ALBERT

Description: Genome instability, epigenetic remodelling and structural chromosomal rearrangements are hallmarks of cancer. However, the coordinated epigenetic effects of constitutional chromosomal rearrangements that disrupt genes associated with congenital neurodevelopmental diseases are poorly understood. To understand the genetic–epigenetic interplay at breakpoints of chromosomal translocations disrupting CG-rich loci, we quantified epigenetic modifications at DLGAP4 ( SAPAP4), a key post-synaptic density 95 (PSD95) associated gene, truncated by the chromosome translocation t(8;20)(p12;q11.23), co-segregating with cerebellar ataxia in a five-generation family. We report significant epigenetic remodelling of the DLGAP4 locus triggered by the t(8;20)(p12;q11.23) translocation and leading to dysregulation of DLGAP4 expression in affected carriers. Disruption of DLGAP4 results in monoallelic hypermethylation of the truncated DLGAP4 promoter CpG island. This induced hypermethylation is maintained in somatic cells of carriers across several generations in a t(8;20) dependent-manner however, is erased in the germ cells of the translocation carriers. Subsequently, chromatin remodelling of the locus-perturbed monoallelic expression of DLGAP4 mRNAs and non-coding RNAs in haploid cells having the translocation. Our results provide new mechanistic insight into the way a balanced chromosomal rearrangement associated with a neurodevelopmental disorder perturbs allele-specific epigenetic mechanisms at breakpoints leading to the deregulation of the truncated locus.

Description: We conducted blinded psychiatric assessments of 26 Amish subjects (52 ± 11 years) from four families with prevalent bipolar spectrum disorder, identified 10 potentially pathogenic alleles by exome sequencing, tested association of these alleles with clinical diagnoses in the larger Amish Study of Major Affective Disorder (ASMAD) cohort, and studied mutant potassium channels in neurons. Fourteen of 26 Amish had bipolar spectrum disorder. The only candidate allele shared among them was rs78247304, a non-synonymous variant of KCNH7 (c.1181G〉A, p.Arg394His). KCNH7 c.1181G〉A and nine other potentially pathogenic variants were subsequently tested within the ASMAD cohort, which consisted of 340 subjects grouped into controls subjects and affected subjects from overlapping clinical categories (bipolar 1 disorder, bipolar spectrum disorder and any major affective disorder). KCNH7 c.1181G〉A had the highest enrichment among individuals with bipolar spectrum disorder ( 2 = 7.3) and the strongest family-based association with bipolar 1 ( P = 0.021), bipolar spectrum ( P = 0.031) and any major affective disorder ( P = 0.016). In vitro, the p.Arg394His substitution allowed normal expression, trafficking, assembly and localization of HERG3/Kv11.3 channels, but altered the steady-state voltage dependence and kinetics of activation in neuronal cells. Although our genome-wide statistical results do not alone prove association, cumulative evidence from multiple independent sources (parallel genome-wide study cohorts, pharmacological studies of HERG-type potassium channels, electrophysiological data) implicates neuronal HERG3/Kv11.3 potassium channels in the pathophysiology of bipolar spectrum disorder. Such a finding, if corroborated by future studies, has implications for mental health services among the Amish, as well as development of drugs that specifically target HERG3/Kv11.3.

Description: Complex III (cytochrome bc 1 ) is a protein complex of the mitochondrial inner membrane that transfers electrons from ubiquinol to cytochrome c . Its assembly requires the coordinated expression of mitochondrial-encoded cytochrome b and nuclear-encoded subunits and assembly factors. Complex III deficiency is a severe multisystem disorder caused by mutations in subunit genes or assembly factors. Sequence-profile-based orthology predicts C11orf83 , hereafter named UQCC3 , to be the ortholog of the fungal complex III assembly factor CBP4 . We describe a homozygous c.59T〉A missense mutation in UQCC3 from a consanguineous patient diagnosed with isolated complex III deficiency, displaying lactic acidosis, hypoglycemia, hypotonia and delayed development without dysmorphic features. Patient fibroblasts have reduced complex III activity and lower levels of the holocomplex and its subunits than controls. They have no detectable UQCC3 protein and have lower levels of cytochrome b protein. Furthermore, in patient cells, cytochrome b is absent from a high-molecular-weight complex III. UQCC3 is reduced in cells depleted for the complex III assembly factors UQCC1 and UQCC2. Conversely, absence of UQCC3 in patient cells does not affect UQCC1 and UQCC2. This suggests that UQCC3 functions in the complex III assembly pathway downstream of UQCC1 and UQCC2 and is consistent with what is known about the function of Cbp4 and of the fungal orthologs of UQCC1 and UQCC2, Cbp3 and Cbp6. We conclude that UQCC3 functions in complex III assembly and that the c.59T〉A mutation has a causal role in complex III deficiency.

Description: Mutations in the photoreceptor-specific gene peripherin-2 ( PRPH-2 , also known as retinal degeneration slow/RDS) cause incurable retinal degeneration with a high degree of phenotypic variability. Patient phenotypes range from retinitis pigmentosa to various forms of macular and pattern dystrophy. Macular and pattern dystrophy in particular are associated with complex, poorly understood disease mechanisms, as severe vision loss is often associated both with defects in the photoreceptors, as well as the choroid and retinal pigment epithelium (RPE). Since there is currently no satisfactory model to study pattern dystrophy disease mechanisms, we generated a knockin mouse model expressing an RDS pattern dystrophy mutation, Y141C. Y141C mice exhibited clinical signs similar to those in patients including late-onset fundus abnormalities characteristic of RPE and choroidal defects and electroretinogram defects. Ultrastructural examination indicated that disc formation was initiated by the Y141C protein, but proper sizing and alignment of discs required wild-type RDS. The biochemical mechanism underlying these abnormalities was tied to defects in the normal process of RDS oligomerization which is required for proper RDS function. Y141C-RDS formed strikingly abnormal disulfide-linked complexes which were localized to the outer segment (OS) where they impaired the formation of proper OS structure. These data support a model of pattern dystrophy wherein a primary molecular defect occurring in all photoreceptors leads to secondary sequellae in adjacent tissues, an outcome which leads to macular vision loss. An understanding of the role of RDS in the interplay between these tissues significantly enhances our understanding of RDS-associated pathobiology and our ability to design rational treatment strategies.

Description: Over the course of the past few decades, there has been an exponential growth in environmental courts and tribunals (ECTs). At present, over 350 of these specialized fora for resolving environmental disputes exist, spanning across every region throughout the world. Some of the ECTs have been more successful but others have been less successful. This article identifies 12 characteristics that experience suggests are required for an environmental court or tribunal to operate successfully in practice, drawing upon examples from multiple jurisdictions. In identifying best practices, both substantive and procedural, from existing ECTs, this article will assist two groups: first, stakeholders who are in the process of planning or creating environmental courts or tribunals in their jurisdictions and, secondly, stakeholders and countries that are looking to improve the functioning and performance of their own ECTs.

Description: Legal education plays an important but under-acknowledged role in anthropogenic environmental change because it shapes and qualifies people to become lawyers, judges and policy makers. Their work can prohibit and legitimate particular environmental practices. The conceptual framework of law, its taxonomy, as taught to students of law, often perpetuates an unsustainable relationship to the environment where it separates questions of entitlement to land and natural resources from questions of responsibility for them. The implication of perpetuating this separation in law curricula is that generations of legal practitioners will remain unlikely to develop a coherent system of environmental law that aligns rights with responsibilities. Environmental education scholar David Orr argues that ‘all education is environmental education’. But legal education often excludes environmental considerations even where these are materially relevant. Given the role of legal education in shaping future law, this article contends that rethinking its categories opens the possibility to create sustainable land use practice laws and policy.

Description: This article utilises the concept of interdisciplinarity as a background against which to reflect on the nature of environmental law scholarship. The article argues that, while interdisciplinary scholarship has some tangible benefits in terms of expanding the perimeters of a discipline, the effects of interdisciplinary work are often exaggerated. In fact, interdisciplinary scholarship may have the unintended consequence of entrenching academic disciplines even further. In light of this, it is argued that environmental law scholarship is best perceived and defined as a deliberative practice which takes place within, and speaks to, a specific community of scholars—an interpretive community. In order to secure a vibrant discipline, the article argues that the community ought to maintain a flexible, open-ended and broadly defined approach to environmental law scholarship.

Description: European Union (EU) legal studies generally picture the Member States’ local and regional authorities as implementers of national and supranational norms rather than independent regulators. Yet, sub-national authorities (SNAs) have become active regulators in the context of climate change mitigation and adaptation, a role not foreseen by EU primary law, which this article understands to constitute the surface of EU law. This article examines regulatory activity of SNAs from the perspective of EU law. It illustrates that sub-national, national, supranational and international actors are engaged in a process of mutual learning and experimentation and that, below its surface, EU law recognises that SNAs are not mere implementers of norms but also independent regulators.

Description: This article presents a fresh analysis of the implications of the 2006 judgment of the Court of Justice of the European Union (CJEU) in Case C-244/05 Bund Naturschutz in Bayern , which clarified the standard of legal protection afforded to sites eligible for adoption as Sites of Community Importance (SCIs) under the EU’s Habitats Directive. The article argues that, as a result of this line of case law, it will be unlawful ( at least in certain cases, and perhaps in all) to apply the Article 6(4) Habitats Directive derogation in respect of eligible sites which have not yet been adopted by the European Commission as SCIs. The Commission appears to have been aware of this potential implication, and acted swiftly to minimise the potentially disruptive impact of the judgment on plans and projects within the EU. The article also considers the relevance of the CJEU’s Sweetman judgment ( C-258/11 ) to the Bund Naturschutz in Bayern line of jurisprudence.

Description: What does the specialised nature of an environment court entitle it to do? The recent decision of the New Zealand Supreme Court in Environmental Defence Society Incorporated v Marlborough District Council (‘the King Salmon case’)[2014] NZSC 38 helps to answer this question. For the past 20 years, the New Zealand Environment Court has decided applications within a framework of the broadly defined statutory purpose of sustainable resource management. The King Salmon case narrows this wide discretion. This article analyses the implications of the decision, suggesting that it helps to delineate between functions of specialist environment courts that may be considered appropriate (adjudicative and legislative fact finding) and decision-making that strays too far into the policy-sphere.

Description: This article compares the protection from unnecessary suffering afforded to wild animals with that afforded to domesticated animals and animals under human control. It considers various forms of species-specific biodiversity- and conservation-based protection for wild animals, under legislation such as the Wildlife and Countryside Act 1981 and the Conservation of Habitats and Species Regulations 2010, as well as the general protection from intentionally inflicted unnecessary suffering afforded to wild mammals under the Wild Mammals (Protection) Act 1996. The article then compares the standard of protection afforded to wild animals with that afforded to non-wild animals under section 4 of the Animal Welfare Act 2006, which criminalises unnecessary suffering unreasonably caused to non-wild animals.

Description: In recent years, an increasing number of reports have been focused on the structure and biological role of non-canonical nucleic acid secondary structures. Many of these studies involve the use of oligonucleotides that can often adopt a variety of structures depending on the experimental conditions, and hence change the outcome of an assay. The knowledge of the structure(s) formed by oligonucleotides is thus critical to correctly interpret the results, and gain insight into the biological role of these particular sequences. Herein we demonstrate that size-exclusion HPLC (SE-HPLC) is a simple yet surprisingly powerful tool to quickly and effortlessly assess the secondary structure(s) formed by oligonucleotides. For the first time, an extensive calibration and validation of the use of SE-HPLC to confidently detect the presence of different species displaying various structure and/or molecularity, involving 〉110 oligonucleotides forming a variety of secondary structures (antiparallel, parallel, A-tract bent and mismatched duplexes, triplexes, G-quadruplexes and i-motifs, RNA stem loops), is performed. Moreover, we introduce simple metrics that allow the use of SE-HPLC without the need for a tedious calibration work. We show that the remarkable versatility of the method allows to quickly establish the influence of a number of experimental parameters on nucleic acid structuration and to operate on a wide range of oligonucleotide concentrations. Case studies are provided to clearly illustrate the all-terrain capabilities of SE-HPLC for oligonucleotide secondary structure analysis. Finally, this manuscript features a number of important observations contributing to a better understanding of nucleic acid structural polymorphism.

