Serial analysis of gene expression in the southern cattle tick following acaricide treatment of larvae from organophosphate resistant and susceptible strains

Organophosphate resistant and susceptible tick larvae from laboratory strains of the southern cattle tick, Rhipicephalus (Boophilus) microplus were exposed to low doses of the organophosphate (OP) acaricide, coumaphos. Serial analysis of gene expression (SAGE) was used to analyse differential gene expression in response to OP treatment and to compare the responses of OP-treated and -untreated resistant and susceptible tick larvae. An R. microplus Gene Index was used as an EST database to identify genes which corresponded to SAGE tags whose abundance changed in response to acaricide exposure. Relative quantitative RT-PCR was used to confirm the differential expression results from the SAGE experiments. Of particular interest is a SAGE tag which corresponds to a cytochrome P450-like EST in the Gene Index which was more abundant in untreated OP resistant larvae compared to untreated OP susceptible larvae. This SAGE tag was also more abundant in OP resistant larvae treated with OP compared to OP susceptible larvae treated with OP.     

云南省景洪市鼠类及媒介蜱中伯氏疏螺旋体感染状况调查

目的了解云南省景洪市鼠类及媒介蜱中伯氏疏螺旋体的感染状况及其携带的病原体特征。方法2018年3月在景洪市景讷和大渡岗2个乡镇7个调查点采集蜱标本，在勐罕、勐养、嘎洒、景讷4个乡镇4个调查点采集鼠的肾脏、膀胱标本，提取样本DNA；采用实时定量PCR进行伯氏疏螺旋体recA基因检测；对recA基因阳性样本用巢式PCR扩增5S ~ 23S rRNA基因间隔区，并对扩增产物进行测序及序列同源性比较。结果共采集牛、羊寄生蜱724只，经鉴定均为微小牛蜱；35只鼠均为黄胸鼠；524只蜱及35份鼠标本伯氏疏螺旋体培养结果均为阴性。 对200份蜱recA基因检测发现阳性3份；35份鼠标本均为阴性。 对3份阳性标本的5S ~ 23S rRNA序列同源性进行分析，初步判定其为伽氏疏螺旋体。结论云南省景洪市蜱中存在伽氏疏螺旋体感染，微小牛蜱很可能是其传播媒介，应加强对当地人群、宿主及媒介的调查和监测。     

Expression and immunolocalization of a Boophilus microplus cathepsin L-like enzyme

Efforts are being undertaken to control tick infestations that cause important economic losses. A cathepsin L-like endopeptidase of Boophilus microplus was expressed in Escherichia coli; the recombinant enzyme was capable of hydrolysing gelatin, tick vitellin and bovine haemoglobin. In this paper we focus on the expression and local of synthesis of this enzyme in the tick. RT-PCR experiments showed that this endopeptidase is transcribed in the gut of partially engorged tick females. In immunoblotting, polyclonal antibodies against the recombinant enzyme reacted with proteins of larvae older than 5 days, of fully and partially engorged female gut. In immunolocalization experiments the enzyme was localized in probable secretory cells of the gut. Based on our findings we postulate that BmCL1 may be involved in haemoglobin degradation in the B. microplus gut. This enzyme may be used as target for the control of this parasite.     

胃癌组织SERPINH1基因表达水平与其病理及预后关系研究

目的探讨胃癌组织SERPINH1基因表达水平与其病理及预后的关系;探讨SERPINH1在胃癌中的作用机制。方法收集TCGA和GEO公共数据库的胃癌数据,对胃癌组织样本的SERPINH1基因表达数据及其对应的临床信息进行病理指标的回顾性分析和生存分析;利用基因集富集分析(GSEA)方法分析与SERPINH1表达相关的功能性基因集合,探究SERPINH1的作用机制。结果 421例胃癌样本中,SERPINH1高表达组与低表达组之间肿瘤分级、N分期、转移无显著性差异(P0.05),但SERPINH1高表达与肿瘤浸润深度(T分期)显著相关(P=0.049),表达水平越高,浸润深度越大。生存分析中,SERPINH1高表达患者的预后明显差于低表达患者[P0.001,HR(95%CI):1.97(1.61~2.41)]。基因集富集分析发现,SERPINH1高表达的样本中富集了肿瘤信号通路、肿瘤微环境等相关基因集。69例胃癌及癌旁组织的基因表达芯片数据也提示,SERPINH1在胃癌组织中的表达明显升高(P0.000 1),且具有较大诊断价值(AUC=0.988 1)。结论 SERPINH1基因高表达与胃癌的发生、发展相关,具有较大的临床意义。     

