EffectorK,a comprehensive resource to mine for Ralstonia,Xanthomonas, and other published effector interactors in the Arabidopsis proteome

Pathogens deploy effector proteins that interact with host proteins to manipulate the host physiology to the pathogen's own benefit. However, effectors can also be recognized by host immune proteins, leading to the activation of defence responses. Effectors are thus essential components in determining the outcome of plant–pathogen interactions. Despite major efforts to decipher effector functions, our current knowledge on effector biology is scattered and often limited. In this study, we conducted two systematic large-scale yeast two-hybrid screenings to detect interactions between Arabidopsis thaliana proteins and effectors from two vascular bacterial pathogens: Ralstonia pseudosolanacearum and Xanthomonas campestris. We then constructed an interactomic network focused on Arabidopsis and effector proteins from a wide variety of bacterial, oomycete, fungal, and invertebrate pathogens. This network contains our experimental data and protein–protein interactions from 2,035 peer-reviewed publications (48,200 Arabidopsis–Arabidopsis and 1,300 Arabidopsis–effector protein interactions). Our results show that effectors from different species interact with both common and specific Arabidopsis interactors, suggesting dual roles as modulators of generic and adaptive host processes. Network analyses revealed that effector interactors, particularly “effector hubs” and bacterial core effector interactors, occupy important positions for network organization, as shown by their larger number of protein interactions and centrality. These interactomic data were incorporated in EffectorK, a new graph-oriented knowledge database that allows users to navigate the network, search for homology, or find possible paths between host and/or effector proteins. EffectorK is available at www.effectork.org and allows users to submit their own interactomic data.     

Timing is everything

Cell adhesion to the extracellular matrix elicits a temporal reorganization of the actin cytoskeleton that is regulated first by Rac1 and later by RhoA. The signaling mechanisms controlling late stage RhoA activation are incompletely understood. Net1A is a RhoA/RhoB-specific guanine nucleotide exchange factor that is required for cancer cell motility. The ability of Net1A to stimulate RhoA activation is negatively regulated by nuclear sequestration. However, mechanisms controlling the plasma membrane localization of Net1A had not previously been reported. Recently we have shown that Rac1 activation stimulates plasma membrane relocalization and activation of Net1A. Net1A relocalization is independent of its catalytic activity and does not require its C-terminal pleckstrin homology or PDZ interacting domains. Rac1 activation during cell adhesion stimulates a transient relocalization of Net1A that is terminated by proteasomal degradation of Net1A. Importantly, plasma membrane localization of Net1A is required for efficient myosin light chain phosphorylation, focal adhesion maturation, and cell spreading. These data show for the first time a physiological mechanism controlling Net1A relocalization from the nucleus. They also demonstrate a previously unrecognized role for Net1A in controlling actomyosin contractility and focal adhesion dynamics during cell adhesion.     

云南省国家级和省级自然保护区森林生态服务功能价值评估

采取文献查阅、资料数据处理、统计分析等研究方法,选取合理、成熟、可操作的森林生态服务评估体系和方法（LY/T 1721-2008）,测算出云南省国家级、省级自然保护区森林生态系统在涵养水源、保育土壤、固碳释氧、积累营养物质、净化大气环境、生物多样性保护等6类生态系统服务功能的物质量和价值量,并从森林类型、质量、立地状况等多方面进行了分析。经评估,云南省自然保护区森林生态系统服务年总价值为2009.02亿元。其中,涵养水源价值为538.75亿元;保育土壤价值为493.79亿元;固碳释氧价值为122.09亿元;积累营养物质价值为16.11亿元;净化大气环境价值为83.21亿元;生物多样性保护价值为755.07亿元。保护区每年每公顷森林生态系统服务价值平均为12.31万元,相当于全国平均水平的2.9倍,云南省平均水平的2.4倍。     

Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol

Objectives

The sequencing by the PolyA selection is the most common approach for library preparation. With limited amount or degraded RNA, alternative protocols such as the NuGEN have been developed. However, it is not yet clear how the different library preparations affect the downstream analyses of the broad applications of RNA sequencing.

Methods and Materials

Eight human mammary epithelial cell (HMEC) lines with high quality RNA were sequenced by Illumina’s mRNA-Seq PolyA selection and NuGEN ENCORE library preparation. The following analyses and comparisons were conducted: 1) the numbers of genes captured by each protocol; 2) the impact of protocols on differentially expressed gene detection between biological replicates; 3) expressed single nucleotide variant (SNV) detection; 4) non-coding RNAs, particularly lincRNA detection; and 5) intragenic gene expression.