Description: Single-molecule manipulation (SMM) techniques use applied force, and measured elastic response, to reveal microscopic physical parameters of individual biomolecules and details of biomolecular interactions. A major hurdle in the application of these techniques is the labeling method needed to immobilize biomolecules on solid supports. A simple, minimally-perturbative labeling strategy would significantly broaden the possible applications of SMM experiments, perhaps even allowing the study of native biomolecular structures. To accomplish this, we investigate the use of functionalized locked nucleic acid (LNA) oligomers as biomolecular handles that permit sequence-specific binding and immobilization of DNA. We find these probes form bonds with DNA with high specificity but with varied stability in response to the direction of applied mechanical force: when loaded in a shear orientation, the bound LNA oligomers were measured to be two orders of magnitude more stable than when loaded in a peeling, or unzipping, orientation. Our results show that LNA provides a simple, stable means to functionalize dsDNA for manipulation. We provide design rules that will facilitate their use in future experiments.

Description: Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds.

Description: Decitabine (5-aza-2'-deoxycytidine) is a DNA methyltransferase inhibitor and an archetypal epigenetic drug for the therapy of myeloid leukemias. The mode of action of decitabine strictly depends on the incorporation of the drug into DNA. However, DNA incorporation and ensuing genotoxic effects of decitabine have not yet been investigated in human cancer cell lines or in models related to the approved indication of the drug. Here we describe a robust assay for the quantitative determination of decitabine incorporation rates into DNA from human cancer cells. Using a panel of human myeloid leukemia cell lines we show appreciable amounts of decitabine incorporation that closely correlated with cellular drug uptake. Decitabine incorporation was also detectable in primary cells from myeloid leukemia patients, indicating that the assay is suitable for biomarker analyses to predict drug responses in patients. Finally, we also used next-generation sequencing to comprehensively analyze the effects of decitabine incorporation on the DNA sequence level. Interestingly, this approach failed to reveal significant changes in the rates of point mutations and genome rearrangements in myeloid leukemia cell lines. These results indicate that standard rates of decitabine incorporation are not genotoxic in myeloid leukemia cells.

Description: A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/ .

Description: The understanding of folding and function of RNA molecules depends on the identification and classification of interactions between ribonucleotide residues. We developed a new method named ClaRNA for computational classification of contacts in RNA 3D structures. Unique features of the program are the ability to identify imperfect contacts and to process coarse-grained models. Each doublet of spatially close ribonucleotide residues in a query structure is compared to clusters of reference doublets obtained by analysis of a large number of experimentally determined RNA structures, and assigned a score that describes its similarity to one or more known types of contacts, including pairing, stacking, base–phosphate and base–ribose interactions. The accuracy of ClaRNA is 0.997 for canonical base pairs, 0.983 for non-canonical pairs and 0.961 for stacking interactions. The generalized squared correlation coefficient (GC 2 ) for ClaRNA is 0.969 for canonical base pairs, 0.638 for non-canonical pairs and 0.824 for stacking interactions. The classifier can be easily extended to include new types of spatial relationships between pairs or larger assemblies of nucleotide residues. ClaRNA is freely available via a web server that includes an extensive set of tools for processing and visualizing structural information about RNA molecules.

Description: The Prp19-associated complex is required for spliceosome activation by stabilizing the binding of U5 and U6 on the spliceosome after the release of U4. The complex comprises at least eight proteins, among which Ntc90 and Ntc77 contain multiple tetratricopeptide repeat (TPR) elements. We have previously shown that Ntc90 is not involved in spliceosome activation, but is required for the recruitment of essential first-step factor Yju2 to the spliceosome. We demonstrate here that Ntc77 has dual functions in both spliceosome activation and the first catalytic step in recruiting Yju2. We have identified an amino-terminal region of Ntc77, which encompasses the N-terminal domain and the first three TPR motifs, dispensable for spliceosome activation but required for stable interaction of Yju2 with the spliceosome. Deletion of this region had no severe effect on the integrity of the NTC, binding of NTC to the spliceosome or spliceosome activation, but impaired splicing and exhibited a dominant-negative growth phenotype. Our data reveal functional roles of Ntc77 in both spliceosome activation and the first catalytic step, and distinct structural domains of Ntc77 required for these two steps.

Description: Polarization in classical Be stars results from Thomson scattering of the unpolarized light from the Be star in the circumstellar disc. Theory and observations agree that the maximum degree of polarization from isolated Be stars is 4 per cent. We report on the first optical polarimetric observations of the Be/X-ray binary EXO 2030+375. We find that the optical ( R -band) light is strongly linearly polarized with a degree of polarization of 19 per cent, the highest ever measured either in a classical or Be/X-ray binary. We argue that the interstellar medium cannot account for this high-polarization degree and that a substantial amount must be intrinsic to the source. We propose that it may result from the alignment of non-spherical ferromagnetic grains in the Be star disc due to the strong neutron star magnetic field.

Description: An intraplate slow earthquake was detected in northernmost Hokkaido, Japan, by a dense network of the global navigation satellite system. Transient abnormal acceleration of 〈12 mm was observed during the period 2012 July to 2013 January (~5.5 months) at several sites. The spatial displacement distribution suggests that a localized tectonic event caused localized deformation. Estimated fault parameter indicates very shallow-dip reverse faulting in the uppermost crust, with a total seismic moment of 1.75E + 17 N m ( M w 5.4). This fault geometry is probably consistent with detachment structure indicated by geological studies. A simultaneous earthquake swarm with the maximum magnitude M 4.1 suggests a possibility that the slow slip triggered the seismic activity for unknown reasons. This slow earthquake is slower than its moment would indicate, with a duration–magnitude scaling relationship unlike either regular earthquakes or subduction slow slip events. This result indicates that even if the area is under different physical property from subduction zones, slow earthquake can occur by some causes. Slow earthquakes exist in remote regions away from subduction zones and might play an important role in strain release and tectonic activity.

Description: We studied ionospheric responses to the 2012 April 11 M w 8.6 North Sumatra earthquake using total electron content (TEC) measurements with the regional Global Navigation Satellite System network. This earthquake ruptured the oceanic lithosphere off the Indian Ocean coast of North Sumatra, and is known as the largest strike-slip earthquake ever recorded. Coseismic ionospheric disturbances (CIDs) with rapid TEC enhancement of a few TEC units propagated northward with a speed of acoustic waves (~1 km s –1 ). Resonant atmospheric oscillation with a frequency ~4 mHz have been found as monochromatic oscillation of TEC lasting for an hour after the main shock and the largest aftershock. We compared CID amplitudes of 21 earthquakes world-wide with moment magnitudes ( M w ) 6.6–9.2. They roughly obeyed a law such that CID amplitude increases by two orders of magnitude for the M w increase of three. The 2012 North Sumatra earthquakes slightly deviated negatively from the trend possibly reflecting their strike-slip mechanisms, that is small vertical crustal movements for their magnitudes.

Description: In autumn 2012, the new release 05 (RL05) of monthly geopotencial spherical harmonics Stokes coefficients (SC) from Gravity Recovery and Climate Experiment (GRACE) mission was published. This release reduces the noise in high degree and order SC, but they still need to be filtered. One of the most common filtering processing is the combination of decorrelation and Gaussian filters. Both of them are parameters dependent and must be tuned by the users. Previous studies have analyzed the parameters choice for the RL05 GRACE data for oceanic applications, and for RL04 data for global application. This study updates the latter for RL05 data extending the statistics analysis. The choice of the parameters of the decorrelation filter has been optimized to: (1) balance the noise reduction and the geophysical signal attenuation produced by the filtering process; (2) minimize the differences between GRACE and model-based data and (3) maximize the ratio of variability between continents and oceans. The Gaussian filter has been optimized following the latter criteria. Besides, an anisotropic filter, the fan filter, has been analyzed as an alternative to the Gauss filter, producing better statistics.

Description: We present high-resolution tomographic images in source areas of 26 large crustal earthquakes ( M 6.0–7.2) which occurred in Northeast Japan (Tohoku) during the past 120 yr from 1894 to 2014. Prominent low-velocity (low- V ) and high Poisson's ratio (high- ) anomalies are revealed in the crust and mantle wedge under the source areas. Beneath the volcanic front and backarc areas, the low- V and high- zones reflect arc-magma related high-temperature anomalies which are produced by joint effects of corner flow in the mantle wedge and fluids from dehydration of the subducting Pacific slab. The hot anomalies cause locally thinning and weakening of the brittle seismogenic layer above them. Low-frequency micro-earthquakes are observed in the lower crust and uppermost mantle in or around the low- V zones, which reflect ascending of arc magma and fluids from the mantle wedge to the crust. No volcano and magma exist in the forearc area due to low temperature there, hence the low- V zones in the forearc reflect fluids from the slab dehydration. The ascending fluids may have produced a ‘water wall’ in the mantle wedge and crust beneath the forearc area. When the water enters active faults in the crust, the fault-zone friction is reduced and so large earthquakes can be induced. These results indicate that the nucleation of a large earthquake is not entirely a mechanical process, but is closely associated with subduction dynamics and physical and chemical properties of rocks in the crust and upper mantle. In particular, arc magma and fluids play an important role in the seismogenesis.

Description: We present two estimators to quantify the angular power spectrum of the sky signal directly from the visibilities measured in radio interferometric observations. This is relevant for both the foregrounds and the cosmological 21-cm signal buried therein. The discussion here is restricted to the Galactic synchrotron radiation, the most dominant foreground component after point source removal. Our theoretical analysis is validated using simulations at 150 MHz, mainly for GMRT and also briefly for Low-Frequency Array. The Bare Estimator uses pairwise correlations of the measured visibilities, while the Tapered Gridded Estimator uses the visibilities after gridding in the uv plane. The former is very precise, but computationally expensive for large data. The latter has a lower precision, but takes less computation time which is proportional to the data volume. The latter also allows tapering of the sky response leading to sidelobe suppression, an useful ingredient for foreground removal. Both estimators avoid the positive bias that arises due to the system noise. We consider amplitude and phase errors of the gain, and the w -term as possible sources of errors. We find that the estimated angular power spectrum is exponentially sensitive to the variance of the phase errors but insensitive to amplitude errors. The statistical uncertainties of the estimators are affected by both amplitude and phase errors. The w -term does not have a significant effect at the angular scales of our interest. We propose the Tapered Gridded Estimator as an effective tool to observationally quantify both foregrounds and the cosmological 21-cm signal.

Description: We extend the theory of astrophysical maser propagation through a medium with a Zeeman-split molecular response to the case of a non-uniform magnetic field, and allow a component of the electric field of the radiation in the direction of propagation: a characteristic of radiation with orbital angular momentum. A classical reduction of the governing equations leads to a set of nine differential equations for the evolution of intensity-like parameters for each Fourier component of the radiation. Four of these parameters correspond to the standard Stokes parameters, whilst the other five represent the z -component of the electric field, and its coupling to the conventional components in the x – y -plane. A restricted analytical solution of the governing equations demonstrates a non-trivial coupling of the Stokes parameters to those representing orbital angular momentum: the z -component of the electric field can grow from a background in which only Stokes- I is non-zero. A numerical solution of the governing equations reveals radiation patterns with a radial and angular structure for the case of an ideal quadrupole magnetic field perpendicular to the propagation direction. In this ideal case, generation of radiation orbital angular momentum, like polarization, can approach 100 per cent.

