Rat organic anion transporting protein 1A1 (Oatp1a1): purification and phosphopeptide assignment

Rat organic anion transporting protein 1a1 (oatp1a1), a hepatocyte basolateral plasma membrane protein, mediates transport of various amphipathic compounds. Our previous studies indicated that serine phosphorylation of a single tryptic peptide inhibits its transport activity without changing its cell surface content. The site of phosphorylation is unknown and was the subject of the present study. Following immunoaffinity chromatographic purification from rat liver, oatp1a1 was subjected to trypsin digestion and MALDI-TOF. Except for predicted N-glycosylated peptides, 97% of oatp1a1 tryptic peptides were observed. A single tryptic phosphopeptide was found in the C-terminus (aa 626-647), existing in unphosphorylated or singly or doubly phosphorylated forms and sensitive to alkaline phosphatase treatment. The beta-elimination reaction resulted in a mass loss of 98 or 196 Da from this peptide, and subsequent Michael addition with cysteamine increased masses by the predicated 77 and 154 Da, indicating that oatp1a1 can be singly or doubly phosphorylated at serine or threonine residues in the C-terminal sequence SSATDHT (aa 634-640). Subsequent tandem MS/MS analysis revealed that phosphorylation at S634 accounted for all singly phosphorylated peptide, while phosphorylation at S634 and S635 accounted for all doubly phosphorylated peptide. These findings identify the site of oatp1a1 phosphorylation and demonstrate that it is an ordered process, in which phosphorylation at S634 precedes that at S635. The mechanism by which phosphorylation results in loss of transport activity in hepatocytes remains to be established. Whether phosphorylation near the C-terminus inhibits C-terminal oligomerization of oatp1a1, required for normal transport function, can be speculated upon but is as yet unknown.     

A meta‐analysis on growth,physiological, and biochemical responses of woody species to ground‐level ozone highlights the role of plant functional types

The carbon‐sink strength of temperate and boreal forests at midlatitudes of the northern hemisphere is decreased by ozone pollution, but knowledge on subtropical evergreen broadleaved forests is missing. Taking the dataset from Chinese studies covering temperate and subtropical regions, effects of elevated ozone concentration ([O₃]) on growth, biomass, and functional leaf traits of different types of woody plants were quantitatively evaluated by meta‐analysis. Elevated mean [O₃] of 116 ppb reduced total biomass of woody plants by 14% compared with control (mean [O₃] of 21 ppb). Temperate species from China were more sensitive to O₃ than those from Europe and North America in terms of photosynthesis and transpiration. Significant reductions in chlorophyll content, chlorophyll fluorescence parameters, and ascorbate peroxidase induced significant injury to photosynthesis and growth (height and diameter). Importantly, subtropical species were significantly less sensitive to O₃ than temperate ones, whereas deciduous broadleaf species were significantly more sensitive than evergreen broadleaf and needle‐leaf species. These findings suggest that carbon‐sink strength of Chinese forests is reduced by present and future [O₃] relative to control (20–40 ppb). Given that (sub)‐tropical evergreen broadleaved species dominate in Chinese forests, estimation of the global carbon‐sink constraints due to [O₃] should be re‐evaluated.     

Concentration‐ and flux‐based dose–responses of isoprene emission from poplar leaves and plants exposed to an ozone concentration gradient

Concentration‐ and flux‐based O₃ dose–responses of isoprene emission from single leaves and whole plants were developed. Two poplar clones differing in O₃ sensitivity were exposed to five O₃ levels in open‐top chambers for 97 d: charcoal‐filtered ambient air (CF), non‐filtered ambient air (NF) and NF plus 20 ppb (NF + 20), 40 ppb (NF + 40) and 60 ppb (NF + 60). At both leaf and plant level, isoprene emission was significantly decreased by NF + 40 and NF + 60 for both clones. Although intra‐specific variability was found when the emissions were up‐scaled to the whole plant, both leaf‐ and plant‐level emissions decreased linearly with increasing concentration‐based (AOT40, cumulative exposure to hourly O₃ concentrations >40 ppb) and flux‐based indices (POD_Y, cumulative stomatal uptake of O₃ > Y nmol O₃ m^?2 PLA s^?1). AOT40‐ and POD₇‐based dose–responses performed equally well. The two clones responded differently to AOT40 and similarly to POD_Y (with a slightly higher R² for POD₇) when the emission was expressed as change relative to clean air. We thus recommend POD₇ as a large‐scale risk assessment metric to estimate isoprene emission responses to O₃ in poplar.     

