ALBERT

Description: Motivation: An ever-increasing body of evidence supports the importance of B cell receptor immunoglobulin (BcR IG) sequence restriction, alias stereotypy, in chronic lymphocytic leukemia (CLL). This phenomenon accounts for ~30% of studied cases, one in eight of which belong to major subsets, and extends beyond restricted sequence patterns to shared biologic and clinical characteristics and, generally, outcome. Thus, the robust assignment of new cases to major CLL subsets is a critical, and yet unmet, requirement. Results: We introduce a novel application, ARResT/AssignSubsets, which enables the robust assignment of BcR IG sequences from CLL patients to major stereotyped subsets. ARResT/AssignSubsets uniquely combines expert immunogenetic sequence annotation from IMGT/V-QUEST with curation to safeguard quality, statistical modeling of sequence features from more than 7500 CLL patients, and results from multiple perspectives to allow for both objective and subjective assessment. We validated our approach on the learning set, and evaluated its real-world applicability on a new representative dataset comprising 459 sequences from a single institution. Availability and implementation: ARResT/AssignSubsets is freely available on the web at http://bat.infspire.org/arrest/assignsubsets/ Contact: nikos.darzentas@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Although we are nearing a consensus that most ultraluminous X-ray sources (ULXs) below 10 41 erg s –1 represent stellar mass black holes accreting in a super-Eddington ‘ultraluminous’ accretion state, little is yet established of the physics of this extreme accretion mode. Here, we use a combined X-ray spectral and timing analysis of an XMM–Newton sample of ULXs to investigate this new accretion regime. We start by suggesting an empirical classification scheme that separates ULXs into three classes based on the spectral morphologies observed by Gladstone et al.: a singly peaked broadened disc class, and two-component hard ultraluminous and soft ultraluminous regimes, with the spectra of the latter two classes dominated by the harder and softer component, respectively. We find that at the lowest luminosities ( L X  〈 3 10 39 erg s –1 ) the ULX population is dominated by sources with broadened disc spectra, whilst ULXs with two-component spectra are seen almost exclusively at higher luminosities, suggestive of a distinction between ~Eddington and super-Eddington accretion modes. We find high levels of fractional variability are limited to ULXs with soft ultraluminous spectra, and a couple of the broadened disc sources. Furthermore, the variability in these sources is strongest at high energies, suggesting it originates in the harder of the two spectral components. We argue that these properties are consistent with current models of super-Eddington emission, where a massive radiatively driven wind forms a funnel-like geometry around the central regions of the accretion flow. As the wind provides the soft spectral component this suggests that inclination is the key determinant in the observed two-component X-ray spectra, which is very strongly supported by the variability results if this originates due to clumpy material at the edge of the wind intermittently obscuring our line-of-sight to the spectrally hard central regions of the ULX. The pattern of spectral variability with luminosity in two ULXs that straddle the hard/soft ultraluminous regime boundary is consistent with the wind increasing at higher accretion rates, and thus narrowing the opening angle of the funnel. Hence, this work suggests that most ULXs can be explained as stellar mass black holes accreting at and above the Eddington limit, with their observed characteristics dominated by two variables: accretion rate and inclination.

Description: We extend the Kolmogorov–Smirnov (K–S) test to multiple dimensions by suggesting a $\mathbb {R}^n \rightarrow [0,1]$ mapping based on the probability content of the highest probability density region of the reference distribution under consideration; this mapping reduces the problem back to the one-dimensional case to which the standard K–S test may be applied. The universal character of this mapping also allows us to introduce a simple, yet general, method for the validation of Bayesian posterior distributions of any dimensionality. This new approach goes beyond validating software implementations; it provides a sensitive test for all assumptions, explicit or implicit, that underlie the inference. In particular, the method assesses whether the inferred posterior distribution is a truthful representation of the actual constraints on the model parameters. We illustrate our multidimensional K–S test by applying it to a simple two-dimensional Gaussian toy problem, and demonstrate our method for posterior validation in the real-world astrophysical application of estimating the physical parameters of galaxy clusters parameters from their Sunyaev–Zel'dovich effect in microwave background data. In the latter example, we show that the method can validate the entire Bayesian inference process across a varied population of objects for which the derived posteriors are different in each case.

Description: Spinocerebellar ataxia type 6 (SCA6) belongs to the family of CAG/polyglutamine (polyQ)-dependent neurodegenerative disorders. SCA6 is caused by abnormal expansion in a CAG trinucleotide repeat within exon 47 of CACNA1A , a bicistronic gene that encodes α1A, a P/Q-type calcium channel subunit and a C-terminal protein, termed α1ACT. Expansion of the CAG/polyQ region of CACNA1A occurs within α1ACT and leads to ataxia. There are few animal models of SCA6. Here, we describe the generation and characterization of the first Drosophila melanogaster models of SCA6, which express the entire human α1ACT protein with a normal or expanded polyQ. The polyQ-expanded version of α1ACT recapitulates the progressively degenerative nature of SCA6 when expressed in various fly tissues and the presence of densely staining aggregates. Additional studies identify the co-chaperone DnaJ-1 as a potential therapeutic target for SCA6. Expression of DnaJ-1 potently suppresses α1ACT-dependent degeneration and lethality, concomitant with decreased aggregation and reduced nuclear localization of the pathogenic protein. Mutating the nuclear importer karyopherin α3 also leads to reduced toxicity from pathogenic α1ACT. Little is known about the steps leading to degeneration in SCA6 and the means to protect neurons in this disease are lacking. Invertebrate animal models of SCA6 can expand our understanding of molecular sequelae related to degeneration in this disorder and lead to the rapid identification of cellular components that can be targeted to treat it.

