Towards online multiresolution community detection in large-scale networks

The investigation of community structure in networks has aroused great interest in multiple disciplines. One of the challenges is to find local communities from a starting vertex in a network without global information about the entire network. Many existing methods tend to be accurate depending on a priori assumptions of network properties and predefined parameters. In this paper, we introduce a new quality function of local community and present a fast local expansion algorithm for uncovering communities in large-scale networks. The proposed algorithm can detect multiresolution community from a source vertex or communities covering the whole network. Experimental results show that the proposed algorithm is efficient and well-behaved in both real-world and synthetic networks.     

Mutational analysis of N381, a key trimer contact residue in Tsr, the Escherichia coli serine chemoreceptor

Chemoreceptors such as Tsr, the serine receptor, function in trimer-of-dimer associations to mediate chemotactic behavior in Escherichia coli. The two subunits of each receptor homodimer occupy different positions in the trimer, one at its central axis and the other at the trimer periphery. Residue N381 of Tsr contributes to trimer stability through interactions with its counterparts in a central cavity surrounded by hydrophobic residues at the trimer axis. To assess the functional role of N381, we created and characterized a full set of amino acid replacements at this Tsr residue. We found that every amino acid replacement at N381 destroyed Tsr function, and all but one (N381G) of the mutant receptors also blocked signaling by Tar, the aspartate chemoreceptor. Tar jamming reflects the formation of signaling-defective mixed trimers of dimers, and in vivo assays with a trifunctional cross-linking reagent demonstrated trimer-based interactions between Tar and Tsr-N381 mutants. Mutant Tsr molecules with a charged amino acid or proline replacement exhibited the most severe trimer formation defects. These trimer-defective receptors, as well as most of the trimer-competent mutant receptors, were unable to form ternary signaling complexes with the CheA kinase and with CheW, which couples CheA to receptor control. Some of the trimer-competent mutant receptors, particularly those with a hydrophobic amino acid replacement, may not bind CheW/CheA because they form conformationally frozen or distorted trimers. These findings indicate that trimer dynamics probably are important for ternary complex assembly and that N381 may not be a direct binding determinant for CheW/CheA at the trimer periphery.     

维生素E对体外培养的人脐静脉内皮细胞白介素-8表达的影响

目的探讨维生素E(α-生育酚)对人脐静脉内皮细胞(HUVEC)白介素-8(IL-8)表达的影响.方法体外培养HUVEC,将其随机分为正常对照组和实验组,实验组细胞在用激动剂脂多糖(LPS)刺激之前,分别给予0、10、20、30mg/Lα-生育酚,然后在6h、24h、48h三个时段,利用双抗体夹心酶联免疫吸附技术(ELISA)和原位杂交技术(ISH)检测各组细胞IL-8蛋白表达及mRNA表达水平.结果 (1)正常对照组IL-8有基础表达;(2)与正常对照组比较,ELISA和ISH的结果均显示LPS能够明显诱导IL-8高表达:蛋白表达增强约28倍(P<0.01),mRNA表达增强约4.3倍(P<0.01);(3)维生素E能够抑制LPS诱导的IL-8的表达:ELISA结果显示20mg/L-48hα-T处理组作用最强,IL-8蛋白表达减少72.7%(P<0.01);ISH结果显示20mg/L -24hα-T处理组作用最强,IL-8mRNA表达减少73.2%(P<0.01).结论维生素E可显著抑制LPS诱导的HUVEC高表达IL-8,表明维生素E可通过影响对动脉粥样硬化有重要作用的IL-8的表达来发挥其抗动脉粥样硬化作用.     

The Protective Mechanism for the Blood–Brain Barrier Induced by Aminoguanidine in Surgical Brain Injury in Rats

This study was performed to investigate the mechanism of blood–brain barrier (BBB) permeability change, which was induced by aminoguanidine (AG) after surgical brain injury (SBI) in rats. Compared to control group, AG (150 mg/kg, i.p.) significantly reduced Evans blue extravasation into brain tissue at 24 h after surgical resection, it also induced a 32% decrease of malondialdehyde (MDA) values and a 1.1-fold increase of the glutathione (GSH) levels at 12 h after injury. The expression of inducible nitric oxide synthase (iNOS) reached the peak value at 24 h after SBI, which was significantly attenuated after AG treatment. In addition, ZO-1 protein was up-regulated by AG (150 mg/kg) treatment at 24 h after SBI. Our results indicated that AG could protect the BBB after SBI, which could be correlated with antioxidative property, the down-regulation of iNOS and up-regulation of tight junction protein expression.     

Expression of P2Y receptors in the rat anterior pituitary

In this study, the distribution patterns of P2Y₁, P2Y₂ P2Y₄, P2Y₆, P2Y₁₂, and P2Y₁₃ receptors in the anterior pituitary cells of rat were studied with double-labeling immunofluorescence and Western blot. The results showed that P2Y receptors were widely expressed in the anterior pituitary. P2Y₁ and P2Y₄ receptors were found to be expressed in the majority of gonadotrophs and thyrotrophs, P2Y₂ receptors were expressed in a small subpopulation of lactotrophs and almost all the folliculo-stellate cells, that were also stained with S100 protein immunoreactivity. P2Y₆ receptors were expressed in macrophages. P2Y₁₃ receptors were expressed in a small subpopulation of cells in the rat anterior pituitary, the identity of which needs to be clarified. P2Y₁ and P2Y₄ receptors are co-expressed in some gonadotrophs and thyrotrophs. Corticotrophs and somatotrophs were found not to express P2Y receptors in this study. FSH and TSH were shown to coexist in the same endocrine cells in rat anterior pituitary. The present data suggests that purines and/or pyrimidines could be involved in regulating the functions of gonadotrophs and thyrotrophs via P2Y₁ and P2Y₄ receptors, some lactotrophs via P2Y₂ receptors, and folliculo-stellate cells via P2Y₂ receptors in the rat anterior pituitary.     

