Real-time polymerase chain reaction-based exponential sample amplification for microarray gene expression profiling

Conventional approaches to target labeling for gene expression analysis using microarray technology typically require relatively large amounts of RNA, a serious limitation when the available sample is limited. Here we describe an alternative exponential sample amplification method by using quantitative real-time polymerase chain reaction (QRT-PCR) to follow the amplification and eliminate the overamplified cDNA which could distort the quantitative ratio of the starting mRNA population. Probes generated from nonamplified, PCR-amplified, and real-time-PCR-amplified cDNA samples were generated from lipopolysaccharide-treated and nontreated mouse macrophages and hybridized to mouse cDNA microarrays. Signals obtained from the three protocols were compared. Reproducibility and reliability of the methods were determined. The Pearson correlation coefficients for replica experiments were r=0.927 and r=0.687 for QRT-PCR-amplification and PCR-overamplification protocols, respectively. Chi2 test showed that overamplification resulted in major biases in expression ratios, while these alterations could be eliminated by following the cycling status with QRT-PCR. Our exponential sample amplification protocol preserves the original expression ratios and allows unbiased gene expression analysis from minute amounts of starting material.     

Analysis of differential gene expression in the central nervous system of Schistocerca gregaria by differential display PCR

Within the optic lobes, the mushroom bodies or other parts of the insect brain, information is processed in an area-specific manner. To study the molecular basis of the abilities of the respective areas, the central nervous system of the desert locust Schistocerca gregaria was dissected into different parts, the optic lobes, the “midbrain”, and the thoracic ganglia. Using a simple electrophoretic approach we were able to show area-specific expression of proteins exclusively present in the optic lobes. To study brain area-specific gene expression in more detail, we adapted the differential display polymerase chain reaction to the specific needs of this project. A number of differentially expressed amplicons were identified. The majority of them could be reamplified and their differential expression verified by northern blot analysis. To demonstrate the efficiency of the approach two amplicons with complementary expression patterns were further analysed. Accepted: 31 August 1997     

芹菜韧皮部蛋白基因的分离与表达分析

韧皮部蛋白在维持植物形态,物质转运以及植物伤口保护等方面起着重要作用。本研究以地域来源和性状特性差异均较大的两个芹菜品种‘六合黄心芹’和‘美国西芹’为试验材料,利用RT-PCR技术获得这两种芹菜韧皮部蛋白基因的cDNA序列。结果显示：这两种芹菜来源的韧皮部蛋白基因全长均为546 bp,编码181个氨基酸。两者核苷酸序列有3个位点的不同,分别为：88G/A、399T/C和489T/C;在氨基酸序列上有一个位点的不同,为30T/A。预测其蛋白质分子量为19 kD,pI值为9.18。‘六合黄心芹’和‘美国西芹’的韧皮部蛋白与忽地笑等植物的韧皮部蛋白相似度较高,在保守位置分别具有5个亮氨酸残基和4个色氨酸残基。实时定量PCR表达分析表明,该基因主要在芹菜的茎和根等部位表达,具有明显的组织特异性。     

Comparison of gene expression between left atria and left ventricles from non-diseased humans

We examine the reliability and accuracy of gene array technology in analyzing differences in gene expression between human non-diseased left atrium and left ventricle. We have used cDNA gene arrays and validated those data by carefully designed quantitative real-time polymerase chain reaction (PCR). We have identified pitfalls using cDNA gene array technology based on comparisons with other gene array studies and with changes reported for the levels of expression of the genes corresponding to these cDNAs. The high error rate reported here underscores the cautionary comments reported by others in this field.     