Description: Two mafic eruptive products from Vesuvius, a tephrite and a trachybasalt, have been crystallized in the laboratory to constrain the nature of primitive Vesuvius magmas and their crustal evolution. Experiments were performed at high temperatures (from 1000 to ≥1200°C) and both at 0·1 MPa and at high pressures (from 50 to 200 MPa) under H 2 O-bearing fluid-absent and H 2 O- and CO 2 -bearing fluid-present conditions. Experiments started from glass except for a few that started from glass plus San Carlos olivine crystals to force olivine saturation. Melt H 2 O concentrations reached a maximum of 6·0 wt % and experimental f O 2 ranged from NNO – 0·1 to NNO + 3·4 (where NNO is nickel–nickel oxide buffer). Clinopyroxene (Mg# up to 93) is the liquidus phase for the two investigated samples; it is followed by leucite for H 2 O in melt 〈3 wt %, and by phlogopite (Mg# up to 81) for H 2 O in melt 〉3 wt %. Olivine (Fo 85 ) crystallized spontaneously in only one experimental charge. Plagioclase was not found. Upon progressive crystallization of clinopyroxene, glass K 2 O and Al 2 O 3 contents strongly increase whereas MgO, CaO and CaO/Al 2 O 3 decrease; the residual melts follow the evolution of Vesuvius whole-rocks from trachybasalt to tephrite, phonotephrite and to tephriphonolite. Concentrations of H 2 O and CO 2 in near-liquidus 200 MPa glasses and primitive melt inclusions from the literature overlap. The earliest evolutionary stage, corresponding to the crystallization of Fo-rich olivine, was reconstructed by the olivine-added experiments. They show that the primitive Vesuvius melts are trachybasalts (K 2 O ~ 4·5–5·5 wt %, MgO = 8–9 wt %, Mg# = 75–80, CaO/Al 2 O 3 = 0·9–0·95) that crystallize Fo-rich olivine (90–91) as the liquidus phase between 1150 and 1200°C and from 300 to 〈200 MPa. Primitive Vesuvius melts are volatile-rich (1·5–4·5 wt % H 2 O and 600–4500 ppm CO 2 in primitive melt inclusions) and oxidized (from NNO + 0·4 to NNO + 1·2). Assimilation of carbonate wall-rocks by ascending primitive magmas can account for the disappearance of olivine from crystallization sequences and explains the lack of rocks representative of olivine-crystallizing magmas. A correlation between carbonate assimilation and the type of feeding system is proposed: carbonate assimilation is promoted for primitive magma batches of small volumes. In contrast, for longer-lived, large-volume, less frequently recharged, hence more evolved, cooler reservoirs, magma–carbonate interaction is limited. Primitive magmas from Vesuvius and other Campanian volcanoes have similar redox states. However, the Cr# of Vesuvius spinels is distinctive and therefore the peridotitic component in the mantle source of Vesuvius differs from that of the other Campanian magmas.

Description: Peridotite xenoliths exhumed by Quaternary alkaline magmatism in the Tahalgha district, southern Hoggar, represent fragments of the subcontinental lithospheric mantle beneath the boundary between the two major structural domains of the Tuareg Shield: the ‘Polycyclic Central Hoggar’ to the east and the ‘Western Hoggar’, or ‘Pharusian Belt’, to the west. Samples were collected from volcanic centres located on both sides of a major lithospheric shear zone at 4°35' separating these two domains. Although showing substantial variations in their deformation microstructures, equilibrium temperatures and modal and chemical compositions, the studied samples do not display any systematic changes of these features across the 4°35' fault. The observed variations rather record small-scale heterogeneities distributed throughout the study area and reflecting the widespread occurrence of vein conduits and metasomatized wall-rocks related to trans-lithospheric melt circulation during the Cenozoic. These features include partial annealing of pre-existing deformation microstructures, post-deformation metasomatic reactions, and trace-element enrichment, coupled with heating from 750–900°C (low-temperature lherzolites) to 900–1150°C (intermediate- T lherzolites and high- T harzburgites and wehrlites). Trace-element modelling confirms that the range of rare earth element (REE) variations observed in the Tahalgha clinopyroxenes may be accounted for by reactive porous flow involving a single stage of basaltic melt infiltration into a light REE (LREE)-depleted protolith. Whole-rock compositions record the final entrapment of disequilibrium metasomatic melts upon thermal relaxation of the veins–wall-rock system. The striking correlations between equilibrium temperatures and trace-element enrichment favor a scenario in which the high-temperature peridotites record advective heat transport along melt conduits, whereas the intermediate- and low-temperature lherzolites reflect conductive heating of the host Mechanical Boundary Layer. This indicates that the lithosphere did not reach thermal equilibrium, suggesting that the inferred heating event was transient and was rapidly erased by thermal relaxation down to the relatively low-temperature present-day geotherm. The low- T (〈900°C) deformed lherzolites (porphyroclastic to equigranular) are characterized by only incipient annealing and LREE-depleted clinopyroxene compositions. They were only weakly affected by the Cenozoic events and could represent relatively well-preserved samples from rejuvenated Pan-African lithosphere. Extensive lithospheric rejuvenation occurred either regionally during the Pan-African orogeny, as a result of lithospheric delamination or thermomechanical erosion after thickening, or more locally along the meridional shear zones. The low- T Tahalgha lherzolites are comparable with lherzolites from Etang de Lherz, southern France, interpreted as lithospheric mantle rejuvenated by melt-induced refertilization during a late stage of the Variscan orogeny.

Description: Hydrothermal experiments were conducted at 200 MPa and 900–1018°C to determine the solubilities, fluid(s)–melt partitioning, and mixing properties of H 2 O, CO 2 , S, Cl, and F in phonolitic–trachytic melts saturated in vapor, vapor plus saline liquid, or saline liquid. The bulk compositions and S, Cl, and F concentrations of the run-product glasses were determined by electron microprobe and the H 2 O and CO 2 contents by Fourier-transform infrared spectroscopy (FTIR). A new parameterization was developed to calculate molar absorption coefficients for FTIR analysis of carbonate in glasses and applied to the run-product glasses. The concentrations of volatiles in the fluid(s) were determined by mass-balance calculations and checked with chloridometer analysis and gravimetry. The range in oxygen fugacity of these experiments is NNO to NNO + 2 (where NNO is nickel–nickel oxide buffer). The phonolitic–trachytic melts dissolved up to 7·5 wt % H 2 O, 0·94 wt % Cl, 0·73 wt % CO 2 , 0·75 wt % F, and 0·16 wt % S, and the integrated bulk fluid(s) contained up to 99 mol % H 2 O, 34 mol % Cl, 82 mol % CO 2 , 1·7 mol % F, and 3·7 mol % S. The mixing relationships of H 2 O, CO 2 , and Cl in melt versus fluid(s) are complex and strongly non-ideal at these pressure–temperature conditions, particularly with two fluid phases stable. The concentrations of H 2 O and CO 2 in melt change with the addition of Cl ± S to the system, and the solubility of Cl in melt varies with S. The reductions in H 2 O and CO 2 solubility in melt exceed those resulting from simple dilution of the coexisting fluid(s) owing to addition of other volatiles. The partitioning of H 2 O and CO 2 between fluid(s) and melt varies as a function of fluid(s) and melt composition. The experimental data are applied to phonolitic and related magmas of Mt. Somma–Vesuvius, Italy, Mt. Erebus, Antarctica, and Cripple Creek, USA, to better interpret processes of fluid(s) exsolution in eruptive and mineralizing systems. Application of the experimental results also provides constraints on eruptive and mineralizing fluid(s) compositions.

Description: A halo merger tree forms the essential backbone of a semi-analytic model for galaxy formation and evolution. Recent studies have pointed out that extracting merger trees from numerical simulations of structure formation is non-trivial; different tree building algorithms can give differing merger histories. These differences should be carefully understood before merger trees are used as input for models of galaxy formation. We investigate the impact of different halo merger trees on a semi-analytic model. We find that the z  = 0 galaxy properties in our model show differences between trees when using a common parameter set. The star formation history of the universe and the properties of satellite galaxies can show marked differences between trees with different construction methods. Independently calibrating the semi-analytic model for each tree can reduce the discrepancies between the z  = 0 global galaxy properties, at the cost of increasing the differences in the evolutionary histories of galaxies. Furthermore, the underlying physics implied can vary, resulting in key quantities such as the supernova feedback efficiency differing by factors of 2. Such a change alters the regimes where star formation is primarily suppressed by supernovae. Therefore, halo merger trees extracted from a common halo catalogue using different, but reliable, algorithms can result in a difference in the semi-analytic model. Given the uncertainties in galaxy formation physics, however, these differences may not necessarily be viewed as significant.

Description: We simulate the evolution of dense-cool clumps embedded in the intracluster medium (ICM) of cooling flow clusters of galaxies in response to multiple jet-activity cycles, and find that the main heating process of the clumps is mixing with the hot shocked jets’ gas, the bubbles, while shocks have a limited role. We use the pluto hydrodynamical code in two dimensions with imposed axisymmetry, to follow the thermal evolution of the clumps. We find that the inflation process of hot bubbles, which appear as X-ray deficient cavities in observations, is accompanied by complicated induced vortices inside and around the bubbles. The vorticity induces efficient mixing of the hot bubbles’ gas with the ICM and cool clumps, resulting in a substantial increase of the temperature and entropy of the clumps. For the parameters used by us, heating by shocks barely competes with radiative cooling, even after 25 consecutive shocks excited during 0.5 Gyr of simulation. Some clumps are shaped to filamentary structure that can turn to observed optical filaments. We find that not all clumps are heated. Those that cool to very low temperatures will fall in and feed the central supermassive black hole, hence closing the feedback cycle in what is termed the cold feedback mechanism.

Description: The pulsar IGR J16393–4643 belongs to a class of highly absorbed supergiant high-mass X-ray binaries (HMXBs), characterized by a very high column density of absorbing matter. We present the results of simultaneous broad-band pulsation and spectrum analysis from a 44-ks Suzaku observation of the source. The orbital intensity profile created with the Swift Burst Alert Telescope ( Swift –BAT) light curve shows an indication of IGR J16393–4643 being an eclipsing system with a short eclipse semi-angle E  ~ 17°. For a supergiant companion star with a 20-R radius, this implies an inclination of the orbital plane in the range 39°–57°, whereas for a main-sequence B star as the companion with a 10-R radius, the inclination of the orbital plane is in the range 60°–77°. Pulse profiles created for different energy bands have complex morphology, which shows some energy dependence and increases in pulse fraction with energy. We have also investigated broad-band spectral characteristics, phase-averaged spectra and resolving the pulse phase into peak and trough phases. The phase-averaged spectrum has a very high N H (~ 3 10 23  cm –2 ) and is described by a power law ( ~ 0.9) with a high-energy cut-off above 20 keV. We find a change in the spectral index in the peak and trough phases, implying an underlying change in the source spectrum.

Description: A large class of flat axially symmetric solutions to the Vlasov–Poisson system is constructed with the property that the corresponding rotation curves are approximately flat, slightly decreasing or slightly increasing. The rotation curves are compared with measurements from real galaxies and satisfactory agreement is obtained. These facts raise the question whether the observed rotation curves for disc galaxies may be explained without introducing dark matter. Furthermore, it is shown that for the ansatz we consider stars on circular orbits do not exist in the neighbourhood of the boundary of the steady state.

Description: This paper presents a detailed analysis of two-armed spiral structure in a sample of galaxies from the Spitzer Infrared Nearby Galaxies Survey, with particular focus on the relationships between the properties of the spiral pattern in the stellar disc and the global structure and environment of the parent galaxies. Following Paper I , we have used a combination of Spitzer Space Telescope mid-infrared imaging and visible multicolour imaging to isolate the spiral pattern in the underlying stellar discs, and we examine the systematic behaviours of the observed amplitudes and shapes (pitch angles) of these spirals. In general, spiral morphology is found to correlate only weakly at best with morphological parameters such as stellar mass, gas fraction, disc/bulge ratio, and v flat . In contrast to weak correlations with galaxy structure, a strong link is found between the strength of the spiral arms and tidal forcing from nearby companion galaxies. This appears to support the longstanding suggestion that either a tidal interaction or strong bar is a necessary condition for driving grand-design spiral structure. The pitch angles of the stellar arms are only loosely correlated with the pitch angles of the corresponding arms traced in gas and young stars. We find that the strength of the shock in the gas and the contrast in the star formation rate are strongly correlated with the stellar spiral amplitude.

