ALBERT

Description: Pagan is one of the largest volcanoes along the Mariana arc volcanic front. It has a maximum elevation of 570 m (Mt. Pagan), but its submarine flanks descend to 2000–3000 m below sea level, and are unexplored. Bathymetric mapping and ROV Hyper-Dolphin dives (HPD1147 and HPD1148) on the submarine NE and SW flanks of Pagan were carried out during cruise NT10-12 of R.V. Natsushima in July 2010. There are no systematic compositional differences between subaerial lavas reported in the literature and differentiated submarine lavas collected in HPD1148, with 〈7 wt % MgO, suggesting they are derived from the same magmatic system. However, these differentiated lavas show complexities including magma mixing; thus we concentrate on magnesian submarine lavas (〉7 wt % MgO). Twenty least-fractionated basalts (48·5–50 wt % SiO 2 ) collected during HPD1147 extend to higher MgO (10–11 wt %) and Mg# (66–70) than the subaerial lavas. Olivine (up to Fo 94 ) and spinel (Cr# up to 0·8) compositions suggest that these Pagan primitive magmas formed from high degrees of mantle melting. Two basalt types can be distinguished based on their geochemistry at similar (10–11 wt %) MgO; these erupted recently, 500 m apart. Both contain clinopyroxene and olivine phenocrysts and are referred to as COB1 and COB2. Lower TiO 2 , FeO, Na 2 O, K 2 O, incompatible trace element abundances, and Nb/Yb suggest that COB1 formed from higher degrees of mantle melting. In addition, light rare earth element (LREE) enrichment and higher Th/Nb in COB2 contrast with LREE depletion and lower Th/Nb in COB1. Higher Ba/Th and Ba/Nb and lower Th/Nb indicate that the main subduction addition in COB1 was dominated by hydrous fluid, whereas that in COB2 was dominated by sediment melt. Sr–Nd–Pb–Hf isotopes are also consistent with this interpretation. These observations suggest that the subduction component responsible for the greater degree of melting of the COB1 source was mostly hydrous fluid. The origin of such different metasomatic agents resulted in different primary magmas forming in the same volcano. Both hydrous fluid and sediment melt components may have unmixed from an originally homogeneous supercritical fluid in or above the subducting slab below the volcanic front. These may have been added separately to the mantle wedge peridotite (mantle diapir) and resulted in two neighboring but completely different primary magmas from the same diapir. Moreover, these primitive lavas suggest that even for intra-oceanic arcs assimilation–fractional crystallization is inevitable when these magmas evolve in the crust and, in addition, that phlogopite is present in their mantle residue and thus played an important role in their genesis.

Description: The structure of the nucleosome has been solved at atomic resolution, and the genome-wide nucleosome positions have been clarified for the budding yeast Saccharomyces cerevisiae . However, the genome-wide three-dimensional arrangement of nucleosomal arrays in the nucleus remains unclear. Several studies simulated overall interphase chromosome architectures by introducing the putative persistence length of the controversial 30-nm chromatin fibres into the modelling and using data-fitting approaches. However, the genome-folding mechanism still could not be linked with the chromosome shapes, to identify which structures or properties of chromatin fibres or DNA sequences determine the overall interphase chromosome architectures. Here we demonstrate that the paths of nucleosomal arrays and the chromatin architectures themselves are determined principally by the physical properties of genomic DNA and the nucleus size in yeast. We clarified the flexibilities and persistence lengths of all linker DNAs of the organism, deduced their spatial expanses and simulated the architectures of all 16 interphase chromosomes in the nucleus, at a resolution of beads-on-a-string chromatin fibre. For the average spatial distance between two given loci in a chromosome, the model predictions agreed well with all experimental data reported to date. These findings suggest a general mechanism underlying the folding of eukaryotic genomes into interphase chromosomes.

Description: CENP-B is a widely conserved centromeric satellite DNA-binding protein, which specifically binds to a 17-bp DNA sequence known as the CENP-B box. CENP-B functions positively in the de novo assembly of centromeric nucleosomes, containing the centromere-specific histone H3 variant, CENP-A. At the same time, CENP-B also prevents undesired assembly of the CENP-A nucleosome through heterochromatin formation on satellite DNA integrated into ectopic sites. Therefore, improper CENP-B binding to chromosomes could be harmful. However, no CENP-B eviction mechanism has yet been reported. In the present study, we found that human Nap1, an acidic histone chaperone, inhibited the non-specific binding of CENP-B to nucleosomes and apparently stimulated CENP-B binding to its cognate CENP-B box DNA in nucleosomes. In human cells, the CENP-B eviction activity of Nap1 was confirmed in model experiments, in which the CENP-B binding to a human artificial chromosome or an ectopic chromosome locus bearing CENP-B boxes was significantly decreased when Nap1 was tethered near the CENP-B box sequence. In contrast, another acidic histone chaperone, sNASP, did not promote CENP-B eviction in vitro and in vivo and did not stimulate specific CENP-B binding to CENP-A nucleosomes in vitro . We therefore propose a novel mechanism of CENP-B regulation by Nap1.

