BACKGROUND & AIMS: :The regulatory locus sae is a two-component system in Staphylococcus aureus that regulates many important virulence factors, including alpha-toxin (encoded by hla) at the transcriptional level. The SarA homologs Rot and SarT were previously shown to be repressors of hla in selected S. aureus backgrounds. To delineate the interaction of rot and sae and the contribution of sarT to hla expression, an assortment of rot and sae isogenic single mutants, a rot sae double mutant, and a rot sae sarT markerless triple mutant were constructed from wild-type strain COL. Using Northern blot analysis and transcriptional reporter gene green fluorescent protein, fusion, and phenotypic assays, we found that the repression of hla by rot is dependent on sae. A rot sae sarT triple mutant was not able to rescue the hla defect of the rot sae double mutant. Among the three sae promoters, the distal sae P3 promoter is the strongest in vitro. Interestingly, the sae P3 promoter activities correlate with hla expression in rot, rot sae, and rot sae sarT mutants of COL. Transcriptional study has also shown that rot repressed sae, especially at the sae P3 promoter. Collectively, our data implicated the importance of sae in the rot-mediated repression of hla in S. aureus.

背景与目标： ：调控基因座sae是金黄色葡萄球菌的两部分系统，在转录水平上调控许多重要的毒力因子，包括α-毒素（由hla编码）。先前显示，SarA同系物Rot和SarT在选定的金黄色葡萄球菌背景中是hla的阻遏物。为了描述腐烂和sae的相互作用以及sarT对hla表达的贡献，从野生型菌株COL构建了腐烂和sae等基因单突变体，腐烂sae双突变体和腐烂sae sarT无标记三重突变体。使用Northern印迹分析和转录报告基因绿色荧光蛋白，融合和表型分析，我们发现腐烂对hla的抑制作用取决于sae。 rot sae sarT三突变体无法挽救rot sae double突变体的hla缺陷。在这三个sae启动子中，远端sae P3启动子在体外最强。有趣的是，SAE P3启动子活性与COL的rot，rot sae和rot sae sarT突变体中的hla表达相关。转录研究还显示腐烂抑制了sae，特别是在sae P3启动子处。总的来说，我们的数据暗示了sae在金黄色葡萄球菌的腐烂介导的hla抑制中的重要性。

BACKGROUND & AIMS: :Staphylococcus aureus subverts innate defenses during infection in part by killing host immune cells to exacerbate disease. This human pathogen intercepts host cues and activates a transcriptional response via the S. aureus exoprotein expression (SaeR/SaeS [SaeR/S]) two-component system to secrete virulence factors critical for pathogenesis. We recently showed that the transcriptional repressor CodY adjusts nuclease (nuc) gene expression via SaeR/S, but the mechanism remained unknown. Here, we identified two CodY binding motifs upstream of the sae P1 promoter, which suggested direct regulation by this global regulator. We show that CodY shares a binding site with the positive activator SaeR and that alleviating direct CodY repression at this site is sufficient to abrogate stochastic expression, suggesting that CodY represses sae expression by blocking SaeR binding. Epistasis experiments support a model that CodY also controls sae indirectly through Agr and Rot-mediated repression of the sae P1 promoter. We also demonstrate that CodY repression of sae restrains production of secreted cytotoxins that kill human neutrophils. We conclude that CodY plays a previously unrecognized role in controlling virulence gene expression via SaeR/S and suggest a mechanism by which CodY acts as a master regulator of pathogenesis by tying nutrient availability to virulence gene expression.IMPORTANCE Bacterial mechanisms that mediate the switch from a commensal to pathogenic lifestyle are among the biggest unanswered questions in infectious disease research. Since the expression of most virulence genes is often correlated with nutrient depletion, this implies that virulence is a response to the lack of nourishment in host tissues and that pathogens like S. aureus produce virulence factors in order to gain access to nutrients in the host. Here, we show that specific nutrient depletion signals appear to be funneled to the SaeR/S system through the global regulator CodY. Our findings reveal a strategy by which S. aureus delays the production of immune evasion and immune-cell-killing proteins until key nutrients are depleted.

