Coupling of an indicator-free electrochemical DNA biosensor with polymerase chain reaction for the detection of DNA sequences related to the apolipoprotein E

This paper describes a disposable indicator-free electrochemical DNA biosensor applied to the detection of apolipoprotein E (apoE) sequences in PCR samples. In the indicator-free assays, the duplex formation was detected by measuring the electrochemical signal of the guanine base of nucleic acids. The biosensor format involved the immobilisation of an inosine-modified (guanine-free) probe onto a screen-printed electrode (SPE) transducer and the detection of the duplex formation in connection with the square-wave voltammetric measurement of the oxidation peak of the guanine of the target sequence.The indicator-free scheme has been characterised using 23-mer oligonucleotides as model: parameters affecting the hybridisation assay such as probe immobilisation conditions, hybridisation time, use of hybridisation accelerators were examined and optimised.The analysis of PCR samples (244 bp DNA fragments, obtained by amplification of DNA extracted from human blood) required a further optimisation of the experimental procedure. In particular, a lower steric hyndrance of the probe modified surface was essential to allow an efficient hybridisation of the target DNA fragment. Negative controls have been performed using the PCR blank and amplicons unrelated to the immobilised probe. A 10 min hybridisation time allowed a full characterisation of each sample.     

Durbin-Watson statistic as a morphological estimator of information content

The present work proposes a new approach for the evaluation of the information content in latent variables, and therefore, for the determination of the regression model dimensionality. Several examples are provided, using simulated, real-world, and reference datasets. The results showed that the application of the Durbin-Watson (DW) criterion could be used for the determination of the number of latent variables. Moreover, the method is straightforward in its implementation and could help in the understanding of model behaviour, particularly in complex datasets. A comparison is made with cross-validation techniques for the case of reference datasets, showing the potential of the Durbin-Watson criterion in the characterisation of the regression model. The advantages and disadvantages of this procedure (compared to cross-validation) are discussed. The properties of the information content of the regression vectors (loadings p, w and b vectors) are shown as well as how to use them for the current purpose.     

Genotyping of exons 1 to 20 in Duchenne muscular dystrophy by universal multiplex PCR and short‐end capillary electrophoresis

One rapid CE method was established to diagnose Duchenne muscular dystrophy (DMD). DMD is a severe recessive inherited disorder frequently caused by gene deletions. Among them, exons 1–20 account for nearly 30% of occurrences. In this study, the universal multiplex PCR was used to enhance the fluorescently labeling efficiency, which was performed only by one universal fluorescent primer. After PCR, a short‐end injection CE (short‐end CE) speeded up the genotyping of the DMD gene. This method involved no extra purification, and was completed within 9 min. The CE conditions contained a polymer solution of 1.5% hydroxylethylcellulose in 1× TBE buffer at 6 kV for separation. This method was applied to test six DMD patients and one healthy male person. The results showed good agreement with those of multiplex ligation‐dependent probe amplification. This method can be applied for clinical diagnosis of DMD disease. Accurate diagnosis of the DMD gene is the best way to prevent the disease.     

A rapid and effective method for silver staining of PCR products separated in polyacrylamide gels

With the development of molecular quantitative genetics, particularly, genetic linkage map construction, quantitative trait loci mapping or genes fine mapping and association analysis etc., more and more PCR products separated in polyacrylamide gels need to be silver‐stained. However, conventional silver‐staining procedures are complicated and time‐consuming as they require a lot of preparation and handling of several solutions prior to use. In this study, a simple and rapid protocol for silver staining of PCR products was developed. The number of steps was reduced compared to conventional protocols, thus achieving detection of PCR products in 7 min, saving time and resources. Fixation and staining solution and developing solution in present staining procedure allowed a reutilization for 12 and 8 times, respectively, reducing the cost greatly. Meanwhile, the sensitivity was significantly improved with the improved method and the minimum of 0.097 ng/μL of DNA amount can be detected in denaturing polyacrylamide gel. The protocol developed in this study will facilitate the development of molecular quantitative genetics.     

Isometric artifacts from polymerase chain reaction-massively parallel sequencing analysis of short tandem repeat loci: An emerging issue from a new technology?

