Next-generation sequencing to generate interactome datasets

Next-generation sequencing has not been applied to protein-protein interactome network mapping so far because the association between the members of each interacting pair would not be maintained in en masse sequencing. We describe a massively parallel interactome-mapping pipeline, Stitch-seq, that combines PCR stitching with next-generation sequencing and used it to generate a new human interactome dataset. Stitch-seq is applicable to various interaction assays and should help expand interactome network mapping.     

TLR4 signaling-induced heme oxygenase upregulation in the acute lung injury: role in hemorrhagic shock and two-hit induced lung inflammation

Resuscitated hemorrhagic shock is believed to promote the development of acute lung injury (ALI) by priming the immune system for an exaggerated inflammatory response to a second trivial stimulus. This work explored effects of TLR4 on hemorrhage-induced ALI and “second-hit” responses, and further explore the mechanisms involved in “second-hit” responses. Expression of HO-1, IL-10, lung W/D and MPO markedly increased at nearly all time-points examined in HSR/LPS group as compared with sham/LPS group in WT mice. In HSR/LPS mice, the induced amount of IL-10 and the expressions of HO-1 of WT mice were significantly higher compared with TLR-4d/d. This study provides in vivo evidence that pulmonary infections after LPS instillation contribute to local tissue release of pro-inflammatory mediators after HSR systemic. Activation of TLR4 might induce HO-1 expression and HO-1 modulates proinflammatory responses that are triggered via TLR4 signaling.     

酱香型白酒酿造酒醅中酵母菌多样性研究

为解析酱香型白酒酿造酒醅中酵母菌的菌群结构,获取酒醅中的主要酵母菌,采用高通量测序法分析酱香型白酒酒醅中酵母菌多样性及主要功能菌群,同时采用可培养分离方法获取酒醅中酵母菌活性菌株。从酱香型白酒下沙至五轮次酒醅中共检出59个属、129个种的酵母菌,分离得到酵母菌活性菌株41种,检测到的酵母菌种类与获得的酵母菌活菌在各香型白酒中最多。不同时期酒醅中的酵母菌种类和数量差异明显,其中下沙、造沙轮次以Pichia kudriavzevii为绝对优势酵母菌;一至五轮次随着轮次的递增,酒醅中优势酵母菌的种类增多,其中主要的优势酵母菌有Pichia kudriavzevii、Pichia manshurica、Zygosaccharomyces bailii、Saccharomyces cerevisiae、Candida apicola。酱香型白酒酒醅中蕴藏着极其丰富的酵母菌资源,对酵母菌菌群结构的解析有助于科学地认识酱香型白酒酿造过程中产酒与风味代谢机理,为发酵过程的调控提供一定依据。     

凡纳滨对虾肠道红杆菌科细菌富集碳源筛选及其定向分离

【目的】红杆菌科(Rhodobacteraceae)细菌为凡纳滨对虾肠道微生物的优势类群,在健康对虾肠道中具有较高的相对丰度,是指示对虾健康的关键类群,探究对虾肠道红杆菌科细菌定向富集和分离方法,可为对虾养殖益生菌菌剂的研发提供基础。【方法】利用16S rRNA基因高通量测序技术研究不同碳源添加对凡纳滨对虾肠道中红杆菌科细菌的富集作用,筛选对红杆菌科细菌有显著富集作用的碳源;利用纯培养技术从红杆菌科细菌富集的样品中定向分离红杆菌科细菌,并对其进行鉴定和遗传多样性分析。【结果】添加短链脂肪酸(乙酸、丙酸、丁酸、戊酸)和碳酸氢钠对红杆菌科细菌有显著富集作用,主要富集到Cribrihabitans、Tritonibacter、Rhodovulum、Ruegeria、Sagittula和Thalassobius属相关菌株;对红杆菌科细菌相对丰度最高的样品进行稀释涂布培养,共分离纯化出303株细菌,分属于2门12科,其中红杆菌科细菌为主导类群共119株,主要包括Tritonibacter (90株)、Phaeobacter (25株)、Sulfitobacter (1株)、Ruegeria (1...     

A green and effective method for the determination of metalaxyl enantiomers in tobacco and soil by supercritical fluid chromatography–tandem mass spectrometry

We reported a new methodology for the stereoselective determination of metalaxyl enantiomers in tobacco and soil. The QuEChERS (quick, easy, cheap, effective, rugged, and safe) method was used for the extraction and clean-up of the tobacco and soil samples. Separation of the metalaxyl enantiomers was performed on an ACQUITY UPC2 Trefoil CEL1 chiral column coupled with supercritical fluid chromatography with tandem mass spectrometry (SFC-MS/MS), and the run time was only 5 minutes. Under the optimized conditions, the recoveries for the enantiomers were between 78.2% and 93.3% with intraday relative standard deviations (RSDs) ranging from 1.1% to 5.4%. The limit of detection (LOD) for the enantiomers in tobacco and soil varied from 0.005 to 0.007 mg/kg, and the limit of quantitation (LOQ) ranged from 0.017 to 0.020 mg/kg. In this method, only a small amount of methanol was consumed to obtain a rapid stereoselective separation. This proposed method showed good accuracy and precision and might be suitable for fast enantioselective determination of metalaxyl in food and environmental samples. The developed method was further validated by application to the analysis of authentic samples.     