基因表达差异显示分析技术在创伤研究中的应用

基因是细胞增殖,分化,成熟等各项生命活动的调控中心,也是许多痢疾发生,发展和转归的决定性因素。基因表达的变化必然导致细胞,组织,器官乃至整个机体的各种异常。包括创伤在内的各种内外刺激,都可不同程度地引起基因表达的变化,最终妨碍机体健康。随着生物信息学的逐渐兴起和分子生物学的不断发展并向其他学科的逐渐渗透,业已建立起一系列研究基因表达变化的切实可行的技术手段（即“基因表达差异分析技术”,如DNA微阵列）,对捕获基因表达的种种变化具有重要价值。这些技术已经在肿瘤及其他疾病的研究中得到广泛应用,近几年也逐渐进入创伤研究领域,在一定程度上推动了创伤研究的发展。     

Combined expression patterns of QTL-linked candidate genes best predict thermotolerance in Drosophila melanogaster

Knockdown resistance to high temperature (KRHT) is a thermal adaptation trait in Drosophila melanogaster. Here we used quantitative real-time PCR (qRT-PCR) to test for possible associations between KRHT and the expression of candidate genes within quantitative trait loci (QTL) in eight recombinant inbred lines (RIL). hsp60 and hsc70-3 map within an X-linked QTL, while CG10383, catsup, ddc, trap1, and cyp6a13 are linked in a KRHT-QTL on chromosome 2. hsc70-3 expression increased by heat-hardening. Principal Components analysis revealed that catsup, ddc and trap1 were either co-expressed or combined in their expression levels. This composite expression variable (e-PC1) was positively associated to KRHT in non-hardened RIL. In heat-hardened flies, hsp60 was negatively related to hsc70-3 on e-PC2, with effects on KRHT. These results are consistent with the notion that QTL can be shaped by expression variation in combined candidate loci. We found composite variables of gene expression (e-PCs) that best correlated to KRHT. Network effects with other untested linked loci are apparent because, in spite of their associations with KRHT phenotypes, e-PCs were sometimes uncorrelated with their QTL genotype.     

Gene expression profiling of human diseases by serial analysis of gene expression

Until recently, the approach to understanding the molecular basis of complex syndromes such as cancer, coronary artery disease, and diabetes was to study the behavior of individual genes. However, it is generally recognized that expression of a number of genes is coordinated both spatially and temporally and that this coordination changes during the development and progression of diseases. Newly developed functional genomic approaches, such as serial analysis of gene expression (SAGE) and DNA microarrays have enabled researchers to determine the expression pattern of thousands of genes simultaneously. One attractive feature of SAGE compared to microarrays is its ability to quantify gene expression without prior sequence information or information about genes that are thought to be expressed. SAGE has been successfully applied to the gene expression profiling of a number of human diseases. In this review, we will first discuss SAGE technique and contrast it to microarray. We will then highlight new biological insights that have emerged from its application to the study of human diseases.     

锦鲤Hepcidin基因的克隆及其组织特异性表达分析

【目的】克隆锦鲤hepcidin全长cDNA序列(k-hepc),并获得此基因在鱼体内的表达模式。【方法】利用RT-PCR和RACE PCR的方法,从锦鲤肝脏中克隆锦鲤hepcidin的全长cDNA,进行序列测定和分析;锦鲤经肌肉注射维氏气单胞菌0、4、8、12、24和48 h后,分别取其肝、脾、肾、肠、脑、心、肌肉和鳃组织,采用实时荧光定量PCR的方法,以β-actin为内参基因,检测k-hepc基因的表达量。【结果】锦鲤抗菌肽(GenBank登录号KC795559)全长755 bp,编码序列276 bp,编码91个氨基酸,包括信号肽、原肽和成熟肽,成熟肽C端含有8个半胱氨酸,可形成4个分子内二硫键。与已报道的普通鲤鱼hepcidin氨基酸序列的一致性为93%,与其他鱼类hepcidin氨基酸序列的一致性为29%?93%。在本研究所检测的正常锦鲤的组织中,k-hepc均有表达,其中在肝组织中表达量最高,鳃组织中表达量最低。经维氏气单胞菌感染后,k-hepc在肝和心组织中的表达量明显增加,在其余组织中变化不显著。【结论】k-hepc编码的蛋白是Hepcidin家族的成员之一。锦鲤Hepcidin的表达主要受内在调节因素影响。     

