寡核苷酸探针悬浮芯片在病原体检测中的应用

悬浮芯片与固体芯片、荧光定量PCR并列成为核酸序列鉴定中的重要的分子生物学工具,并在病原菌检测方面显示出不同的应用领域.悬浮芯片能同时检测多种病原菌,具有处理多样本能力、使用灵活、低成本等特点,适合对未知样本检测及环境监控.能够在生物安全、公共卫生、工农业生产中发挥重要作用;而固体芯片能耦联成千上百个探针,但由于在多样本处理、成本方面欠缺,因此适合于对重要的未知病原体的鉴定;荧光定量PCR具较好特异性、灵敏度,以及多样本处理能力,但在高通量方面欠缺.适合有目的地检测已知病原体.目前已建立三种基于悬浮芯片的检测方法:多重PCR扩增、通用引物扩增16S/23S rDNA、直接对实际样本杂交检测.多重PCR具较好特异性,但其多重能力还难以满足悬浮芯片的高通量的需要;通用引物具较好灵敏度及扩增多靶分子能力,但也存在交叉反应等缺陷.同时,采用PCR扩增方法,悬浮芯片检测的是PCR产物,不能客观反应实际样本中存在病原菌数量及是否具生命力.直接杂交环境样本尽管避免了PCR的缺陷,但在灵敏度方面非常欠缺.目前,在环境样本处理上,仍然缺乏有效的、高通量、自动化的方法,不能满足PCR与悬浮芯片多样本检测的需要.     

悬浮芯片在核酸和蛋白质检测中的应用

悬浮芯片是近年来兴起的一种新型检测技术,不同于固相基因芯片,它整合了高分子化学、分子生物学、免疫学、激光检测、微流体、高速数字信号处理、计算机分析等方面的先进技术,能够对少量样本进行高通量的定性、定量检测。主要综述了悬浮芯片技术的基本原理,并概要介绍了其在核酸和蛋白质检测中的应用。悬浮芯片技术在核酸和蛋白质检测中有着显著的优点,如高通量、操作简便、重复性好、灵敏度高、线性范围宽等,不但可以广泛应用于科学研究领域,而且还将逐渐普及于临床诊断实验室,具有广阔的应用前景。     

复合式悬液芯片系统在病原学检测中的临床应用

复合式悬液芯片系统（multiplex suspension array system,MSAS）由悬浮芯片和微流体芯片组成,具有高通量精确定量的特点,而且具有较高的准确性和重复性,在多种蛋白质分子的同时精确定量和大规模样品检测方面有着很大的应用优势,其应用领域覆盖感染性疾病的快速诊断、细胞因子、信号通路、肿瘤标志物、流行病学病原体的筛查、蛋白质的相互作用、单核苷酸多态性（SNP）的研究等。就MSAS在病原学检测中的应用作一简要综述。     

开发应用于Bio-Plex悬液芯片系统抗IL-17A的单克隆抗体

利用大肠杆菌(E.coli)表达的IL-17A单体蛋白免疫小鼠,通过杂交瘤技术获得针对IL-17A的单克隆抗体,用Bio-Plex悬浮芯片技术筛选出能通过双抗夹心法识别IL-17A的高亲和力单克隆抗体对,最终实现用Bio-Plex悬浮芯片技术定量检测样品中IL-17A含量的研究目标。     

七重呼吸道病毒液相芯片核酸检测技术的初步建立

由呼吸道病毒引起的疾病严重威胁着人类的生命健康,为了建立一种快速高通量的呼吸道病毒核酸检测方法,本研究将多重PCR技术同液相芯片技术结合起来,针对呼吸道合胞病毒A型和B型、乙型流感病毒Victoria系和Yamagata系、甲型流感病毒H1型和H3型以及新冠病毒等常见的七种呼吸道病毒,初步建立了七重呼吸道病毒液相芯片核酸检测技术,评价了方法的特异性、敏感性和重复性,并使用来自安徽省疾控的25份临床急性期样本核酸对方法进行验证。结果显示,建立起的基于液相芯片多重核酸检测方法可特异性识别七种目标呼吸道病毒的靶基因序列,与包括副流感病毒在内的9种非目标呼吸道病毒无交叉反应。对七种病毒核酸进行十倍稀释液相检测,其中H3、BV、RSVB可以检出10²拷贝/μL,BY、RSVA和SARS-CoV-2可以检出10³拷贝/μL,对H1的检测限为10⁴拷贝/μL。25份样本核酸检测结果与实际相符。结果表明,本研究建立的七重呼吸道病毒液相芯片核酸检测技术具有特异性强、敏感性高、稳定性好等特点,可用于临床样本的快速检测,为呼吸道类传染病的液相...     

cDNA芯片差异表达基因检测的非转换方法

cDNA微阵列数据中包含许多变异因素,用于检测差异表达基因和其它统计分析前,必须将这些“噪音”剔除。对数比法（背景校正、对数比转换和数据标准化）已经被广泛应用于cDNA微阵列数据分析中,然而这种方法却存在着一些亟待解决的缺陷。对此,该文提出一种非转换方法,它可免去对数比的转化过程,直接在背景校正后进行数据标准化,可以有效剔除实验“噪音”。研究结果表明：在检测差异表达基因的效率方面,非转换方法比常规的对数比法具有更好的稳健性和更高的检测功效,基因检出率和准确性大大提高。     

