ALBERT

Description: Next-generation sequencing has been widely used for the genome-wide profiling of histone modifications, transcription factor binding and gene expression through chromatin immunoprecipitated DNA sequencing (ChIP-seq) and cDNA sequencing (RNA-seq). Here, we describe a versatile library construction method that can be applied to both ChIP-seq and RNA-seq on the widely used Illumina platforms. Standard methods for ChIP-seq library construction require nanograms of starting DNA, substantially limiting its application to rare cell types or limited clinical samples. By minimizing the DNA purification steps that cause major sample loss, our method achieved a high sensitivity in ChIP-seq library preparation. Using this method, we achieved the following: (i) generated high-quality epigenomic and transcription factor-binding maps using ChIP-seq for murine adipocytes; (ii) successfully prepared a ChIP-seq library from as little as 25 pg of starting DNA; (iii) achieved paired-end sequencing of the ChIP-seq libraries; (iv) systematically profiled gene expression dynamics during murine adipogenesis using RNA-seq and (v) preserved the strand specificity of the transcripts in RNA-seq. Given its sensitivity and versatility in both double-stranded and single-stranded DNA library construction, this method has wide applications in genomic, epigenomic, transcriptomic and interactomic studies.

Description: Author(s): G. M. Pang, Z. Y. Nie, A. Wang, D. Singh, W. Xie, W. B. Jiang, Y. Chen, R. P. Singh, M. Smidman, and H. Q. Yuan The noncentrosymmetric superconductor Re 6 Zr has attracted much interest due to the observation of broken time-reversal symmetry in the superconducting state. Here we report an investigation of the superconducting gap structure of Re 6 Zr single crystals by measuring the magnetic penetration depth shif... [Phys. Rev. B 97, 224506] Published Thu Jun 07, 2018

Description: The factors and processes that control trace-element partitioning among co-crystallizing cumulus minerals in layered intrusions have long been controversial. Here we address this issue using new laser ablation ICP-MS trace element data for magnetite, ilmenite, and clinopyroxene from the Panzhihua layered intrusion in the Emeishan large igneous province, SW China. The cumulus minerals display strong Ni, Co, and Cr depletions, indicative of parental magmas low in concentration of these elements probably due to prior sulfide removal and the fractionation of chromite or Cr-magnetite in a staging magma chamber at depth. Both magnetite and clinopyroxene show cyclical variations in some transition elements (e.g., Cr, V, and Ni) along the stratigraphic section. The average concentrations of these transition elements in magnetite are positively correlated with those in clinopyroxene, likely resulting from co-crystallization of magnetite and clinopyroxene. The incompatible element (e.g., Zr, Hf, and Nb) concentrations of the cumulus minerals from the Lower Zone are highly variable compared to those of the Middle and Upper Zones. These large variations in trace element compositions are attributed to a "trapped liquid shift" in the Lower Zone. Ilmenite crystals from the Panzhihua intrusion may have undergone extensive modification of transition elements during subsolidus re-equilibration with magnetite, leading to the decoupled variations of transition elements in ilmenite across the Lower Zone stratigraphy. Our study indicates that systematic trace element variations of the main cumulus mineral assemblage, rather than a single mineral, need to be considered to better constrain the magmatic differentiation and elemental fractionation of layered intrusions.

Description: Dominant climatic factors controlling the lifetime peak intensity of typhoons are determined from six decades of Pacific typhoon data. We find that upper ocean temperatures in the low-latitude northwestern Pacific (LLNWP) and sea surface temperatures in the central equatorial Pacific control the seasonal average lifetime peak intensity by setting the rate and duration of typhoon intensification, respectively. An anomalously strong LLNWP upper ocean warming has favored increased intensification rates and led to unprecedentedly high average typhoon intensity during the recent global warming hiatus period, despite a reduction in intensification duration tied to the central equatorial Pacific surface cooling. Continued LLNWP upper ocean warming as predicted under a moderate [that is, Representative Concentration Pathway (RCP) 4.5] climate change scenario is expected to further increase the average typhoon intensity by an additional 14% by 2100.

Description: Article BRAF inhibitors often show skin-hyperproliferative side effects in melanoma patients. Here, the authors demonstrate that BRAF inhibitors can be used to enhance skin wound healing through the MAPK- ERK pathway activation that positively regulates the proliferation of keratinocytes. Nature Communications doi: 10.1038/ncomms12348 Authors: Helena Escuin-Ordinas, Shuoran Li, Michael W. Xie, Lu Sun, Willy Hugo, Rong Rong Huang, Jing Jiao, Felipe Meira de-Faria, Susan Realegeno, Paige Krystofinski, Ariel Azhdam, Sara Marie D. Komenan, Mohammad Atefi, Begoña Comin-Anduix, Matteo Pellegrini, Alistair J. Cochran, Robert L. Modlin, Harvey R. Herschman, Roger S. Lo, William H. McBride, Tatiana Segura, Antoni Ribas