Identification and mRNA expression profile of glutamate receptor-like gene in quinclorac-resistant and susceptible Echinochloa crus-galli

Animal ionotropic glutamate receptors (iGluRs) function as Ca^2 + ion channels during excitatory neurotransmission in nerve cells. Here, a glutamate receptor-like gene (GLR) was identified and characterized from a plant — Echinochloa crus-galli. The GLR gene was designated EcGLR1 with GenBank no: JX518597. It has a 2793 bp open reading frame predicted to encode a 101.7 kDa protein. Sequence alignment showed that EcGLR1 is a GLR homologue. Its expression in response to quinclorac treatment was assessed by real-time PCR in near-isogenic lines of quinclorac-resistant (R) and susceptible (S) biotypes of E. crus-galli. The expression of EcGLR1 in the seedling leaf and root at least increased 5 times in the S plants and 22 times in the R plants after exposure to quinclorac. In the adult plant leaves, roots and stems, its expression increased 11–14 times in the S plants and 23–25 times in the R plants after quinclorac stimulation. In the seed, its expression was 4 times less in the S plants than that in the R plants, but after treatment, the levels all increased by about 24 times in the two biotypes. EcGLR1 expression was 1–4 times greater in the R plants than in that in the S plants, and after treatment by quinclorac, the difference increased to a ratio of 4 to 9. Its expression was higher in all tissues tested of R biotypes than in that of S plants before or after quinclorac treatment. The results of this study provide basic information for the further research of function of the EcGLR1 in resistance to quinclorac in E. crus-galli.     

Comparative analysis of gene expression profiles in ruminal tissue from Holstein dairy cows fed high or low concentrate diets

Cattle are often fed high concentrate (HC) diets to increase productivity, although HC diets cause changes in ruminal environment such as pH reduction. Despite those well-documented changes in cattle fed HC diets, there is currently a paucity of data describing the molecular events regulating the ruminal environment. Our objective was to gain an understanding of which genes are differentially expressed in ruminal tissue from Holstein cows fed a HC comparing to low concentrate (LC) diet using microarray analysis using a bovine 24 k microarray. A total of 5,200 differentially expressed genes (DEG) were detected for cows fed HC relative to LC. The DEG were firstly annotated with gene ontology (GO) and Kyoto encyclopedia of Genes and Genomes (KEGG), indicating that the DEG were associated with catalytic activity and MAPK pathway, respectively. Further characterization using GeneCodis identified patterns of interrelated annotations for the DEG to elucidate the relationships among annotation groups revealed that a cAMP-dependent protein kinase A catalytic subunit beta (PRKACB), may be associated with ruminal tissue maintenance. The results contributed to understanding of the regulatory mechanisms at the mRNA level for Holstein cows fed at different concentrate ratio diets.     

Involvement of differential gene expression and mRNA stability in the developmental regulation of the hsp 30 gene family in heat-shocked Xenopus laevis embryos