新城疫液相芯片快速检测方法的建立

目的：建立可检测新城疫病毒（Newcastle disease virus,NDV）的液相芯片快速检测技术。方法：用DNAStar软件对GEN-BANK中NDV的NP基因进行序列分析设计NDV特异性探针并标记生物素,利用该探针与荧光编码微球偶联后与抽提的NDV病毒RNA的RT-PCR产物杂交反应,用液相芯片检测仪（Liquichip 200）检测荧光信号建立了NDV快速液相芯片检测方法。结果：检测结果显示,该法具有较好的特异性,不与H5AIV和H9AIV反应;检测灵敏度达到150个EID50;该法与鸡胚病毒分离法检出NDV的符合率达到97.1%。结论：初步建立了检测NDV的液相芯片技术,为进一步搭建NDV全新快速高通量检测平台奠定了基础,也为其他同类病毒的快速高通量检测提供了借鉴和经验。     

快速老化小鼠海马差异表达cDNA芯片的制作

老年性痴呆(Alzheimer’s disease,AD)是老年人群中最普遍的痴呆类型,是一种神经退行性紊乱疾病,目前临床上还没有有效的治疗方法。快速老化小鼠亚系P8(senescence-accelerated mouse prone8,SAMP8)是研究增龄相关性认知缺陷机制以及研究脑老化机制的良好动物,同时也是研究AD较为理想的实验动物模型之一。cDNA芯片技术可以同时规模研究成千上万个基因的表达,尤其适于AD这种多机制、多靶标、多途径的复杂疾病的研究,为了揭示AD的发病机制,发现用于治疗AD的药物靶标,以SAMP8和SAMR1海马抑制消减cDNA文库中的cDNA片段为材料,以β-actin和G3PDH为内参,设计了16×(1×14)点阵方案,并点制了含有3136个点的SAM海马差异表达cDNA芯片。芯片背景均匀一致,点的大小均一,排列规则整齐。在靶分子与探针杂交过程中,进行了杂交条件和洗涤芯片的优化。将杂交结果进行统计分析,选择差异表达的cDNA进行测序并进行生物信息学分析,用实时定量RT-PCR对部分基因的表达进行了验证,检测了芯片筛选结果的可靠性。该芯片的成功制备为进一步进行差异表达基因的筛选和研究提供了良好的手段,并将成为揭示SAMP8脑老化和AD发病机制的有力手段。     

DNA芯片技术中利用内标对数据归一化后检测基因的表达变化

在DNA芯片技术中 ,通过反转录反应 ,由mRNA合成带有荧光标记物的cDNA的过程中 ,往往要参入已知质量的poly(A) + RNA ,以对DNA芯片的检测灵敏度进行归一化处理 .通过体外转录的方法 ,以真核生物的cDNA克隆中的DNA片段为模板合成poly(A) +RNA ,对之定量后 ,以不同的质量比参入到样品的反转录体系中 ,代表不同的RNA拷贝丰度 ,从而对DNA芯片检测的灵敏度进行了定量 ,并得到DNA芯片上杂交点的荧光信号强度与基因表达的RNA拷贝数成正相关的关系 .利用含有内标的DNA芯片检测了热击反应后酵母细胞的基因表达变化 ,结果与Northern印迹方法检测结果是相符的     

Determination of multiple redox-active compounds by high-performance liquid chromatography with coulometric multi-electrode array system

Studies of the antioxidant defense system and the related metabolic pathways are often complicated by cumbersome analytical methods, which require separate and multi-step extraction and chemical reaction procedures. Further, assaying multiple parameters is limited because of the usual small sample amounts. High-performance liquid chromatography coupled with a coulometric multi-electrode array system provides us high specificity and sensitivity to measure electrochemically oxidizable compounds in biological samples. In contrast to previously reported methods with two columns in series and a complex gradient elution profile, we have developed an automated procedure to simultaneously measure multiple redox-active low-molecular weight compounds that utilizes a single column with a simplified binary gradient profile. No other chemical reactions are necessary. In order to reduce the running time and yet achieve a reproducible retention time by the auto sampler injection, our gradient elution profile was modified to produce a shorter equilibration time, stable retention time, and a reduced cost per test.     

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     

Cytoplasmic polyhedrosis virus-induced differential gene expression in two silkworm strains of different susceptibility

Digital gene expression (DGE) was performed to investigate the gene expression profiles of 4008 and p50 silkworm strains at 48 h after oral infection with BmCPV. 3,668,437 clean tags were identified in the BmCPV-infected p50 silkworms and 3,540,790 clean tags in the control p50. By contrast, 4,498,263 clean tags were identified in the BmCPV-infected 4008 silkworms and 4,164,250 clean tags in the control 4008. A total of 691 differentially expressed genes were detected in the infected 4008 DGE library and 185 were detected in the infected p50 DGE library, respectively. The expression profiles identified some important differentially expressed genes involved in signal transduction, enzyme activity and apoptotic changes, some of which were verified using quantitative real-time PCR (qRT-PCR). These results provide important clues on the molecular mechanism of BmCPV invasion and resistance mechanism of silkworms against BmCPV infection.     