Description: The early stages of magmatic processes operating at mantle depths beneath continental arcs are poorly known. The chemical compositions of minerals and rocks, mineral Sr–Nd–Hf–O isotopes and zircon U–Pb ages of garnet clinopyroxenite dykes from the Shenglikou peridotite massif (North Qaidam Orogen, NE Tibet, China) were studied to constrain their sources and genesis, and the dynamic processes that controlled pyroxenite formation beneath an early Paleozoic active continental margin. Major-element compositions of bulkrocks suggest that the pyroxenitic protoliths were cumulates segregated from a melt, which was extracted from a peridotite-dominated mantle source. Bulk-rock and mineral trace-element patterns show strong enrichment in fluid-mobile elements (e.g. Cs, Rb, Ba, Th, U, K, Pb and Li) and marked negative anomalies in the high field strength elements relative to rare earth elements, similar to the characteristics of melts derived from a volatile-rich sub-arc mantle. Enriched Sr and Nd initial isotopic compositions at 500 Ma ( 87 Sr/ 86 Sr of 0·70919–0·71774 and Nd of –16·3 to –3·4) are in contrast to the highly radiogenic Hf isotope compositions (similar to those of the depleted-mantle reservoir) and to the uncontaminated upper-mantle 18 O V-SMOW (garnet: 5·6 ± 0·3, 2SD, n = 61; zircon: 5·9 ± 0·3, 2SD, n = 28). These decoupled isotopic signatures suggest that the melt source was located in a convective mantle wedge (controlling the Hf and O isotopes) that had been pervasively metasomatized by fluids from a subducted Proto-Tethys oceanic slab (controlling the Sr–Nd isotopes and highly incompatible elements). Zircons with two groups of U–Pb ages (430 ± 5 Ma and 401 ± 7 Ma) were generated by recrystallization events, corresponding to UHP metamorphism and a major uplift stage during the North Qaidam orogeny, respectively. The combined evidence reveals a picture of continental arc magmatism at mantle depths and subsequent continental collision. The subduction of the Proto-Tethys oceanic slab beneath the southern Qilian margin triggered flux melting of the metasomatized convective mantle wedge and generated hydrous arc magmas. These primitive magmas intruded into the overlying lithospheric mantle and segregated the cumulates parental to the Shenglikou pyroxenites. Subsequent continental subduction incorporated fragments of the mantle-wedge peridotite (containing pyroxenite dykes) at ~430 Ma and carried them to shallow depths during exhumation at ~400 Ma.

Description: Using a new high-resolution dataset, this study presents evidence for short length scale 18 O/ 16 O heterogeneity in the mantle source region of young (age 12 ka bp ) Icelandic basalts. The dataset comprises secondary ion mass spectrometry determinations of 18 O/ 16 O in single compositional zones of plagioclase crystals from the primitive Borgarhraun flow in northern Iceland, along with trace and major element data from the same zones. The presence of mantle under Iceland with 18 O below typical mid-ocean ridge basalt (MORB) values of ~5·5 ± 0·3 (VSMOW) has previously been disputed, because variability in 18 O in many Icelandic basalts is also known to be caused by the interaction of basaltic melts with crustal lithologies that have been altered by low- 18 O meteoric water. Primitive basalt flows, such as Borgarhraun, and their macrocrysts are the most likely candidates to retain a mantle 18 O signature. However, the role of crustal processes in generating the low 18 O in olivine crystals from these flows has not unequivocally been ruled out. By making intra-crystal analyses in Borgarhraun plagioclase it has been possible in this study to obtain a detailed record of the chemical and isotopic compositions of the melts that crystallized the plagioclase zones. The variability observed in trace element compositions of the early crystallized anorthitic plagioclase zones (80·9–89·4 mol % anorthite) is firstly shown to arise from melt compositional variability, and equilibrium melt concentrations of Sr, La and Y are then calculated from the crystal concentrations of these elements using carefully selected partition coefficients. The ranges of incompatible trace element ratios (La/Y, Sr/Y) in these equilibrium melts reflect a range of compositions of fractional mantle melts, a result that is in agreement with previous proposals for the cause of variability in trace element indices of Borgarhraun olivine-hosted melt inclusions and clinopyroxene compositional zones. Correlations observed between La/Y and Sr/Y in the melts in equilibrium with the Borgarhraun plagioclase zones and the 18 O of these zones therefore support the hypothesis that the mantle under Iceland is heterogeneous in 18 O/ 16 O. Such correlations have not previously been observed in intra-crystal data from Iceland, and provide strong evidence that mantle material with abnormally low 18 O may exist in the form of readily fusible heterogeneities alongside ambient mantle with MORB-like 18 O (+5·5) on a length scale of 〈100 km. The lowest 18 O of plagioclase that is attributed to a mantle origin in this study is 4·5 ± 0·4, equating to a melt equivalent value of 4·3 ± 0·5 or an olivine equivalent value of 3·8 ± 0·5.

Description: Mafic to ultramafic intrusions of the Qullinaaraaluk suite (Q-suite) were emplaced into the Ungava craton of the Northeastern Superior Province during an episode of intense igneous activity and crustal reworking from c. 2·74 to 2·70 Ga. Orthopyroxene-rich Q-suite intrusions from the Hudson Bay Terrane and southwestern Rivière Arnaud Terrane, and orthopyroxene-poor Q-suite intrusions from the north–central Rivière Arnaud Terrane indicate the existence of at least two Q-suite magma types: a subalkaline magma parental to the orthopyroxene-rich intrusions and a transitional magma parental to the orthopyroxene-poor intrusions. Both types of intrusions are characterized by light rare earth element (LREE)-enriched, high field strength element (HFSE)-depleted trace element profiles that reflect, in large part, contamination by the tonalite–trondhjemite–granodiorite-dominated crust. Near-chondritic to strongly sub-chondritic initial Nd (2·72 Ga) values (+2 to –10) of the Q-suite intrusions reflect the combined effects of both the amount of crustal contamination and the age-dependent isotopic composition of the contaminant. The inferred trace element profiles of the uncontaminated Q-suite magmas were probably flat to LREE-depleted. The transitional magmas that produced the least evolved dunitic cumulates of the Q-suite were ferropicrites (MgO ~14 wt %, FeO TOT ~17 wt %). In contrast, the magmas parental to the primitive Q-suite harzburgites were Fe-rich, high-Mg basalts (MgO ~11 wt %; FeO ~14 wt %). The high Fe contents of the Q-suite magmas are incompatible with derivation from a pyrolitic mantle [Mg-number ~0·90, Mg/(Mg + Fe TOT )] and require sources significantly enriched in iron (Mg-number ≤0·79). Both magma types are also characterized by relatively low Ni contents suggesting derivation from source regions depleted in Ni relative to pyrolitic mantle peridotite. Differences in the major element compositions of the subalkaline and transitional parental magmas may reflect compositional diversity among the Fe-rich mantle sources. Comparisons with melting experiments on compositions analogous to the Martian mantle suggest that the Q-suite magmas may rather be generated by different degrees of melting of a common source with an Fe content slightly lower than that of the Homestead L5 ordinary chondrite (Mg-number = 0·77). The Fe-rich picritic to high-Mg basaltic magmas last equilibrated with garnet-free harzburgitic to lherzolitic residues at upper mantle pressures (≤5 GPa). The craton-wide occurrence of c. 2·72–2·70 Ga Q-suite mafic to ultramafic plutons suggests that underplating by Fe-rich mantle melts may have had a key role in the c. 2·74–2·70 Ga cratonization of the Northeastern Superior Province.

Description: Arc basalts are more oxidized than mid-ocean ridge basalts, but it is unclear whether this difference is due to differentiation processes in the Earth’s crust or to a fundamental difference in the oxygen fugacity of their mantle sources. Distinguishing between these two hypotheses is important for understanding redox-sensitive processes related to arc magmatism, and thus more broadly how Earth materials cycle globally. We present major, volatile, and trace element concentrations in combination with Fe 3+ /Fe ratios determined in olivine-hosted glass inclusions and submarine glasses from five Mariana arc volcanoes and two regions of the Mariana Trough. For single eruptions, Fe 3+ /Fe ratios vary along liquid lines of descent that are either slightly oxidizing (olivine + clinopyroxene + plagioclase fractionation, CO 2 ± H 2 O degassing) or reducing (olivine + clinopyroxene + plagioclase ± magnetite fractionation, CO 2 + H 2 O + S degassing). Mariana samples are consistent with a global relationship between calc-alkaline affinity and both magmatic H 2 O and magmatic oxygen fugacity, where wetter, higher oxygen fugacity magmas display greater affinity for calc-alkaline differentiation. We find, however, that low-pressure differentiation cannot explain the majority of variations observed in Fe 3+ /Fe ratios for Mariana arc basalts, requiring primary differences in magmatic oxygen fugacity. Calculated oxygen fugacities of primary mantle melts at the pressures and temperatures of melt segregation are significantly oxidized relative to mid-ocean ridge basalts (~QFM, where QFM is quartz–fayalite–magnetite buffer), ranging from QFM + 1·0 to QFM + 1·6 for Mariana arc basalts, whereas back-arc related samples record primary oxygen fugacities that range from QFM + 0·1 to QFM + 0·5. This Mariana arc sample suite includes a diversity of subduction influences, from lesser influence of a homogeneous H 2 O-rich component in the back-arc, to sediment melt- and fluid-dominated influences along the arc. Primary melt oxygen fugacity does not correlate significantly with sediment melt contributions (e.g. Th/La), nor can it be attributed to previous melt extraction in the back-arc. Primary melt oxygen fugacity correlates strongly with indices of slab fluids (e.g. Ba/La) from the Mariana Trough through the Mariana arc, increasing by 1·5 orders of magnitude as Ba/La increases by a factor of 10 relative to mid-ocean ridge basalts. These results suggest that contributions from the slab to the mantle wedge may be responsible for the elevated oxygen fugacity recorded by Mariana arc basalts and that slab fluids are potentially very oxidized.

Description: Magma mixing and crystal mush disaggregation are important processes in basaltic magma reservoirs. We carried out a detailed petrological and geochemical study on a highly plagioclase-phyric eruption within the Eastern Volcanic Zone of Iceland—the Skuggafjöll eruption—to investigate crystal storage and transport processes within a single magmatic system. Crystal content and phase proportions vary between samples: the least phyric samples have phase proportions similar to the low-pressure, three-phase gabbro eutectic (plg:cpx:ol ~ 11:6:3), whereas highly phyric samples are strongly enriched in plagioclase (plg:cpx:ol ~ 8:1:1). Statistically significant geochemical variability in 28 whole-rock samples collected across the eruption can be accounted for by variable accumulation of a troctolitic assemblage containing plagioclase and olivine in an approximately 9:1 ratio. Two macrocryst assemblages are defined using compositional and textural information recorded in QEMSCAN® images: a primitive assemblage of high-anorthite plagioclase (An 〉83 ) and high-forsterite olivine (Fo 〉84 ), and an evolved assemblage of low-anorthite plagioclase (An 〈79 ), low-forsterite olivine (Fo 〈82 ) and clinopyroxene (Mg# ~ 82). Plagioclase and olivine have strongly bimodal composition distributions whereas the composition distribution of clinopyroxene is unimodal. The mean trace element composition of melt inclusions hosted within high-forsterite olivine and high-anorthite plagioclase macrocrysts is the same (mean Ce/Y ~ 0·47–0·48), confirming that both primitive macrocryst phases crystallized from the same distribution of melts. Clinopyroxene macrocrysts and matrix glasses are in Ce/Yb equilibrium with each other, indicating that the evolved assemblage crystallized from melts with a more incompatible trace element-enriched composition (mean Ce/Y ~ 0·65–71) than the primitive assemblage. Variability in whole-rock, macrocryst and melt inclusion compositions suggests that the Skuggafjöll magma experienced two stages of crystallization. Primitive macrocrysts crystallized first from incompatible trace element-depleted melts within a shallow crustal magma reservoir. These primitive macrocrysts were subsequently stored in crystal mushes that ultimately disaggregated into an evolved and incompatible trace element-enriched magma from which the evolved assemblage crystallized. On average, ~17% of the erupted magma at Skuggafjöll is composed of accumulated macrocrysts entrained from crystal mushes. The timescale between mush disaggregation and eruption, during which crystal accumulation occurred, was short—of the order of years—according to simple diffusion calculations. Striking petrological similarities between Skuggafjöll and other highly phyric eruptions both in Iceland and along mid-ocean ridges indicate that crystal accumulation by mush disaggregation is likely to be an important mechanism for generating highly phyric magmas in basaltic plumbing systems.

