ALBERT

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: 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.

Description: Pan-genome ortholog clustering tool ( PanOCT ) is a tool for pan-genomic analysis of closely related prokaryotic species or strains. PanOCT uses conserved gene neighborhood information to separate recently diverged paralogs into orthologous clusters where homology-only clustering methods cannot. The results from PanOCT and three commonly used graph-based ortholog-finding programs were compared using a set of four publicly available strains of the same bacterial species. All four methods agreed on ~70% of the clusters and ~86% of the proteins. The clusters that did not agree were inspected for evidence of correctness resulting in 85 high-confidence manually curated clusters that were used to compare all four methods.

Description: Although biallelic mutations in non-collagen genes account for 〈10% of individuals with osteogenesis imperfecta, the characterization of these genes has identified new pathways and potential interventions that could benefit even those with mutations in type I collagen genes. We identified mutations in FKBP10 , which encodes the 65 kDa prolyl cis–trans isomerase, FKBP65, in 38 members of 21 families with OI. These include 10 families from the Samoan Islands who share a founder mutation. Of the mutations, three are missense; the remainder either introduce premature termination codons or create frameshifts both of which result in mRNA instability. In four families missense mutations result in loss of most of the protein. The clinical effects of these mutations are short stature, a high incidence of joint contractures at birth and progressive scoliosis and fractures, but there is remarkable variability in phenotype even within families. The loss of the activity of FKBP65 has several effects: type I procollagen secretion is slightly delayed, the stabilization of the intact trimer is incomplete and there is diminished hydroxylation of the telopeptide lysyl residues involved in intermolecular cross-link formation in bone. The phenotype overlaps with that seen with mutations in PLOD2 (Bruck syndrome II), which encodes LH2, the enzyme that hydroxylates the telopeptide lysyl residues. These findings define a set of genes, FKBP10 , PLOD2 and SERPINH1 , that act during procollagen maturation to contribute to molecular stability and post-translational modification of type I procollagen, without which bone mass and quality are abnormal and fractures and contractures result.

Description: Mitochondrial DNA (mtDNA) mutations cause a variety of mitochondrial disorders for which effective treatments are lacking. Emerging data indicate that selective mitochondrial degradation through autophagy (mitophagy) plays a critical role in mitochondrial quality control. Inhibition of mammalian target of rapamycin (mTOR) kinase activity can activate mitophagy. To test the hypothesis that enhancing mitophagy would drive selection against dysfunctional mitochondria harboring higher levels of mutations, thereby decreasing mutation levels over time, we examined the impact of rapamycin on mutation levels in a human cytoplasmic hybrid (cybrid) cell line expressing a heteroplasmic mtDNA G11778A mutation, the most common cause of Leber's hereditary optic neuropathy. Inhibition of mTORC1/S6 kinase signaling by rapamycin induced colocalization of mitochondria with autophagosomes, and resulted in a striking progressive decrease in levels of the G11778A mutation and partial restoration of ATP levels. Rapamycin-induced upregulation of mitophagy was confirmed by electron microscopic evidence of increased autophagic vacuoles containing mitochondria-like organelles. The decreased mutational burden was not due to rapamycin-induced cell death or mtDNA depletion, as there was no significant difference in cytotoxicity/apoptosis or mtDNA copy number between rapamycin and vehicle-treated cells. These data demonstrate the potential for pharmacological inhibition of mTOR kinase activity to activate mitophagy as a strategy to drive selection against a heteroplasmic mtDNA G11778A mutation and raise the exciting possibility that rapamycin may have therapeutic potential for the treatment of mitochondrial disorders associated with heteroplasmic mtDNA mutations, although further studies are needed to determine if a similar strategy will be effective for other mutations and other cell types.

Description: Although attempts have been made to constrain the stellar types of optical counterparts to ultraluminous X-ray sources (ULXs), the detection of optical variability instead suggests that they may be dominated by reprocessed emission from X-rays which irradiate the outer accretion disc. Here, we report results from a combined X-ray and optical spectral study of a sample of ULXs, which were selected for having broadened disc-like X-ray spectra and known optical counterparts. We simultaneously fit optical and X-ray data from ULXs with a new spectral model of emission from an irradiated, colour-temperature-corrected accretion disc around a black hole, with a central Comptonizing corona. We find that the ULXs require reprocessing fractions of ~10 –3 , which is similar to sub-Eddington thermal dominant state black hole binaries (BHBs), but less than has been reported for ULXs with soft ultraluminous X-ray spectra. We suggest that the reprocessing fraction may be due to the opposing effects of self-shielding in a geometrically thick supercritical accretion disc and reflection from far above the central black hole by optically thin material ejected in a natal super-Eddington wind. Then, the higher reprocessing fractions reported for ULXs with wind-dominated X-ray spectra may be due to enhanced scattering on to the outer disc via the stronger wind in these objects. Alternatively, the accretion discs in these ULXs may not be particularly geometrically thick, rather they may be similar in this regard to the thermal dominant state BHBs.

