Over-expression of Arabidopsis DnaJ (Hsp40) contributes to NaCl-stress tolerance

DnaJ (Hsp40), a heat shock protein, is a molecular chaperones responsive to various environmental stress. To analyze the protective role of DnaJ, we obtained sense transgenic Arabidopsis plants that constitutively expressed elevated levels of DnaJ. In this study, sense transgenic plants show large thinner, fade color and malformed leaves, as well as less floss of back leaves. Plants with enhanced levels of DnaJ in their transgenic sense lines exhibited tolerance to NaCl stress. Under 120 mM NaCl, root length was higher in transgenic sense plants than wild-type plants. In vitro expression system, DnaJ protein shows tolerance to high NaCl. These results suggest that over-expression of DnaJ can confer NaCl-stress tolerance

Distinct control mechanism of fine-grained sediments from Yellow River and Kyushu supply in the northern Okinawa Trough since the last glacial

© 2017. American Geophysical Union. All Rights Reserved. High-resolution multiproxy records, including clay minerals and Sr-Nd-Pb isotopes of the clay-sized silicate fraction of sediments from IODP Site U1429 in the northern Okinawa Trough, provide reliable evidence for distinct control mechanism on fine-grained sediments input from the Yellow River and the southern Japanese Islands to the northern Okinawa Trough since 34 ka BP. Provenance analysis indicates that the sediments were mainly derived from the Yellow River and the island of Kyushu. Since the last glacial, clay-sized sediments transported from the Yellow River to the study site were strongly influenced by sea-level fluctuation. During low sea-level stage (∼34–14 ka BP), the paleo-Yellow River mouth was positioned closer to the northern Okinawa Trough, favoring large fluvial discharge or even direct input of detrital sediments, which resulted about four times more flux of clay-sized sediments supply to the study area as during the relatively high sea-level stage (∼14–0 ka BP). The input of Kyushu-derived clay-sized sediments to the study site was mainly controlled by the Kuroshio Current and Tsushima Warm Current intensity, with increased input in phase with weakened Kuroshio Current/Tsushima Warm Current. Our study suggests that the Kuroshio Current was very likely flowed into the Okinawa Trough and thus influenced the fine-grained sediment transport in the area throughout the last glacial and deglacial. During ∼34–11 ka BP, the Kyushu clay-sized sediment input was mainly controlled by the Kuroshio Current. Since ∼11 ka BP, the occurrence of Tsushima Warm Current became important in influencing the Kyushu fine-grained sediment input to the northern Okinawa Trough

Integrated Bio-Entity Network: A System for Biological Knowledge Discovery

A significant part of our biological knowledge is centered on relationships between biological entities (bio-entities) such as proteins, genes, small molecules, pathways, gene ontology (GO) terms and diseases. Accumulated at an increasing speed, the information on bio-entity relationships is archived in different forms at scattered places. Most of such information is buried in scientific literature as unstructured text. Organizing heterogeneous information in a structured form not only facilitates study of biological systems using integrative approaches, but also allows discovery of new knowledge in an automatic and systematic way. In this study, we performed a large scale integration of bio-entity relationship information from both databases containing manually annotated, structured information and automatic information extraction of unstructured text in scientific literature. The relationship information we integrated in this study includes protein–protein interactions, protein/gene regulations, protein–small molecule interactions, protein–GO relationships, protein–pathway relationships, and pathway–disease relationships. The relationship information is organized in a graph data structure, named integrated bio-entity network (IBN), where the vertices are the bio-entities and edges represent their relationships. Under this framework, graph theoretic algorithms can be designed to perform various knowledge discovery tasks. We designed breadth-first search with pruning (BFSP) and most probable path (MPP) algorithms to automatically generate hypotheses—the indirect relationships with high probabilities in the network. We show that IBN can be used to generate plausible hypotheses, which not only help to better understand the complex interactions in biological systems, but also provide guidance for experimental designs

Aspergillus Myosin-V Supports Polarized Growth in the Absence of Microtubule-Based Transport

