Polymerase chain reaction-restriction fragment length polymorphism analysis of mitochondrial cytb gene from species of dairy interest

Species identification plays an important role in food allergy prevention and food substitution detection that can reduce the commercial value of a product. For these reasons, many molecular methods have been developed to determine species origin; among them, polymerase chain reaction (PCR)-based methods were successfully applied to processed or unprocessed foodstuffs. An updated PCR-RFLP (restriction fragment length polymorphism) method of the cytb gene was developed for the identification of the 4 species of main interest in the dairy industry (Bos, Ovis, Capra, Bubalus). The comparative analysis of the 92 cytb sequences available in the database belonging to the 4 species allowed identification of 2 highly conserved regions, which were used to design 2 oligonucleotides for the PCR amplification of a 275 base-pair (bp) cytb fragment. The in silico analysis allowed identification of a set of species-specific restriction endonucleases (HaeIII, TaqI, and MwoI), which generated easily analyzable species-specific restriction profiles of the 275 bp cytb DNA fragment. The system was developed for both purified DNA and DNA extracted from meat or dairy products and finally tested on mixed samples, indicating its applicability to foodstuffs.     

Detection and identification of multiple genetically modified events using DNA insert fingerprinting

Current screening and event-specific polymerase chain reaction (PCR) assays for the detection and identification of genetically modified organisms (GMOs) in samples of unknown composition or for the detection of non-regulated GMOs have limitations, and alternative approaches are required. A transgenic DNA fingerprinting methodology using restriction enzyme digestion, adaptor ligation, and nested PCR was developed where individual GMOs are distinguished by the characteristic fingerprint pattern of the fragments generated. The inter-laboratory reproducibility of the amplified fragment sizes using different capillary electrophoresis platforms was compared, and reproducible patterns were obtained with an average difference in fragment size of 2.4 bp. DNA insert fingerprints for 12 different maize events, including two maize hybrids and one soy event, were generated that reflected the composition of the transgenic DNA constructs. Once produced, the fingerprint profiles were added to a database which can be readily exchanged and shared between laboratories. This approach should facilitate the process of GMO identification and characterization.     

Platinum nanoparticle-facilitated reflective surfaces for non-contact temperature control in microfluidic devices for PCR amplification

The polymerase chain reaction (PCR) is critical for amplification of target sequences of DNA or RNA that have clinical, biological or forensic relevance. While extrinsic Fabry-Perot interferometry (EFPI) has been shown to be adequate for non-contact temperature sensing, the difficulty in defining a reflective surface that is semi-reflective, non-reactive for PCR compatibility and adherent for thermal bonding has limited its exploitation. Through the incorporation of a reflective surface fabricated using a thermally driven self-assembly of a platinum nanoparticle monolayer on the surface of the microfluidic chamber, an enhanced EFPI signal results, allowing for non-contact microfluidic temperature control instrumentation that uses infrared-mediated heating, convective forced-air cooling, and interferometic temperature sensing. The interferometer is originally calibrated with a miniature copper-constantan thermocouple in the PCR chamber resulting in temperature sensitivities of -22.0 to -32.8 nm·°C(-1), depending on the chamber depth. This universal calibration enables accurate temperature control in any device with arbitrary dimensions, thereby allowing versatility in various applications. Uniquely, this non-contact temperature control for PCR thermocycling is applied to the amplification of STR loci for human genetic profiling, where nine STR loci are successfully amplified for human identification using the EFPI-based non-contact thermocycling.     