Developmental competence and gene expression of immature oocytes following liquid helium vitrification in bovine

The objective of this study was to develop an effective ultra-rapid vitrification method and evaluate its effect on maturation, developmental competence and development-related gene expression in bovine immature oocytes. Bovine cumulus oocyte complexes were randomly allocated into three groups: (1) controls, (2) liquid nitrogen vitrification, and (3) liquid helium vitrification. Oocytes were vitrified and then warmed, the percentage of morphologically normal oocytes in liquid helium group (89.0%) was significantly higher (P < 0.05) than that of the liquid nitrogen group (81.1%). When the vitrified–thawed oocytes were matured in vitro for 24 h, the maturation rate in liquid helium group (50.6%) was higher (P < 0.05) than liquid nitrogen group (42.6%). Oocytes of liquid helium vitrification had higher cleavage and blastocyst rates (41.1% and 10.0%) than that of liquid nitrogen vitrification (33.0% and 4.5%; P < 0.05) after in vitro fertilization. Moreover, the expression of GDF9 (growth/differentiation factor-9), BAX (apoptosis factor) and ZAR1 (zygote arrest 1) was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) when the vitrified–thawed oocytes were matured 24 h. The expression of these genes was altered after vitrification. Expression of GDF9 and BAX in the liquid helium vitrification group was not significantly different from that of the control, however there were significant differences between the liquid nitrogen vitrification group and control. In conclusion, it was feasible to use liquid helium for vitrifying bovine immature oocytes. There existed an association between the compromised developmental competence and the altered expression levels of these genes for the vitrified oocytes.     

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq

Background

Massively parallel cDNA sequencing (RNA-seq) experiments are gradually superseding microarrays in quantitative gene expression profiling. However, many biologists are uncertain about the choice of differentially expressed gene (DEG) analysis methods and the validity of cost-saving sample pooling strategies for their RNA-seq experiments. Hence, we performed experimental validation of DEGs identified by Cuffdiff2, edgeR, DESeq2 and Two-stage Poisson Model (TSPM) in a RNA-seq experiment involving mice amygdalae micro-punches, using high-throughput qPCR on independent biological replicate samples. Moreover, we sequenced RNA-pools and compared their results with sequencing corresponding individual RNA samples.

Results

False-positivity rate of Cuffdiff2 and false-negativity rates of DESeq2 and TSPM were high. Among the four investigated DEG analysis methods, sensitivity and specificity of edgeR was relatively high. We documented the pooling bias and that the DEGs identified in pooled samples suffered low positive predictive values.

Conclusions

Our results highlighted the need for combined use of more sensitive DEG analysis methods and high-throughput validation of identified DEGs in future RNA-seq experiments. They indicated limited utility of sample pooling strategies for RNA-seq in similar setups and supported increasing the number of biological replicate samples.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1767-y) contains supplementary material, which is available to authorized users.     

HCV E2区基因在真核表达系统中的表达

以原核表达载体pET-E2为模板,用PCR的方法重新扩增出带有适于真核表达载体多克隆位点的E2基因,PCR产物经纯化并双酶切后与相同处理的真核表达载体pSecTag2/Hygro连接并转化大肠杆菌DH5α感受态细胞,重组表达载体在大量扩增并纯化后再转染COS7细胞,收集的培养上清经过Ni-柱纯化,用ELISA进行血清检测显示,6份HCV阳性血清中有4份检出有E2抗体,而5份HCV阴性血清也有一份检出有E2抗体。     

Modeling and optimization of the baculovirus expression vector system in batch suspension culture

A mathematical model has been developed that predicts the cell population dynamics and production of recombinant protein and infective extracellular virus progeny by insect cells after infection with baculovirus in batch suspension culture. Infection in the model is based on the rate of virus attachment to suspended insect cells under culture conditions. The model links the events following infection with the sequence of gene expression in the baculovirus replicative cycle. Substrate depletion is used to account for the decrease in product yield observed when infecting at high cell densities. Model parameters were determined in shaker flasks for two media: serum-supplemented IPL-41 medium and serum free Sf900II medium. There was good agreement between model predictions and the results from an independent series of experiments performed to validate the mode. The model predicted: (1) the optimal time of infection at high multiplicity of infection: (2) the timing and magnitude of recombinant protein production in a 2-L bioreactor; and (3) the timing and magnitude of recombinant protein production at multiplicities of infection from 0.01 to 100 plaque-forming units per cell. Through its ability to predict optimal infection strategies in batch suspension culture, the model has use in the design and optimization of large-scale systems for the production of recombinant products using the baculovirus expression vector system. (c) 1994 John Wiley & Sons, Inc.