Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations

Drought is a major stress for plants, creating a strong selection pressure for traits that enable plant growth and survival in dry environments. Many drought responses are conserved species‐wide responses, while others vary among populations distributed across heterogeneous environments. We tested how six populations of the widely distributed California valley oak (Quercus lobata) sampled from contrasting climates would differ in their response to soil drying relative to well‐watered controls in a common environment by measuring ecophysiological traits in 93 individuals and gene expression (RNA‐seq) in 42 individuals. Populations did not differ in their adjustment of turgor loss point during soil drying, suggesting a generalized species‐wide response. Differential expression analysis identified 689 genes with a common response to treatment across populations and 470 genes with population‐specific responses. Weighted gene co‐expression network analysis (WGCNA) identified groups of genes with similar expression patterns that may be regulated together (gene modules). Several gene modules responded differently to water stress among populations, suggesting regional differences in gene network regulation. Populations from sites with a high mean annual temperature responded to the imposed water stress with significantly greater changes in gene module expression, indicating that these populations may be locally adapted to respond to drought. We propose that this variation among valley oak populations provides a mechanism for differential tolerance to the increasingly frequent and severe droughts in California.     

EGFR配体生物学效应的多样性

表皮生长因子受体（epidermal growth factor receptor, EGFR）的配体作为一类重要的信号分子参与了细胞功能的调节,并且和机体发育、器官形成、组织修复与稳态维持,以及疾病的发生密切相关。虽然这些信号分子具有序列和结构上的相似性,但由于这些信号分子结构上的细微差异以及它们受体信号传导上的复杂性,造成了这些信号分子（配体）生物学效应的多样性。目前,从结构和机制上,对于单个信号分子的生物学效应已有较为深入的研究,但这些信号分子之间以及信号分子与受体之间的调控网络较为复杂,并且这种调控网络对信号的精细、有序和多样化转导至关重要。本文对EGFR配体的结构及配体生物学效应多样性的分子机制进行回顾,并对未来的研究方向提出展望。     

世界竹子清单更新

编研世界竹子清单(World Checklist of Bamboos,WCB)是竹学的一项基础性工作。文中更正了2016年由世界禾草权威英国皇家植物园——Kew园领衔出版的World Checklist of Bamboos and Rattans竹子部分统计数据,实际为1665种,而非其自述的1642种;持续汇集全球竹种,时间更新至2018年底,WCB(2018)已禀赋计130个竹属,包含1700个竹种。     

络合型含铁材料对砷胁迫下水稻生理生化特性及砷累积的影响

土壤重金属与农产品质量息息相关.本研究通过设置砷胁迫条件下水稻种植盆栽试验,分析络合型含铁材料不同施用时期和不同施用量对水稻SPAD值、抗氧化酶(SOD、POD、CAT)活性以及水稻砷吸收、累积的影响.结果表明,砷胁迫对水稻SOD、POD、CAT活性有着不同程度的抑制作用,添加络合型含铁材料可以降低水稻MDA含量,缓解砷对水稻光合作用和SOD、POD、CAT活性的抑制;同时能减少水稻对土壤砷的吸收和累积.与移栽前添加络合型含铁材料相比,选择水稻孕穗期前添加络合型含铁材料,水稻砷吸收的抑制效果较好;水稻植株地上部砷含量与络合型含铁材料的添加浓度呈显著负相关,孕穗期前添加0.2 g·kg-1络合型含铁材料对水稻植株砷的吸收抑制效果最好,水稻植株地上部砷含量降低59.22%.     

Immuno-spin trapping analyses of DNA radicals

Immuno-spin trapping is a highly sensitive method for detecting DNA radicals in biological systems. This technique involves three main steps: (i) in situ and real-time trapping of DNA radicals with the nitrone spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), thus forming DMPO-DNA nitrone adducts (referred to here as nitrone adducts); (ii) purification of nitrone adducts; and (iii) analysis of nitrone adducts by heterogeneous immunoassays using Abs against DMPO. In experiments, DMPO is added prior to the formation of free radicals. It diffuses easily through all cell compartments and is present when DNA free radicals are formed as a result of oxidative damage. Due to its low toxicity, DMPO can be used in cells at high enough concentrations to out-compete the normal reactions of DNA radicals, thus ensuring a high yield of DNA nitrone adducts. Because both protein and DNA nitrone adducts are formed, it is important that the DNA be pure in order to avoid misinterpretations. Depending on the model under study, this protocol can be completed in as few as 6 h.     

The frequency of occurrence and discriminatory power of compounds found in human scent across a population determined by SPME-GC/MS

The composition of human scent collected from the hands is of interest to the medical community as a mechanism to diagnose disease and the forensic community as a means to investigate canine scent discriminations. An extensive survey of the volatile organic compounds (VOCs) identified in the headspace of hand odor samples utilizing solid phase micro-extraction gas chromatography/mass spectrometry (SPME-GC/MS) has been conducted to determine the constituents of the human base odor profile. Sixty-three compounds were extracted from the collected odor samples. The composition included acids, alcohols, aldehydes, hydrocarbons, esters, ketones and nitrogen-containing compounds. The majority of the compounds detected (79.4%) were present in less than one third of the individuals sampled. Spearman correlation coefficient comparisons at a match/no-match threshold of 0.9 produced a distinguish ability of 99.67% across the population.     