Practical integration of polymerase chain reaction amplification and electrophoretic analysis in microfluidic devices for genetic analysis

An integrated system of a silicon-based microfabricated polymerase chain reaction (microPCR) chamber and microfabricated electrophoretic glass chips have been developed. The PCR chamber was made of silicon and had aluminum heaters and temperature sensors integrated on the glass anodically bonded cover. Temperature uniformity in the reaction chamber was +/-0.3 degrees C using an improved novel "joint-heating" scheme. Thermal cycling was digitally controlled with a temperature accuracy of +/- 0.2 degrees C. Small operating volumes together with high thermal conductivity of silicon made the device well suited to rapid cycling; 16 s/cycle were demonstrated. For analysis of the PCR products, the chamber output was transferred to the glass microchip by pressure. Analysis time of PCR amplified genomic DNA was obtained in the microchip in less than 180 s. The analysis procedure employed was reproducible, simple and practical by using viscous sieving solutions of hydroxypropylmethylcellulose and dynamically coated microchip channels with poly(vinylpyrrolidone). DNA fragments that differ in size by 18 base pairs (bp) were resolved. Analysis of genomic male and female amplified DNA by microPCR was achieved in microchip, and application of the integrated microPCR-microchip for the identification of bird sex was tested. Genomic DNA samples from several bird species such as pigeon and chicken were analyzed. Hence, the system could be used as well to determine the sex of avian species.     

A review of the DNA standard reference materials developed by the National Institute of Standards and Technology

The Standard Reference Materials Program at the US National Institute of Standards and Technology (NIST) has three human DNA standard reference materials (SRM 2390, SRM 2391a, and SRM 2392) currently available [1, 2]. Both the DNA profiling SRM 2390 and the polymerase chain reaction (PCR)-based DNA profiling SRM 2391a are intended for use in forensic and paternity identifications, for instructional law enforcement, or for non-clinical research purposes and are not intended for clinical diagnostics. The mitochondrial DNA (mtDNA) SRM 2392 is to provide standardization and quality control when performing PCR and sequencing any segment or the entire 16,569 base pairs that comprise human mitochondrial DNA. SRM 2392 is designed for use by the forensic, medical, and toxicological communities for human identification, disease diagnosis or mutation detection.     

Development of a real-world direct interface for integrated DNA extraction and amplification in a microfluidic device

Integrated DNA extraction and amplification have been carried out in a microfluidic device using electro-osmotic pumping (EOP) for fluidic control. All the necessary reagents for performing both DNA extraction and polymerase chain reaction (PCR) amplification were pre-loaded into the microfluidic device following encapsulation in agarose gel. Buccal cells were collected using OmniSwabs [Whatman?, UK] and manually added to a chaotropic binding/lysis solution pre-loaded into the microfluidic device. The released DNA was then adsorbed onto a silica monolith contained within the DNA extraction chamber and the microfluidic device sealed using polymer electrodes. The washing and elution steps for DNA extraction were carried out using EOP, resulting in transfer of the eluted DNA into the PCR chamber. Thermal cycling, achieved using a Peltier element, resulted in amplification of the Amelogenin locus as confirmed using conventional capillary gel electrophoresis. It was demonstrated that the PCR reagents could be stored in the microfluidic device for at least 8 weeks at 4 °C with no significant loss of activity. Such methodology lends itself to the production of 'ready-to-use' microfluidic devices containing all the necessary reagents for sample processing, with many obvious applications in forensics and clinical medicine.     

Minireview: Whole-cell,Nucleotide, and Enzyme Inhibition-based Biosensors for the Determination of Arsenic

Arsenic is a natural and highly toxic environmental contaminant and is intensely connected with human health. It can cause DNA damage, mutations, neurological disorders, and cancer. In previous few decades, large numbers of biosensors for recognition and identification of arsenic both qualitatively and quantitatively have been developed. The biosensor is a logical device that is usually used for identification of a particular or a group of analytes in samples. This review aims at various advancements made in the improvement of biosensors for arsenic detection such as whole cell-based, nucleotide-based, and enzyme inhibition-based biosensors. The review focuses on the technology used for development of arsenic biosensor along with their advantages and limitations.     