Description: We combine photometry from the Ultra Deep Survey (UDS), Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) UDS and CANDELS the Great Observatories Origins Deep Survey-South (GOODS-S) surveys to construct the galaxy stellar mass function probing both the low- and high-mass end accurately in the redshift range 0.3 〈  z  〈 3. The advantages of using a homogeneous concatenation of these data sets include meaningful measures of environment in the UDS, due to its large area (0.88 deg 2 ), and the high-resolution deep imaging in CANDELS ( H 160  〉 26.0), affording us robust measures of structural parameters. We construct stellar mass functions for the entire sample as parametrized by the Schechter function, and find that there is a decline in the values of and of α with higher redshifts, and a nearly constant M * up to z  ~ 3. We divide the galaxy stellar mass function by colour, structure, and environment and explore the links between environmental overdensity, morphology, and the quenching of star formation. We find that a double Schechter function describes galaxies with high Sérsic index ( n  〉 2.5), similar to galaxies which are red or passive. The low-mass end of the n  〉 2.5 stellar mass function is dominated by blue galaxies, whereas the high-mass end is dominated by red galaxies. This shows that there is a possible link between morphological evolution and star formation quenching in high mass galaxies, which is not seen in lower mass systems. This in turn suggests that there are strong mass-dependent quenching mechanisms. In addition, we find that the number density of high-mass systems is elevated in dense environments, suggesting that an environmental process is building up massive galaxies quicker in over densities than in lower densities.

Description: We analyse a sample of 26 active galactic nuclei (AGN) with deep XMM–Newton observations, using principal component analysis (PCA) to find model-independent spectra of the different variable components. In total, we identify at least 12 qualitatively different patterns of spectral variability, involving several different mechanisms, including five sources which show evidence of variable relativistic reflection (MCG–6-30-15, NGC 4051, 1H 0707–495, NGC 3516 and Mrk 766) and three which show evidence of varying partial covering neutral absorption (NGC 4395, NGC 1365 and NGC 4151). In over half of the sources studied, the variability is dominated by changes in a power-law continuum, both in terms of changes in flux and power-law index, which could be produced by propagating fluctuations within the corona. Simulations are used to find unique predictions for different physical models, and we then attempt to qualitatively match the results from the simulations to the behaviour observed in the real data. We are able to explain a large proportion of the variability in these sources using simple models of spectral variability, but more complex models may be needed for the remainder. We have begun the process of building up a library of different principal components, so that spectral variability in AGN can quickly be matched to physical processes. We show that PCA can be an extremely powerful tool for distinguishing different patterns of variability in AGN, and that it can be used effectively on the large amounts of high-quality archival data available from the current generation of X-ray telescopes. We will make our PCA code available upon request to the lead author.

Description: Using N -body simulations we study the phenomenon of radial orbit instability occurring in dark matter haloes of the size of a dwarf galaxy. We carried out simulations of seven spherical models, with the same standard NFW (Navarro, Frenk & White) density profile but different anisotropy profiles of particle orbits. Four of them underwent instability: two with a constant positive anisotropy, one with an anisotropic core and an isotropic envelope and one with a very small isotropic core and an anisotropic envelope. Haloes affected by the instability become approximately axisymmetric and prolate, with the profile of the shortest-to-longest axis ratio increasing with radius. The lower limit for the central value of this axis ratio is 0.3 for an NFW halo. The density profiles of the haloes did not change significantly, whereas the velocity distributions became axisymmetric. The angular momentum modulus rose due to large-amplitude oscillations of its components perpendicular to the symmetry axis of the halo. We also studied orbits of individual particles assigning them to classical orbit families in triaxial potentials. We find that the membership of a given particle in a family depends on its initial angular momentum modulus and its components along the principal axes of matter distribution.

Description: We present a study of the prevalence and luminosity of active galactic nuclei (AGN; traced by optical spectra) as a function of both environment and galaxy interactions. For this study, we used a sample of more than 250 000 galaxies drawn from the Sloan Digital Sky Survey and, crucially, we controlled for the effect of both stellar mass and central star formation activity. Once these two factors are taken into account, the effect of the local density of galaxies and of one-on-one interactions is minimal in both the prevalence of AGN activity and AGN luminosity. This suggests that the level of nuclear activity depends primarily on the availability of cold gas in the nuclear regions of galaxies and that secular processes can drive the AGN activity in the majority of cases. Large-scale environment and galaxy interactions only affect AGN activity in an indirect manner, by influencing the central gas supply.

Description: We report the results of the photometric and spectroscopic monitoring campaign of the transient SN 2007sv. The observables are similar to those of Type IIn supernovae, a well-known class of objects whose ejecta interact with pre-existing circumstellar material (CSM). The spectra show a blue continuum at early phases and prominent Balmer lines in emission; however, the absolute magnitude at the discovery of SN 2007sv ( M R  = –14.25 ± 0.38) indicate it to be most likely a supernova impostor. This classification is also supported by the lack of evidence in the spectra of very high velocity material as expected in supernova ejecta. In addition, we find no unequivocal evidence of broad lines of α- and/or Fe-peak elements. The comparison with the absolute light curves of other interacting objects (including Type IIn supernovae) highlights the overall similarity with the prototypical impostor SN 1997bs. This supports our claim that SN 2007sv was not a genuine supernova, and was instead a supernova impostor, most likely similar to the major eruption of a luminous blue variable.

Description: The Cosmicflows-2 catalogue is a compendium of peculiar velocity measurements. While it has many objects in common with the COMPOSITE catalogue, a previously analysed collection of peculiar velocity data found to give an unexpectedly large bulk flow on large scales, the data in Cosmicflows-2 have been reanalysed to ensure consistency between distances measured using different methods. In particular, a focus on accurate distances led the authors of the Cosmicflows-2 to not correct for homogeneous or inhomogeneous Malmquist bias, both or which are corrected for in the COMPOSITE compilation. We find remarkable agreement between the COMPOSITE and the Cosmicflows-2 if the small EFAR sample of clusters located in two dense superclusters is removed from both surveys, giving results that are inconsistent with the cold dark matter standard model with Planck central parameters at the 98 per cent level. On smaller scales we find overall agreement between data sets and consistency with the standard model.

Description: We quantify the stellar abundances of neutron-rich r-process nuclei in cosmological zoom-in simulations of a Milky Way-mass galaxy from the Feedback In Realistic Environments project. The galaxy is enriched with r-process elements by binary neutron star (NS) mergers and with iron and other metals by supernovae. These calculations include key hydrodynamic mixing processes not present in standard semi-analytic chemical evolution models, such as galactic winds and hydrodynamic flows associated with structure formation. We explore a range of models for the rate and delay time of NS mergers, intended to roughly bracket the wide range of models consistent with current observational constraints. We show that NS mergers can produce [r-process/Fe] abundance ratios and scatter that appear reasonably consistent with observational constraints. At low metallicity, [Fe/H]  –2, we predict there is a wide range of stellar r-process abundance ratios, with both supersolar and subsolar abundances. Low-metallicity stars or stars that are outliers in their r-process abundance ratios are, on average, formed at high redshift and located at large galactocentric radius. Because NS mergers are rare, our results are not fully converged with respect to resolution, particularly at low metallicity. However, the uncertain rate and delay time distribution of NS mergers introduce an uncertainty in the r-process abundances comparable to that due to finite numerical resolution. Overall, our results are consistent with NS mergers being the source of most of the r-process nuclei in the Universe.

Description: We present time series spectroscopy of two short period cataclysmic variables, CC Scl and V2051 Oph, to test the efficiency of Doppler-tomography-based methods in constraining orbital parameters of evolved cataclysmic variables. We find that the Ca ii triplet lines offer superior diagnostics, revealing emission components from the mass donors and sharp images of the accretion discs. Furthermore, we use Monte Carlo methods to estimate the uncertainties from ensembles of Doppler maps. We compare our new methods against traditional radial velocity methods and show that they offer a valid route towards system parameter determination. Our analysis of CC Scl suggests a low mass ratio of q  = 0.08 ± 0.03 with a primary velocity of K 1  = 37 ± 14 km s –1 . This mass ratio is in between the pre- and post-period minimum status, however our K 1 solution favours a post-period minimum system. Our derived parameters for V2051 Oph ( q  = 0.18 ± 0.05, K 1  = 97 ± 10 km s –1 ) are in agreement with the eclipse solution ( q  = 0.19 ± 0.03), offering a direct validation of our methods.

Description: We present NuSTAR observations of the bright Seyfert 2 galaxy NGC 2110 obtained in 2012, when the source was at the highest flux level ever observed, and in 2013, when the source was at a more typical flux level. We include archival observations from other X-ray satellites, namely XMM–Newton , Suzaku , BeppoSAX , Chandra and Swift . Simultaneous NuSTAR and Swift broad-band spectra (in the 3–80 keV range) indicate a cutoff energy E c  〉 210 keV, with no detectable contribution from Compton reflection. NGC 2110 is one of the very few sources where no evidence for distant Compton-thick scattering is found and, by using temporal information collected over more than a decade, we investigate variations of the iron Kα line on time-scales of years. The Fe Kα line is likely the sum of two components: one constant (originating from distant Compton-thick material) and the other one variable and linearly correlated with the source flux (possibly arising from Compton-thin material much closer to the black hole).

Description: Angiosperm mitochondrial genomes exhibit many unusual properties, including heterogeneous nucleotide composition and exceptionally large and variable genome sizes. Determining the role of nonadaptive mechanisms such as mutation bias in shaping the molecular evolution of these unique genomes has proven challenging because their dynamic structures generally prevent identification of homologous intergenic sequences for comparative analyses. Here, we report an analysis of angiosperm mitochondrial DNA sequences that are derived from inserted plastid DNA ( mtpts ). The availability of numerous completely sequenced plastid genomes allows us to infer the evolutionary history of these insertions, including the specific nucleotide substitutions and indels that have occurred because their incorporation into the mitochondrial genome. Our analysis confirmed that many mtpts have a complex history, including frequent gene conversion and multiple examples of horizontal transfer between divergent angiosperm lineages. Nevertheless, it is clear that the majority of extant mtpt sequence in angiosperms is the product of recent transfer (or gene conversion) and is subject to rapid loss/deterioration, suggesting that most mtpts are evolving relatively free from functional constraint. The evolution of mtpt sequences reveals a pattern of biased mutational input in angiosperm mitochondrial genomes, including an excess of small deletions over insertions and a skew toward nucleotide substitutions that increase AT content. However, these mutation biases are far weaker than have been observed in many other cellular genomes, providing insight into some of the notable features of angiosperm mitochondrial architecture, including the retention of large intergenic regions and the relatively neutral GC content found in these regions.

Description: Dusty, star-forming galaxies have a critical role in the formation and evolution of massive galaxies in the Universe. Using deep far-infrared imaging in the range 100–500 μm obtained with the Herschel telescope, we investigate the dust-obscured star formation (SF) in the galaxy cluster XDCP J0044.0-2033 at z  = 1.58, the most massive cluster at z  〉 1.5, with a measured mass M 200  = 4.7 $^{+1.4}_{-0.9}$  10 14  M . We perform an analysis of the spectral energy distributions (SEDs) of 12 cluster members (5 spectroscopically confirmed) detected with ≥3 significance in the PACS maps, all ultraluminous infrared galaxies. The individual star formation rates (SFRs) lie in the range 155–824 M yr –1 , with dust temperatures of 24–35 K. We measure a strikingly high amount of SF in the cluster core, SFR (〈250 kpc) ≥ 1875 ± 158 M yr –1 , four times higher than the amount of SF in the cluster outskirts. This scenario is unprecedented in a galaxy cluster, showing for the first time a reversal of the SF–density relation at z ~ 1.6 in a massive cluster.

Description: Polycyclic aromatic hydrocarbons (PAHs) are believed to be the small-size tail of the interstellar carbonaceous dust grain population. Their vibrational emission is the most widely accepted source of the aromatic near-infrared features, and their rotational radiation is a likely explanation for the dust-correlated anomalous microwave emission (AME). Yet, no individual interstellar PAH molecule has been identified to date. It was recently recognized that quasi-symmetric planar PAHs ought to have a well identifiable comb-like rotational spectrum, and suggested to search for them in spectroscopic data with matched-filtering techniques. We report the results of the first such search, carried out with the Green Bank Telescope, and targeting the star-forming region IC 348 in the Perseus molecular cloud, a known source of AME. Our observations amounted to 16.75 h and spanned a 3-GHz-wide band extending from 23.3 to 26.3 GHz. Using frequency switching, we achieved a sensitivity of 0.4 mJy per 0.4 MHz channel (1). The non-detection of comb-like spectra allowed us to set upper bounds on the abundance of specific quasi-symmetric PAH molecules (specified uniquely by their moments of inertia) of approximately 0.1 per cent of the total PAH abundance. This bound generically applies to PAHs with approximately 15–100 carbon atoms.