云南省西北地区家畜体表蜱类形态学与分子生物学鉴定

目的 调查云南省西北地区家畜体表蜱的种类及其种群遗传进化情况。方法 采集家畜体表寄生的蜱虫,经形态学鉴定后,用PCR法扩增蜱样本的16S rDNA和ITS2基因片段,测序后进行序列分析。结果 共采集成蜱样本1 275只,经形态学鉴定为1科3属4种,其中微小扇头蜱1 263只（占99.1%）,卵形硬蜱7只（占0.6%）,锐跗硬蜱4只（占0.3%）,未知血蜱1只（占0.1%）。样品分子鉴定结果与形态学鉴定结果一致。16S rDNA序列分析显示,蜱P6与印度微小扇头蜱（EU918188）的相似性最高为99.8%,与中国云南微小扇头蜱（JX051062）的相似性99.4%;蜱P2与美国卵形硬蜱（U95900）的相似性最高为93.8%;蜱P1与日本锐跗硬蜱（AB105167）的相似性最高为95.9%;蜱P4与澳大利亚parva血蜱（JX573136）的相似性为90.5%,与中国云南长角血蜱（JX051064）的相似性为88.7%。ITS2序列分析显示,蜱P6与来自老挝（KC503276）、中国云南（KC203364）的微小扇头蜱的相似性均为99.9%;蜱P2与日本卵形硬蜱（D88857）的相似性最高为96.1%;蜱P1与日本锐跗硬蜱（AB605168）的相似性最高为95.3%;蜱P4与罗马尼亚Haemaphysalis parva血蜱（FN296282）的相似性最高为91.0%。结论 云南地区家畜体表存在微小扇头蜱、卵形硬蜱、锐跗硬蜱和一种与parva血蜱相关的新型血蜱。     

CLDN23基因在结肠癌中的临床意义和预后价值

摘要：目的?检测CLDN23基因在结肠癌中的表达情况，分析其临床意义和预后价值。方法?登录癌症基因图谱数据库(the cancer genome atlas，TCGA)下载结肠癌转录本测序数据和相应患者的临床病理资料，使用R 3.6.0软件提取并分析CLDN23基因在结肠癌中的表达情况。根据CLDN23基因在结肠癌患者中表达水平的中位值，将结肠癌患者分为高、低表达2组，使用卡方检验分析CLDN23基因表达与患者临床病理参数的关系，使用Log rank检验分析2组之间总体生存率的差异。利用单因素和多因素Cox回归分析CLDN23基因在结肠癌中的预后价值。结果?与正常组织相比，CLDN23基因在结肠癌组织中显著下调(P<0.001)。Log rank检验分析结果提示，低表达组患者的总体生存率较高表达组患者更低(P=0.018)。多因素Cox回归分析结果提示，CLDN23基因可作为结肠癌患者的独立预后因子(HR=1.47,95%CI:1.09～1.96,P=0.01)。结论?CLDN23基因在结肠癌组织中表达下调，与结肠癌恶性进展相关，可作为结肠癌的预后因子和潜在的分子标志物。     

基于生物信息学方法对抑郁症小鼠脑组织差异基因表达的分析

目的:基于生物信息学方法分析抑郁症小鼠海马和杏仁核等脑组织中差异表达基因及其可能的生物学功能.方法:选取GEO数据库中数据集GSE151807,利用R软件及Limma包进行差异基因的筛选;对数据集GSE151807基因表达矩阵进行基因集富集分析;利用David在线分析工具对差异基因进行基因本体论(GO)富集分析和KEG...     