Microfabricated PCR-electrochemical device for simultaneous DNA amplification and detection

Microfabricated silicon/glass-based devices with functionalities of simultaneous polymerase chain reaction (PCR) target amplification and sequence-specific electrochemical (EC) detection have been successfully developed. The microchip-based device has a reaction chamber (volume of 8 microl) formed in a silicon substrate sealed by bonding to a glass substrate. Electrode materials such as gold and indium tin oxide (ITO) were patterned on the glass substrate and served as EC detection platforms where DNA probes were immobilized. Platinum temperature sensors and heaters were patterned on top of the silicon substrate for real-time, precise and rapid thermal cycling of the reaction chamber as well as for efficient target amplification by PCR. DNA analyses in the integrated PCR-EC microchip start with the asymmetric PCR amplification to produce single-stranded target amplicons, followed by immediate sequence-specific recognition of the PCR product as they hybridize to the probe-modified electrode. Two electrochemistry-based detection techniques including metal complex intercalators and nanogold particles are employed in the microdevice to achieve a sensitive detection of target DNA analytes. With the integrated PCR-EC microdevice, the detection of trace amounts of target DNA (as few as several hundred copies) is demonstrated. The ability to perform DNA amplification and EC sequence-specific product detection simultaneously in a single reaction chamber is a great leap towards the realization of a truly portable and integrated DNA analysis system.     

Dot-blot amperometric genosensor for detecting a novel determinant of beta-lactamase resistance in Staphylococcus aureus

A new electrochemical hybridisation genosensor for the detection of resistant bacteria has been developed. This device relies on the immobilisation of a 50-mer oligonucleotide target, unique to a novel determinant of beta-lactamase resistance in Staphylococcus aureus, onto an electrochemical transducer. This genosensor is based on a concept adapted from classical dot-blot DNA analysis, but implemented in an electrochemical biosensor configuration. Amperometric transduction and an enzyme label method, that increases the genosensor sensitivity, are the main features of this new approach. In addition to the adapted dot-blot format, a double hybridisation assay, in which two different labelled probes were used, is reported. This procedure, if combined with polymerase chain reaction (PCR), allows determination of the genotype of an antibiotic-resistant organism in a shorter time than that required to perform traditional phenotypic susceptibility testing. Its characteristics are ideal for implementation in a kit form.     

Quantification of DNA in forensic samples

Quantification of DNA in a forensic sample is of major importance for proper DNA amplification and STR profiling. Several methods have been developed to quantify DNA, from basic UV spectrometry, through gel-based techniques, to dye staining, blotting techniques, and, very recently, DNA amplification methods (polymerase chain reaction, PCR). Early techniques simply measured total DNA, but newer techniques can specifically measure human DNA while excluding non-human DNA (foodstuff, animal, or bacterial contamination). These newer assays can be faster and less expensive than traditional methods, making them ideal for the busy forensic laboratory. This paper reviews classic and newer quantification techniques and presents methods recently developed by the authors on the basis of PCR of Alu sequences.     

A valveless microfluidic device for integrated solid phase extraction and polymerase chain reaction for short tandem repeat (STR) analysis

A valveless microdevice has been developed for the integration of solid phase extraction (SPE) and polymerase chain reaction (PCR) on a single chip for the short tandem repeat (STR) analysis of DNA from a biological sample. The device consists of two domains--a SPE domain filled with silica beads as a solid phase and a PCR domain with an ~500 nL reaction chamber. DNA from buccal swabs was purified and amplified using the integrated device and a full STR profile (16 loci) resulted. The 16 loci Identifiler? multiplex amplification was performed using a non-contact infrared (IR)-mediated PCR system built in-house, after syringe-driven SPE, providing an ~80-fold and 2.2-fold reduction in sample and reagent volumes consumed, respectively, as well as an ~5-fold reduction in the overall analysis time in comparison to conventional analysis. Results indicate that the SPE-PCR system can be used for many applications requiring genetic analysis, and the future addition of microchip electrophoresis (ME) to the system would allow for the complete processing of biological samples for forensic STR analysis on a single microdevice.     