背景与目标： 金黄色葡萄球菌在感染过程中破坏了先天防御，部分原因是杀死宿主免疫细胞使疾病恶化。该人类病原体拦截宿主线索，并通过金黄色葡萄球菌外蛋白表达（SaeR / SaeS [SaeR / S]）两组分系统激活转录反应，以分泌对发病机理至关重要的毒力因子。我们最近显示，转录抑制因子CodY通过SaeR / S调节核酸酶（nuc）基因表达，但机制仍不清楚。在这里，我们确定了sae P1启动子上游的两个CodY结合基序，提示该全局调控子直接调控。我们显示CodY与阳性激活剂SaeR共享一个结合位点，并且在该位点减轻直接CodY抑制作用足以消除随机表达，这表明CodY通过阻断SaeR结合来抑制sae表达。上位性实验支持CodY还通过Agr和Rot介导的sae P1启动子阻遏间接控制sae的模型。我们还证明CodY抑制sae抑制杀死人类嗜中性粒细胞的分泌性细胞毒素的产生。我们得出的结论是CodY在通过SaeR / S控制毒力基因表达中起着前所未有的作用，并提出了一种机制，通过该机制将CodY通过将营养素的利用与毒力基因的表达联系起来作为发病机理的主要调节剂。与致病的生活方式相称是传染病研究中最大的未解决问题之一。由于大多数毒力基因的表达通常与营养耗竭相关，因此这意味着毒力是对宿主组织中缺乏营养的一种反应，而金黄色葡萄球菌等病原体会产生毒力因子以获取宿主中的养分。在这里，我们表明特定的营养耗尽信号似乎通过全球监管机构CodY漏斗到SaeR / S系统中。我们的发现揭示了一种策略，通过该策略金黄色葡萄球菌可以延迟免疫逃逸和免疫细胞杀灭蛋白的产生，直到关键营养物质耗尽为止。

BACKGROUND & AIMS: :This paper describes an investigation of the complex internal regulatory circuitry of the staphylococcal sae locus and the impact of modifying this circuitry on the expression of external genes in the sae regulon. The sae locus contains four genes, the saeR and S two-component signalling module (TCS), and saeP and Q, two upstream genes of hitherto unknown function. It is expressed from two promoters, P(A)sae, which transcribes only the TCS, and P(C)sae, which transcribes the entire locus. A bursa aurealis (bursa) transposon insertion in saeP in a derivative of Staphylococcus aureus NCTC 8325 has a profound effect on sae function. It modifies the activity of the TCS, changing the expression of many genes in the sae regulon, even though transcription of the TCS (from P(A)sae) is not interrupted. Moreover, these effects are not due to disruption of saeP since an in-frame deletion in saeP has essentially no phenotype. The phenotype of S. aureus strain Newman is remarkably similar to that of the saeP : : bursa and this similarity is explained by an amino acid substitution in the Newman saeS gene that is predicted to modify profoundly the signalling function of the protein. This concurrence suggests that the saeP : : bursa insertion affects the signalling function of saeS, a suggestion that is supported by the ability of an saeQR clone, but not an saeR clone, to complement the effects of the saeP : : bursa insertion.

背景与目标： ：本文描述了葡萄球菌sae基因座的复杂内部调控电路的研究，以及修改此电路对sae regulon中外部基因表达的影响。 sae基因座包含四个基因，即saeR和S两组分信号传导模块（TCS），以及saeP和Q，这是迄今未知功能的两个上游基因。它由两个启动子表达，即仅转录TCS的P（A）sae和转录整个基因座的P（C）sae。在金黄色葡萄球菌NCTC 8325衍生物中的saeP中插入金黄色囊（bursa）转座子对sae功能有深远的影响。它改变了TCS的活性，改变了sae regulon中许多基因的表达，即使TCS的转录（来自P（A）sae）也没有中断。此外，这些作用不是由于saeP的破坏所致，因为saeP的读框内缺失基本上没有表型。金黄色葡萄球菌Newman的表型与saeP :: Burs的表型非常相似，这种相似性可以通过Newman saeS基因中的氨基酸取代来解释，该氨基酸取代预计会显着改变蛋白的信号传导功能。这种一致表明saeP :: bursa插入会影响saeS的信号传导功能，这一建议得到saeQR克隆（而不是saeR克隆）补充saeP :: bursa插入效果的支持。

