Validation of Zebrafish （Danio redo） Reference Genes for Quantitative Real-time RT-PCR Normalization

The normalization of quantitative real time RT-PCR （qRT-PCR） is important to obtain accurate gene expression data. The most common method for qRT-PCR normalization is to use reference, or housekeeping genes. However, there is emerging evidence that even reference genes can be regulated under different conditions, qRT-PCR has only recently been used in terms of zebrafish gene expression studies and there is no validated set of reference genes. This study characterizes the expression of nine possible reference genes during zebrafish embryonic development and in a zebrafish tissue panel. All nine reference genes exhibited variable expression. The fl-actin, EFlot and Rpll3ot genes comprise a validated reference gene panel for zebrafish developmental time course studies, and the EF1 or, Rpll3α and 18S rRNA genes are more suitable as a reference gene panel for zebrafish tissue analysis. Importantly, the zebrafish GAPDH gene appears unsuitable as reference gene for both types of studies.     

Independence and reproducibility across microarray platforms

Microarrays have been widely used for the analysis of gene expression, but the issue of reproducibility across platforms has yet to be fully resolved. To address this apparent problem, we compared gene expression between two microarray platforms: the short oligonucleotide Affymetrix Mouse Genome 430 2.0 GeneChip and a spotted cDNA array using a mouse model of angiotensin II-induced hypertension. RNA extracted from treated mice was analyzed using Affymetrix and cDNA platforms and then by quantitative RT-PCR (qRT-PCR) for validation of specific genes. For the 11,710 genes present on both arrays, we assessed the relative impact of experimental treatment and platform on measured expression and found that biological treatment had a far greater impact on measured expression than did platform for more than 90% of genes, a result validated by qRT-PCR. In the small number of cases in which platforms yielded discrepant results, qRT-PCR generally did not confirm either set of data, suggesting that sequence-specific effects may make expression predictions difficult to make using any technique.     

RNA integrity and the effect on the real-time qRT-PCR performance

The assessment of RNA integrity is a critical first step in obtaining meaningful gene expression data. Working with low-quality RNA may strongly compromise the experimental results of downstream applications which are often labour-intensive, time-consuming, and highly expensive. Using intact RNA is a key element for the successful application of modern molecular biological methods, like qRT-PCR or micro-array analysis. To verify RNA quality nowadays commercially available automated capillary-electrophoresis systems are available which are on the way to become the standard in RNA quality assessment. Profiles generated yield information on RNA concentration, allow a visual inspection of RNA integrity, and generate approximated ratios between the mass of ribosomal sub-units. In this review, the importance of RNA quality for the qRT-PCR was analyzed by determining the RNA quality of different bovine tissues and cell culture. Independent analysis systems are described and compared (OD measurement, NanoDrop, Bioanalyzer 2100 and Experion). Advantage and disadvantages of RNA quantity and quality assessment are shown in performed applications of various tissues and cell cultures. Further the comparison and correlation between the total RNA integrity on PCR performance as well as on PCR efficiency is described. On the basis of the derived results we can argue that qRT-PCR performance is affected by the RNA integrity and PCR efficiency in general is not affected by the RNA integrity. We can recommend a RIN higher than five as good total RNA quality and higher than eight as perfect total RNA for downstream application.     

Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns

Single-cell quantitative real-time PCR (qRT-PCR) combined with high-throughput arrays allows the analysis of gene expression profiles at a molecular level in approximately 11 h after cell sample collection. We present here a high-content microfluidic real-time platform as a powerful tool for comparatively investigating the regulation of developmental processes in single cells. This approach overcomes the limitations involving heterogeneous cell populations and sample amounts, and may shed light on differential regulation of gene expression in normal versus disease-related contexts. Furthermore, high-throughput single-cell qRT-PCR provides a standardized, comparative assay for in-depth analysis of the mechanisms underlying human pluripotent stem cell self-renewal and differentiation.     