Description: As is well known, it is necessary to derive stellar parameters from massive amounts of spectral data automatically and efficiently. However, in traditional automatic methods such as artificial neural networks (ANNs) and kernel regression (KR), it is often difficult to optimize the algorithm structure and determine the optimal algorithm parameters. Gaussian process regression (GPR) is a recently developed method that has been proven to be capable of overcoming these difficulties. Here we apply GPR to derive stellar atmospheric parameters from spectra. Through evaluating the performance of GPR on Sloan Digital Sky Survey (SDSS) spectra, Medium resolution Isaac Newton Telescope Library of Empirical Spectra (MILES) spectra, ELODIE spectra and the spectra of member stars of galactic globular clusters, we conclude that GPR can derive stellar parameters accurately and precisely, especially when we use data preprocessed with principal component analysis (PCA). We then compare the performance of GPR with that of several widely used regression methods (ANNs, support-vector regression and KR) and find that with GPR it is easier to optimize structures and parameters and more efficient and accurate to extract atmospheric parameters.

Description: Galaxy–galaxy weak lensing is a direct probe of the mean matter distribution around galaxies. The depth and sky coverage of the Canada–France–Hawaii Telescope Legacy Survey yield statistically significant galaxy halo mass measurements over a much wider range of stellar masses (10 8.75 to 10 11.3 M ) and redshifts (0.2 〈  z  〈 0.8) than previous weak lensing studies. At redshift z  ~ 0.5, the stellar-to-halo mass ratio (SHMR) reaches a maximum of 4.0 ± 0.2 per cent as a function of halo mass at ~10 12.25 M . We find, for the first time from weak lensing alone, evidence for significant evolution in the SHMR: the peak ratio falls as a function of cosmic time from 4.5 ± 0.3 per cent at z  ~ 0.7 to 3.4 ± 0.2 per cent at z  ~ 0.3, and shifts to lower stellar mass haloes. These evolutionary trends are dominated by red galaxies, and are consistent with a model in which the stellar mass above which star formation is quenched ‘downsizes’ with cosmic time. In contrast, the SHMR of blue, star-forming galaxies is well fitted by a power law that does not evolve with time. This suggests that blue galaxies form stars at a rate that is balanced with their dark matter accretion in such a way that they evolve along the SHMR locus. The redshift dependence of the SHMR can be used to constrain the evolution of the galaxy population over cosmic time.

Description: Here we conducted an integrative multi-omics analysis to understand how cancers harbor various types of aberrations at the genomic, epigenomic and transcriptional levels. In order to elucidate biological relevance of the aberrations and their mutual relations, we performed whole-genome sequencing, RNA-Seq, bisulfite sequencing and ChIP-Seq of 26 lung adenocarcinoma cell lines. The collected multi-omics data allowed us to associate an average of 536 coding mutations and 13,573 mutations in promoter or enhancer regions with aberrant transcriptional regulations. We detected the 385 splice site mutations and 552 chromosomal rearrangements, representative cases of which were validated to cause aberrant transcripts. Averages of 61, 217, 3687 and 3112 mutations are located in the regulatory regions which showed differential DNA methylation, H3K4me3, H3K4me1 and H3K27ac marks, respectively. We detected distinct patterns of aberrations in transcriptional regulations depending on genes. We found that the irregular histone marks were characteristic to EGFR and CDKN1A, while a large genomic deletion and hyper-DNA methylation were most frequent for CDKN2A. We also used the multi-omics data to classify the cell lines regarding their hallmarks of carcinogenesis. Our datasets should provide a valuable foundation for biological interpretations of interlaced genomic and epigenomic aberrations.

Description: Alkylative damage to DNA can be induced by environmental chemicals, endogenous metabolites and some commonly prescribed chemotherapeutic agents. The regioisomeric N 3-, O 2 - and O 4 -ethylthymidine ( N 3-, O 2 - and O 4 -EtdT, respectively) represent an important class of ethylated DNA lesions. Using nonreplicative double-stranded vectors containing an N 3-EtdT, O 2 -EtdT or O 4 -EtdT at a defined site in the template strand, herein we examined the effects of these lesions on DNA transcription mediated by single-subunit T7 RNA polymerase or multisubunit human RNA polymerase II in vitro and in human cells. We found that O 4 -EtdT is highly mutagenic and exclusively induces the misincorporation of guanine opposite the lesion, whereas N 3-EtdT and O 2 -EtdT display promiscuous miscoding properties during transcription. In addition, N 3-EtdT and O 2 -EtdT were found to inhibit strongly DNA transcription in vitro and in certain human cells. Moreover, N 3-EtdT, but not O 2 -EtdT or O 4 -EtdT, is an efficient substrate for transcription-coupled nucleotide excision repair. These findings provide new important insights into how these alkylated DNA lesions compromise the flow of genetic information, which may help to understand the risk of these lesions in living cells.

Description: In the liver Wnt-signaling contributes to the metabolic fate of hepatocytes, but the precise role of the TCF7L2 in this process is unknown. We employed a temporal RNA-Seq approach to examine gene expression 3–96 h following Tcf7l2 silencing in rat hepatoma cells, and combined this with ChIP-Seq to investigate mechanisms of target gene regulation by TCF7L2. Silencing Tcf7l2 led to a time-dependent appearance of 406 differentially expressed genes (DEGs), including key regulators of cellular growth and differentiation, and amino acid, lipid and glucose metabolism. Direct regulation of 149 DEGs was suggested by strong proximal TCF7L2 binding (peak proximity score 〉 10) and early mRNA expression changes (≤18 h). Indirect gene regulation by TCF7L2 likely occurred via alternate transcription factors, including Hnf4a , Foxo1 , Cited2 , Myc and Lef1 , which were differentially expressed following Tcf7l2 knock-down. Tcf7l2 -silencing enhanced the expression and chromatin occupancy of HNF4α, and co-siRNA experiments revealed that HNF4α was required for the regulation of a subset of metabolic genes by TCF7L2, particularly those involved in lipid and amino-acid metabolism. Our findings suggest TCF7L2 is an important regulator of the hepatic phenotype, and highlight novel mechanisms of gene regulation by TCF7L2 that involve interplay between multiple hepatic transcriptional pathways.

Description: 5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs ( rrn5 ) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella . Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator.

Description: Mammalian splicing regulatory protein RNA-binding motif protein 4 (RBM4) has an alanine repeat-containing C-terminal domain (CAD) that confers both nuclear- and splicing speckle-targeting activities. Alanine-repeat expansion has pathological potential. Here we show that the alanine-repeat tracts influence the subnuclear targeting properties of the RBM4 CAD in cultured human cells. Notably, truncation of the alanine tracts redistributed a portion of RBM4 to paraspeckles. The alanine-deficient CAD was sufficient for paraspeckle targeting. On the other hand, alanine-repeat expansion reduced the mobility of RBM4 and impaired its splicing activity. We further took advantage of the putative coactivator activator (CoAA)-RBM4 conjoined splicing factor, CoAZ, to investigate the function of the CAD in subnuclear targeting. Transiently expressed CoAZ formed discrete nuclear foci that emerged and subsequently separated—fully or partially—from paraspeckles. Alanine-repeat expansion appeared to prevent CoAZ separation from paraspeckles, resulting in their complete colocalization. CoAZ foci were dynamic but, unlike paraspeckles, were resistant to RNase treatment. Our results indicate that the alanine-rich CAD, in conjunction with its conjoined RNA-binding domain(s), differentially influences the subnuclear localization and biogenesis of RBM4 and CoAZ.

Description: Efficient transcription of the HIV-1 genome is regulated by Tat, which recruits P-TEFb from the 7SK small nuclear ribonucleoprotein (snRNP) and other nucleoplasmic complexes to phosphorylate RNA polymerase II and other factors associated with the transcription complex. Although Tat activity is dependent on its binding to the viral TAR sequence, little is known about the cellular factors that might also assemble onto this region of the viral transcript. Here, we report that the splicing factor SRSF1 (SF2/ASF) and Tat recognize overlapping sequences within TAR and the 7SK RNA. SRSF1 expression can inhibit Tat transactivation by directly competing for its binding to TAR. Additionally, we provide evidence that SRSF1 can increase the basal level of viral transcription in the absence of Tat. We propose that SRSF1 activates transcription in the early stages of viral infection by recruiting P-TEFb to TAR from the 7SK snRNP. Whereas in the later stages, Tat substitutes for SRSF1 by promoting release of the stalled polymerase and more efficient transcriptional elongation.

Description: We describe the identification and characterization of novel homing endonucleases using genome database mining to identify putative target sites, followed by high throughput activity screening in a bacterial selection system. We characterized the substrate specificity and kinetics of these endonucleases by monitoring DNA cleavage events with deep sequencing. The endonuclease specificities revealed by these experiments can be partially recapitulated using 3D structure-based computational models. Analysis of these models together with genome sequence data provide insights into how alternative endonuclease specificities were generated during natural evolution.

Description: Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3'-5' turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The ‘ratchet helix’ is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues along the ratchet helix alters in vitro activity in Mtr4 and TRAMP and causes slow growth phenotypes in vivo . We also identify a residue on the ratchet helix that influences Mtr4 affinity for polyadenylated substrates. Previous work indicated that deletion of the arch domain has minimal effect on Mtr4 unwinding activity. We now show that combining the arch deletion with ratchet helix mutations abolishes helicase activity and produces a lethal in vivo phenotype. These studies demonstrate that the ratchet helix modulates helicase activity and suggest that the arch domain plays a previously unrecognized role in unwinding substrates.

Description: Recent evidence points to a role of chromatin in regulation of alternative pre-mRNA splicing (AS). In order to identify novel chromatin regulators of AS, we screened an RNAi library of chromatin proteins using a cell-based high-throughput in vivo assay. We identified a set of chromatin proteins that regulate AS. Using simultaneous genome-wide expression and AS analysis, we demonstrate distinct and non-overlapping functions of these chromatin modifiers on transcription and AS. Detailed mechanistic characterization of one dual function chromatin modifier, the H3K9 methyltransferase EHMT2 (G9a), identified VEGFA as a major chromatin-mediated AS target. Silencing of EHMT2, or its heterodimer partner EHMT1, affects AS by promoting exclusion of VEGFA exon 6a, but does not alter total VEGFA mRNA levels. The epigenetic regulatory mechanism of AS by EHMT2 involves an adaptor system consisting of the chromatin modulator HP1, which binds methylated H3K9 and recruits splicing regulator SRSF1. The epigenetic regulation of VEGFA is physiologically relevant since EHMT2 is transcriptionally induced in response to hypoxia and triggers concomitant changes in AS of VEGFA. These results characterize a novel epigenetic regulatory mechanism of AS and they demonstrate separate roles of epigenetic modifiers in transcription and alternative splicing.

Description: N 6 A methylation is the most abundant RNA modification occurring within messenger RNA. Impairment of methylase or demethylase functions are associated with severe phenotypes and diseases in several organisms. Beside writer and eraser enzymes of this dynamic RNA epigenetic modification, reader proteins that recognize this modification are involved in numerous cellular processes. Although the precise characterization of these reader proteins remains unknown, preliminary data showed that most potential reader proteins contained a conserved YT521-B homology (YTH) domain. Here we define the YTH domain of rat YT521-B as a N 6 -methylated adenosine reader domain and report its solution structure in complex with a N 6 -methylated RNA. The structure reveals a binding preference for NGANNN RNA hexamer and a deep hydrophobic cleft for m 6 A recognition. These findings establish a molecular function for YTH domains as m 6 A reader domains and should guide further studies into the biological functions of YTH-containing proteins in m 6 A recognition.

Description: Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html .