BACKGROUND & AIMS: :Global regulatory locus sae consists of a two-component signal transduction system coded by saeR and saeS genes that upregulates the transcription of several exoproteins. Northern analysis carried out in this study reveals the synthesis at late and post-exponential phases of a cotranscript of saeR and saeS structural genes of about 2.4 kb. This transcript is diminished in the isogenic agr:: tetM mutant. Likewise, transcriptional fusion experiments show that sae expression is downregulated in the agr null mutant. Complementation analyses with plasmids carrying fragments of about 1.2 or 0.2 kbp upstream of saeR-saeS genes, which restore fully or only partially, respectively, the wild-type phenotype to the sae mutant, are in agreement with two initiation start points of transcription revealed by primer extension experiments. This work, as well as previous studies, reveals a complex hierarchical regulatory network involving several loci that control the expression of virulence determinants in S. aureus.

背景与目标： ：全球调节基因座sae由由saeR和saeS基因编码的两组分信号转导系统组成，该系统上调了几种外蛋白的转录。在这项研究中进行的Northern分析揭示了在晚期和指数后阶段​​合成约2.4 kb的saeR和saeS结构基因的共转录本。该转录本在等基因agr :: tetM突变体中减少。同样，转录融合实验表明在agr null突变体中sae表达被下调。用携带saeR-saeS基因上游约1.2或0.2 kbp片段的质粒进行的互补分析，分别将野生型表型分别完全或部分还原为sae突变体，这与两个揭示的转录起始点一致。引物延伸实验。这项工作以及以前的研究揭示了一个复杂的分级监管网络，其中涉及几个控制金黄色葡萄球菌毒力决定簇表达的基因座。

BACKGROUND & AIMS: INTRODUCTION:Myositis specific autoantibodies (MSAs) are useful in the diagnosis of idiopathic inflammatory myopathies and in the definition of disease subsets. The aim of this study was to set up an unlabelled protein immunoprecipitation technique for MSA identification in the sera of myositis patients, in order to identify and investigate new antibody reactivity, undetectable by currently used methods. METHODS:Sera of 183 patients with connective tissue diseases (75 adult dermatomyositis, 12 juvenile dermatomyositis, 43 polymyositis, 53 other connective tissue diseases) and 30 healthy controls were screened by an in-house procedure of unlabelled protein immunoprecipitation. In the same sera MSAs and myositis associated antibodies were determined by immunoblotting and immunoprecipitation for RNA. RESULTS:The analytical specificity of unlabelled protein immunoprecipitation was demonstrated by testing reference sera with known antibody reactivity. Sera from five patients, affected with dermatomyositis (5/75=7%), immunoprecipitated two proteins of 40 and 90 kDa apparent molecular weights respectively, consistent with the subunits of the small ubiquitin like modifier activating enzyme heterodimer (SAE1/SAE2). The identity of putative SAE immunoprecipitated proteins was confirmed by immunoblotting on immunoprecipitates using commercial monospecific antibodies to SAE1 and SAE2. Major clinical features were compared between anti-SAE positive and negative patients. Interestingly, anti-SAE positive patients had mainly skin and muscle manifestations while dysphagia, interstitial lung disease, arthritis and constitutional symptoms were absent. CONCLUSIONS:Unlabelled protein immunoprecipitation is a specific analytical approach, appropriate for the identification of the recently described anti-SAE autoantibody. We confirmed the role of anti-SAE antibody as marker of dermatomyositis.