Results

Sequences from the NuGEN protocol had lower (75%) alignment rate than the PolyA (over 90%). The NuGEN protocol detected fewer genes (12–20% less) with a significant portion of reads mapped to non-coding regions. A large number of genes were differentially detected between the two protocols. About 17–20% of the differentially expressed genes between biological replicates were commonly detected between the two protocols. Significantly higher numbers of SNVs (5–6 times) were detected in the NuGEN samples, which were largely from intragenic and intergenic regions. The NuGEN captured fewer exons (25% less) and had higher base level coverage variance. While 6.3% of reads were mapped to intragenic regions in the PolyA samples, the percentages were much higher (20–25%) for the NuGEN samples. The NuGEN protocol did not detect more known non-coding RNAs such as lincRNAs, but targeted small and “novel” lincRNAs.

Conclusion

Different library preparations can have significant impacts on downstream analysis and interpretation of RNA-seq data. The NuGEN provides an alternative for limited or degraded RNA but it has limitations for some RNA-seq applications.     

新疆准噶尔盆地北缘中中新世早期的原圆齿鼠(Promylagaulinae,Mylagaulidae)(英文)

<正>1988年吴文裕描述了产自新疆准噶尔盆地北缘铁尔斯哈巴合地点哈拉玛盖组下部层位的一枚圆齿鼠的P4,定名为Sinomylagaulus halamagaiensis。1997年中国科学院古脊椎动物与古人类研究所新疆考察队又在铁尔斯哈巴合的哈拉玛盖组下部层位中采集到两枚p4。1988年的研究工作仅依据一枚上前臼齿(P4),标本的稀缺决定了当时研究成果的局限性。新材料无疑为认识新疆的圆齿鼠类提供了新的信息     

先天性肛门直肠畸形大鼠后肠发育中Fibronectin与Laminin β1的表达及意义

该文采用全反式维甲酸(ATRA)构建SD大鼠肛门直肠畸形模型(n=32),探究FN1(fibronectin 1)与LAMB1(laminin β1)在大鼠胚胎后肠发育过程的表达及意义。对照组与模型组均于E11.5~E16.5、E18.5、E20.5剖宫取胎,记录胎鼠身长、体质量、尾长、大体形态。qRT-PCR、Western blot、免疫组织化学检测FN1与LAMB1 mRNA及蛋白在对照组及模型组胚胎后肠发育中的表达。对照组生长发育指标在各个时间点均优于模型组,差异具有统计学意义(P<0.05)。FN1与LAMB1在胚胎后肠发育中呈连续动态表达。对照组中,qRT-PCR、Western blot、免疫组织化学结果显示二者表达高峰为E15.5,主要均匀分布于泄殖腔上皮黏膜层和基底膜。在模型组中,二者mRNA和蛋白表达水平在E11.5~E16.5均显著上调,表达高峰较对照组滞后出现在E16.5,差异具有统计学意义(P<0.05),免疫组织化学结果提示,二者在泄殖腔中呈现出高表达和分布不均匀的改变。与对照组相比,ATRA诱导的肛门直肠畸形模型组胚胎生长发育滞后,后肠发育中FN1与LAMB1表达上调且峰值延迟,可能与先天性肛门直肠畸形发生有关。     

应用SRAP标记分析福瑞鲤及其原始亲本的遗传结构

摘要：应用SRAP分子标记对建鲤（Cyprinus carpio var. jian）、黄河鲤（C.c.haematopterus）和福瑞鲤（FFRC Strain Common Carp,C.carpio）进行遗传结构分析。结果显示,筛选出的10个多态性较好的引物组合共扩增出110个位点,其中多态性位点92个,平均多...     

基于样方数据的云南松林分生长模型研究——以云南省保山市杨柳白族彝族乡为例

以云南省保山市杨柳白族彝族乡实地调查的86块云南松样地数据,使用非线性拟合的方法拟合优选常用树木生长方程,建立了包括地位指数、密度指数、平均直径和蓄积量的生长模型。经验生长方程Schumacher的拟合度与其它方程相近,但模型中参数变异系数均比其余方程低,为地位指数、平均直径和蓄积量的最优方程。