ALBERT

Description: Abstract This study analyzes the summertime precipitation bias over the Central United States and its relationship to the simulated large‐scale environment and the convection scheme in the Energy Exascale Earth System Model Atmosphere Model version 1. This relationship is mainly examined in a set of short‐term hindcasts initialized with realistic large‐scale conditions for the summer of 2011. Besides the uniform 1° model resolution, we adopt Regionally Refined Meshes to increase the model resolution to 0.25° over the contiguous United States. Additional five‐year Atmospheric Model Intercomparison Project simulations are conducted to confirm that the results from the hindcasts are consistent with the climate runs. We find that the summertime dry precipitation bias over the Great Plains and the wet bias over the Rockies cannot be reduced simultaneously by changing resolution or tuning parameters. As for the diurnal cycle, Energy Exascale Earth System Model Atmosphere Model version 1 captures the general diurnal variation of the large‐scale moisture transport and the large‐scale upward motion over the Central United States. However, the diurnal cycle of precipitation over the Great Plains is out of phase with the diurnal variation of the large‐scale environment because the convective precipitation dominates the total precipitation and its diurnal cycle, and it does not directly respond to the local moisture convergence and the large‐scale upward motion. These results reemphasize the importance of improving the coupling of the convection to the large‐scale environment in reducing the summer precipitation bias over the Central United States in climate models with the resolution of ~0.25°.

Description: 〈sec〉〈st〉Synopsis〈/st〉〈p〉〈textbox textbox-type="graphic"〉〈p〉〈inline-fig〉〈/inline-fig〉〈/p〉〈/textbox〉〈/p〉 〈p〉The RNA-binding protein ALYREF functions in coupling nuclear export and 3'-end processing of polyadenylated mRNAs. New data identify a parallel mechanism for ALYREF also linking 3'-end processing to nuclear export of non-polyadenylated, replication-dependent histone mRNAs.〈/p〉 〈p〉 〈l type="unord"〉〈li〉〈p〉ALYREF prevalently binds to a 3' region of histone mRNAs in an SLBP-dependent manner.〈/p〉〈/li〉 〈li〉〈p〉ALYREF promotes histone pre-mRNA processing by ensuring U7-snRNP recruitment.〈/p〉〈/li〉 〈li〉〈p〉The TREX complex facilitates histone mRNA export by recruiting NXF1.〈/p〉〈/li〉 〈li〉〈p〉3'-end processing promotes ALYREF recruitment and histone mRNA export.〈/p〉〈/li〉〈/l〉 〈/p〉〈/sec〉

Description: The Journal of Physical Chemistry B DOI: 10.1021/acs.jpcb.6b06306

Description: We present an improved procedure of generating initial conditions (ICs) for climate model hindcast experiments with specified sea surface temperature and sea ice. The motivation is to minimize errors in the ICs and lead to a better evaluation of atmospheric parameterizations' performance in the hindcast mode. We apply state variables (horizontal velocities, temperature and specific humidity) from the operational analysis/reanalysis for the atmospheric initial states. Without a data assimilation system, we apply a two-step process to obtain other necessary variables to initialize both the atmospheric (e.g., aerosols and clouds) and land models (e.g., soil moisture). First, we nudge only the model horizontal velocities towards operational analysis/reanalysis values, given a 6-hour relaxation time scale, to obtain all necessary variables. Compared to the original strategy in which horizontal velocities, temperature and specific humidity are nudged, the revised approach produces a better representation of initial aerosols and cloud fields which are more consistent and closer to observations and model's preferred climatology. Second, we obtain land ICs from an offline land model simulation forced with observed precipitation, winds, and surface fluxes. This approach produces more realistic soil moisture in the land ICs. With this refined procedure, the simulated precipitation, clouds, radiation, and surface air temperature over land are improved in the Day 2 mean hindcasts. Following this procedure, we propose a “Core” integration suite which provides an easily repeatable test allowing model developers to rapidly assess the impacts of various parameterization changes on the fidelity of modelled cloud-associated processes relative to observations. This article is protected by copyright. All rights reserved.

Description: The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi . Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solved NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH 2 -) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH 2 towards the metal-ligand water molecule, where a dioxygen O 2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably because the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.