Description: Fanconi anaemia (FA) is a genome instability disease caused by defects in the FA DNA repair pathway that senses and repairs damage caused by DNA interstrand crosslinks. At least 8 of the 16 genes found mutated in FA encode proteins that assemble into the FA core complex, a multisubunit monoubiquitin E3 ligase. Here, we show that the RuvBL1 and RuvBL2 AAA+ ATPases co-purify with FA core complex isolated under stringent but native conditions from a vertebrate cell line. Depletion of the RuvBL1-RuvBL2 complex in human cells causes hallmark features of FA including DNA crosslinker sensitivity, chromosomal instability and defective FA pathway activation. Genetic knockout of RuvBL1 in a murine model is embryonic lethal while conditional inactivation in the haematopoietic stem cell pool confers profound aplastic anaemia. Together these findings reveal a function for RuvBL1-RuvBL2 in DNA repair through a physical and functional association with the FA core complex. Surprisingly, depletion of RuvBL1-RuvBL2 leads to co-depletion of the FA core complex in human cells. This suggests that a potential mechanism for the role of RuvBL1-RuvBL2 in maintaining genome integrity is through controlling the cellular abundance of FA core complex.

Description: Assuming the generalized Riemann hypothesis, we prove a quantitative estimate for the number of simple zeros on the critical line for $L$ -functions attached to classical holomorphic newforms.

Description: In this paper, we consider a $\mathbb {Q}$ -Fano $3$ -fold weighted complete intersection of codimension $2$ in the $85$ families listed in Iano-Fletcher's list and determine which cycle is a maximal center or not. For each maximal center, we construct either a birational involution which untwists the maximal singularity or a Sarkisov link centered at the cycle to another explicitly described Mori fiber space. As a consequence, nineteen families are proved to be birationally rigid and the remaining $66$ families are proved to be birationally non-rigid.

Description: We present 1000 mock galaxy catalogues (mocks) for the analysis of the low-redshift sample (LOWZ; effective redshift z  ~ 0.32) of the Baryon Oscillation Spectroscopic Survey (BOSS) Data Releases 10 and 11. These mocks have been created following the PTHalos method revised to include new developments. The main improvement is the introduction of a redshift dependence in the halo occupation distribution in order to account for the change of the galaxy number density with redshift. These mock galaxy catalogues are used in the analyses of the LOWZ galaxy clustering by the BOSS collaboration.

Description: We present two new catalogues of superclusters of galaxies out to a redshift of z  = 0.15, based on the Abell/ACO cluster redshift compilation maintained by one of us (HA). The first of these catalogues, the all-sky Main SuperCluster Catalogue (MSCC), is based on only the rich (A-) Abell clusters, and the second one, the Southern SuperCluster Catalogue (SSCC), covers declinations  〈 –17° and includes the supplementary Abell S-clusters. A tunable Friends-of-Friends algorithm was used to account for the cluster density decreasing with redshift and for different selection functions in distinct areas of the sky. We present the full list of Abell clusters used, together with their redshifts and supercluster memberships and including the isolated clusters. The SSCC contains about twice the number of superclusters than MSCC for  〈 –17°, which we found to be due to (1) new superclusters formed by A-clusters in their cores and surrounded by S-clusters (50 per cent), (2) new superclusters formed by S-clusters only (40 per cent), (3) redistribution of member clusters by fragmentation of rich (multiplicity m 〉 15) superclusters (8 per cent), and (4) new superclusters formed by the connection of A-clusters through bridges of S-clusters (2 per cent). Power-law fits to the cumulative supercluster multiplicity function yield slopes of α = –2.0 and α = –1.9 for MSCC and SSCC, respectively. This power-law behaviour is in agreement with the findings for other observational samples of superclusters, but not with that of catalogues based on cosmological simulations.

Description: We use two cosmological simulations of structure formation in the cold dark matter (CDM) scenario to study the evolutionary histories of dark matter haloes and to characterize the Lagrangian regions from which they form. We focus on haloes identified at redshift z id  = 0 and show that the classic ellipsoidal collapse model systematically overestimates their collapse times. If one imposes that halo collapse takes place at z id , this model requires starting from a significantly lower linear density contrast than what is measured in the simulations at the locations of halo formation. We attempt to explain this discrepancy by testing two key assumptions of the model. First, we show that the tides felt by collapsing haloes due to the surrounding large-scale structure evolve non-linearly. Although this effect becomes increasingly important for low-mass haloes, accounting for it in the ellipsoidal collapse model only marginally improves the agreement with N -body simulations. Second, we track the time evolution of the physical volume occupied by forming haloes and show that, after turnaround, it generally stabilizes at a well-defined redshift, z c  〉  z id , contrary to the basic assumption of extended Press–Schechter theory based on excursion sets. We discuss the implications of this result for understanding the origin of the mass dependence and scatter in the linear threshold for halo formation. Finally, we show that, when tuned for collapse at z c , a modified version of the ellipsoidal collapse model that also accounts for the triaxial nature of protohaloes predicts their linear density contrast in an unbiased way.

Description: The polarimetric measurement on the prompt phase of GRB 100826A shows that the polarization angle changes ~90° between two adjacent time intervals. We will show that this phenomenon can be naturally interpreted in the framework of the magnetic-dominated jet (MDJ) model. The MDJ model suggests that the bulk Lorentz factor of the outflow increases as r 1/3 , until reaching a saturated value sat . Electrons move in the globally ordered magnetic field advected by the jet from the central engine and produce synchrotron photons. The polarized synchrotron photons travel alone the jet direction and then collide with the cold electrons at the front of the jet. After the Compton scattering process, these photons escape from the jet and are detected by the observer locating slightly off-axis. If photons are emitted before the bulk Lorentz factor saturates, the change of polarization angle is a natural result of the acceleration of the outflow.

Description: The origin of trace hydrogen in white dwarfs (WDs) with He-dominated atmospheres is a long-standing problem, one that cannot satisfactorily be explained by the historically favoured hypothesis of accretion from the interstellar medium. Here we explore the possibility that the gradual accretion of exo-Oort cloud comets, which are a rich source of H, contributes to the apparent increase of trace H with WD cooling age. We determine how often remnant exo-Oort clouds, freshly excited from post-main-sequence stellar mass loss, dynamically inject comets inside the WD's Roche radius. We improve upon previous studies by considering a representative range of single WD masses (0.52–1.00 M ) and incorporating different cloud architectures, giant branch stellar mass loss, stellar flybys, Galactic tides and a realistic escape ellipsoid in self-consistent numerical simulations that integrate beyond 8 Gyr ages of WD cooling. We find that ~10 –5 of the material in an exo-Oort cloud is typically amassed on to the WD, and that the H deposits accumulate even as the cloud dissipates. This accumulation may account for the relatively large amount of trace H, 10 22 –10 25  g, that is determined frequently among WDs with cooling ages ≥1 Gyr. Our results also reaffirm the notion that exo-Oort cloud comets are not the primary agents of the metal budgets observed in polluted WD atmospheres.

Description: In this work, we investigate the statistical computation of the Boltzmann entropy of statistical samples. For this purpose, we use both histogram and kernel function to estimate the probability density function of statistical samples. We find that, due to coarse-graining, the entropy is a monotonic increasing function of the bin width for histogram or bandwidth for kernel estimation, which seems to be difficult to select an optimal bin width/bandwidth for computing the entropy. Fortunately, we notice that there exists a minimum of the first derivative of entropy for both histogram and kernel estimation, and this minimum point of the first derivative asymptotically points to the optimal bin width or bandwidth. We have verified these findings by large amounts of numerical experiments. Hence, we suggest that the minimum of the first derivative of entropy be used as a selector for the optimal bin width or bandwidth of density estimation. Moreover, the optimal bandwidth selected by the minimum of the first derivative of entropy is purely data-based, independent of the unknown underlying probability density distribution, which is obviously superior to the existing estimators. Our results are not restricted to one-dimensional, but can also be extended to multivariate cases. It should be emphasized, however, that we do not provide a robust mathematical proof of these findings, and we leave these issues with those who are interested in them.

Description: HD 76431 is a slow rotating post-HB star that shows an underabundance of helium by 0.5 dex relative to the solar value. These observational facts suggest that atomic diffusion could be active in its atmosphere. We have used the MMT and Bok spectra to estimate the atmospheric parameters of the target star using the model atmospheres and synthetic spectra calculated with tlusty and synspec . The derived values of the effective temperature, surface gravity, and helium abundance are consistent with those obtained by Ramspeck et al. It appears that non-local thermodynamic equilibrium (NLTE) effects are not important for HD 76431. We have used Stokes I spectra from ESPaDOnS at CFHT to perform an abundance analysis and a search for observational evidence of vertical stratification of the abundance of certain elements. The results of our abundance analysis are in good agreement with previously published data with respect to average abundances. Our numerical simulations show that carbon and nitrogen reveal signatures of vertical abundance stratification in the atmosphere of HD 76431. It appears that the carbon abundance increases towards the deeper atmospheric layers. Nitrogen also shows a similar behaviour, but in deeper atmospheric layers we obtain a significant dispersion for the estimates of its abundance. To our knowledge, this is the first demonstration of vertical abundance stratification of metals in a post-HB star and up to now it is the hottest star to show such stratification features. We also report the detection of two Si iii and one Ti iii emission lines in the spectra of HD 76431 that were not detected in previous studies.

Description: The Exoplanet Euclid Legacy Survey (ExELS) proposes to determine the frequency of cold exoplanets down to Earth mass from host separations of ~1 au out to the free-floating regime by detecting microlensing events in Galactic bulge. We show that ExELS can also detect large numbers of hot, transiting exoplanets in the same population. The combined microlensing+transit survey would allow the first self-consistent estimate of the relative frequencies of hot and cold sub-stellar companions, reducing biases in comparing ‘near-field’ radial velocity and transiting exoplanets with ‘far-field’ microlensing exoplanets. The age of the bulge and its spread in metallicity further allows ExELS to better constrain both the variation of companion frequency with metallicity and statistically explore the strength of star–planet tides. We conservatively estimate that ExELS will detect ~4100 sub-stellar objects, with sensitivity typically reaching down to Neptune-mass planets. Of these, ~600 will be detectable in both Euclid's VIS (optical) channel and Near Infrared Spectrometer and Photometer (NISP)- H -band imager, with ~90 per cent of detections being hot Jupiters. Likely scenarios predict a range of 2900–7000 for VIS and 400–1600 for H band. Twice as many can be expected in VIS if the cadence can be increased to match the 20-min H -band cadence. The separation of planets from brown dwarfs via Doppler boosting or ellipsoidal variability will be possible in a handful of cases. Radial velocity confirmation should be possible in some cases, using 30 m-class telescopes. We expect secondary eclipses, and reflection and emission from planets to be detectable in up to ~100 systems in both VIS and NISP- H . Transits of ~500 planetary-radius companions will be characterized with two-colour photometry and ~40 with four-colour photometry (VIS, YJH ), and the albedo of (and emission from) a large sample of hot Jupiters in the H band can be explored statistically.

Description: Motivated by the picture of a thin accretion disc around a black hole, radiating mainly in the direction perpendicular to its plane, we study the motion of test particles interacting with a test geodesic radiation flux originating in the equatorial plane of a Schwarzschild space–time and propagating initially in the perpendicular direction. We assume that the interaction with the test particles is modelled by an effective term corresponding to the Thomson-type interaction which governs the Poynting–Robertson effect. After approximating the individual photon trajectories adequately, we solve the continuity equation approximately in order to find a consistent flux density with a certain plausible prescribed equatorial profile. The combined effects of gravity and radiation are illustrated in several typical figures which confirm that the particles are generically strongly influenced by the flux. In particular, they are both collimated and accelerated in the direction perpendicular to the disc, but this acceleration is not enough to explain highly relativistic outflows emanating from some black hole–disc sources. The model can however be improved in a number of ways before posing further questions which are summarized in concluding remarks.

Description: It is now known that unwanted noise and unmodeled artifacts such as batch effects can dramatically reduce the accuracy of statistical inference in genomic experiments. These sources of noise must be modeled and removed to accurately measure biological variability and to obtain correct statistical inference when performing high-throughput genomic analysis. We introduced surrogate variable analysis (sva) for estimating these artifacts by (i) identifying the part of the genomic data only affected by artifacts and (ii) estimating the artifacts with principal components or singular vectors of the subset of the data matrix. The resulting estimates of artifacts can be used in subsequent analyses as adjustment factors to correct analyses. Here I describe a version of the sva approach specifically created for count data or FPKMs from sequencing experiments based on appropriate data transformation. I also describe the addition of supervised sva (ssva) for using control probes to identify the part of the genomic data only affected by artifacts. I present a comparison between these versions of sva and other methods for batch effect estimation on simulated data, real count-based data and FPKM-based data. These updates are available through the sva Bioconductor package and I have made fully reproducible analysis using these methods available from: https://github.com/jtleek/svaseq .

