诱变酒酒球菌中抗酸候选基因ATPase和FtsH的表达差异分析及功能验证

为研究胁迫条件下具有不同表达趋势的抗酸候选基因ATPase和FtsH是否可以提高菌株的抗酸性,利用实时荧光定量PCR(RT-qPCR)测定诱变酒酒球菌抗酸菌株b1和酸敏菌株b2中ATPase和FtsH在pH 4.8(最适条件)和pH 3.0(胁迫条件)ATB培养基中的相对表达量,分析其表达趋势;从b1中克隆ATPase和FtsH,分别命名为ATPase1和FtsH1,从b2中克隆ATPase和FtsH,分别命名为ATPase2和FtsH2,分析序列差异;将ATPase1,ATPase2,FtsH1和FtsH2分别在植物乳杆菌XJ25中做功能验证,构成重组植物乳杆菌a1,a2,f1和f2。以含空载体的植物乳杆菌con为对照,于pH 3.2的MRS培养基中测定重组植物乳杆菌的生长能力。定量结果表明ATPase在菌株b1和b2中表达量均显著上调;FtsH在b1中不变,在b2中显著上调。ATPase1和ATPase2在功能结构域内有3处非同义突变,FtsH1和FtsH2在跨膜结构域内有1处非同义突变。功能验证结果表明:a1和a2的生长能力均强于con,且a1和a2生长能力无差异;f1生长能力强于con,f2生长能力与con无差异。由此可知ATPase1,ATPase2和FtsH1均可以提高菌株抗酸性。     

肺炎克雷伯菌CRP蛋白表达与纯化及生物学特征分析

目的:原核表达获得肺炎克雷伯菌KP1_RS23625基因（crp）编码的CRP蛋白,并解析CRP蛋白具体的生物学功能。方法:首先克隆肺炎克雷伯菌crp基因,并亚克隆至pET-28a（+）质粒构建重组蛋白表达载体;然后体外原核诱导表达、纯化目的蛋白并进行SDS-PAGE电泳分析。进一步通过生物学信息方法分析CRP蛋白的生物学功能:利用ProtParam、Protscale、SignalP4.1 Service、TMHMM Server v.2.0、SOPMA、SWISS-MODEL软件分别分析目的蛋白理化性质、疏水性、信号肽、跨膜区域、二级与三级结构等一般生物学特征;并借助CDD数据库、Net Phos 3.1 Sever在线软件预测蛋白的功能结构域、磷酸化位点等功能特征;进一步利用ATRING 11.0交互式数据库进行蛋白质交联互作分析。结果:成功构建了重组目的蛋白表达载体pET-28a-crp,并通过原核诱导表达与镍柱亲和吸附法表达、纯化获得CRP目的蛋白;蛋白电泳结果显示CRP蛋白为水溶性蛋白,包括标签蛋白（约4 kDa）的重组目的蛋白分子质量约27 kDa。对CRP蛋白的生物信息学分析结果显示:CRP蛋白大小23.65 kDa、为亲水性蛋白;无跨膜结构域、无信号肽;蛋白二级结构主要由α螺旋与不规则卷曲构成,其中α-螺旋占比40%以上,结构较松散;同时成功构建了三级结构模型;CRP蛋白结构域分析表明含有1个功能结构域,属PRK11753超级家族;修饰位点及蛋白注释分析显示目的蛋白含20个磷酸化位点,与多个蛋白具有交互作用。结论:本研究利用基因工程方法成功获得了较高纯度肺炎克雷伯菌CRP蛋白,并通过生物信息学手段解析了其生物学特征,为肺炎克雷伯菌感染的临床治疗提供理论基础。     

不同培养条件下酿酒酵母菌的转录组差异分析

从组学水平分析富硒条件下酿酒酵母菌(Saccharomyces cerevisiae)内在分子机制,为酿酒酵母菌富硒研究及富硒基因的挖掘利用提供理论依据。该研究以不加硒培养的酿酒酵母菌作为对照组Kb,以加20μg/mL硒培养的酿酒酵母菌为实验组Se,利用Illumina高通量测序平台对两组进行转录组测序,通过生物信息学方法对数据进行分析处理。结果表明,转录组测序共获得6445个Unigenes,分别有1401个(21.74%)、3665个(56.87%)、5630个(87.35%)、6112个(94.83%)、6077个(94.29%)、5059个(78.49%)Unigenes被注释到GO、KEGG、COG、NR、Swiss Prot和Pfam数据库,共有6150个(95.42%)Unigenes得到注释。在GO功能注释中,共得到41个GO功能小类,在KEGG代谢通路分析时,获得了113条KEGG通路。该转录组测序数据质量高,结果覆盖面广,为酿酒酵母菌富硒基因挖掘和研究提供了一定的理论参考。     

花生主要过敏原Ara h 1线性B细胞表位的预测及鉴定

花生过敏由于其高致敏率和致敏严重性而引起了人们的广泛关注。Ara h 1是花生中的主要过敏原,属于Cupin超家族,通过抗原表位识别结合免疫球蛋白E引发花生过敏。本研究采用生物信息学分析花生主要过敏原Cupin超家族Ara h 1线性B细胞表位氨基酸组成,及其与Ara h 1二级、三级结构之间关系,通过质谱分析Ara h 1氨基酸序列中的抗消化肽段,并分析抗消化肽段与预测线性B细胞表位的关系。结果表明,Ara h 1的线性B细胞表位富含亲水性氨基酸和带电氨基酸;其二级结构没有明显的分布规律,具有一定的回转折叠结构;分析Ara h 1三级结构发现,表位主要位于单体之间的疏水相互作用区域,部分表位埋入三聚体构象内部;Ara h 1抗消化序列与表位之间存在部分重叠。综上,质谱检测体外模拟胃肠道消化肽段并结合表位生物信息学分析可以作为鉴定Cupin超家族线性B细胞表位的新方法。     