背景与目标： 简介：肌炎特异性自身抗体（MSA）可用于诊断特发性炎症性肌病和定义疾病亚型。这项研究的目的是建立一种未标记的蛋白质免疫沉淀技术，用于肌炎患者血清中MSA的鉴定，以鉴定和研究新抗体的反应性，这是当前使用的方法无法检测到的。
方法：采用内部未标记蛋白免疫沉淀方法筛选了183例结缔组织疾病患者（75例成人皮肌炎，12例青少年皮肌炎，43例多发性肌炎，53例其他结缔组织疾病）和30例健康对照者的血清。在同一血清中，通过免疫印迹和RNA免疫沉淀测定了MSA和肌炎相关抗体。
结果：通过检测具有已知抗体反应性的参考血清，证明了未标记蛋白质免疫沉淀的分析特异性。来自五名患有皮肌炎（5/75 = 7％）的患者的血清分别免疫沉淀了40和90 kDa表观分子量的两种蛋白质，这与小泛素样修饰因子激活酶异二聚体（SAE1 / SAE2）的亚基一致。通过使用针对SAE1和SAE2的商业单特异性抗体对免疫沉淀物进行免疫印迹来确认推定的SAE免疫沉淀蛋白的身份。比较了抗SAE阳性和阴性患者的主要临床特征。有趣的是，抗SAE阳性的患者主要表现为皮肤和肌肉表现，而吞咽困难，间质性肺病，关节炎和体质症状却不存在。
结论：未标记的蛋白质免疫沉淀是一种特定的分析方法，适用于鉴定最近描述的抗SAE自身抗体。我们证实了抗SAE抗体作为皮肌炎的标志物的作用。

BACKGROUND & AIMS: :The cytotoxic alpha-toxin (encoded by hla) of Staphylococcus aureus is regulated by three loci, agr, sarA and sae, in vitro. Here, we assess the regulation of hla in a guinea pig model of device-related infection by quantifying RNAIII (the effector molecule of agr) and hla directly in exudates accumulating in infected devices without subculturing of the bacteria. LightCycler reverse transcription-polymerase chain reaction (RT-PCR) was used to quantify the transcripts. Strains RN6390 and Newman expressed considerably smaller amounts of RNAIII in the guinea pig than during in vitro growth. The residual RNAIII expression decreased during the course of infection and was negatively correlated with bacterial densities. As with RNAIII, the highest hla expression was detected in both strains early in infection. Even in strain Newman, a weak hla producer in vitro, a pronounced expression of hla was observed during infection. Likewise, four S. aureus isolates from cystic fibrosis (CF) patients expressed Q1hla despite an inactive agr during device-related infection as in the CF lung. Mutation of agr and sarA in strain Newman and RN6390 had no consequence for hla expression in vivo. In contrast, the mutation in sae resulted in severe downregulation of hla in vitro as well as in vivo. In conclusion, S. aureus seems to be provided with regulatory circuits different from those characterized in vitro to ensure alpha-toxin synthesis during infections.

背景与目标： 金黄色葡萄球菌的细胞毒性α-毒素（由hla编码）在体外受三个基因座agr，sarA和sae的调节。在这里，我们通过定量RNAIII（agr的效应分子）和直接在被感染设备中积聚的渗出物中的hla来评估设备相关感染的豚鼠模型中hla的调节，而无需对细菌进行传代培养。使用LightCycler逆转录-聚合酶链反应（RT-PCR）定量转录本。与体外生长期间相比，RN6390和Newman菌株在豚鼠中表达的RNAIII量要少得多。 RNAIII的残留表达在感染过程中降低，并且与细菌密度呈负相关。与RNAIII一样，在感染早期，两种菌株均检测到最高的hla表达。即使在体外弱于HLA产生者的纽曼菌株中，在感染过程中也观察到了Hla的明显表达。同样，尽管在设备相关的感染过程中，如在CF肺部感染时agr不活跃，但来自囊性纤维化（CF）患者的4株金黄色葡萄球菌分离物仍表达Q1hla。 Newman和RN6390菌株中agr和sarA的突变对体内hla表达没有影响。相反，sae的突变导致体内外hla严重下调。总之，金黄色葡萄球菌似乎具有不同于体外表征的调节回路，以确保感染期间α-毒素的合成。

BACKGROUND & AIMS: :Currently, sedation in endoscopic procedures is considered a necessary condition and a criterion of quality in digestive endoscopy. The role of SAE in conventional endoscopic procedures is clearly established in clinical guidelines, but this is not so clear in complex endoscopic procedures, such as ERCP. In recent years, numerous studies have been published, with results similar to those noticed in this article, endorsing the safety, efficacy and efficiency of SAE, when performed by properly trained staff.