Description: The distribution of all recognized biotic elements was mapped on five extensive surfaces of the Middle Triassic Guanling Formation exposed in quarries near Luoping, Yunnan Province, China. A 0.5 m 2 grid was overlain on the surfaces, and all recognizable fossils were located by placing them in one of nine quadrants within the grid. A total of 240 m 2 were mapped, and each specimen observed was recorded as one of 15 categories, subsequently grouped as pelagic, benthic, and other (bone, trace fossils, algae). The pelagic component, fish, thylacocephalans, and mysidaceans, dominated all layers. The benthic component was sparse on all surfaces; epifaunal, vagrant organisms were the dominant forms, suggesting that the substrate was unsuitable for infaunal and sessile epifaunal organisms. Shrimp and bivalves dominated the benthic organisms. Two of the surfaces were overwhelmingly dominated by mysidaceans, and one was dominated by thylacocephalans, suggesting that their remains documented periodic mass kills of swarming, pelagic organisms. Scanning electron microscope analysis of the bedding surfaces revealed nothing remarkable about the sediment, suggesting that the cause of death of the organisms was likely due to an event within the water column, possibly an algae bloom, not recorded in the sediment record.

Description: Aims Understanding relationships between vegetation and environments is of importance for ecosystem restoration and management. However, information on how environments influence the floristic patterns of shrublands is lack, especially in the subtropical China. In this study, we explored how environments regulate species composition of shrublands at landscape scale in mid-subtropical China. Methods We investigated species composition and measured the climate and soil environments for 207 shrubland plots in mid-subtropical China (24°39'–30°08'N, 108°47'–114°15'E). We applied a hierarchical cluster analysis and indicator species analysis based on the Bray–Curtis similarity index to identify the main shrubland types and employed principal coordinate analysis (PCoA) to explore the relationship between floristic composition and environment. Important Findings We identified four shrubland types occurring in different environmental conditions. Montane shrubland, dominated by species suitable for cool climates (e.g. Rhododendron simsii ), were distributed in steep areas at comparatively high altitudes; foothill shrubland, dominated by mesophilous species (e.g. Loropetalum chinense ), were distributed in low mountains and hills; pioneer shrubland, dominated by fast grow and short-life cycles species (e.g. Rhus chinensis ), were distributed at low altitudes with dense population; and finally, limestone shrubland, dominated by calcicole plants (e.g. Coriaria nepalensis ), were distributed in the extensive karst areas. Communities occurring in high pH soils were completely separated from those in low pH soils according to the hierarchical cluster analysis. PCoA ordination associated the four types with distinct edaphic and climatic gradients. Soil pH explained 63.3% of variation in PCoA, followed by soil depth and soil bulk density.

Description: 〈span〉〈div〉Abstract〈/div〉The Chengchao Fe skarn deposit (280 Mt @ 45% Fe; nearly half of the total Fe reserve has an ore grade higher than 53 wt %) is the largest high-grade magnetite skarn deposit in the Middle-Lower Yangtze River metallogenic belt. The magnetite orebodies and skarns occur mainly along the contact zones between granitic (129 ± 2 Ma) rocks and diorite (133 ± 1 Ma) and Triassic strata. The paragenesis of the Chengchao deposit includes the following five stages: Na-K alteration stage (albite + K-feldspar), prograde skarn stage (garnet + pyroxene), retrograde skarn stage (magnetite + phlogopite + amphibole), sulfate-sulfide stage (anhydrite + pyrite ± garnet ± magnetite), and carbonate stage (calcite).Four generations of garnet and magnetite with distinct textures are recognized. The elemental compositions and fluid inclusion data of the three generations of garnet from the prograde skarn stage indicate fluctuating changes in the oxygen fugacity during their precipitation. Some magnetite grains from the retrograde skarn stage are characterized by well-developed zonation with respect to Al, K, Ca, and Si, with concentrations of up to hundreds of parts per million. The higher contents of (V + Ti) and (Al + Mn) in Mt2 relative to Mt1 (0.8 and 2,321 ppm for Mt1, and 182 and 10,315 ppm for Mt2, respectively) may be indicative of increasing fluid temperatures from episodic magmatic events. Fluid inclusion data show that the fluids responsible for the prograde skarn stage have high temperature (〉750°C), high salinity (〉50 wt % NaCl equiv) and high Fe concentration (e.g., magnetite and pyrite daughter crystals within garnet and pyroxene). Oxygen and hydrogen isotope data suggest that magmatic water was dominant during the prograde skarn stage and that increasing percentages of meteoric water were involved during later stages. Multiple episodic incursions of Fe-rich fluids, which were probably related to the emplacement of granitic rocks and diorite, were crucial for controlling the formation of the high-grade Chengchao Fe skarn deposit.〈/span〉

Description: Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region...