TYMP基因在肾透明细胞癌中的表达及临床意义

目的:阐述胸苷磷酸化酶(thymidine phosphorylase,TYMP)基因在肾透明细胞癌(clear cell renal cellcarcinoma,CCRCC)中的表达及临床意义。方法:利用Oncomine及GEPIA数据库分析T YMP基因在正常肾组织及CCRCC组织中的表达差异;通过GEPIA数据库进行TYMP基因表达程度与病理分期的相关性分析;利用OncoLnc数据库对TYMP基因的表达水平与CCRCC患者生存率作Kaplan-Meier生存分析和log-rank检验;经MethHC数据库分析CCRCC组织和正常肾组织中T YMP启动子区DNA甲基化水平的差异;利用String-DB数据库分析与TYMP蛋白相互作用的蛋白;最后通过The Human Protein Atlas数据库分析TYMP蛋白在正常肾组织及CCRCC组织中的表达差异。结果:在mRNA及蛋白水平上,TYMP在CCRCC组织较正常肾组织中显著高表达,且TYMP mRNA表达水平越高,CCRCC病理分期越高;与TYMP基因低表达组相比,TYMP基因高表达的CCRCC患者总体生存率明显降低;CCRCC组织中TYMP启动子区DNA甲基化水平较正常组织甲基化水平显著降低;同时,与TYMP蛋白相关的蛋白有TK2,NT5M,CDA,UPRT,NT5C,UPP2,UMPS,TK1,UPP1和DPYD等,主要参与嘧啶核苷的合成、分解、代谢,转移戊糖基、蛋白质同源聚合等生物过程。结论:大样本数据挖掘能迅速获取CCRCC组织中TYMP基因表达的相关信息,为深入研究TYMP基因在CCRCC发生发展中的作用机制及预后奠定基础。     

In vivo time-dependent gene expression of cationic lipid-based emulsion as a stable and biocompatible non-viral gene carrier

To make stable and biocompatible non-viral gene carriers for therapeutic gene therapy, we developed a cationic lipid-based emulsion (CLE) prepared by an oil-in-water (O/W) emulsion method, wherein squalene oil was used as an oil core and the cationic lipid, 1,2-dioleoyl-sn-glycero-3-trimethylammonium-propane (DOTAP), was employed as an emulsifier. To evaluate in vivo characteristics such as toxicity and time-dependent gene expression, a bioluminescence reporter gene in pCMV-luc plasmid DNA was simply mixed with CLE in aqueous condition, resulting in a CLE/DNA complex. The CLE/DNA complex was optimized to form a compact and stable nano-sized particle by adding different amounts of plasmid DNA, and an optimal cationic lipid-to-DNA (C/D) weight ratio of 4 was identified. Freshly prepared CLE/DNA complex, with a C/D of 4, showed a high transfection efficiency and minimal cytotoxicity in vitro, compared to controls of a liposome (DOTAP)/DNA complex and a branched poly(ethyleneimine) (Mw = 25 kDa) (bPEI)/DNA complex, respectively. The in vivo characteristics of the CLE/DNA complex were evaluated after intravenous injection into Balb/c mice. Time-dependent gene expression data in vivo were obtained using a non-invasive, whole animal bioluminescence imaging system. These data showed that the CLE/DNA complex offered prolonged high-level gene expression for 1 week, particularly in the liver and spleen. On the other hand, the controls of DOTAP/DNA complex and bPEI/DNA complex showed a relatively lower gene expression, because of the unstable and toxic properties of the control carriers. Our in vivo gene expression data demonstrate the potential of the CLE/DNA complex as a non-viral gene carrier for in vivo gene delivery.     

Microarray analysis of mouse ear tissue exposed to bis-(2-chloroethyl) sulfide: gene expression profiles correlate with treatment efficacy and an established clinical endpoint

Bis-(2-chloroethyl) sulfide (sulfur mustard; SM) is a potent alkylating agent. Three treatment compounds have been shown to limit SM damage in the mouse ear vesicant model: dimercaprol, octyl homovanillamide, and indomethacin. Microarrays were used to determine gene expression profiles of biopsies taken from mouse ears after exposure to SM in the presence or absence of treatment compounds. Mouse ears were topically exposed to SM alone or were pretreated for 15 min with a treatment compound and then exposed to SM. Ear tissue was harvested 24 h after exposure for ear weight determination, the endpoint used to evaluate treatment compound efficacy. RNA extracted from the tissues was used to generate microarray probes for gene expression profiling of therapeutic responses. Principal component analysis of the gene expression data revealed partitioning of the samples based on treatment compound and SM exposure. Patterns of gene responses to the treatment compounds were indicative of exposure condition and were phenotypically anchored to ear weight. Pretreatment with indomethacin, the least effective treatment compound, produced ear weights close to those treated with SM alone. Ear weights from animals pretreated with dimercaprol or octyl homovanillamide were more closely associated with exposure to vehicle alone. Correlation coefficients between gene expression level and ear weight revealed genes involved in mediating responses to both SM exposure and treatment compounds. These data provide a basis for elucidating the mechanisms of response to SM and drug treatment and also provide a basis for developing strategies to accelerate development of effective SM medical countermeasures.     