An integrated biosensor platform for extraction and detection of nucleic acids

The development of portable systems for analysis of nucleic acids (NAs) is crucial for the evolution of biosensing in the context of future healthcare technologies. The integration of NA extraction, purification, and detection modules, properly actuated by microfluidics technologies, is a key point for the development of portable diagnostic systems. In this paper, we describe an integrated biosensor platform based on a silicon–plastic hybrid lab-on-disk technology capable of managing NA extraction, purification, and detection processes in an integrated format. The sample preparation process is performed by solid-phase extraction technology using magnetic beads on a plastic disk, while detection is done through quantitative real-time polymerase chain reaction (qRT-PCR) on a miniaturized silicon device. The movement of sample and reagents is actuated by a centrifugal force induced by a disk actuator instrument. The assessment of the NA extraction and detection performance has been carried out by using hepatitis B virus (HBV) DNA genome as a biological target. The quantification of the qRT-PCR chip in the hybrid disk showed an improvement in sensitivity with respect to the qRT-PCR commercial platforms, which means an optimization of time and cost. Limit of detection and limit of quantification values of about 8 cps/reaction and 26 cps/reaction, respectively, were found by using analytical samples (synthetic clone), while the results with real samples (serum with spiked HBV genome) indicate that the system performs as well as the standard methods.     

黄瓜全基因组热激转录因子(HSFs)的鉴定与表达分析

热激转录因子 (Heat shock factors, HSFs) 普遍存在于整个生物界。尽管植物HSFs的DNA 结合域具有较高的保守性, 但其结构特征、生物功能具有多样化的特点。本文利用黄瓜(Cucumis sativus L.)全基因组测序结果, 运用生物信息学方法鉴定了黄瓜HSFs, 并对其数量、序列特征、染色体定位以及系统发育关系等进行分析。结果表明, 黄瓜至少含有21个HSFs基因家族成员, 编码184～560个氨基酸, 分子量21.2~62.3 kDa, 等电点(PI)4.70~9.10; 序列比对发现这些成员都具有转录因子特有的DNA结合域(DNA binding domain, DBD); 染色体定位分析表明, 除Csa026480之外, 其余HSFs不均匀分布在黄瓜7条染色体上。从拟南芥(Arabidopsis thaliana)和黄瓜HSFs系统发育树可以看出, 这些转录因子分为3个分支, 其中Ⅰ分支进一步可分为3类(A、B、C类), 系统发育分析揭示黄瓜HSFs蛋白存在9对直系同源蛋白, 3对旁系同源蛋白, 表明HSF转录因子基因家族的多样化发生在黄瓜和拟南芥分化之前。EST表达分析发现这些热激转录因子参与黄瓜的果实、雌花和两性花的发育与形成; 通过qRT-PCR分析, 发现这些基因在黄瓜苗期应对高温热激响应中表达水平存在显著的差异。研究结果为进一步分析黄瓜热激转录因子奠定了基础。     

不同波长光源对新蚜虫疠霉产孢能力的影响及霉菌蓝光受体基因的克隆和表达分析

光在调控真菌的多种生理过程中发挥着重要作用。为探究光照对新蚜虫疠霉Pandora neoaphidis产孢的影响,本文研究了不同波长光源(蓝光、绿光、白光、红光、黄光)和无光黑暗条件对新蚜虫疠霉分生孢子弹射能力的影响,通过cDNA末端的快速扩增(RACE)对新蚜虫疠霉的蓝光受体蛋白基因pnwc-1进行克隆并对其进行生物信息学分析,利用qRT-PCR对蓝光光源不同照射时长下pnwc-1的表达量进行了定量分析。结果表明,蓝色光源(波长460–465nm)照射后的新蚜虫疠霉菌丝产生的分生孢子数量显著高于其他波长光源,排序为:蓝光>绿光>白光>红光>黄光>无光。另外,分析克隆获得的全长为2 423bp的pnwc-1基因发现,其编码的蛋白具有蓝光受体蛋白典型的保守结构域,同源比对结果显示新蚜虫疠霉与接合菌门真菌归为一类但相对独立。qRT-PCR的定量分析结果表明随着照射时长增加,蓝光处理能显著提高pnwc-1的表达量,而且pnwc-1的相对表达量与累积产孢量存在正相关(R2=0.9798)。本研究为后续蓝光及其受体基因功能的深入研究提供了实验基础,并促进以新蚜虫疠霉为代表的虫霉目真菌在害虫生物防治中的应用。