乙烯诱导水仙成花相关代谢物和基因的筛选与分析

为了解乙烯诱导水仙(Narcissus tazetta var. chinensis)成花的生理和分子机制,利用代谢组和转录组测序技术,筛选乙烯诱导水仙成花的差异表达代谢物和基因。结果表明,乙烯处理的侧芽检测到12个差异表达代谢物(DEM),包括7个上调,5个下调,其中,(±)7-表茉莉酸、多巴胺、亚精胺可能与乙烯诱导水仙成花正相关,而吲哚及其衍生物呈负相关。转录组共获得1 021个差异表达基因(DEG),包括615个上调,406个下调,在DEG中鉴定筛选了45个与乙烯信号传导和开花相关的差异表达基因。乙烯诱导水仙成花启动可能先激活水仙鳞茎内源植物激素(尤其乙烯)信号通路的变化,与开花促进基因FPF1和MADS15的上调表达密切相关。9个基因的qRT-PCR结果验证了RNA-Seq的正确性。这些差异表达的代谢物和基因在水仙成花启动过程中可能具有重要作用。     

Identification and expression analysis of lncRNA in seven organs of Rhinopithecus roxellana

Long non-coding RNA (lncRNA) represents a new direction to identify expression profiles and regulatory mechanisms in various organisms. Here, we report the first dataset of lncRNAs of the golden snub-nosed monkey (GSM), including 12,557 putative lncRNAs identified from seven organs. Compared with mRNA, GSM lncRNA had fewer exons and isoforms, and longer length. LncRNA showed more obvious tissue-specific expression than mRNA. However, for the top ten most abundant genes in each organ, mRNAs expression was more tissue-specific than lncRNAs. By identification of specifically expressed lncRNAs and mRNAs in each organ, it indicates that the expression of SEG-lncRNA (specifically expressed lncRNA) and SEG-mRNA (specifically expressed mRNA) had high correlation. In particular, combined our lncRNA and mRNA data, we identified 92 heart SEG-lncRNAs targeted ten mRNA genes in the oxidative phosphorylation pathway and upregulated the expression of these target genes such as ND4, ATP6, and ATP8. These may contribute to GSM adaption to its high-elevation environment. We also identified 171 liver SEG-lncRNAs, which targeted 27 genes associated with the metabolism of xenobiotics and leaded to high expression of these target genes in liver. These lncRNAs may play important roles in GSM adaptation to a folivory diet.

     

6种绿化树种的气孔特性与臭氧剂量的响应关系

采用开顶式气室装置研究5种臭氧(O_3)浓度对6种绿化树种,即杨树基因型‘546’(Populus deltoides cv.‘55/56’×P.deltoides cv.‘Imperial’)和‘107’(P.euramericana cv.‘74/76’)、白蜡(Fraxinus chinensis)、法桐(Platanus orientalis)、洋槐(Robinia pseudoacacia)、国槐(Sophora japonica)的气孔密度、开度和大小的影响。结果表明,随着O_3浓度的升高,气孔密度、开度和大小均显著降低,不同树种的各项气孔特征指标之间均存在显著性差异,O_3处理、树种、采样时期以及O_3和树种之间、采样时期和树种之间存在显著交互作用。6种树种的各项气孔指标与O_3剂量(AOT40,小时O_3浓度大于40nmol/mol的累计值)间具有显著的线性负相关关系(P0.05),即随着O_3浓度的升高而显著降低。为深入研究环境变化背景下城市植物的叶组织结构和功能在适应地表O_3污染方面提供理论证据。     