不同抗性泡核桃对褐斑病病原菌侵染的生理生化响应北大核心CSCD

以抗病和感病泡核桃无性系为实验材料,人工接种褐斑病病原菌后测定不同时期叶片中保护酶活性、总酚、类黄酮、叶绿素含量等相关生理生化指标,探讨不同抗性泡核桃响应褐斑病病原菌侵染的生理生化差异。结果表明:(1)接种病原菌后,感病无性系64叶片带菌率随着侵染时间的增加而升高,且显著高于抗病无性系199(P<0.05)。(2)抗病无性系199和感病无性系64叶片的SOD、POD、CAT、APX和PPO活性随着侵染时间均呈现先升高后降低的变化趋势,其中SOD、POD和APX活性均在16 d时达到最大值;与较感病无性系相比,接种后抗病无性系的POD和APX活性较强;在接种前期(1~16 d),感病无性系PPO活性高于抗病无性系,后期(16~34 d)CAT活性也较抗病无性系高。(3)抗病无性系叶片叶绿素含量始终高于感病无性系;抗病无性系MDA含量在接种后无明显变化,而感病无性系先增加后降低,其细胞膜脂过氧化较重。(4)两个无性系叶片可溶性蛋白和可溶性糖含量变化较平缓,且差异不显著,在接种后期(34 d)有升高的趋势;接种5 d以后,感病无性系叶片类黄酮和总酚含量始终显著高于抗病无性系。研究发现,泡核桃抗病无性系叶片带菌率较低,较难受到侵染,并且通过提高POD和APX活性以及积累较多叶绿素、可溶性蛋白和可溶性糖来应对病原菌侵染引起的氧化胁迫,抑制病原菌的繁殖,从而提高其抗病能力。     

The cis-Regulatory Atlas of the Mouse Immune System

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Associations of physical activity with gut microbiota in pre-adolescent children

[Purpose] To determine whether physical activity (PA), primarily the recommended 60 minutes of moderate-to-vigorous PA, is associated with gut bacterial microbiota in 10-year-old children.[Methods] The Block Physical Activity Screener, which provides minutes/day PA variables, was used to determine whether the child met the PA recommendations. 16S rRNA sequencing was performed on stool samples from the children to profile the composition of their gut bacterial microbiota. Differences in alpha diversity metrics (richness, Pielou’s evenness, and Faith’s phylogenetic diversity) by PA were determined using linear regression, whereas beta diversity (unweighted and weighted UniFrac) relationships were assessed using PERMANOVA. Taxon relative abundance differentials were determined using DESeq2.[Results] The analytic sample included 321 children with both PA and 16S rRNA sequencing data (mean age [SD] =10.2 [0.8] years; 54.2% male; 62.9% African American), where 189 (58.9%) met the PA recommendations. After adjusting for covariates, meeting the PA recommendations as well as minutes/day PA variables were not significantly associated with gut richness, evenness, or diversity (p ≥ 0.19). However, meeting the PA recommendations (weighted UniFrac R² = 0.014, p = 0.001) was significantly associated with distinct gut bacterial composition. These compositional differences were partly characterized by increased abundance of Megamonas and Anaerovorax as well as specific Christensenellaceae_R-7_group taxa in children with higher PA.[Conclusion] Children who met the recommendations of PA had altered gut microbiota compositions. Whether this translates to a reduced risk of obesity or associated metabolic diseases is still unclear.     

Phosphoproteomic analysis of thrombin- and p38 MAPK-regulated signaling networks in endothelial cells

Endothelial dysfunction is a hallmark of inflammation and is mediated by inflammatory factors that signal through G protein–coupled receptors including protease-activated receptor-1 (PAR1). PAR1, a receptor for thrombin, signals via the small GTPase RhoA and myosin light chain intermediates to facilitate endothelial barrier permeability. PAR1 also induces endothelial barrier disruption through a p38 mitogen-activated protein kinase–dependent pathway, which does not integrate into the RhoA/MLC pathway; however, the PAR1-p38 signaling pathways that promote endothelial dysfunction remain poorly defined. To identify effectors of this pathway, we performed a global phosphoproteome analysis of thrombin signaling regulated by p38 in human cultured endothelial cells using multiplexed quantitative mass spectrometry. We identified 5491 unique phosphopeptides and 2317 phosphoproteins, four distinct dynamic phosphoproteome profiles of thrombin-p38 signaling, and an enrichment of biological functions associated with endothelial dysfunction, including modulators of endothelial barrier disruption and a subset of kinases predicted to regulate p38-dependent thrombin signaling. Using available antibodies to detect identified phosphosites of key p38-regulated proteins, we discovered that inhibition of p38 activity and siRNA-targeted depletion of the p38α isoform increased basal phosphorylation of extracellular signal–regulated protein kinase 1/2, resulting in amplified thrombin-stimulated extracellular signal–regulated protein kinase 1/2 phosphorylation that was dependent on PAR1. We also discovered a role for p38 in the phosphorylation of α-catenin, a component of adherens junctions, suggesting that this phosphorylation may function as an important regulatory process. Taken together, these studies define a rich array of thrombin- and p38-regulated candidate proteins that may serve important roles in endothelial dysfunction.