Description: : Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies. Therefore, we create the Annotated Scaffold Database (ASDB), a computer-readable and systematic target-annotated scaffold database, to serve such needs. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets and medical indications. The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets. The scaffolds consist of 3032 scaffolds derived from drugs and 5163 scaffolds derived from natural products. For given scaffolds, scaffold-target networks can be generated from the database to demonstrate the relations of scaffolds and targets. Availability and implementation: ASDB is freely available at http://www.rcdd.org.cn/asdb/ with the major web browsers. Contact: junxu@biochemomes.com or xujun9@mail.sysu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Partial melting plays an important role in the geodynamics of continental subduction zones. This is identified from a suite of ultrahigh-pressure (UHP) migmatites in the Sulu orogen through a combined study of zircon U-Pb ages, trace elements, and oxygen isotopes, as well as rock-forming mineral and inclusion compositions. The results indicate two episodes of partial melting in the subducted continental crust during continental collision, providing insights into subduction channel processes. The first episode of anatexis is indicated by the occurrence of nanogranites, not only in zircon, garnet, and monazite from diatexite, but also in zircon cores from leucosome. The anatectic zircon exhibits U-Pb ages of 230–227 Ma and flat rare earth element (REE) patterns with weak or no negative Eu anomalies, and it contains mineral inclusions of coesite and garnet + amphibole. Newly grown zircon grains in the diatexite and zircon cores in the leucosome exhibit high 18 O values of 8.3–17.3, indicating a metasedimentary protolith. The host rocks show high A/CNK (= molar ratio of Al 2 O 3 /[CaO + Na 2 O + K 2 O]) values and the occurrence of peritectic garnet in the diatexite. Thus, the diatexite was produced by partial melting of metasedimentary rocks. The Ti-in-zircon thermometry, the garnet-phengite Fe-Mg partition thermometry for mineral inclusions in the zircon, and the occurrence of coesite inclusions in zircon indicate partial melting at 650–800 °C and 2.5–3.0 GPa, corresponding to high-pressure (HP) to UHP conditions. On the other hand, the second episode of anatexis is recorded by newly grown zircon grains in metatexite and zircon rims in leucosome, which show U-Pb ages of 218–214 Ma, oscillatory zoning, steep heavy (H) REE patterns with negative Eu anomalies, low temperatures of 550–700 °C, and significant variations in Th, U, Nb, and Ta contents. The Zr-in-titanite thermometry for nanogranite-bearing titanite and the garnet-phengite Fe-Mg partition thermometry for mineral inclusions in the leucosome zircon rims indicate anatexis at 800–850 °C and 1.0–1.5 GPa. The zircon in the metatexite exhibits low 18 O values of –1.5–3.5 and Neoproterozoic U-Pb ages for relict magmatic cores, indicating the protolith of a low 18 O UHP metagranite. The two episodes of anatexis yield zircon domains with a series of differences not only in U-Pb age, but also in geochemical composition. Thus, protoliths with different origins were involved in the anatexis, with a possible difference in spatial positions. The UHP metasedimentary rocks atop the deeply subducted continental crust would have undergone the first episode of anatexis during the final subduction, whereas their underlying metagranite would have undergone the second episode of anatexis during the exhumation of deeply subducted crust. In either case, the breakdown of UHP hydrous minerals during exhumation is the key for the partial melting of UHP metamorphic rocks in the continental subduction channel.

Description: Histone acetyltransferase PCAF accelerates apoptosis by repressing a GLI1/BCL2/BAX axis in hepatocellular carcinoma Cell Death and Disease 6, e1712 (April 2015). doi:10.1038/cddis.2015.76 Authors: X Gai, K Tu, C Li, Z Lu, L R Roberts & X Zheng

Description: The human-climate-ecosystem interactions in the past were valuable for today’s human beings who face the challenge of global change. The multi-proxy reconstruction of climate change impacts and social responses and the comparative study between typical periods form an effective tool for elucidating the mechanisms of the interactions. In this paper, with a reconstruction of the proxy series of famine, migration and wars, the most typical social consequences related to climate change and disasters (flood/drought) in North China in 1470–1911 were quantitatively described, and two typical periods of human-climate interaction with similar climate change backgrounds (cold periods of the ‘Little Ice Age’), which were the late Ming dynasty (1560–1644) and late Qing dynasty (1780–1911), were selected and compared. It is determined that the climate deterioration (rapid cooling and increasing extreme disasters) in the late 16th and 18th centuries both resulted in severe social consequences characterized by more famine and popular unrest. The differences were that the climatic impacts in the late Ming were much more serious, and interregional migration, which was an effective responsive measure in the late Qing, was not important in the late Ming; they were primarily influenced by three factors based on the analytical framework of the impacts of historical climate change and social responses: (1) climate deterioration in the late Ming was more severe (more rapid cooling and more extreme disasters), (2) social system were more sensitive to climate change in the late Ming because of its mode of agricultural production (especially cropping system and crop species), and (3) the capacity of social response to climate disaster, especially disaster relief and refugee settlement, was considerably greater in the late Qing.

Description: As an important mechanism for adaptation to heterogeneous environment, plastic responses of correlated traits to environmental alteration may also be genetically correlated, but less is known about the underlying genetic basis. We describe a statistical model for mapping specific quantitative trait loci (QTLs) that control the interrelationship of phenotypic plasticity between different traits. The model is constructed by a bivariate mixture setting, implemented with the EM algorithm to estimate the genetic effects of QTLs on correlative plastic response. We provide a series of procedure that test (1) how a QTL controls the phenotypic plasticity of a single trait; and (2) how the QTL determines the correlation of environment-induced changes of different traits. The model is readily extended to test how epistatic interactions among QTLs play a part in the correlations of different plastic traits. The model was validated through computer simulation and used to analyse multi-environment data of genetic mapping in winter wheat, showing its utilization in practice.