Identification of the clonal complexes of Staphylococcus aureus strains by determination of the conservation patterns of small genomic islets

Aims:  To investigate the clonality of Staphylococcus aureus isolates, it is important to identify their clonal complexes (CCs) with multilocus sequence typing (MLST). However, it is expensive to carry out MLST analyses for many isolates. The aim of this study, therefore, was to develop a cost-effective method to identify CCs by determining the conservation pattern of 'small genomic islets' (SGIs). SGIs are nonconserved regions between strains and have single or multiple open-reading frames (ORFs).
Methods and Results:  The whole-genome sequences of nine strains were compared in order to select 16 SGIs. The conservation patterns of the 16 SGIs (islet patterns) were investigated in 136 S. aureus isolates, which were classified into 21 CCs. The islet patterns (IPs) exhibited a one-to-one correspondence with the CCs, except for isolates belonging to CC1, CC5 and CC8. The IPs typical of strains belonging to CC1, CC5 and CC8 differed between those of sequence type 1 (ST1) and ST188 (CC1), ST5 and ST6 (CC5) and ST8 and ST239 (CC8).
Significance and Impact of the Study:  The CCs of many isolates can be identified in an easy and inexpensive manner by detecting these 16 SGIs. Emergent clones, particularly methicillin-resistant ones, can be identified by examining numerous islets by IP analysis.     

应用siRNA技术探讨MCF-7乳腺癌细胞分泌的VEGF对树突状细胞的影响

为探讨MCF-7乳腺癌细胞分泌的血管内皮生长因子（ vascular endothelial growth factor, VEGF）对树突状细胞（dendritic cell, DC）功能及其分化的影响,针对VEGF基因设计siRNA（small interfering RNA, siRNA),采用脂质体转染法以100 nmol/L最佳转染浓度导入MCF-7乳腺癌细胞（siRNA组）,以脂质体Lipofectamine　2000TM转染MCF-7 乳腺癌细胞培养上清培养正常DC作为对照（对照组）,采用ELISA法检测经siRNA 干扰VEGF基因后的MCF-7 乳腺癌细胞分泌的VEGF因子含量, Western 印迹检测VEGF蛋白表达,以探讨siRNA的基因沉默效果;以siRNA组和对照组培养上清分别培养外周血单个核细胞,用流式细胞仪检测所诱导DC表型CD1a、CD80、CD83、CD86和HLA-DR的表达,用MTT法检测转染前后两组DC 诱导的细胞毒性T淋巴细胞（cytotoxic T lymphocyte, CTL）对MCF-7细胞的细胞毒作用.结果显示,MCF-7 乳腺癌细胞培养上清能明显抑制正常DC分化成熟及抗原递呈能力,干扰VEGF基因后MCF-7 乳腺癌细胞培养上清对DC的影响明显降低,CD80、CD83、CD86和HLA-DR的表达较对照组显著升高,而CD1a表达下降（P＜0.01）.转染前后DC 诱导的CTL对MCF-7细胞的杀伤活性有明显差异（P＜0.01）.由此可见,siRNA可靶向抑制MCF-7乳腺癌细胞VEGF的表达,下调VEGF后的MCF-7 细胞上清对DC分化成熟及功能的抑制作用明显降低,从而推测VEGF在肿瘤的发生、发展和免疫抑制方面可能起着重要的作用.     

解读AGO蛋白结构及其功能

RNA沉默是由小RNA特异向导和RNA诱导的沉默复合物（RISC）切割或者抑制靶标mRNA翻译的一种调控系统. 作为RISC的核心成分,AGO蛋白(argonaute proteins)由N末端、PAZ、MID和PIWI 4个结构域组成. PAZ区能非序列特异性识别结合双链小RNA 3′末端悬垂的2个核苷酸,MID与PIWI界面处的“保守口袋”识别结合小RNA 5′端第1位核苷酸,PIWI区具有切割mRNA的催化中心. 根据系统进化学分析,AGO蛋白家族分为3个组：AGO like、PIWI-like和GROUP3. 拟南芥共编码10种AGO蛋白.目前已经证实,具有切割活性的为AtAGO1、AtAGO4和AtAGO7,三者参与的小RNA通路也已得到确认. 在拟南芥10种AGO蛋白中,AtAGO1与AtAGO10、AtAGO1与AtAGO7、AtAGO4与AtAGO6存在功能上的部分冗余.     