Multiplex polymerase chain reaction method for detection of bovine materials in foodstuffs

Rapid identification of bovine materials in animal foodstuffs is essential for effective control of a potential source of bovine spongiform encephalophathy. A convenient polymerase chain reaction (PCR)-based assay was developed for detection and identification of a bovine-specific genomic DNA sequence in foodstuffs. Simultaneously the assay assessed the DNA quality of the experiment system by amplification of a highly conserved eucaryotic DNA region of the 18-S ribosomal gene, helping to check the reliability of the test result. The amplified bovine-specific PCR product was a genomic DNA fragment of lactoferrin, a low copy gene that was different from a commonly used bovine-specific mitochondria sequence for identification of bovine materials. The specificity of this method was confirmed by the absence of detectable homologous PCR product using reference foodstuff samples that lacked bovine-derived meat and bonemeals, or genomic DNA samples from vertebrates whose offals are commonly included in animal feeds. This method could detect the presence of bovine material in foodstuffs when the samples contained > 0.02% bovine-derived meat and bone meal. Furthermore, it was not affected by prolonged heat treatment. The specificity, convenience, and sensitivity of this method suggest that it can be used for the routine detection of bovine-derived materials.     

DNA analysis on microfabricated electrophoretic devices with bubble cells

Microfluidic devices with bubble cells have been fabricated on poly(methyl methacrylate) (PMMA) plates and have been employed for the analysis of DNA using polyethylene oxide (PEO) solutions. First, the separation channel was fabricated using a wire-imprinting method. Then, wires with greater sizes or a razor blade glued in a polycarbonate plate was used to fabricate bubble cells, with sizes of 190-650 microm. The improvements in resolution and sensitivity have been achieved for large DNA (> 603 base pair, bp) using such devices, which depend on the geometry of the bubble cell. The main contributor for optimal resolution is mainly due to DNA migration at lower electric field strengths inside the bubble cell. On the other hand, slight losses of resolution for small DNA fragments have been found mainly due to diffusion, supported by the loss of resolution when separating two small solutes. With a bubble cell of 75 microm (width) x 500 microm (depth), the sensitivity improvement up to 17-fold has been achieved for the 271 bp fragment in the separation of PhiX-174/HaeIII DNA restriction fragments. We have also found that a microfluidic device with a bubble cell of 360 microm x 360 microm is appropriate for DNA analysis. Such a device has been used for separating DNA ranging from 8 to 2176 bp and polymerase chain reaction (PCR) products amplified after 30 cycles, with rapidity and improvements in the sensitivity as well as resolution.     

Universal optical assays based on multi-component nanoprobes for genomic deoxyribonucleic acid and proteins

In this report, we developed a universal assay method for both genomic DNA and proteins by using enzyme-based multi-component optical nanoprobes. The nanoprobes are gold nanoparticles assembled with bio-recognizing and signaling elements. We firstly demonstrated that the nanoprobes could detect unpurified asymmetric polymerase chain reaction (PCR) product from genomic DNA of Escherichia coli, with the sensitivity approximately 10 times higher than that of quantitative real-time PCR assay. The limit of detection (LOD) of our nanoprobe-based method is less than 10 pg template DNA (target DNA). Using DNA aptamers as recognition elements, we also showed that as few as 0.1 nM thrombin could be colorimetrically detected with high specificity. These results indicated that the enzyme-based multi-component nanoprobes have the capability to work with real biological samples, and have the potential in various biological and clinical applications.     

疑似蛇毒液样品的纳升级超高效液相色谱-高分辨质谱分析鉴定

针对5个疑似蛇毒毒液及其沾染样品,基于纳升级超高效液相色谱-四极杆-静电场轨道阱高分辨质谱（Nano LC-MS/HRMS）技术,结合尺寸排阻色谱分离,建立了一种蛋白质种类及物种归属的严格鉴定方法。5个样品经尺寸排阻色谱分离后均得到3个洗脱峰,分别冻干后以胰蛋白酶进行溶液内酶解处理并进行液相色谱-高分辨质谱分析鉴定。首先采用全扫描-数据依赖型MS/MS（Full MS/dd MS²）采集模式对样品中的肽段信息进行非靶向采集,依次与Swiss-Prot、蛇亚目（Serpentes）、游蛇科（Colubroidea）、眼镜蛇科（Elapidae）、眼镜蛇亚科（Elapinae）、眼镜蛇属（Naja）蛋白质数据库逐级收缩比对;再筛选符合肽谱匹配度、肽段错误发现率小于1%和特征肽段数目大于等于2的蛋白质,共鉴定到32种蛋白质均来自中华眼镜蛇（Naja atra）,可归属于Naja atra的10个家族,主要为三指毒素、金属蛋白酶、磷脂酶A2等。最后,采用平行反应监测模式选取每种蛋白质的两条特征肽段进行靶向验证,当两条特征肽段均满足“至少75%的y⁺和b⁺离子的Δm/z小于5 ppm”时,方认为鉴定到了样品中的某一蛋白质。最终鉴定出5个样品均含有Naja atra蛇毒。此鉴定方法研究系统、严格,可为蛇毒中毒司法鉴定以及毒药物研究等提供有效的技术支持。     