基于表达谱芯片技术的食管鳞状细胞癌相关差异基因的筛选及功能研究

目的利用食管鳞状细胞癌细胞相关基因芯片数据,筛选与食管癌显著相关的关键基因,并对关键基因所在的模块进行功能研究。方法从基因表达数据库 GEO 数据库中下载数据 GSE17351（数据共10个样本,正常和食管鳞状细胞癌样本组织各5个）,利用 R软件包做数据预处理和差异表达分析,选取差异表达基因（FDR ＜ 0.05及差异值 ＞2或＜ -2）。然后对差异表达基因进行生物信息学分析,首先投入 String 在线分析工具获得差异表达基因的蛋白-蛋白相互作用网络（score ＞0.9）,统计网络中各个节点的度,挑选出最关键的主效基因（hub基因）。然后利用Cytoscape软件插件 Mcode对整个网络进行网络模块化,并通过插件Bingo（P value＜ 0.05）对hub基因所在的模块进行功能注释,推测模块中影响基因特异性表达导致食管癌的机制和方式。结果通过比较正常和患病者食管鳞状细胞癌表达数据,筛选到600个差异表达的基因,构建了包含268对差异表达基因产物蛋白对的相互作用网络。找到最关键 hub 基因 TOP2A。得到1个包括hub基因在内由5个差异表达基因组成的模块,模块功能最显著富集在染色体分离和浓缩;发现与多种癌症相关的基因TOP2A共同起染色体活动基因 NCAPG。结论食管鳞癌的发生与最关键基因 TOP2A的异常表达有关,推测与之功能发生作用的基因 NCAPG 基因通过与 TOP2A 相同的机制和方式（染色体中前期活动）影响着癌症特异性基因的表达。     

黏液型与非黏液型铜绿假单胞菌Cif基因表达研究

目的 比较黏液型和非黏液型铜绿假单胞菌囊性纤维化跨膜传导调节体抑制因子(Cif)基因表达差异,并结合临床资料比较对应患者白细胞(WBC)及C反应蛋白(CRP)等炎症指标的不同。方法 采用逆转录PCR和实时荧光定量PCR检测两种型别铜绿假单胞菌Cif基因的表达量。收集相应患者临床数据比较WBC数和CRP水平及其与Cif基因表达的相关性。结果 黏液型铜绿假单胞菌Cif基因表达量显著高于非黏液型铜绿假单胞菌,差异有统计学意义(t=2.09,P<0.05),黏液型铜绿假单胞菌组和非黏液型铜绿假单胞菌组的患者其WBC数和CRP水平差异无统计学意义(t=0.65,0.60,P>0.05); Cif基因表达与CRP水平相关性极弱(a=-0.061,R²=0.04),与WBC数相关性也极弱(a=0.095,R²=0.029)。结论 Cif基因表达可能与黏液型铜绿假单胞菌生物被膜的形成有关,可能为铜绿假单胞菌新的毒力因子。     

PITX1基因在肺腺癌中的表达及临床预后意义

目的:探讨同源域转录因子1(paired like homeodomain 1,PITX1)基因在肺腺癌组织和正常组织中的表达水平及其与临床病理特征和预后之间的相关性。方法:综合利用肿瘤基因组图谱(The Cancer Genome Atlas,TCGA)数据库和基因表达数据库(Gene Expression Omnibus,GEO)中的GSE130779和GSE85841数据集,分析PITX1基因在肺腺癌患者癌组织及癌旁组织中的表达水平,并利用实时荧光定量PCR法在40例肺腺癌患者组织中验证PITX1基因的表达水平。同时利用COX回归分析PITX1基因与肺腺癌患者的总生存期(overall survival,OS)和无复发生存期(recurrence-free survival,RFS)之间的相关性,进而分析其表达水平与肺腺癌患者临床病理特征之间的相关性。结果:基于TCGA和GEO数据库分析结果显示PITX1基因在肺腺癌组织中显著高表达(P<0.01),实时荧光定量PCR结果显示PITX1基因在肺腺癌组织的表达量显著高于癌旁正常组织(P<0.001),其相对表达量分别为1.064±0.077和0.641±0.044。COX回归分析显示PITX1基因的表达水平与肺腺癌患者的TNM分期、淋巴结转移状态和肿瘤大小显著相关(均P<0.05)。同时,上调PITX1的表达水平与肺腺癌患者的OS和RFS呈负相关。结论:PITX1基因在肺腺癌组织中显著高表达,且与肺腺癌患者的预后显著相关。     