原核生物中小RNA的功能及研究进展

在原核生物基因组中,除了tRNA、rRNA和mRNA这3种我们很熟悉的RNA以外,目前已经知道还含有许多编码非常规调控的RNA。这些RNA的长度为50～400核苷酸,通常由原核生物的基因间区编码,但并不翻译成蛋白质,因此被称为非编码小RNA（sRNA）,简称小RNA或非编码RNA。近年来,随着生物信息学和分子生物学技术的不断发展,在原核生物体内陆续发现了上百种sRNA分子,这些sRNA分子具有多样的生物学功能,作为一类新发现的基因表达调控子已经引起了高度的重视。     

基因枪在RNA干扰中的应用研究进展

RNA干扰（RNA interference,RNAi）是指双链RNA（double-strand RNA,dsRNA）特异性降解同源mRNA,从而引发基因转录后水平沉默的现象,是一种高效、高特异性抑制基因表达的途径。自1998年Fire等发现RNA干扰现象以来,其特异性降解目的基因的优势吸引了众多研究者的目光。本文在简要综述RNAi技术在基因功能研究、抗病毒治疗,肿瘤基因治疗等领域的应用后,重点归纳了基因枪技术在RNAi研究即siRNA导入细胞中的应用,并简单分析其优势与意义。     

The Emerging Role of the RAB25 Small GTPase in Cancer

RAB25, a member of the rat sarcoma (RAS) family of small GTPase, has been implicated in the pathophysiology of ovarian, breast and other cancers. Its role in endosomal transport and recycling of cell-surface receptors and signaling proteins presents a novel paradigm for the disruption of cellular pathways and promotion of tumor development and aggressiveness. Variations in structure and post-translational modifications control the localization of RAS superfamily proteins to specific subcellular compartments and recruitment of downstream effectors, allowing these small GTPases to function as sophisticated modulators of a complex and diverse range of cellular processes. Here, we review the link between RAB25 and tumor development and current knowledge regarding its possible roles in cancer.     

一种特异性识别小细胞肺癌细胞的小分子肽

应用“一个珠子一个化合物”的组合化学肽库技术,筛选得到特异性识别小细胞肺癌细胞(DMS53)的小分子肽.初次筛选共得到32个与DMS53阳性结合的珠子,经氨基酸序列分析后发现,含有cNGRXXXc或cXNGRXXc肽链结构的序列共有10个.再次合成三种有代表性的小分子肽,发现cFNGRQQc与DMS53的结合率明显高于其他小分子肽.选择cFNGRQQc作进一步的细胞特异性研究,发现cFNGRQQc与DMS53的粘附特异性明显高于其他细胞系,对cFNGRQQc的结构分析显示,-NGR-及六肽长度对小分子肽与DMS53细胞的粘附非常重要.用抗整合素、E-cadherin、NCAM及ICAM的抗体或多肽阻断小分子肽与DMS53细胞表面的相应受体结合,未见明显的阻断效应.小分子肽与DMS53细胞表面的结合位点有待于进一步证实.     

植物生长素极性运输调控机理的研究进展

生长素极性运输特异地调控植物器官发生、发育和向性反应等生理过程。本文综述和分析了生长素极性运输的调控机制。分子遗传和生理学研究证明极性运输这一过程是由生长素输入载体和输出载体活性控制的。小G蛋白ARF附属蛋白GEF和GAP分别调控输出载体（PINI）和输入载体（AUX1）的定位和活性。并影响高尔基体等介导的细胞囊泡运输系统,小G蛋白ROP也参与输出载体PIN2活性的调节。本文基于作者的研究工作提出小G蛋白在调控生长素极性运输中的可能作用模式。     

Ubiquitination and SUMOylation of annexin A1 and helicase activity

Background

While annexin A1 in nuclei is proposed to be involved in cell transformation, its functions remain poorly understood. Since annexin A1 has the consensus motif, ¹⁶⁰LKRD, for SUMOylation as well as Ks, acceptors for ubiquitination that regulates localization and functions of proteins, we investigated SUMOylation and ubiquitination of annexin A1.

Methods

SUMOylation and ubiquitination of bovine annexin A1 were biochemically tested in vitro by purified proteins, and were confirmed by cell experiments with L5178 lymphoma cells. Effects of the modifications on DNA helicase activity were measured by ssDNA binding activity and by dsDNA unwinding activity.

Results

SUMOylation of annexin A1 was catalyzed by Ubc9, while its ubiquitination was by Rad6-Rad 18. Ubiquitinated annexin A1 had higher affinity for damaged DNA, and promoted in vitro translesion DNA synthesis by Pol β. In mouse lymphoma L5178Y tk(+/−) cells, levels of SUMOylated annexin A1 decreased by DNA damaging agents, MMS or As³⁺, whereas those of ubiquitinated annexin A1 increased under the same conditions.

Conclusion

These observations suggest but do not necessarily prove that ubiquitinated annexin A1 in nuclei may be involved in DNA damage response, while SUMOylated annexin A1 functions in proliferation–differentiation.

Significance

Ubiquitination of annexin A1 may play an important role in mutagenesis, an initial step of cell transformation.