Genome Sequence of Staphylococcus capitis QN1, Which Causes Infective Endocarditis

Staphylococcus capitis is a subtype of coagulase-negative staphylococci (CoNS) which could emerge as a significant pathogen causing infective endocarditis, prosthetic valve endocarditis, and late-onset sepsis. We isolated S. capitis strain QN1 from the skin swab sample of a female. Here we prepared a genome sequence for this strain consisting of 30 contigs totaling 2,430,101 bases and a GC content of 32.76%.     

2016年动物胃肠道微生物组研究十大亮点成果

动物胃肠道微生物对生产性能提高具有重要的作用,因此营养、微生物组与生产表型的互作研究已经成为国际研究热点。综述了2016年动物胃肠道微生物组学研究取得的十项重要成果,这些成果通过组学方法,研究了瘤胃纤维分解菌和尿素分解菌的功能基因多样性,揭示了微生物群落与日粮营养素、宿主基因型、环境的互作关系,阐明了反刍动物生产表型相关的瘤胃微生物种类和功能;首次构建猪肠道微生物组参考基因集,解析猪全肠道黏膜微生物组成,阐明了猪增重相关肠道微生物种类。这十大亮点成果将为国内动物营养学家开展动物胃肠道微生物组学研究提供参考。     

A systems-biology analysis of feedback inhibition in the Sho1 osmotic-stress-response pathway

BACKGROUND: A common property of signal transduction systems is that they rapidly lose their ability to respond to a given stimulus. For instance in yeast, the mitogen-activated protein (MAP) kinase Hog1 is activated and inactivated within minutes, even when the osmotic-stress stimulus is sustained. RESULTS: Here, we used a combination of experimental and computational analyses to investigate the dynamic behavior of Hog1 activation in vivo. Computational modeling suggested that a negative-feedback loop operates early in the pathway and leads to rapid attenuation of Hog1 signaling. Experimental analysis revealed that the membrane-bound osmosensor Sho1 is phosphorylated by Hog1 and that phosphorylation occurs on Ser-166. Moreover, Sho1 exists in a homo-oligomeric complex, and phosphorylation by Hog1 promotes a transition from the oligomeric to monomeric state. A phosphorylation-site mutation (Sho1(S166E)) diminishes the formation of Sho1-oligomers, dampens activation of the Hog1 kinase, and impairs growth in high-salt or sorbitol conditions. CONCLUSIONS: These findings reveal a novel phosphorylation-dependent feedback loop leading to diminished cellular responses to an osmotic-stress stimulus.     

高通量测序技术及其在微生物学研究中的应用

20世纪70年代发明的核酸测序技术为基因组学及其相关学科的发展做出了巨大贡献,本世纪初发展的以Illumina公司的HiSeq 2000,ABI公司的SOLID,和Roche公司的454技术为代表的高通量测序技术又为基因组学的发展注入了新活力.本文在阐述这些技术的基础上,着重讨论了新一代测序技术在微生物领域中的应用.     

Rab39, a novel Golgi-associated Rab GTPase from human dendritic cells involved in cellular endocytosis

Rab GTPases are Ras-like small molecular weight GTP binding proteins that are involved in various steps along the exocytic and endocytic pathways. Here we report that Rab39, a novel Rab protein, is a Golgi-associated protein involved in endocytosis of HeLa cells. Full-length cDNA of Rab39 contains 1251bp with an open reading frame (ORF) of 636bp, which is predicted to encode a 211 aa protein. By blast analysis of Rab39 cDNA and protein sequence with homologues, we find that Rab39 may be a short variant of Rab34. Rab39 contains conserved motifs involved in phosphate/guanosine binding and a microbody C-terminal targeting signal. RT-PCR analysis indicates that Rab39 is mainly detected in epithelial cell lines, and Northern blot analysis shows that Rab39 is expressed ubiquitously in human tissues. By using FITC-BSA as an endocytic tracer, we show that Rab39 can facilitate endocytosis in HeLa cells when expressed either transiently or stably. Confocal microscopy examination of Rab39 subcellular localization suggests that Rab39 is associated with Golgi-associated organelles. Our findings demonstrate that Rab39 is a novel Rab GTPase involved in cellular endocytosis.     