TDP1基因表达水平在肺腺癌患者预后中的价值研究

目的探究TDP1基因mRNA在肺腺癌组织中的表达及其与患者预后之间的关系。方法以TCGA数据库内登记的肺腺癌患者的临床信息及TDP1表达情况为研究数据,通过UALCAN数据库挖掘分析工具对TDP1基因mRNA的表达情况进行分析,并通过Kaplan-Meier生存分析法分析TDP1表达水平与患者总生存期(OS)之间的关系。结果肺腺癌组织中TDP1基因mRNA的表达水平高于正常肺组织(P=0.0000),TDP1基因mRNA的高表达与更差的OS相关(P=0.0057)。亚组分析中,TDP1基因mRNA的表达水平在男性患者和女性患者之间无显著差异(P=0.9412),在不同种族人群间的表达水平也无显著差异(P>0.05),但在女性患者及高加索患者中,TDP1基因mRNA的高表达均与更差的OS相关(女性患者:P=0.031;高加索患者:P=0.016)。结论 TDP1在肺腺癌组织中呈高表达,与更短的OS相关,提示TDP1可能在肺腺癌发生发展过程中有驱动作用,TDP1可作为肺腺癌治疗的下一个潜在靶点,但其内在机制需要更多的基础与临床研究予以揭示。     

基于Oncomine和GEPIA数据库分析 NFE2L3基因在结直肠癌中的表达及其临床意义

目的通过挖掘Oncomine和GEPIA数据库中的相关数据,分析NFE2L3基因在结直肠癌中的表达及临床意义。 方法检索Oncomine和GEPIA数据库中有关结直肠癌的数据并结合文献资料进行二次综合分析。癌与正常组织之间基因表达差异采用t检验,采用单因素方差分析比较不同临床分期之间基因表达的差异,采用Pearson相关分析进行相关性研究,采用Kaplan-Meier方法进行生存分析。 结果Oncomine数据库中共收集了334项关于NFE2L3基因在不同类型癌与正常组织中表达的比较的研究结果,表达差异有统计学意义的研究结果有55个。其中共有21项研究涉及NFE2L3基因在结直肠癌组织和正常结直肠组织中的表达,共包括1000个样本。与对照组相比结直肠癌组织中NFE2L3 mRNA表达显著高于结直肠正常组织（P<0.05）。GEPIA数据库中分析发现NFE2L3基因的表达与错配修复基因MLH1、MSH2、MSH6和PMS2的表达均呈显著相关性（P<0.05）;NFE2L3基因与结直肠癌的临床分期与预后生存（总生存率和无病生存率）均不具有相关性（P>0.05）。 结论NFE2L3 mRNA在结直肠癌组织中呈高表达,并与影响结肠癌发生的错配修复基因的表达关系密切。     

乳腺癌组织中肿瘤转移相关基因1和基质金属蛋白酶的表达及其临床意义

目的 研究乳腺癌组织中肿瘤转移相关基因1(MTA1)蛋白和基质金属蛋白酶-9(MMP-9)的表达及其与临床病理资料之间的关系.方法 应用免疫组化SP法检测56例乳腺癌组织中MTA1、MMP-9蛋白的表达.结果 56例乳腺癌组织中39例MTA1蛋白阳性表达(69.6%),41例MMP-9蛋白阳性表达(73.2%),MTA1和MMP-9的高表达与乳腺癌组织学分级、临床分期和淋巴结转移关系密切(均P＜0.05).结论 MTA1和MMP-9蛋白的表达可以作为判断乳腺癌预后及术后综合治疗的生物学指标.     

Implications for powering biomarker discovery studies

This study examined variations in gene expression between FFPE blocks within tumors of individual patients. Microarray data were used to measure tumor heterogeneity within and between patients and disease states. Data were used to determine the number of samples needed to power biomarker discovery studies. Bias and variation in gene expression were assessed at the intrapatient and interpatient levels and between adenocarcinoma and squamous samples. A mixed-model analysis of variance was fitted to gene expression data and model signatures to assess the statistical significance of observed variations within and between samples and disease states. Sample size analysis, adjusted for sample heterogeneity, was used to determine the number of samples required to support biomarker discovery studies. Variation in gene expression was observed between blocks taken from a single patient. However, this variation was considerably less than differences between histological characteristics. This degree of block-to-block variation still permits biomarker discovery using either macrodissected tumors or whole FFPE sections, provided that intratumor heterogeneity is taken into account. Failure to consider intratumor heterogeneity may result in underpowered biomarker studies that may result in either the generation of longer gene signatures or the inability to identify a viable biomarker. Moreover, the results of this study indicate that a single biopsy sample is suitable for applying a biomarker in non-small-cell lung cancer.