背景与目标： 目前，内窥镜手术中的镇静被认为是消化内窥镜检查的必要条件和质量标准。 SAE在常规内窥镜手术中的作用已在临床指南中明确确立，但在复杂的内窥镜手术（例如ERCP）中尚不清楚。近年来，已经发表了无数研究，其结果与本文中提到的结果相似，认可了由经过适当培训的人员进行的SAE的安全性，有效性和效率。

BACKGROUND & AIMS: :Our previous studies showed that both Sae and Fur are required for the induction of eap and emp expression in low iron. In this study, we show that expression of sae is also iron-regulated, as sae expression is activated by Fur in low iron. We also demonstrate that both Fur and Sae are required for full induction of the oxidative stress response and expression of non-covalently bound surface proteins in low-iron growth conditions. In addition, Sae is required for the induced expression of the important virulence factors isdA and isdB in low iron. Our studies also indicate that Fur is required for the induced expression of the global regulators Agr and Rot in low iron and a number of extracellular virulence factors such as the haemolysins which are also Sae- and Agr-regulated. Hence, we show that Fur is central to a complex regulatory network that is required for the induced expression of a number of important S. aureus virulence determinants in low iron.

背景与目标： ：我们以前的研究表明，Sae和Fur都需要在低铁条件下诱导eap和emp表达。在这项研究中，我们显示sae的表达也是铁调节的，因为sae的表达被低铁中的Fur激活。我们还证明，在低铁生长条件下，完全诱导氧化应激反应和表达非共价结合的表面蛋白都需要Fur和Sae。另外，在低铁条件下，重要的毒力因子isdA和isdB的诱导表达需要Sae。我们的研究还表明，在低铁和许多细胞外毒力因子（如溶血素（也受Sae和Agr调节））的诱导表达中，Fur是诱导整体调节剂Agr和Rot表达所必需的。因此，我们表明，对于低铁中许多重要的金黄色葡萄球菌毒力决定因子的诱导表达，复杂的调控网络至关重要。

BACKGROUND & AIMS: :We characterized the sae operon, a global regulator for virulence gene expression in Staphylococcus aureus. A Tn917 sae mutant was obtained by screening a Tn917 library of the agr mutant ISP479Mu for clones with altered hemolytic activity. Sequence analysis of the sae operon revealed two additional open reading frames (ORFs) (ORF3 and ORF4) upstream of the two-component regulatory genes saeR and saeS. Four overlapping sae-specific transcripts (T1 to T4) were detected by Northern blot analysis, and the transcriptional initiation points were mapped by primer extension analysis. The T1, T2, and T3 mRNAs are probably terminated at the same stem-loop sequence downstream of saeS. The T1 message (3.1 kb) initiates upstream of ORF4, T2 (2.4 kb) initiates upstream of ORF3, and T3 (2.0 kb) initiates in front of saeR. T4 (0.7 kb) represents a monocistronic mRNA encompassing ORF4 only. sae-specific transcripts were detectable in all of the 40 different clinical S. aureus isolates investigated. Transcript levels were at maximum during the post-exponential growth phase. The sae mutant showed a significantly reduced rate of invasion of human endothelial cells, consistent with diminished transcription and expression of fnbA. The expression of type 5 capsular polysaccharide is activated in the sae mutant of strain Newman, as shown by immunofluorescence and promoter-reporter fusion experiments. In summary, the sae operon constitutes a four-component regulator system which acts on virulence gene expression in S. aureus.

背景与目标： ：我们表征了sae operon，它是金黄色葡萄球菌中毒力基因表达的全球调节物。通过筛选agr突变体ISP479Mu的Tn917文库中具有改变的溶血活性的克隆来获得Tn917 sae突变体。 sae操纵子的序列分析揭示了两个成分的调控基因saeR和saeS上游的两个额外的开放阅读框（ORF）（ORF3和ORF4）。通过Northern印迹分析检测到四个重叠的sae特异性转录物（T1至T4），并且通过引物延伸分析来绘制转录起始点。 T1，T2和T3 mRNA可能在saeS下游的相同茎环序列处终止。 T1消息（3.1 kb）在ORF4的上游启动，T2（2.4 kb）在ORF3的上游启动，而T3（2.0 kb）在saeR前面启动。 T4（0.7 kb）代表仅包含ORF4的单顺反子mRNA。在所研究的40种不同临床金黄色葡萄球菌分离株中，均可检测到sae特异的转录本。在指数后的生长阶段，转录物水平最高。 sae突变体显示出人类内皮细胞的侵袭率显着降低，这与fnbA转录和表达的减少相一致。如免疫荧光和启动子-报告子融合实验所示，在纽曼菌株的sae突变体中激活了5型荚膜多糖的表达。总之，sae操纵子构成了一个四组分调节系统，该系统作用于金黄色葡萄球菌中的毒力基因表达。