The recent introduction of polymerase chain reaction (PCR)-massively parallel sequencing (MPS) technologies in forensics has changed the approach to allelic short tandem repeat (STR) typing because sequencing cloned PCR fragments enables alleles with identical molecular weights to be distinguished based on their nucleotide sequences. Therefore, because PCR fidelity mainly depends on template integrity, new technical issues could arise in the interpretation of the results obtained from the degraded samples. In this work, a set of DNA samples degraded in vitro was used to investigate whether PCR-MPS could generate “isometric drop-ins” (IDIs; i.e., molecular products having the same length as the original allele but with a different nucleotide sequence within the repeated units). The Precision ID GlobalFiler NGS STR panel kit was used to analyze 0.5 and 1 ng of mock samples in duplicate tests (for a total of 16 PCR-MPS analyses). As expected, several well-known PCR artifacts (such as allelic dropout, stutters above the threshold) were scored; 95 IDIs with an average occurrence of 5.9 IDIs per test (min: 1, max: 11) were scored as well. In total, IDIs represented one of the most frequent artifacts. The coverage of these IDIs reached up to 981 reads (median: 239 reads), and the ratios with the coverage of the original allele ranged from 0.069 to 7.285 (median: 0.221). In addition, approximately 5.2% of the IDIs showed coverage higher than that of the original allele. Molecular analysis of these artifacts showed that they were generated in 96.8% of cases through a single nucleotide change event, with the C > T transition being the most frequent (85.7%). Thus, in a forensic evaluation of evidence, IDIs may represent an actual issue, particularly when DNA mixtures need to be interpreted because they could mislead the operator regarding the number of contributors. Overall, the molecular features of the IDIs described in this work, as well as the performance of duplicate tests, may be useful tools for managing this new class of artifacts otherwise not detected by capillary electrophoresis technology.     

分子生物学手段检测转Bt基因棉花中Cry杀虫蛋白的定性和定量方法

建立了转Bt基因棉花中Cry杀虫蛋白的提取、样品前处理以及酶联免疫(ELISA)定量分析方法,并使用凝胶电泳、普通聚合酶链式反应(PCR)和实时荧光定量PCR等分子生物学手段对转基因棉花中的Bt基因进行定性和定量检测.所建立的苏云金芽孢杆菌杀虫晶体蛋白(Cry1Ab蛋白和Cry1Ac蛋白)标准曲线线性关系良好,相关系数r2均大于0.999,相对标准偏差RSD均小于2.0%.方法简单、快速、重现性和精密度好,可为农业食品行业和环境领域科研人员提供一种简便快速地从转基因棉花中检测Bt毒蛋白的分析方法.     

Evaluation of pharmaceutical activities of G-protein coupled receptor targeted pharmaceuticals in Chinese wastewater effluent

The occurrence of biologically active pharmaceuticals in aquatic environments raised the potential risks to aquatic species. Among these marketed biological active pharmaceuticals, it has been estimated that 40% of them target G-protein-coupled receptors (GPCRs). We have illustrated pharmaceutical activities of GPCR targeted pharmaceuticals in English and Japanese wastewater by the in vitro transforming growth factor-α (TGFα) shedding assay. However, as the most important producer and consumer of pharmaceuticals, the occurrence of GPCR targeted pharmaceuticals in China had remained unclear. In this study, we investigated the pharmaceutical activities of GPCR targeted pharmaceuticals in secondary effluents of Chinese wastewater treatment plants. We discovered antagonistic activities against angiotensin (AT1) receptor at up to 7.2 × 102 ng-valsartan-equivalent quantity/L in Chinese wastewater for the first time as well as agonistic activities against dopamine (D2) receptor. Furthermore, in parallel with the assay, we determined concentrations of GPCR targeted pharmaceuticals in target wastewater by liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS). Through the comparison of predicted antagonistic activities calculated by concentrations and potency values from the assay, we found that the measured antagonistic activities against AT1 receptor from the assay were higher than the predicted AT1 activities from valsartan, irbesartan, and losartan, indicating the potential existence of other unknown AT1 antagonists in wastewater.     

Influence of the solvent quality on the AhR mediated Procept assay measurement of dioxin and dioxin-like compounds

Polychlorodibenzo-p-dioxins, polychorodibenzofurans and “dioxin-like” polychlorinated biphenyls are widespread persistent organic pollutants sharing a similar toxicological pathway mediated by the aryl-hydrocarbon receptor (AhR). Since the confirmatory method for their measurement at trace levels in complex matrices (using isotopic dilution and gas chromatography-high resolution mass spectrometry) remains time and cost-consuming, growing efforts of the scientific community have been focused on the development of screening approaches, including AhR mediated assays. Unfortunately, AhR ligands are highly diverse and agonistic/antagonistic effects can be observed on procedural blanks and/or sample extracts. In this study, the influence of solvent grade quality on the response of a DNA-binding AhR mediated assay used for screening dioxins has been investigated. Our results demonstrated a very critical impact of this parameter with both strong agonistic and antagonistic effects observed for any tested solvent lot. A small silver nitrate silica column removed partly these interfering compounds and then can be recommended as final purification step. Some preferable grades can be identified and selected in order to guarantee the best possible performances. However, it appears necessary to test every new lot, even if a grade appeared previously compliant.