Identification of new human cadherin genes using a combination of protein motif search and gene finding methods

We have combined protein motif search and gene finding methods to identify genes encoding proteins containing specific domains. Particularly, we have focused on finding new human genes of the cadherin superfamily proteins, which represent a major group of cell-cell adhesion receptors contributing to embryonic neuronal morphogenesis. Models for three cadherin protein motifs were generated from over 100 already annotated cadherin domains and used to search the complete translated human genome. The genomic sequence regions containing motif "hits" were analyzed by eukaryotic GeneMark.hmm to identify the exon-intron structure of new genes. Three new genes CDH-J, PCDH-J and FAT-J were found. The predicted proteins PCDH-J and FAT-J were classified into protocadherin and FAT-like subfamilies, respectively, based on the number and organization of cadherin domains and presence of subfamily-specific conserved amino acid residues. Expression of FAT-J was shown in almost all tested tissues. The exon-intron organization of CDH-J was experimentally verified by PCR with specifically designed primers and its tissue-specific expression was demonstrated. The described methodology can be applied to discover new genes encoding proteins from families with well-characterized structural and functional domains.     

RNA干扰抑制肾小管上皮细胞TSP1表达和TGF-β1活化

血小板反应蛋白1(TSP1)是转化生长因子-β1(TGF-β1)体内重要的活化因子,而后者又是致肾小管间质纤维化的关键因素。观察了针对TSP1的小双链干扰RNA(siRNA-TSP1),抑制由血管紧张素II(AngII)诱导的肾小管上皮细胞TGF-β1过度活化。将根据人TSP1基因序列设计的特异siRNA-TSP1转染人肾小管上皮细胞系(HK-2),利用Western印迹、RT-PCR、流式细胞仪及ELISA等方法,检测了TSP1、TGF-β1及其信号蛋白Smad2与p-Smad2、纤维连接蛋白(FN)和纤溶酶原激活剂抑制物-1(PAI-1)的基因转录水平、蛋白质表达或蛋白质活性。结果显示,siRNA-TSP1能有效转染HK-2细胞,并以剂量依赖方式显著抑制TSP1的基因转录与合成;其对TGF-β1的合成影响较小,但能明显抑制TGF-β1的活化。此外siRNA-TSP1可阻抑TGF-β1依赖的Smad2磷酸化,减少细胞外基质FN以及PAI-1的合成。研究结果提示,由于TSP1是TGF-β1重要的内源性活化因子,故针对TSP1的RNA干扰能在体外有效抑制TSP1表达并相应调抑了TGF-β1的活化。     

鳄蜥对熟悉和陌生个体气味的辨别

个体辨别对于减少同种争斗以及配偶选择具有重要意义。我们用棉棒粘取鳄蜥(Shinisaurus crocodilurus)尿液作为气味源,以香水作为对照,测定鳄蜥对熟悉个体气味、陌生个体气味以及香水的舔舌次数和舔舌潜伏期,来探讨鳄蜥通过化学信息辨别熟悉和陌生个体的能力。结果显示,不论是雌性还是雄性,对不同个体尿液的舔舌次数均显著高于对香水的,舔舌潜伏期显著短于香水的;尽管雄性对陌生同性个体气味与熟悉同性个体气味的舔舌次数无显著差异,但对前者的舔舌潜伏期显著短于后者;雄性对陌生雌性气味的舔舌次数显著多于熟悉雌性气味的,对前者的舔舌潜伏期显著短于后者;雌性对陌生雄性气味的舔舌潜伏期显著短于对熟悉雄性气味的;雄鳄蜥对陌生雌性气味的舔舌次数显著多于雌鳄蜥对陌生雄性的。结果表明,鳄蜥能辨别同种个体的化学信息,并能通过化学信息来辨别熟悉和陌生个体,推测鳄蜥的这种辨别能力对其领域分配以及繁殖交配有重要作用。