Easy DNA extraction for rapid detection of Panax ginseng C. A. Meyer in commercial ginseng products

An investigation was carried out in order to obtain an easy and rapid detection of Panax ginseng in commercial herbal products by using molecular techniques (polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP)). Two protocols and one commercial kit for DNA extraction were used. Four forms of commercial products were considered, i.e., dried body roots, dried root tails, dried root prongs and dried extracts. The RFLP of DNA amplified products by 18df/28ccr primers, obtained using Inf I, Sau 3A1 and Taq I endonucleases, allowed the identification of P. ginseng and its differentiation from P. quinquefolium. The presence of adulterants, as Mirabilis jalapa L. and Phytolacca acinosa Roxb. was excluded in the examined commercial samples. P. ginseng was detected in 63% of the considered samples according to the declaration of the labels, whereas negative results were obtained with the dried extract form. Therefore, the Invitrogen DNA extraction kit let the easy extraction of useful amounts of DNA and a standardisation of routine work, in comparison with the other molecular protocols so far used.     

Highly sensitive polymerase chain reaction-free quantum dot-based quantification of forensic genomic DNA

Forensic DNA samples can degrade easily due to exposure to light and moisture at the crime scene. In addition, the amount of DNA acquired at a criminal site is inherently limited. This limited amount of human DNA has to be quantified accurately after the process of DNA extraction. The accurately quantified extracted genomic DNA is then used as a DNA template in polymerase chain reaction (PCR) amplification for short tandem repeat (STR) human identification. Accordingly, highly sensitive and human-specific quantification of forensic DNA samples is an essential issue in forensic study. In this work, a quantum dot (Qdot)-labeled Alu sequence was developed as a probe to simultaneously satisfy both the high sensitivity and human genome selectivity for quantification of forensic DNA samples. This probe provided PCR-free determination of human genomic DNA and had a 2.5-femtogram detection limit due to the strong emission and photostability of the Qdot. The Qdot-labeled Alu sequence has been used successfully to assess 18 different forensic DNA samples for STR human identification.     

Non‐hybridization single nucleotide polymorphism detection and genotyping assay through direct discrimination of single base mutation by capillary electrophoretic separation of single‐stranded DNA

The significant demands for single nucleotide polymorphism detection and genotyping assays have grown. Most common assays are based on the recognition of the target sequence by the hybridization with its specific probe having the complementary sequence of the target. Herein, a simple, label‐free, and economical non‐hybridization assay was developed for single nucleotide polymorphism detection and genotyping, based on the direct discrimination of single base mutation by simple capillary electrophoresis separation for single‐stranded DNA in an acidic electrophoretic buffer solution containing urea. Capillary electrophoresis separation of single‐base sequential isomers of DNA was achieved due to charge differences resulting from the different protonation properties of the DNA bases. Single nucleotide polymorphism detection and genotyping were achieved by discriminating the electropherogram pattern change, that is, peak number in the electropherogram, obtained by the proposed method. The successful practical application of the proposed method was demonstrated through single nucleotide polymorphism detection and genotyping on a known gene region of 84‐mer, in which guanine to adenine single‐base mutation is commonly observed, using a human hair sample in combination with genomic DNA extraction, polymerase chain reaction amplification, DNA purification from polymerase chain reaction products, and capillary electrophoresis separation.