Four complete hsp 30 genes have been isolated from Xenopus laevis: hsp 30A, hsp 30B (a pseudogene), hsp 30C, and hsp 30D. The hsp 30A and hsp 30C genes are first heat inducible at the early tailbud stage, as determined by RNase protection and RT-PCR assays. In this study, we determined by RT-PCR that the hsp 30D gene was first heat inducible (33^oC for 1 h) at the mid-tailbud stage, approximately 1 day later in development than hsp 30A and hsp 30C. Furthermore, using Northern blot analysis, we detected the presence of very low levels of hsp 30 mRNA at the heat-shocked late blastula stage. The relative levels of these pre-tailbud (PTB) hsp 30 mRNAs increased at the gastrula and neurula stage followed by a dramatic enhancement in heat shocked tail-bud and tadpole stage embryos (50- to 100- fold relative to late blastula). Interestingly, treatment of blastula or gastrula embryos at high temperatures (37^oC for 1 h) or with the protein synthesis inhibitor, cycloheximide, followed by heat shock, led to enhanced accumulation of the pre-tailbud (PTB) hsp 30 mRNAs. hsp 70, hsp 87, and actin messages were not stabilized at high temperatures or by cycloheximide treatment. Finally, hsp 30D mRNA was not detected by RT-PCR analysis of cycloheximidetreated, heat-shocked blastula stage embryos, confirming that it is not a member of the PTB hsp 30 mRNAs. This study indicates that differential gene expression and mRNA stability are involved in the regulation of hsp 30 gene expression during early Xenopus laevis development. © 1995 Wiley-Liss, Inc.     

白念珠菌抗氧化基因体外表达研究

目的检测白念珠菌体外抗氧化及调节转录的基因表达情况,进一步了解白念珠菌抗氧化机制在体外生长状态下的作用。方法选取白念珠菌标准株sc5314、3株临床分离保存株及7例临床念珠菌性阴道炎分泌物分离株（白念珠菌）,接种培养鉴定为白念珠菌后,分别将体外SDB振荡培养2 h、6 h、24 h、72 h、120 d的菌液（含未培养0h）,用Trizol法提取总RNA,反转录为cDNA后进行实时荧光定量PCR,检测体外各时间点抗氧化基因及抗氧化转录因子的基因表达情况,运用Ct值比较法进行表达量的相对定量分析。结果与0 h相比,体外6 hSOD2表达增加7.47倍,经Wilcoxon配对符号秩和检验显示P值小于0.01,差异具有统计学意义。其他各基因2 h及6 h分别与0 h相比P值均〉0.01,其表达差异不具有统计学意义。体外培养1 d后各基因表达明显增加,CaHog1、CAP1、CAT及SOD5在第3天达最高,分别为24.23、3.34、33.64及14.72倍;SOD2在第1天达最高为68.95倍;CaSkn7在第5天达最高为7.21倍。经Wilcoxon配对符号秩和检验显示SOD5第1天P值为0.013,其余基因表达P均〈0.01,表达差异具有统计学意义。结论当外界营养逐渐耗竭时,白念珠菌会动态加强抗氧化基因的表达,以抵抗机体内、外产生的氧化压力,其中SOD2可能是最早增加表达的抗氧化基因,3条抗氧化感受通路的转录调节基因均有增加表达,提示3条抗氧化感受通路在适应体外营养限制过程中起了重要作用。     

小鼠基因转录表达分析中内参基因的优选

目的 建立小鼠基因转录表达分析中内参基因的选择方法.方法 以C57BL/6J和C3H/HeJ两个品系3个不同组织及2个不同发育阶段为研究对象,应用反转录实时定量PCR技术,评价GAPDH(glyceraldehyde-3-phosphate dehydrogenase)、HPRTl(hypoxanthine phosphoribosyl transferase)、B2M(β2-microglobulin)、PPIA(peptidylprolyl isomerase A)、ACTB(Actin-beta)和18S rRNA(18S ribosomal RNA)等6个看家基因在下丘脑、垂体与卵巢中mRNA水平的表达稳定性.结果 GeNorm统计分析表明,GAPDH和HPRT1表达最为稳定,PPIA等次之,B2M在不同组织和发育阶段中都几乎无表达.结论 成功筛选到GAPDH和HPRT1两个稳定表达的看家基因,证实了小鼠基因表达转录分析中内参基因选择的必要性和可行性.     

