$ cannot be complete physical models as presented. Either $V_{\rm peak}$ truly is a better predictor of stellar mass at $z\sim 0$ and it remains to be seen how the correlation between stellar mass and $V_{\rm peak}$ comes about, or SHAM models are missing vital component(s) that significantly affect galaxy clustering.Comment: 25 pages, 22 figures, submitted to MNRAS, comments welcom

The Immitigable Nature of Assembly Bias: The Impact of Halo Definition on Assembly Bias

Dark matter halo clustering depends not only on halo mass, but also on other properties such as concentration and shape. This phenomenon is known broadly as assembly bias. We explore the dependence of assembly bias on halo definition, parametrized by spherical overdensity parameter, $\Delta$. We summarize the strength of concentration-, shape-, and spin-dependent halo clustering as a function of halo mass and halo definition. Concentration-dependent clustering depends strongly on mass at all $\Delta$. For conventional halo definitions ($\Delta \sim 200\mathrm{m}-600\mathrm{m}$), concentration-dependent clustering at low mass is driven by a population of haloes that is altered through interactions with neighbouring haloes. Concentration-dependent clustering can be greatly reduced through a mass-dependent halo definition with $\Delta \sim 20\mathrm{m}-40\mathrm{m}$ for haloes with $M_{200\mathrm{m}} \lesssim 10^{12}\, h^{-1}\mathrm{M}_{\odot}$. Smaller $\Delta$ implies larger radii and mitigates assembly bias at low mass by subsuming altered, so-called backsplash haloes into now larger host haloes. At higher masses ($M_{200\mathrm{m}} \gtrsim 10^{13}\, h^{-1}\mathrm{M}_{\odot}$) larger overdensities, $\Delta \gtrsim 600\mathrm{m}$, are necessary. Shape- and spin-dependent clustering are significant for all halo definitions that we explore and exhibit a relatively weaker mass dependence. Generally, both the strength and the sense of assembly bias depend on halo definition, varying significantly even among common definitions. We identify no halo definition that mitigates all manifestations of assembly bias. A halo definition that mitigates assembly bias based on one halo property (e.g., concentration) must be mass dependent. The halo definitions that best mitigate concentration-dependent halo clustering do not coincide with the expected average splashback radii at fixed halo mass.Comment: 19 pages, 13 figures. Updated to published version. Main result summarized in Figure 1

How to Optimally Constrain Galaxy Assembly Bias: Supplement Projected Correlation Functions with Count-in-cells Statistics

Most models for the connection between galaxies and their haloes ignore the possibility that galaxy properties may be correlated with halo properties other than mass, a phenomenon known as galaxy assembly bias. Yet, it is known that such correlations can lead to systematic errors in the interpretation of survey data. At present, the degree to which galaxy assembly bias may be present in the real Universe, and the best strategies for constraining it remain uncertain. We study the ability of several observables to constrain galaxy assembly bias from redshift survey data using the decorated halo occupation distribution (dHOD), an empirical model of the galaxy--halo connection that incorporates assembly bias. We cover an expansive set of observables, including the projected two-point correlation function $w_{\mathrm{p}}(r_{\mathrm{p}})$, the galaxy--galaxy lensing signal $\Delta \Sigma(r_{\mathrm{p}})$, the void probability function $\mathrm{VPF}(r)$, the distributions of counts-in-cylinders $P(N_{\mathrm{CIC}})$, and counts-in-annuli $P(N_{\mathrm{CIA}})$, and the distribution of the ratio of counts in cylinders of different sizes $P(N_2/N_5)$. We find that despite the frequent use of the combination $w_{\mathrm{p}}(r_{\mathrm{p}})+\Delta \Sigma(r_{\mathrm{p}})$ in interpreting galaxy data, the count statistics, $P(N_{\mathrm{CIC}})$ and $P(N_{\mathrm{CIA}})$, are generally more efficient in constraining galaxy assembly bias when combined with $w_{\mathrm{p}}(r_{\mathrm{p}})$. Constraints based upon $w_{\mathrm{p}}(r_{\mathrm{p}})$ and $\Delta \Sigma(r_{\mathrm{p}})$ share common degeneracy directions in the parameter space, while combinations of $w_{\mathrm{p}}(r_{\mathrm{p}})$ with the count statistics are more complementary. Therefore, we strongly suggest that count statistics should be used to complement the canonical observables in future studies of the galaxy--halo connection.Comment: Figures 3 and 4 show the main results. Published in Monthly Notices of the Royal Astronomical Societ

SUSY-QCD Effect on Top-Charm Associated Production at Linear Collider

We evaluate the contribution of SUSY-QCD to top-charm associated production at next generation linear colliders. Our results show that the production cross section of the process $e^+e^-\to t\bar c{or}\bar t c$ could be as large as 0.1 fb, which is larger than the prediction of the SM by a factor of $10^8$.Comment: version to appear in PR

The Scots at the Battle of Neville's Cross, 17 October 1346

This is an analysis of the loyalties and political rivalries of the army of David II of Scotland at the battle of Neville's Cross in 1346 where that king was apparently deserted by some of his subjects and led off to eleven years' captivity in England

T-Violation in K+→μ+νγK^+ \to \mu^+ \nu \gamma Decay And Supersymmetry

Measurement of the transverse muon polarization $P^{\bot}_{\mu}$ in the $K^+ \rightarrow \mu^+\nu\gamma$ decay will be attempted for the first time at the ongoing KEK E246 experiment and also at a proposed BNL experiment. We provide a general analysis of how $P^{\bot}_{\mu}$ is sensitive to the physical $CP$-violating phases in new physics induced four-Fermi interactions, and then we calculate the dominant contributions to $P^{\bot}_{\mu}$ from squark family mixings in generic supersymmetric models. Estimates of the upper bounds on $P^{\bot}_{\mu}$ are also given. It is found that a supersymmetry-induced right-handed quark current from $W$ boson exchange gives an upper limit on $P^{\bot}_{\mu}$ as large as a few per cent, whereas with charged-Higgs-exchange induced pseudoscalar interaction, $P^{\bot}_{\mu}$ is no larger than a few tenths of a per cent. Possible correlations between the muon polarization measurements in $K^+ \rightarrow \mu^+\nu\gamma$ and $K^+ \rightarrow \pi^0\mu^+\nu$ decays are discussed, and distinctive patterns of this correlation from squark family-mixings and from the three-Higgs-doublet model are noted.Comment: Revtex, 29 pages including 4 epsf figure