油茶甘油二酯激酶基因（CoDGK3）的克隆与表达分析

以油茶转录组数据为基础,采用RT-PCR和RACE技术,根据Unigene序列设计油茶甘油二酯激酶基因(Co DGK)RACE引物,分离克隆了DGK基因全长c DNA序列,命名为Co DGK3(Gene Bank登录号:KM068056),基因全长1 568 bp,开放阅读框1 455 bp,编码485个氨基酸;氨基酸同源比对及序列分析表明油茶与其它物种的DGK氨基酸序列具有较高的相似性,其中与麻风树和毛果杨相似性最高,达到78%;利用生物学软件对蛋白质进行生物信息学分析,获得其结构特点及理化性质;分析转录组数据中DGK相关的Unigene序列RTKM值和对Co DGK3基因实施实时荧光定量PCR,结果表明Co DGK3在油茶种子发育各时期表达量变化差异不大,并且发现转录组数据分析和实时荧光定量分析的结果变化规律一致,证明了转录组测序的有效性。     

生物信息学导论课程与进阶课程比较

本文根据生物信息学是一门交叉学科的特点,在分析国内外高校相关课程设置的基础上,系统比较了生物信息学导论课程和进阶课程的差异和共性,提出了有针对性的内容安排方法和教学方式.笔者总结了授课过程的几个要点,即概念清楚、围绕主线、因材施教和加强实践,并在生物信息学课程教学中取得较好的效果.     

Boosting and Microarray Data

We have found one reason why AdaBoost tends not to perform well on gene expression data, and identified simple modifications that improve its ability to find accurate class prediction rules. These modifications appear especially to be needed when there is a strong association between expression profiles and class designations. Cross-validation analysis of six microarray datasets with different characteristics suggests that, suitably modified, boosting provides competitive classification accuracy in general.Sometimes the goal in a microarray analysis is to find a class prediction rule that is not only accurate, but that depends on the level of expression of few genes. Because boosting makes an effort to find genes that are complementary sources of evidence of the correct classification of a tissue sample, it appears especially useful for such gene-efficient class prediction. This appears particularly to be true when there is a strong association between expression profiles and class designations, which is often the case for example when comparing tumor and normal samples.     

基于字典的DNA序列压缩算法研究及应用*

在现有DNA序列数据压缩算法的基础上,以DNA序列数据的存储效率及生物学解释综合考虑,设计并实现了基于字典的DNA序列压缩算法DNADCompress.算法核心包括重复子串字典建立、字典项筛选、字串压缩编码三方面.实验数据表明,数据压缩算法压缩效果达到常用DNA序列压缩算法水平,并为序列生物学解释提供了基础.     

Polyphenol Supplementation Reverses Age-Related Changes in Microglial Signaling Cascades

Microglial activity in the aging neuroimmune system is a central player in aging-related dysfunction. Aging alters microglial function via shifts in protein signaling cascades. These shifts can propagate neurodegenerative pathology. Therapeutics require a multifaceted approach to understand and address the stochastic nature of this process. Polyphenols offer one such means of rectifying age-related decline. Our group used mass spectrometry (MS) analysis to explicate the complex nature of these aging microglial pathways. In our first experiment, we compared primary microglia isolated from young and aged rats and identified 197 significantly differentially expressed proteins between these groups. Then, we performed bioinformatic analysis to explore differences in canonical signaling cascades related to microglial homeostasis and function with age. In a second experiment, we investigated changes to these pathways in aged animals after 30-day dietary supplementation with NT-020, which is a blend of polyphenols. We identified 144 differentially expressed proteins between the NT-020 group and the control diet group via MS analysis. Bioinformatic analysis predicted an NT-020 driven reversal in the upregulation of age-related canonical pathways that control inflammation, cellular metabolism, and proteostasis. Our results highlight salient aspects of microglial aging at the level of protein interactions and demonstrate a potential role of polyphenols as therapeutics for age-associated dysfunction.     

Target Score—A Proteomics Data Selection Tool Applied to Esophageal Cancer Identifies GLUT1-Sialyl Tn Glycoforms as Biomarkers of Cancer Aggressiveness

Esophageal cancer (EC) is a life-threatening disease, demanding the discovery of new biomarkers and molecular targets for precision oncology. Aberrantly glycosylated proteins hold tremendous potential towards this objective. In the current study, a series of esophageal squamous cell carcinomas (ESCC) and EC-derived circulating tumor cells (CTCs) were screened by immunoassays for the sialyl-Tn (STn) antigen, a glycan rarely expressed in healthy tissues and widely observed in aggressive gastrointestinal cancers. An ESCC cell model was glycoengineered to express STn and characterized in relation to cell proliferation and invasion in vitro. STn was found to be widely present in ESCC (70% of tumors) and in CTCs in 20% of patients, being associated with general recurrence and reduced survival. Furthermore, STn expression in ESCC cells increased invasion in vitro, while reducing cancer cells proliferation. In parallel, an ESCC mass spectrometry-based proteomics dataset, obtained from the PRIDE database, was comprehensively interrogated for abnormally glycosylated proteins. Data integration with the Target Score, an algorithm developed in-house, pinpointed the glucose transporter type 1 (GLUT1) as a biomarker of poor prognosis. GLUT1-STn glycoproteoforms were latter identified in tumor tissues in patients facing worst prognosis. Furthermore, healthy human tissues analysis suggested that STn glycosylation provided cancer specificity to GLUT1. In conclusion, STn is a biomarker of worst prognosis in EC and GLUT1-STn glycoforms may be used to increase its specificity on the stratification and targeting of aggressive ESCC forms.