植物LEAFY 同源基因的研究进展

本文就近10年来LEAFY(简写为LFY)同源基因的研究进展做了综合分析。通过对19种植物中已分离到的LFY同源基因的序列比较分析发现: LFY同源基因编码区核苷酸和氨基酸序列同源性都较高;在双子叶植物基因组中, 拷贝数却有所不同。该基因的表达特性显示其在不同植物中表达的时间和空间有所差异。根据已知序列推导的氨基酸序列构建的系统进化树表明, 单子叶植物与裸子植物的亲缘关系近于双子叶与裸子植物的亲缘关系。上述研究资料为植物成花机理研究提供了重要参考, 且在研究植物系统进化方面也具有重要的意义。     

Crisis-Like Behavior in China's Stock Market and Its Interpretation

In order for China to play a bigger, more positive role in the world, it is important for China to have a healthy capital market. This perception motivates us to examine the health of China''s capital market, especially the severity of the overall loss of the listed companies in China and the effects of accounting irregularities on the losses. We show the overall loss of the listed companies was very severe, in particular, crisis-like behavior emerged in the fourth quarter of 2002, 2004, 2005, and 2008. We further observe that loss in the fourth quarter was much greater than the average loss of the first three quarters in the same year. The most straightforward interpretation of this loss pattern is that companies underreported losses in the first three quarters, to boost their stock values in most time of the year. However, in the fourth quarter, accounting balance of the whole year dictated that the reported loss in the fourth quarter had to be much greater than the actual loss. Fortunately, such irregularity has been greatly reduced, thanks to the accounting reforms in China in 2007.     

转酮酶在癌症中的作用及其机制研究进展

肿瘤细胞的一大重要特征是代谢水平的改变。戊糖磷酸途径作为细胞产生NADPH和五碳糖的主要通路,在肿瘤发生发展过程中发挥着重要功能。转酮酶是戊糖磷酸途径中的关键酶之一,越来越多的研究表明其与癌症病人预后具有显著相关性。作为肿瘤诊断、治疗的潜在靶标,转酮酶具有重要的研究价值。我们就目前癌症研究中对转酮酶的研究进展做简要综述。     

黄芪对镉致大鼠睾丸支持细胞超微结构及波形蛋白、E-钙粘蛋白表达改变的保护作用

目的 探讨黄芪对镉致大鼠睾丸支持细胞损伤的保护作用.方法 21只成年雄性SD大鼠随机分成镉组(0.1％氯化镉腹腔内注射,1mg/Kg体重/天,5天/周,处理后1、2、3、4周取材)、镉加黄芪组(注射氯化镉的同时注射黄芪,10g/Kg体重/天,5天/周,处理后2、4周取材)和对照组(腹腔内注射等量生理盐水).睾丸取材作光镜、免疫组织化学染色和图像分析及超微结构观察.结果 光镜H.E染色对照组支持细胞核不规则,染色浅,核仁明显,镉处理后胞浆内有空泡形成,镉加黄芪组支持细胞未见明显改变.对照组波形蛋白阳性产物在支持细胞靠近基室腔的胞浆中表达,E-钙粘蛋白阳性产物则主要定位于生精上皮近腔室的支持细胞和部分生精细胞胞浆中.镉处理后支持细胞胞浆中波形蛋白和E-钙粘蛋白阳性产物表达的平均光密度值均明显降低(P＜0.05),镉加黄芪组阳性产物表达虽较对照组减弱但明显高于相应镉组(P＜0.05).镉处理组支持细胞胞质特化区和紧密连接破坏,镉加黄芪组支持细胞超微病变较相应镉组为轻.结论 镉降低大鼠睾丸支持细胞波形蛋白和E-钙粘蛋白的表达并造成支持细胞的超微结构损伤,黄芪具有较好的保护效果.     

NF-κB激活gp96转录从而促进肝细胞生长、细胞周期进展和细胞转化

【目的】探讨乙肝感染中gp96上调的机制及其可能发挥的病理学机制。【方法】首先通过生物信息学、Real-time PCR、荧光报告基因和Western blot研究NF-κB激活gp96表达的机制。进一步通过在肝细胞中过表达或敲低gp96的水平,运用CCK-8法和流式检测分析gp96对肝细胞增殖、凋亡,和细胞周期的影响,通过检测肝细胞EMT发生和细胞集落形成实验,分析gp96对于HCC发生的作用。【结果】NF-κB与gp96启动子上NF-κB结合位点结合,激活gp96的表达。实验结果显示,gp96能够促进肝细胞增殖、抑制凋亡,促进细胞周期从静息期向分裂期的转化,同时促进肝细胞EMT发生和细胞集落的形成。【结论】NF-κB通过活化gp96启动子上调其表达,为HBV慢性感染上调gp96的机制提供了线索,同时提示gp96在慢性炎症引发HCC过程中发挥重要作用。