Microarray gene expression analysis free of reverse transcription and dye labeling

A new microarray system has been developed for gene expression analysis using cationic gold nanoparticles with diameters of 250 nm as a target detection reagent. The approach utilizes nonlabeled target molecules hybridizing with complementary probes on the array, followed by incubation in a colloidal gold solution. The hybridization signal results from the precipitation of nanogold particles on the hybridized spots due to the electrostatic attraction of the cationic gold particles and the anionic phosphate groups in the target DNA backbone. In contrast to conventional fluorescent detection, this nanoparticle-based detection system eliminates the target labeling procedure. The visualization of hybridization signals can be accomplished with a flatbed scanner instead of a confocal laser scanner, which greatly simplifies the process and reduces the cost. The sensitivity is estimated to be less than 2 pg of DNA molecules captured on the array surface. The signal from hybridized spots quantitatively represents the amount of captured target DNA and therefore permits quantitative gene expression analysis. Cross-array reproducibility is adequate for detecting twofold or less signal changes across two microarray experiments.     

Effect of cytokinins on ribosomal RNA gene expression in excised cotyledons of Cucurbita pepo L.

Excised pumpkin (Cucurbita pepo L.) cotyledons were used to investigate the effects of two different types of cytokinins: N⁶-benzyladenine and N₁-(2-chloro-4-pyridyl)-N₂-phenylurea on RNA synthesis in isolated nuclei. Treatment of cotyledons with both cytokinins resulted in a rapid enhancement of nuclear RNA-polymerase-I activity (EC 2.7.7.6). Maximum stimulation of RNA polymerase I, responsible for rRNA synthesis, was observed 4–6 h after the start of cytokinin action. The activity of RNA polymerase II was stimulated much more slowly and to a lesser extent. Uridine 5-monophosphate-uridine analysis of the alkalidigested nascent pre-rRNA chains showed that the stimulation of RNA-polymerase-I activity was the consequence of an increase of the polyribonucleotide-clongation rate. No significant change in the number of transcribing enzyme molecules was defected after hormone treatment (86·10³ RNA-polymerase-I molecules per diploid genome).Indications that de-novo protein synthesis is necessary for cytokinin-mediated RNA-polymerase stimulation were derived from experiments showing inhibition by cycloheximide.Abbreviations BA N⁶-benzyladenine - [PU]-30 N₁-(2-chloro-4-pyridyl)-N₂-phenylurea - UMP undine 5-monophosphate - UTP udine 5-triphosphate     

Preparation of reference strains for validation and comparison of mycoplasma testing methods

Aims: To optimize growth conditions for preparation of stocks of mycoplasma reference strains to obtain highly viable and disperse samples with low ratios of genomic copy (GC) number to that of colony forming units (CFU). These stocks are required for assessment of relative limits of detection (LOD) of alternative nucleic acid testing (NAT)‐based methods in comparison to the conventional microbiological methods. Methods and Results: A kinetics study was used to assess the changes in ratios between the numbers of GC and CFU at different growth phases of six different mycoplasma cultures Acholeplasma laidlawii, Mycoplasma gallisepticum, Mycoplasma arginini, Mycoplasma fermentans, Mycoplasma orale and Mycoplasma pneumoniae. All tested mycoplasmas demonstrated low GC/CFU ratios (≤10) within the log and early stationary growth phases. A significant increase in GC/CFU ratios was observed at the very late stationary and death phases, when the titre of cultures has declined. Similar patterns of GC/CFU profiles were observed for A. laidlawii and Myc. gallisepticum co‐cultured with suspension of Chinese hamster ovary (CHO) cells. Conclusions: Tested mycoplasma strains harvested at the exponential‐early stationary phases of growth demonstrated the lowest GC/CFU ratios and low propensity to form filamentous structures or aggregates under proposed conditions and can be used for the preparation of a mycoplasma reference panel for methods comparability study. Significance and Impact of the Study: This study shows that the preparation and use of viable mycoplasma reference strains with low CG/CFU ratios is the most reliable way to adequately evaluate the LOD of alternative NAT‐based mycoplasma testing methods.