Description: The lack of unambiguous detections of atomic features in the X-ray spectra of ultraluminous X-ray sources (ULXs) has proven a hindrance in diagnosing the nature of the accretion flow. The possible association of spectral residuals at soft energies with atomic features seen in absorption and/or emission and potentially broadened by velocity dispersion could therefore hold the key to understanding much about these enigmatic sources. Here we show for the first time that such residuals are seen in several sources and appear extremely similar in shape, implying a common origin. Via simple arguments we assert that emission from extreme colliding winds, absorption in a shell of material associated with the ULX nebula and thermal plasma emission associated with star formation are all highly unlikely to provide an origin. Whilst CCD spectra lack the energy resolution necessary to directly determine the nature of the features (i.e. formed of a complex of narrow lines or intrinsically broad lines), studying the evolution of the residuals with underlying spectral shape allows for an important, indirect test for their origin. The ULX NGC 1313 X-1 provides the best opportunity to perform such a test due to the dynamic range in spectral hardness provided by archival observations. We show through highly simplified spectral modelling that the strength of the features (in either absorption or emission) appears to anticorrelate with spectral hardness, which would rule out an origin via reflection of a primary continuum and instead supports a picture of atomic transitions in a wind or nearby material associated with such an outflow.

Description: The sliding clamp enhances polymerase processivity and coordinates DNA replication with other critical DNA processing events including translesion synthesis, Okazaki fragment maturation and DNA repair. The relative binding affinity of the sliding clamp for its partners determines how these processes are orchestrated and is essential to ensure the correct processing of newly replicated DNA. However, while stable clamp interactions have been extensively studied; dynamic interactions mediated by the sliding clamp remain poorly understood. Here, we characterize the interaction between the bacterial sliding clamp (β-clamp) and one of its weak-binding partners, the DNA mismatch repair protein MutL. Disruption of this interaction causes a mild mutator phenotype in Escherichia coli , but completely abrogates mismatch repair activity in Bacillus subtilis . We stabilize the MutL-β interaction by engineering two cysteine residues at variable positions of the interface. Using disulfide bridge crosslinking, we have stabilized the E. coli and B. subtilis MutL-β complexes and have characterized their structures using small angle X-ray scattering. We find that the MutL-β interaction greatly stimulates the endonuclease activity of B. subtilis MutL and supports this activity even in the absence of the N-terminal region of the protein.

Description: The known members of the class of hyperluminous X-ray sources (HLXs) are few in number, yet they are of great interest as they are regarded as the likeliest intermediate-mass black hole (IMBH) candidates amongst the wider population of ultraluminous X-ray sources (ULXs). Here we report optical photometry and spectroscopy of an HLX candidate associated with the galaxy IC 4320, that reveal it is a background AGN. We discuss the implications of the exclusion of this object from the small number of well-studied HLXs, that appears to accentuate the difference in characteristics between the good IMBH candidate ESO 243-49 HLX-1 and the small handful of other HLXs.

Description: Fragile X premutation-associated disorders, including Fragile X-associated Tremor Ataxia Syndrome, result from unmethylated CGG repeat expansions in the 5' untranslated region (UTR) of the FMR1 gene. Premutation-sized repeats increase FMR1 transcription but impair rapid translation of the Fragile X mental retardation protein (FMRP), which is absent in Fragile X Syndrome (FXS). Normally, FMRP binds to RNA and regulates metabotropic glutamate receptor (mGluR)-mediated synaptic translation, allowing for dendritic synthesis of several proteins. FMRP itself is also synthesized at synapses in response to mGluR activation. However, the role of activity-dependent translation of FMRP in synaptic plasticity and Fragile X-premutation-associated disorders is unknown. To investigate this question, we utilized a CGG knock-in mouse model of the Fragile X premutation with 120–150 CGG repeats in the mouse Fmr1 5' UTR. These mice exhibit increased Fmr1 mRNA production but impaired FMRP translational efficiency, leading to a modest reduction in basal FMRP expression. Cultured hippocampal neurons and synaptoneurosomes derived from CGG KI mice demonstrate impaired FMRP translation in response to the group I mGluR agonist 3,5-dihydroxyphenylglycine. Electrophysiological analysis reveals enhanced mGluR-mediated long-term depression (mGluR-LTD) at CA3–CA1 synapses in acute hippocampal slices prepared from CGG KI mice relative to wild-type littermates, similar to Fmr1 knockout mice. However, unlike mGluR-LTD in mice completely lacking FMRP, mGluR-LTD in CGG knock-in mice remains dependent on new protein synthesis. These studies demonstrate partially overlapping synaptic plasticity phenotypes in mouse models of FXS and Fragile X premutation disorders and support a role for activity-dependent synthesis of FMRP in enduring forms of synaptic plasticity.