BACKGROUND & AIMS: :Agr and sar are known regulatory loci of Staphylococcus aureus that control the production of several extracellular and cell-wall-associated proteins. A pleiotropic insertional mutation in S. aureus, designated sae, that leads to the production of drastically diminished levels of alpha- and beta-hemolysins and coagulase and slightly reduced levels of protein A has been described. The study of the expression of the genes coding for these exoproteins in the sae::Tn551 mutant (carried out in this work by Northern blot analyses) revealed that the genes for alpha- and beta-hemolysins (hla and hlb) and coagulase (coa) are not transcribed and that the gene for protein A (spa) is transcribed at a somewhat reduced level. These results indicate that the sae locus regulates these exoprotein genes at the transcriptional level. Northern blot analyses also show that the sae mutation does not affect the expression of agr or sar regulatory loci. An sae::Tn551 agr::tetM double mutant has been phenotypically characterized as producing reduced or null levels of alpha-, beta-, and delta-hemolysins, coagulase, and high levels of protein A. Northern blot analyses carried out in this work with the double mutant revealed that hla, hlb, hld, and coa genes are not transcribed, while spa is transcribed at high levels. The fact that coa is not expressed in the sae agr mutant, as in the sae parental strain, while spa is expressed at the high levels characteristic of the agr parental strain, suggests that sae and agr interact in a complex way in the control of the expression of the genes of several exoproteins.

背景与目标： ：Agr和sar是金黄色葡萄球菌的已知调节基因座，它控制几种细胞外和细胞壁相关蛋白的产生。已经描述了在金黄色葡萄球菌中的多效性插入突变，命名为sae，其导致α-和β-溶血素和凝固酶的水平急剧降低的产生以及蛋白A的水平略有降低。对sae :: Tn551突变体中编码这些外蛋白的基因表达的研究（通过Northern blot分析在这项工作中进行）显示，α-和β-溶血素（hla和hlb）和凝固酶（coa）的基因）不会被转录，并且蛋白A（spa）的基因会以某种程度的降低的水平被转录。这些结果表明，sae基因座在转录水平上调节这些外蛋白基因。 Northern印迹分析还显示，sae突变不影响agr或​​sar调控基因座的表达。一个sae :: Tn551 agr :: tetM双突变体在表型上被表征为产生降低的或无效的α-，β-和δ-溶血素，凝固酶和高水平的蛋白A。在这项工作中进行了Northern印迹分析带有双突变体的基因表明，hla，hlb，hld和coa基因不会被转录，而spa会被高水平转录。 coa在sae agr突变体中不表达，如在sae亲本菌株中表达，而spa在agr亲本菌株的高水平特征中表达，这一事实表明sae和agr在复杂的控制中相互作用。几种外蛋白基因的表达

BACKGROUND & AIMS: :In the case of an unexpected high frequency of serious adverse events (SAE), statistical methods are needed to help in the decision making process as to continuation of accrual to the trial. This paper describes an R package, named SAE that implements a method recently developed by defining stopping rules after each observed SAE. The package function control for excessive toxicity either during the trial at the observation of each SAE (function SAE) or during the planning phase of a clinical trial (function DESIGN). This description and the package documentation are complementary to help the users to apply the method. The main difficulty in the implementation of the method is the choice of a priori parameters. Data from an ongoing clinical trial are presented as an example to improve the understanding and the use of the package.

背景与目标： ：如果发生严重不良事件（SAE）的频率异常高，则需要统计方法来帮助决策过程，以继续进行试验。本文介绍了一个名为SAE的R包，该R包实现了一种新近开发的方法，该方法通过在每个观察到的SAE之后定义停止规则来实现。包装功能控制在观察每个SAE的试验期间（功能SAE）或在临床试验的规划阶段（功能设计）的过度毒性。此描述和软件包文档是互补的，以帮助用户应用该方法。该方法实施的主要困难是先验参数的选择。以正在进行的临床试验中的数据为例，以提高对包装的理解和使用。

BACKGROUND & AIMS: :Sepsis associated encephalopathy (SAE) is a poorly understood condition that is associated with severe sepsis and appears to have a negative influence on survival. The incidence of encephalopathy secondary to sepsis is unknown. Amino acid derangements, blood-brain barrier disruption, abnormal neurotransmitters, and direct CNS effect are possible causes of septic encephalopathy. Research has not defined the pathogenesis of SAE.