Description: Initial subduction-related boninitic magmatism occurred between 48 and 44 Ma in the Izu–Bonin–Mariana (IBM) arc. High-Mg adakites and low-Ca boninites have been dredged from the Bonin Ridge fore-arc seamount. Whole-rock 40 Ar/ 39 Ar ages suggest that the boninite (44·0 ± 1·4 Ma) and adakite (43·1 ± 1·0 and 40·8 ± 0·8 Ma) magmatism overlapped, or that the adakite magmatism occurred slightly later than the boninite magmatism. The low-Ca boninites are high-Mg andesites and exhibit U-shaped rare earth element (REE) patterns with an elevated average Mg# of 0·78 [Mg# = Mg/(Mg + Fe) molar ratio] and Ni content of 667 ppm. The high-Mg adakites are andesitic to dacitic in composition; they exhibit markedly high Sr contents and low Y contents and are highly enriched in light REE but depleted in heavy REE, with an average Mg# of 0·79 and Ni content of 433 ppm. A geochemical mass-balance model (Arc Basalt Simulator Version 3) indicates that both magma types could be generated by partial melting of a depleted mantle source fluxed by water-rich slab-derived melts in a hot subduction environment, comparable with the present-day South Chile (ridge subduction) or Southwest Japan (young slab subduction) arcs. An extremely high slab melt flux of 22% is required for the formation of the high-Mg adakite, whereas a low flux of 3% is sufficient for the low-Ca boninite. The low-Ca boninite requires a high-temperature shallow slab (854°C, 2·7 GPa on average), consisting of altered oceanic crust of the Pacific plate and volcaniclastic sediments from HIMU seamounts, and high-temperature shallow mantle melting (1216°C, 0·8 GPa) of depleted Indian mid-ocean ridge basalt (MORB)-type mantle. These modelled conditions are consistent with the occurrence of hot shallow mantle wedge melting in the initial subduction zone at the boundary between Pacific- and Indian-type mantle domains, as suggested by previous studies. In contrast, high-Mg adakite requires a higher temperature and deeper slab (929°C, 4·1 GPa), with the same slab components and slightly deeper but less hot melting (1130°C, 1·1 GPa) of HIMU-type depleted mantle, to satisfy the low Hf isotope ratios. This may occur because of the subsequent cooling of the mantle wedge by the establishment of the subduction system after the boninite magmatism and involvement of a small volume of an isotopically enriched mantle source embedded in the Indian-type mantle. The petrogenetic conditions provide constraints for reconstructing the tectonic settings of the early IBM arc. The hot subduction model would be consistent with the tectonic models with regard to the initiation of subduction associated with fore-arc spreading; this allowed the upwelling of the asthenospheric mantle to generate slab melts from the old Pacific plate slab and hot shallow mantle melting by slab melt fluxing for both boninite and adakite activities.

Description: We study the heating of the cool cores in galaxy clusters by cosmic rays (CRs) accelerated by the central active galactic nuclei (AGNs). We especially focus on the stability of the heating. The CRs stream with Alfvén waves in the intracluster medium (ICM) and heat the ICM. First, assuming that the heating and radiative cooling is balanced, we search steady-state solutions for the ICM and CR profiles of clusters by solving a boundary value problem. The boundary conditions are set so that the solutions are consistent with observations of clusters. We find steady-state solutions if the magnetic fields are strong enough and the association between the magnetic fields and the ICM is relatively weak. Then, we analyse the stability of the solutions via a Lagrangian perturbation analysis and find that the solutions are globally stable. We confirm the results by numerical simulations. Using the steady-state solutions as the initial conditions, we follow the evolution of the profiles for 100 Gyr. We find that the profiles do not evolve on time-scales much larger than cluster lifetimes. These results, as well as consistency with observations of radio mini-haloes, suggest that the CR heating is a promising mechanism to solve the so-called ‘cooling flow problem’.

Description: The plant NADPH oxidases, known as respiratory burst oxidase homologues (Rbohs), play an indispensable role in a wide array of cellular and developmental processes. Arabidopsis thaliana RbohF (AtRbohF)-mediated production of reactive oxygen species (ROS) is involved in biotic and abiotic stress responses. Because of the toxicity of excess amount of ROS, the ROS-producing activity of Rbohs is speculated to be negatively regulated. However, its mechanism is mostly unknown to date. Here, we report the identification of calcineurin B-like protein-interacting protein kinase 26 (CIPK26) as a novel regulatory factor of AtRbohF. We isolated CIPK26 as an AtRbohF-interacting partner by a yeast two-hybrid screen. Our co-immunoprecipitation assay revealed that the CIPK26 protein interacts with the N-terminal region of AtRbohF in Nicotiana benthamiana cell extracts. The fluorescence of both GFP-tagged CIPK26 and AtRbohF was predominantly observed at the cell periphery. We also showed that co-expression of CIPK26 decreases the ROS-producing activity of AtRbohF in HEK293T cells. Together, these results suggest that the direct binding of CIPK26 to AtRbohF negatively modulates ROS production and play a role in the regulation of ROS signalling in plants.