Description: High-throughput techniques have considerably increased the potential of comparative genomics whilst simultaneously posing many new challenges. One of those challenges involves efficiently mining the large amount of data produced and exploring the landscape of both conserved and idiosyncratic genomic regions across multiple genomes. Domains of application of these analyses are diverse: identification of evolutionary events, inference of gene functions, detection of niche-specific genes or phylogenetic profiling. Insyght is a comparative genomic visualization tool that combines three complementary displays: (i) a table for thoroughly browsing amongst homologues, (ii) a comparator of orthologue functional annotations and (iii) a genomic organization view designed to improve the legibility of rearrangements and distinctive loci. The latter display combines symbolic and proportional graphical paradigms. Synchronized navigation across multiple species and interoperability between the views are core features of Insyght. A gene filter mechanism is provided that helps the user to build a biologically relevant gene set according to multiple criteria such as presence/absence of homologues and/or various annotations. We illustrate the use of Insyght with scenarios. Currently, only Bacteria and Archaea are supported. A public instance is available at http://genome.jouy.inra.fr/Insyght . The tool is freely downloadable for private data set analysis.

Description: BRCA1 is involved in many disparate cellular functions, including DNA damage repair, cell-cycle checkpoint activation, gene transcriptional regulation, DNA replication, centrosome function and others. The majority of evidence strongly favors the maintenance of genomic integrity as a principal tumor suppressor activity of BRCA1. At the same time some functional aspects of BRCA1 are not fully understood. Here, a HAC (human artificial chromosome) module with a regulated centromere was constructed for delivery and expression of the 90 kb genomic copy of the BRCA1 gene into BRCA1-deficient human cells. A battery of functional tests was carried out to demonstrate functionality of the exogenous BRCA1. In separate experiments, we investigated the role of BRCA1 in maintenance of heterochromatin integrity within a human functional kinetochore. We demonstrated that BRCA1 deficiency results in a specific activation of transcription of higher-order alpha-satellite repeats (HORs) assembled into heterochromatin domains flanking the kinetochore. At the same time no detectable elevation of transcription was observed within HORs assembled into centrochromatin domains. Thus, we demonstrated a link between BRCA1 deficiency and kinetochore dysfunction and extended previous observations that BRCA1 is required to silence transcription in heterochromatin in specific genomic loci. This supports the hypothesis that epigenetic alterations of the kinetochore initiated in the absence of BRCA1 may contribute to cellular transformation.

Description: Nucleic acids have become a powerful tool in nanotechnology because of their controllable diverse conformational transitions and adaptable higher-order nanostructure. Using single-stranded DNA probes as the pore-caps for various target recognition, here we present an ultrasensitive universal electrochemical detection system based on graphene and mesoporous silica, and achieve sensitivity with all of the major classes of analytes and simultaneously realize DNA logic gate operations. The concept is based on the locking of the pores and preventing the signal-reporter molecules from escape by target-induced the conformational change of the tailored DNA caps. The coupling of ‘waking up’ gatekeeper with highly specific biochemical recognition is an innovative strategy for the detection of various targets, able to compete with classical methods which need expensive instrumentation and sophisticated experimental operations. The present study has introduced a new electrochemical signal amplification concept and also adds a new dimension to the function of graphene-mesoporous materials hybrids as multifunctional nanoscale logic devices. More importantly, the development of this approach would spur further advances in important areas, such as point-of-care diagnostics or detection of specific biological contaminations, and hold promise for use in field analysis.

Description: Many critical processes in the cell involve direct binding between RNAs and proteins, making it imperative to fully understand the physicochemical principles behind such interactions at the atomistic level. Here, we use molecular dynamics simulations and 15 μs of sampling to study the behavior of amino acids and amino acid sidechain analogs in high-concentration aqueous solutions of standard RNA nucleobases. Structural and energetic analysis of simulated systems allows us to derive interaction propensity scales for different amino acid/nucleobase combinations. The derived scales closely match and greatly extend the available experimental data, providing a comprehensive foundation for studying RNA–protein interactions in different contexts. By using these scales, we demonstrate a statistically significant connection between nucleobase composition of human mRNA coding sequences and nucleobase interaction propensities of their cognate protein sequences. For example, pyrimidine density profiles of mRNAs match uracil-propensity profiles of their cognate proteins with a median Pearson correlation coefficient of R = –0.70. Our results provide support for the recently proposed hypotheses that mRNAs and their cognate proteins may be physicochemically complementary to each other and bind, especially if unstructured, with the complementarity level being negatively influenced by mRNA adenine content. Finally, we utilize the derived scales to refine the complementarity hypothesis and closely examine its physicochemical underpinnings.

Description: The 54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the 54 promoters. Here, a predictor called ‘ iPro54-PseKNC ’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k -tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC . For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the 54 promoters.

Description: Telomeres at chromosome ends are normally masked from proteins that signal and repair DNA double strand breaks (DSBs). Bulky DNA lesions can cause DSBs if they block DNA replication, unless they are bypassed by translesion (TLS) DNA polymerases. Here, we investigated roles for TLS polymerase , (pol) in preserving telomeres following acute physical UVC exposure and chronic chemical Cr(VI) exposure, which both induce blocking lesions. We report that pol protects against cytotoxicity and replication stress caused by Cr(VI), similar to results with ultraviolet C light (UVC). Both exposures induce ataxia telangiectasia and Rad3-related (ATR) kinase and pol accumulation into nuclear foci and localization to individual telomeres, consistent with replication fork stalling at DNA lesions. Pol-deficient cells exhibited greater numbers of telomeres that co-localized with DSB response proteins after exposures. Furthermore, the genotoxic exposures induced telomere aberrations associated with failures in telomere replication that were suppressed by pol. We propose that pol's ability to bypass bulky DNA lesions at telomeres is critical for proper telomere replication following genotoxic exposures.

Description: The DNA damage response triggers cell-cycle checkpoints, DNA repair and apoptosis using multiple post-translational modifications as molecular switches. However, how ubiquitination regulates ATR signaling in response to replication stress and single-strand break is still unclear. Here, we identified the deubiquitination enzyme (DUB) USP20 as a pivotal regulator of ATR-related DDR pathway. Through screening a panel of DUBs, we identified USP20 as critical for replication stress response. USP20 is phosphorylated by ATR, resulting in disassociation of the E3 ubiquitin ligase HERC2 from USP20 and USP20 stabilization. USP20 in turn deubiquitinates and stabilizes Claspin and enhances the activation of ATR-Chk1 signaling. These findings reveal USP20 to be a novel regulator of ATR-dependent DNA damage signaling.

Description: Sunlight-induced C to T mutation hotspots in skin cancers occur primarily at methylated CpG sites that coincide with sites of UV-induced cyclobutane pyrimidine dimer (CPD) formation. The C or 5-methyl-C in CPDs are not stable and deaminate to U and T, respectively, which leads to the insertion of A by DNA polymerase and defines a probable mechanism for the origin of UV-induced C to T mutations. We have now determined the photoproduct formation and deamination rates for 10 consecutive T= m CG CPDs over a full helical turn at the dyad axis of a nucleosome and find that whereas photoproduct formation and deamination is greatly inhibited for the CPDs closest to the histone surface, it is greatly enhanced for the outermost CPDs. Replacing the G in a T= m CG CPD with A greatly decreased the deamination rate. These results show that rotational position and flanking sequence in a nucleosome can significantly and synergistically modulate CPD formation and deamination that contribute to C to T mutations associated with skin cancer induction and may have influenced the evolution of the human genome.

Description: We present a discriminative learning method for pattern discovery of binding sites in nucleic acid sequences based on hidden Markov models. Sets of positive and negative example sequences are mined for sequence motifs whose occurrence frequency varies between the sets. The method offers several objective functions, but we concentrate on mutual information of condition and motif occurrence. We perform a systematic comparison of our method and numerous published motif-finding tools. Our method achieves the highest motif discovery performance, while being faster than most published methods. We present case studies of data from various technologies, including ChIP-Seq, RIP-Chip and PAR-CLIP, of embryonic stem cell transcription factors and of RNA-binding proteins, demonstrating practicality and utility of the method. For the alternative splicing factor RBM10, our analysis finds motifs known to be splicing-relevant. The motif discovery method is implemented in the free software package Discrover. It is applicable to genome- and transcriptome-scale data, makes use of available repeat experiments and aside from binary contrasts also more complex data configurations can be utilized.

Description: In Escherichia coli , the ATP-bound form of DnaA (ATP–DnaA) promotes replication initiation. During replication, the bound ATP is hydrolyzed to ADP to yield the ADP-bound form (ADP–DnaA), which is inactive for initiation. The chromosomal site DARS2 facilitates the regeneration of ATP–DnaA by catalyzing nucleotide exchange between free ATP and ADP bound to DnaA. However, the regulatory mechanisms governing this exchange reaction are unclear. Here, using in vitro reconstituted experiments, we show that two nucleoid-associated proteins, IHF and Fis, bind site-specifically to DARS2 to activate coordinately the exchange reaction. The regenerated ATP–DnaA was fully active in replication initiation and underwent DnaA–ATP hydrolysis. ADP–DnaA formed heteromultimeric complexes with IHF and Fis on DARS2 , and underwent nucleotide dissociation more efficiently than ATP–DnaA. Consistently, mutant analyses demonstrated that specific binding of IHF and Fis to DARS2 stimulates the formation of ATP–DnaA production, thereby promoting timely initiation. Moreover, we show that IHF– DARS2 binding is temporally regulated during the cell cycle, whereas Fis only binds to DARS2 in exponentially growing cells. These results elucidate the regulation of ATP–DnaA and replication initiation in coordination with the cell cycle and growth phase.

Description: The virF gene of Shigella , responsible for triggering the virulence cascade in this pathogenic bacterium, is transcriptionally repressed by the nucleoid-associated protein H-NS. The primary binding sites of H-NS within the promoter region of virF have been detected here by footprinting experiments in the presence of H-NS or its monomeric DNA-binding domain (H-NS ctd ), which displays the same specificity as intact H-NS. Of the 14 short DNA fragments identified, 10 overlap sequences similar to the H-NS binding motif. The ‘fast’, ‘intermediate’ and ‘slow’ H-NS binding events leading to the formation of the nucleoprotein complex responsible for transcription repression have been determined by time-resolved hydroxyl radical footprinting experiments in the presence of full-length H-NS. We demonstrate that this process is completed in ≤1 s and H-NS protections occur simultaneously on site I and site II of the virF promoter. Furthermore, all ‘fast’ protections have been identified in regions containing predicted H-NS binding motifs, in agreement with the hypothesis that H-NS nucleoprotein complex assembles from a few nucleation sites containing high-affinity binding sequences. Finally, data are presented showing that the 22-bp fragment corresponding to one of the HNS binding sites deviates from canonical B-DNA structure at three TpA steps.

Description: Human DBC1 (Deleted in Breast Cancer 1; KIAA1967; CCAR2) is a protein implicated in the regulation of apoptosis, transcription and histone modifications. Upon DNA damage, DBC1 is phosphorylated by ATM/ATR on Thr454 and this modification increases its inhibitory interaction with SIRT1, leading to p53 acetylation and p53-dependent apoptosis. Here, we report that the inhibition of SIRT1 by DBC1 in the DNA damage response (DDR) also depends on Chk2, the transducer kinase that is activated by ATM upon DNA lesions and contributes to the spreading of DNA damage signal. Indeed we found that inactivation of Chk2 reduces DBC1-SIRT1 binding, thus preventing p53 acetylation and DBC1-induced apoptosis. These events are mediated by Chk2 phosphorylation of the 11S proteasome activator REG on Ser247, which increases REG-DBC1 interaction and SIRT1 inhibition. Overall our results clarify the mechanisms underlying the DBC1-dependent SIRT1 inhibition and link, for the first time, Chk2 and REG to the ATM-DBC1-SIRT1 axis.