背景与目标： 败血症相关性脑病（SAE）是一种鲜为人知的疾病，与严重的败血症有关，并且似乎对生存产生负面影响。败血症继发性脑病的发病率未知。氨基酸紊乱，血脑屏障破坏，异常神经递质和直接的中枢神经系统作用可能是败血性脑病的原因。研究尚未定义SAE的发病机理。

BACKGROUND & AIMS: :The two-component system SaeRS of Staphylococcus aureus is closely involved in the regulation of major virulence factors. However, little is known about the signals leading to saeRS activation. A total of four overlapping transcripts (T1 to T4) from three different transcription starting points are expressed in the sae operon. We used a beta-galactosidase reporter assay to characterize the putative promoter regions within the saeRS upstream region. The main transcript T2 is probably generated by endoribonucleolytic processing of the T1 transcript. Only two distinct promoter elements (P1 and P3) could be detected within the saeRS upstream region. The P3 promoter, upstream of saeRS, generates the T3 transcript, includes a cis-acting enhancer element and is repressed by saeRS. The most distal P1 promoter is strongly autoregulated, activated by agr, and repressed by sigma factor B. In strain Newman a mutation within the histidine kinase SaeS leads to a constitutively activated sae system. Evaluation of different external signals revealed that the P1 promoter in strain ISP479R and strain UAMS-1 is inhibited by low pH and high NaCl concentrations but activated by hydrogen peroxide. The most prominent induction of P1 was observed at subinhibitory concentrations of alpha-defensins in various S. aureus strains, with the exception of strain ISP479R and strain COL. P1 was not activated by the antimicrobial peptides LL37 and daptomycin. In summary, the results indicate that the sensor molecule SaeS is activated by alteration within the membrane allowing the pathogen to react to phagocytosis related effector molecules.

背景与目标： 金黄色葡萄球菌的两组分系统SaeRS与主要毒力因子的调节密切相关。但是，对于导致saeRS激活的信号知之甚少。来自三个不同转录起点的总共四个重叠转录物（T1至T4）在sae操纵子中表达。我们使用了β-半乳糖苷酶报告基因分析来表征saeRS上游区域内推定的启动子区域。主要成绩单T2可能是由T1成绩单的核糖核酸内切加工产生的。在saeRS上游区域内只能检测到两个不同的启动子元件（P1和P3）。在saeRS上游的P3启动子产生T3转录本，包括一个顺式作用增强子元件，并被saeRS抑制。最远端的P1启动子被强烈自动调节，被agr激活，并被sigma因子B抑制。在纽曼菌株中，组氨酸激酶SaeS内的突变导致组成性激活的sae系统。对不同外部信号的评估表明，菌株ISP479R和UAMS-1中的P1启动子受到低pH和高NaCl浓度的抑制，但被过氧化氢激活。在除金黄色葡萄球菌菌株中亚抑菌素浓度亚抑制浓度下观察到最明显的P1诱导，除了菌株ISP479R和菌株COL。 P1没有被抗菌肽LL37和达托霉素激活。总而言之，结果表明传感器分子SaeS通过膜内的改变被激活，从而使病原体对吞噬作用相关的效应子分子起反应。

BACKGROUND & AIMS: :Small ubiquitin-like modifier (SUMO) family proteins regulate target-protein functions by post-translational modification. However, a potent and selective inhibitor targeting the SUMO pathway has been lacking. Here we describe ML-792, a mechanism-based SUMO-activating enzyme (SAE) inhibitor with nanomolar potency in cellular assays. ML-792 selectively blocks SAE enzyme activity and total SUMOylation, thus decreasing cancer cell proliferation. Moreover, we found that induction of the MYC oncogene increased the ML-792-mediated viability effect in cancer cells, thus indicating a potential application of SAE inhibitors in treating MYC-amplified tumors. Using ML-792, we further explored the critical roles of SUMOylation in mitotic progression and chromosome segregation. Furthermore, expression of an SAE catalytic-subunit (UBA2) S95N M97T mutant rescued SUMOylation loss and the mitotic defect induced by ML-792, thus confirming the selectivity of ML-792. As a potent and selective SAE inhibitor, ML-792 provides rapid loss of endogenously SUMOylated proteins, thereby facilitating novel insights into SUMO biology.