Description: Tools that integrate the complexity of natural systems are needed to facilitate ecosystem-based management (EBM). Loop analysis is an underutilized qualitative tool for EBM that uses information on foodweb links (e.g. predator–prey interactions) and the resulting pathways (cycles) through the foodweb to predict responses to press perturbations. We explore the utility of loop analysis related to management actions: increasing crab abundance and reducing eutrophication in coastal foodwebs. We found that crab-related management actions propagated through the foodweb, with positive and negative impacts. Several negatively impacted species support important fisheries; their declines illustrate the challenge of developing multispecies plans. In our analysis, the management actions decreasing eutrophication reduced most functional groups. However, these predictions were unreliable, suggesting indiscernible bottom-up effects in the foodwebs. Simultaneously managing for crab increases and reducing eutrophication created mostly decreasing abundances in other functional groups and reduced the predictability of the responses. The response to each management action suggests trade-offs between goals, and the qualitatively unreliable predictions could result from variation in the strength of species interactions or indicate knowledge gaps. EBM can benefit from both the explicit articulation of trade-offs and the identification of gaps in our understanding of these systems.

Description: The voltage-sensitive phosphoinositide phosphatases provide a mechanism to couple changes in the transmembrane electrical potential to intracellular signal transduction pathways. These proteins share a domain architecture that is conserved in deuterostomes. However, gene duplication events in primates, including humans, give rise to the paralogs TPTE and TPTE2 that retain protein domain organization but, in the case of TPTE, have lost catalytic activity. Here, we present evidence that these human proteins contain a functional voltage sensor, similar to that in nonmammalian orthologs. However, domains of these human proteins can also generate a noninactivating outward current that is not observed in zebra fish or tunicate orthologs. This outward current has the anticipated characteristics of a voltage-sensitive proton current and is due to the appearance of a single histidine residue in the S4 transmembrane segment of the voltage sensor. Histidine is observed at this position only during the eutherian radiation. Domains from both human paralogs generate proton currents. This apparent gain of proton channel function during the evolution of the TPTE protein family may account for the conservation of voltage sensor domains despite the loss of phosphatase activity in some human paralogs.

Description: The modulation of DNA accessibility by nucleosomes is a fundamental mechanism of gene regulation in eukaryotes. The nucleosome core particle (NCP) consists of 147 bp of DNA wrapped around a symmetric octamer of histone proteins. The dynamics of DNA packaging and unpackaging from the NCP affect all DNA-based chemistries, but depend on many factors, including DNA positioning sequence, histone variants and modifications. Although the structure of the intact NCP has been studied by crystallography at atomic resolution, little is known about the structures of the partially unwrapped, transient intermediates relevant to nucleosome dynamics in processes such as transcription, DNA replication and repair. We apply a new experimental approach combining contrast variation with time-resolved small angle X-ray scattering (TR-SAXS) to determine transient structures of protein and DNA constituents of NCPs during salt-induced disassembly. We measure the structures of unwrapping DNA and monitor protein dissociation from Xenopus laevis histones reconstituted with two model NCP positioning constructs: the Widom 601 sequence and the sea urchin 5S ribosomal gene. Both constructs reveal asymmetric release of DNA from disrupted histone cores, but display different patterns of protein dissociation. These kinetic intermediates may be biologically important substrates for gene regulation.

Description: Palmitoylation, the dynamic post-translational addition of the lipid, palmitate, to proteins by Asp-His-His-Cys-containing palmitoyl acyltransferase (PAT) enzymes, modulates protein function and localization and plays a key role in the nervous system. Huntingtin-interacting protein 14 (HIP14), a well-characterized neuronal PAT, has been implicated in the pathogenesis of Huntington disease (HD), a fatal neurodegenerative disease associated with motor, psychiatric and cognitive symptoms, caused by a CAG expansion in the huntingtin gene ( HTT ). Mice deficient for Hip14 expression develop neuropathological and behavioural features similar to HD, and the catalytic activity of HIP14 is impaired in HD mice, most likely due to the reduced interaction of HIP14 with HTT. Huntingtin-interacting protein 14-like (HIP14L) is a paralog of HIP14, with identical domain structure. Together, HIP14 and HIP14L are the major PATs for HTT. Here, we report the characterization of a Hip14l -deficient mouse model, which develops adult-onset, widespread and progressive neuropathology accompanied by early motor deficits in climbing, impaired motor learning and reduced palmitoylation of a novel HIP14L substrate: SNAP25. Although the phenotype resembles that of the Hip14 –/– mice, a more progressive phenotype, similar to that of the YAC128 transgenic mouse model of HD, is observed. In addition, HIP14L interacts less with mutant HTT than the wild-type protein, suggesting that reduced HIP14L-dependent palmitoylation of neuronal substrates may contribute to the pathogenesis of HD. Thus, both HIP14 and HIP14L may be dysfunctional in the disease.