In the filamentous fungus Aspergillus nidulans, both microtubules and actin filaments are important for polarized growth at the hyphal tip. Less clear is how different microtubule-based and actin-based motors work together to support this growth. Here we examined the role of myosin-V (MYOV) in hyphal growth. MYOV-depleted cells form elongated hyphae, but the rate of hyphal elongation is significantly reduced. In addition, although wild type cells without microtubules still undergo polarized growth, microtubule disassembly abolishes polarized growth in MYOV-depleted cells. Thus, MYOV is essential for polarized growth in the absence of microtubules. Moreover, while a triple kinesin null mutant lacking kinesin-1 (KINA) and two kinesin-3s (UNCA and UNCB) undergoes hyphal elongation and forms a colony, depleting MYOV in this triple mutant results in lethality due to a severe defect in polarized growth. These results argue that MYOV, through its ability to transport secretory cargo, can support a significant amount of polarized hyphal tip growth in the absence of any microtubule-based transport. Finally, our genetic analyses also indicate that KINA (kinesin-1) rather than UNCA (kinesin-3) is the major kinesin motor that supports polarized growth in the absence of MYOV

Modeling forest above-ground biomass dynamics using multi-source data and incorporated models : a case study over the qilian mountains

© 2017 The Author(s) In this work, we present a strategy for obtaining forest above-ground biomass (AGB) dynamics at a fine spatial and temporal resolution. Our strategy rests on the assumption that combining estimates of both AGB and carbon fluxes results in a more accurate accounting for biomass than considering the terms separately, since the cumulative carbon flux should be consistent with AGB increments. Such a strategy was successfully applied to the Qilian Mountains, a cold arid region of northwest China. Based on Landsat Thematic Mapper 5 (TM) data and ASTER GDEM V2 products (GDEM), we first improved the efficiency of existing non-parametric methods for mapping regional forest AGB for 2009 by incorporating the Random Forest (RF) model with the k-Nearest Neighbor (k-NN). Validation using forest measurements from 159 plots and the leave-one-out (LOO) method indicated that the estimates were reasonable (R2 = 0.70 and RMSE = 24.52 tones ha−1). We then obtained one seasonal cycle (2011) of GPP (R2 = 0.88 and RMSE = 5.02 gC m−2 8d−1) using the MODIS MOD_17 GPP (MOD_17) model that was calibrated to Eddy Covariance (EC) flux tower data (2010). After that, we calibrated the ecological process model (Biome-BioGeochemical Cycles (Biome-BGC)) against above GPP estimates (for 2010) for 30 representative forest plots over an ecological gradient in order to simulate AGB changes over time. Biome-BGC outputs of GPP and net ecosystem exchange (NEE) were validated against EC data (R2 = 0.75 and RMSE = 1. 27 gC m−2 d−1 for GPP, and R2 = 0.61 and RMSE = 1.17 gC m−2 d−1 for NEE). The calibrated Biome-BGC was then applied to produce a longer time series for net primary productivity (NPP), which, after conversion into AGB increments according to site-calibrated coefficients, were compared to dendrochronological measurements (R2 = 0.73 and RMSE = 46.65 g m−2 year−1). By combining these increments with the AGB map of 2009, we were able to model forest AGB dynamics. In the final step, we conducted a Monte Carlo analysis of uncertainties for interannual forest AGB estimates based on errors in the above forest AGB map, NPP estimates, and the conversion of NPP to an AGB increment

Rheological behaviors and viscosity prediction model of cementitious composites with various carbon nanotubes

This study aims to understand the effects and mechanisms of length, diameter, and functional group of carbon nanotubes (CNTs) on rheological behaviors of cementitious composites. The experimental results show that the addition of CNTs decreases the flow index and increases the critical shear rate of cementitious composites. CNTs with a sub-micrometer length and small diameter endow cementitious composites with high yield stresses and minimum viscosities. Influenced by the high water absorption of hydroxylic groups, the minimum viscosity of cementitious composites with hydroxyl functionalized CNTs is larger than that of composites with pristine carbon nanotubes (p-CNTs). By contrast, the yield stress and minimum viscosity of cementitious composites with carboxyl functionalized CNTs are smaller than that of cementitious composites with p-CNTs at most contents due to the high dispersion induced by carboxyl groups. The effect mechanisms of CNTs on rheological behaviors can be attributed to adsorption effect and entanglement effect, which are closely related to length, diameter and functionalization groups of CNTs. The established minimum viscosity prediction model considering the influence of CNT physicochemical features can provide guidance for regulating the workability and hardened performance of CNTs modified cementitious composites.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Materials and Environmen