背景与目标： ：小泛素样修饰子（SUMO）家族蛋白通过翻译后修饰来调节靶蛋白的功能。然而，一直缺乏靶向SUMO途径的有效和选择性抑制剂。在这里，我们描述ML-792，这是一种基于机制的SUMO活化酶（SAE）抑制剂，在细胞测定中具有纳摩尔浓度。 ML-792有选择地阻断SAE酶的活性和总SUMOylation，从而减少癌细胞的增殖。此外，我们发现MYC癌基因的诱导增加了癌细胞中ML-792介导的生存能力，从而表明SAE抑制剂在治疗MYC扩增的肿瘤中的潜在应用。使用ML-792，我们进一步探索了SUMOylation在有丝分裂进程和染色体分离中的关键作用。此外，SAE催化亚基（UBA2）S95N M97T突变体的表达挽救了SUMOylation损失和ML-792诱导的有丝分裂缺陷，从而证实了ML-792的选择性。作为一种有效且选择性的SAE抑制剂，ML-792可快速损失内源性SUMO酰化的蛋白质，从而促进对SUMO生物学的新见解。

BACKGROUND & AIMS: BACKGROUND:Protein remote homology detection and fold recognition are central problems in computational biology. Supervised learning algorithms based on support vector machines are currently one of the most effective methods for solving these problems. These methods are primarily used to solve binary classification problems and they have not been extensively used to solve the more general multiclass remote homology prediction and fold recognition problems. RESULTS:We present a comprehensive evaluation of a number of methods for building SVM-based multiclass classification schemes in the context of the SCOP protein classification. These methods include schemes that directly build an SVM-based multiclass model, schemes that employ a second-level learning approach to combine the predictions generated by a set of binary SVM-based classifiers, and schemes that build and combine binary classifiers for various levels of the SCOP hierarchy beyond those defining the target classes. CONCLUSION:Analyzing the performance achieved by the different approaches on four different datasets we show that most of the proposed multiclass SVM-based classification approaches are quite effective in solving the remote homology prediction and fold recognition problems and that the schemes that use predictions from binary models constructed for ancestral categories within the SCOP hierarchy tend to not only lead to lower error rates but also reduce the number of errors in which a superfamily is assigned to an entirely different fold and a fold is predicted as being from a different SCOP class. Our results also show that the limited size of the training data makes it hard to learn complex second-level models, and that models of moderate complexity lead to consistently better results.

背景与目标： 背景：蛋白质远程同源性检测和折叠识别是计算生物学中的核心问题。目前，基于支持向量机的监督学习算法是解决这些问题的最有效方法之一。这些方法主要用于解决二进制分类问题，尚未广泛用于解决更一般的多类远程同源性预测和折叠识别问题。
结果：我们目前对在SCOP蛋白质分类的背景下建立基于SVM的多类别分类方案的许多方法进行了全面评估。这些方法包括直接构建基于SVM的多类模型的方案，采用第二级学习方法来组合由一组基于二进制SVM的分类器生成的预测的方案以及为各个级别的SVM构建和组合二进制分类器的方案。 SCOP层次结构超出了定义目标类的层次结构。
结论：分析不同方法在四个不同数据集上获得的性能，我们发现大多数提议的基于多类SVM的分类方法在解决远程同源性预测和折叠识别问题方面非常有效，并且使用来自二进制模型的预测的方案为SCOP层次结构内的祖先类别构建的结构不仅会导致较低的错误率，而且还会减少将超家族分配给完全不同的折叠并预测来自不同SCOP类的折叠的错误数量。我们的结果还表明，训练数据的数量有限，很难学习复杂的第二级模型，而中等复杂性的模型则可以始终如一地获得更好的结果。