Description: Combinations of histone modifications have significant biological roles, such as maintenance of pluripotency and cancer development, but cannot be analyzed at the single cell level. Here, we visualized a combination of histone modifications by applying the in situ proximity ligation assay, which detects two proteins in close vicinity (~30 nm). The specificity of the method [designated as imaging of a combination of histone modifications (iChmo)] was confirmed by positive signals from H3K4me3/acetylated H3K9, H3K4me3/RNA polymerase II and H3K9me3/H4K20me3, and negative signals from H3K4me3/H3K9me3. Bivalent modification was clearly visualized by iChmo in wild-type embryonic stem cells (ESCs) known to have it, whereas rarely in Suz12 knockout ESCs and mouse embryonic fibroblasts known to have little of it. iChmo was applied to analysis of epigenetic and phenotypic changes of heterogeneous cell population, namely, ESCs at an early stage of differentiation, and this revealed that the bivalent modification disappeared in a highly concerted manner, whereas phenotypic differentiation proceeded with large variations among cells. Also, using this method, we were able to visualize a combination of repressive histone marks in tissue samples. The application of iChmo to samples with heterogeneous cell population and tissue samples is expected to clarify unknown biological and pathological significance of various combinations of epigenetic modifications.

Description: The comet assay has been widely used as a genotoxicity test for detecting primary DNA damage in individual cells. The micronucleus (MN) test is also a well-established assay for detecting clastogenicity and aneugenicity. A combination of the comet assay (COM) and MN test is capable of detecting a variety of genotoxic potentials as an in vitro screening system. Although the in vitro MN test has a robust protocol and Organisation for Economic Co-operation and Development (OECD) test guideline, the in vitro COM does not. To establish a robust protocol for the COM and to compare its sensitivity with that of the MN, we conducted COM and MN concurrently for five genotoxic agents (ethyl methanesulfonate, methyl methanesulfonate, hydrogen peroxide, gamma-rays and mitomycin C) and one non-genotoxic agent (triton X-100), using human lymphoblastoid TK6 cells. Relative cell count (RCC), relative population doubling (RPD), relative increase in cell count (RICC) and relative cell viability determined by trypan blue dye-exclusion assay (TBDE) were employed as cytotoxic measurements. However, the relative cell viability determined by TBDE just after the treatment was not an appropriate parameter of cytotoxicity for the genotoxic agents because it remained constant even at the highest doses, which showed severe cytotoxicity by RCC, RPD and RICC. The results of the COM showed qualitative agreement (positive or negative) with those of the MN except for mitomycin C, which is an interstrand cross-linker. The COM always required higher doses than the MN to detect the genotoxic potential of the genotoxic agents under the test conditions applied here. The doses that induced a comet tail always yielded 〈50% RICC, and do not accord to the OECD test guideline for MN because of their high cytotoxicity. These results are helpful for interpreting the results of the COM and MN in in vitro genotoxic hazard assessments. Further investigation is required to standardise the COM.

Description: We present a stellar mass–metallicity relation at z  ~ 1.4 with an unprecedentedly large sample of ~340 star-forming galaxies obtained with Fibre Multi-Object Spectrograph (FMOS) on the Subaru Telescope. We observed K -band selected galaxies at 1.2 ≤ z ph ≤ 1.6 in the Subaru XMM – Newton Deep Survey/Ultra Deep Survey fields with M *  ≥ 10 9.5 M , and expected F(Hα) ≥ 5 10 –17  erg s –1  cm –2 . Among the observed ~1200 targets, 343 objects show significant Hα emission lines. The gas-phase metallicity is obtained from [N ii ] 6584/Hα line ratio, after excluding possible active galactic nuclei. Due to the faintness of the [N ii ] 6584 lines, we apply the stacking analysis and derive the mass–metallicity relation at z  ~ 1.4. Our results are compared to past results at different redshifts in the literature. The mass–metallicity relation at z  ~ 1.4 is located between those at z  ~ 0.8 and z  ~ 2.2; it is found that the metallicity increases with decreasing redshift from z  ~ 3 to z  ~ 0 at fixed stellar mass. Thanks to the large size of the sample, we can study the dependence of the mass–metallicity relation on various galaxy physical properties. The average metallicity from the stacked spectra is close to the local Fundamental Metallicity Relation (FMR) in the higher metallicity part but 0.1 dex higher in metallicity than the FMR in the lower metallicity part. We find that galaxies with larger E ( B  – V ), B  – R and R  – H colours tend to show higher metallicity by ~0.05 dex at fixed stellar mass. We also find relatively clearer size dependence that objects with smaller half-light radius tend to show higher metallicity by ~0.1 dex at fixed stellar mass, especially in the low-mass part.

Description: The Database of Genotypes and Phenotypes (dbGap, http://www.ncbi.nlm.nih.gov/gap ) is a National Institutes of Health-sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype. Information in dbGaP is organized as a hierarchical structure and includes the accessioned objects, phenotypes (as variables and datasets), various molecular assay data (SNP and Expression Array data, Sequence and Epigenomic marks), analyses and documents. Publicly accessible metadata about submitted studies, summary level data, and documents related to studies can be accessed freely on the dbGaP website. Individual-level data are accessible via Controlled Access application to scientists across the globe.