Flower-specific expression of <Emphasis Type="Italic">Arabidopsis</Emphasis><Emphasis Type="Italic">PCS1</Emphasis> driven by <Emphasis Type="Italic">AGAMOUS</Emphasis> second intron in tobacco decreases the fertility of transgenic plants

The PROMOTION OF CELL SURVIVAL 1 (PCS1) gene, encoding an aspartic protease, has an important role in determining the fate of cells in embryonic development and reproduction processes in Arabidopsis. To explore the potential function of the PCS1 gene in generating reproductive sterility, we placed the PCS1 gene under the control of an 1,869-bp nucleotide sequence from the 3′ end of the second intron (AG-I) of Arabidopsis AGAMOUS and CaMV 35S (–60) minimal promoter [AG-I-35S (–60)::PCS1], and introduced it into tobacco. RT–PCR results demonstrated that the PCS1 gene driven by AG-I-35S (–60) chimeric promoter was expressed only in anthers and carpels in the reproductive tissues of transgenic tobacco. Compared to wild-type plants, all AG-I-35S (–60) and AG-I-35S (–60)::PCS1 transgenic lines showed a normal phenotype throughout the vegetative growth phase. However, during the reproductive stage, most AG-I-35S (–60)::PCS1 transgenic plant anthers displayed delayed dehiscence, failed dehiscence, petalody and hypoplasia, and the pollen grains had different shapes and sizes with a distorted, shrunken, or collapsed morphology. Moreover, three transgenic lines, PCS1-1, PCS1-3 and PCS1-4, showed higher sterility than wild-type and AG-I-35S (–60) transgenic plants, respectively. These results showed that the construct of AG-I-35S (–60)::PCS1 was partially effective at preventing seed set and provided a novel sterility strategy.     

杨树基因组AMT转运蛋白的生物信息学特性

本研究中,通过隐马尔科夫模型(HMM)和杨树蛋白质库搜索,共找到17个杨树铵转运体蛋白(PtAMTs).利用生物信息学方法,我们对杨树家族17条AMT蛋白序列的系统发生和AMT基因组定位进行分析,然后对其氨基酸组成成分、理化性质以及二级结构进行预测和分析,同时还分析了杨树与拟南芥、水稻、番茄、百脉根和欧洲油菜的AMT基因家族之间的联系.二级结构预测结果发现不同成员间氨基酸数目、氨基酸序列间的疏水性存在一定的差异;α-螺旋和无规则卷曲为主要二级结构组成部分.同源性比对分析表明,PtAMT基因家族主要分为2个亚家族,AMT1 (11个成员)和AMT2 (6个成员),基因结果分析表明AMT2亚家族成员不含内含子.杨树AMT蛋白的亚细胞定位分析表明PtAMT主要定位于膜结构上.电子表达图谱分析结果表明:只有XP_002309151和 XP_002334025基因有对应的EST序列,并有相应的电子表达谱,并主要在花蕾表达.     

棕色棉F3'H-羟化酶基因的克隆与生物信息学分析

根据葡萄的类黄酮3′-羟化酶(F3'H)基因全长cDNA序列Blast所得棉花的EST序列设计引物,以开花后16 d(DPA16)的新彩棉5号(xC-5)纤维为材料,利用RACE和RT-PCR技术分离得到了2个类黄酮3′-羟化酶基因cDNA序列,此2个序列编码区完全相同,仅在3'UTR区存在片段长短的差异,推测可能是基因转录后加工方式不同所造成.克隆所获得的棉花F3'H基因编码区全长1 533 bp,编码510个氨基酸,氨基酸序列分析预测表明,该基因所编码蛋白含有一个跨膜结构域,是一种分泌蛋白,定位于内质网上,并含有一段与细胞色素P450功能区相匹配的保守功能域;序列比对结果表明,棉花F3'H基因与其他多个物种的F3'H基因在氨基酸序列上有较高的同源性;聚类分析结果表明,棉花F3'H蛋白与双子叶植物大豆的F3'H亲缘关系较为接近,而与单子叶植物高梁等作物则较远.     

IKK�� downregulation is critical for triggering JNKs-dependent cell apoptotic response in the human hepatoma cells under arsenite exposure

Arsenite has a long history in treating leukemia, which might be also effective in the therapy of other cancers. Our previous published data have demonstrated that arsenite exposure induces apoptosis in the HepG2 human hepatoma cells via activating JNKs/AP-1 pathway, but the upstream signaling events responsible for JNKs (c-Jun N-terminal kinase) cascade activation have not been fully discovered. Since cross-talk between IKK/NF-κB and JNKs pathways under stress conditions is a hot topic, in this article, we investigate the potential roles of IKKα and IKKβ, the catalytic subunits of IKK complexes, in the arsenite-induced JNKs pathway activation in the HepG2 cells. We found that arsenite exposure induced JNKs and AP-1 activation accompanying with a significant reduction of both IKKα and IKKβ expressions. Overexpression of IKKβ, but not of IKKα, inhibited arsenite-induced MKK7/JNKs/AP-1 pathway activation as well as the apoptotic response. Therefore, we conclude that the downregulation of IKKβ expression is the prerequisite signaling event for mediating JNKs pathway activation and the cellular apoptotic response in the HepG2 cells under arsenite exposure. Targeting IKKβ might be helpful to enhance the tumor therapeutic effect of arsenite.