Assessing the Capacity of Plant Species to Accumulate Particulate Matter in Beijing,China

Air pollution causes serious problems in spring in northern China; therefore, studying the ability of different plants to accumulate particulate matter (PM) at the beginning of the growing season may benefit urban planners in their attempts to control air pollution. This study evaluated deposits of PM on the leaves and in the wax layer of 35 species (11 shrubs, 24 trees) in Beijing, China. Differences in the accumulation of PM were observed between species. Cephalotaxus sinensis, Euonymus japonicus, Broussonetia papyriferar, Koelreuteria paniculata and Quercus variabilis were all efficient in capturing small particles. The plants exhibiting high amounts of total PM accumulation (on leaf surfaces and/or in the wax layer), also showed comparatively high levels of PM accumulation across all particle sizes. A comparison of shrubs and trees did not reveal obvious differences in their ability to accumulate particles based on growth form; a combination of plantings with different growth forms can efficiently reduce airborne PM concentrations near the ground. To test the relationships between leaf traits and PM accumulation, leaf samples of selected species were observed using a scanning electron microscope. Growth forms with greater amounts of pubescence and increased roughness supported PM accumulation; the adaxial leaf surfaces collected more particles than the abaxial surfaces. The results of this study may inform the selection of species for urban green areas where the goal is to capture air pollutants and mitigate the adverse effects of air pollution on human health.     

SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization

miRNAs belong to small non-coding RNAs that are related to a number of complicated biological processes. Considerable studies have suggested that miRNAs are closely associated with many human diseases. In this study, we proposed a computational model based on Similarity Constrained Matrix Factorization for miRNA-Disease Association Prediction (SCMFMDA). In order to effectively combine different disease and miRNA similarity data, we applied similarity network fusion algorithm to obtain integrated disease similarity (composed of disease functional similarity, disease semantic similarity and disease Gaussian interaction profile kernel similarity) and integrated miRNA similarity (composed of miRNA functional similarity, miRNA sequence similarity and miRNA Gaussian interaction profile kernel similarity). In addition, the L₂ regularization terms and similarity constraint terms were added to traditional Nonnegative Matrix Factorization algorithm to predict disease-related miRNAs. SCMFMDA achieved AUCs of 0.9675 and 0.9447 based on global Leave-one-out cross validation and five-fold cross validation, respectively. Furthermore, the case studies on two common human diseases were also implemented to demonstrate the prediction accuracy of SCMFMDA. The out of top 50 predicted miRNAs confirmed by experimental reports that indicated SCMFMDA was effective for prediction of relationship between miRNAs and diseases.     

Analysis of co-expression networks for circular RNAs and mRNAs reveals that circular RNAs hsa_circ_0047905, hsa_circ_0138960 and has-circRNA7690-15 are candidate oncogenes in gastric cancer

Accumulating evidence has suggested that circular RNAs (circRNAs) play important roles in oncogenesis and tumor progression. However, our knowledge of circRNAs in gastric cancer (GC) remains limited. To investigate circRNAs involved in GC oncogenesis, we examined differentially-expressed circRNAs and mRNAs in GC tissues and paired noncancerous mucosa tissues using circRNA and mRNA microarrays. Next, we built gene co-expression networks according to the degree of correlation to predict the critical circRNAs in GC. Through bioinformatics analysis, we observed three newly identified circRNAs that are substantially upregulated in GC: hsa_circ_0047905, hsa_circ_0138960 and has-circRNA7690-15. Additionally, hsa_circ_0047905 and hsa_circ_0138960 positively correlated with their parental gene mRNA. Knockdown of hsa_circ_0047905, hsa_circ_0138960 and has-circRNA7690-15 in GC cells, resulted in downregulation of parental gene expression. Functional assays suggested that inhibition of these three circular RNAs suppresses GC cell proliferation and invasion in vitro. Those findings suggest that hsa_circ_0047905, hsa_circ_0138960 and has-circRNA7690-15 might act as tumor promoters in the pathogenesis of gastric cancer.