A novel pathogen detection system based on high‐resolution CE‐SSCP using a triblock copolymer matrix

Although CE‐SSCP analysis combined with 16S ribosomal RNA gene‐specific PCR has enormous potential as a simple and versatile pathogen detection technique, low resolution of CE‐SSCP causes the limited application. Among the experimental conditions affecting the resolution, the polymer matrix is considered to be most critical to improve the resolution of CE‐SSCP analysis. However, due to the peak broadening caused by the interaction between hydrophobic moiety of polymer matrices and DNA, conventional polymer matrices are not ideal for CE‐SSCP analysis. A poly(ethyleneoxide)‐poly(propyleneoxide)‐poly(ethyleneoxide) (PEO‐PPO‐PEO) triblock copolymer, with dynamic coating ability and a propensity to form micelles to minimize exposure of hydrophobic PPO block to DNA, can be an alternative matrix. In this study, we examined the resolution of CE‐SSCP analysis using the PEO‐PPO‐PEO triblock copolymer as the polymer matrix and four same‐sized DNA fragments of similar sequence content. Among 48 commercially available PEO‐PPO‐PEO triblock copolymers, three were selected due to their transparency in the operable range of viscosity and PEO₁₃₇PPO₄₃PEO₁₃₇ exhibited the most effective separation. Significant improvement in resolution allowed discrimination of the similar sequences, thus greatly facilitated CE‐SSCP analysis compared to the conventional polymer matrix. The results indicate that PEO‐PPO‐PEO triblock copolymer may serve as an ideal matrix for high‐resolution CE‐SSCP analysis.     

Sieving properties of end group‐halogenated Pluronic polymer matrix in DNA separation under nondenaturing CE analysis

CE‐SSCP analysis is a well‐established DNA separation method that is based on variations in mobility caused by sequence‐induced differences in the conformation of single‐stranded DNA. The resolution of CE‐SSCP analysis was improved by using a Pluronic polymer matrix, and it has been successfully applied in various genetic analyses. Because the Pluronic polymer forms a micellar cubic structure in the capillary, it provides a stable internal structure for high‐resolution CE‐SSCP analysis. We hypothesized that formation of micellar cubic structure is influenced by the end hydroxyl group of the Pluronic polymer, which affords structural stability through hydrogen bonding. To test this hypothesis, the hydroxyl group was halogenated to eliminate the hydrogen bonding without disturbing the polarity of polymer matrix. CE‐SSCP resolution of two DNA fragments with a single base difference was significantly worse in the halogenated polymer matrices due to band broadening. The viscoelastic properties of control (which has hydroxyl group), chlorinated, and brominated F108 solution upon heating were also investigated by rheological experiments, and we found that gelation was significantly associated with resolution. In this series of experiments, the effect of the hydroxyl group in Pluronic polymer matrix on separation resolution of CE‐SSCP analysis was demonstrated.     

High‐resolution pluronic‐filled microchip CE‐SSCP analysis system via channel width control

Although the resolution of CE‐SSCP has been significantly improved by using a poly(ethyleneoxide)‐poly(propyleneoxide)‐poly(ethyleneoxide) (PEO‐PPO‐PEO; Pluronic^®) triblock copolymer as a separation medium, CE‐SSCP on a microchip format is not widely applicable because their resolution is limited by short channel length. Therefore, a strategy to improve the resolution in channels of limited lengths is highly required for enabling microchip‐based CE‐SSCP. In this study, we developed a high‐resolution CE‐SSCP microchip system by controlling the width of the pluronic‐filled channel. We tested four different channel widths of 180, 240, 300, and 400 μm, and found that 300 μm showed the highest resolution in the separation of two pathogen specific markers. Potential applications of our method in various genetic analyses were also shown by using SNP markers for spinal muscular atrophy.     

A multiplex single nucleotide polymorphism genotyping method using ligase‐based mismatch discrimination and CE‐SSCP

Accuracy, simplicity, and cost‐effectiveness are the most important criteria for a genotyping method for SNPs compatible with clinical use. One method developed for SNP genotyping, ligase‐based discrimination, is considered the simplest for clinical diagnosis. However, multiplex assays using this method are limited by the detection method. Although CE has been introduced as an alternative to error prone microarray‐based detection, the design process and multiplex assay procedure are complicated because of the DNA size‐dependent separation principle. In this study, we developed a simple and accurate multiplex genotyping method using reaction condition‐optimized ligation and high‐resolution CE‐based SSCP. With this high‐resolution CE‐SSCP system, we are able to use similar‐sized probes, thereby eliminating the complex probe design step and simplifying the optimization process. We found that this method could accurately discriminate single‐base mismatches in SNPs of the tp53 gene, used as targets for multiplex detection.     

Comparative analysis of CE‐SSCP to standard RFLP‐CE‐FLA method in quantification of known viral variants within an RNA virus quasispecies

RNA viruses display the highest replication error rate in our biosphere, leading to highly diverse viral populations termed quasispecies. The gold standard method for detection and quantification of variants in a quasispecies is cloning and sequencing, but it is expensive, laborious and time consuming. Therefore, other mutation detection approaches, including SSCP, are often used. In this study, we demonstrate development and the usage of a CE‐SSCP method for quantification of two nearly identical viral variants in heterogenic population of a mumps virus strain and its comparison to RFLP‐CE‐fragment length analysis (RFLP‐CE‐FLA). Analyzed PCR fragments were of the same size (245 bp) with one difference in their nucleotide sequence. The limit of detection of both methods was at 5% of the minor variant. When PCR amplicons of the two variants were pooled, methods' results were very similar. On the contrary, the quantification results of samples in which variants were mixed prior to PCR showed substantial difference between the two methods. Our results indicate that although both methods can be used for detection and monitoring of a specific mutation within a viral population, caution should be taken when quantitative analysis of complex samples is based solely on results of one method.     

A new single‐step quantitative pathogen detection system: Template‐tagging followed by multiplex asymmetric PCR using common primers and CE‐SSCP

Rapid diagnosis of bacterial infection is important for patient management and appropriate therapy during the early phase of bacteria‐induced disease. Among the existing techniques for identifying microbial, CE‐SSCP combined with 16S ribosomal RNA gene‐specific PCR has the benefits of excellent sensitivity, resolution, and reproducibility. However, even though CE‐SSCP can separate PCR products with high‐resolution, multiplex detection and quantification are complicated by primer‐dimer formation and non‐specific amplification. Here, we describe a novel technique for multiplex detection and quantification of pathogens by template‐tagging followed by multiplex asymmetric PCR and subsequent CE‐SSCP. More specifically, we reverse transcribed 16S ribosomal RNAs from seven septicemia‐inducing pathogens, tagged the templates with common end sequences, and amplified them using common primers. The resulting amplicons could be successfully separated by CE‐SSCP and quantified by comparison to an internal standard. This method yielded results that illustrate the potential of this system for diagnosing infectious disease.     

Triblock copolymer matrix‐based capillary electrophoretic microdevice for high‐resolution multiplex pathogen detection

Rapid and simple analysis for the multiple target pathogens is critical for patient management. CE‐SSCP analysis on a microchip provides high speed, high sensitivity, and a portable genetic analysis platform in molecular diagnostic fields. The capability of separating ssDNA molecules in a capillary electrophoretic microchannel with high resolution is a critical issue to perform the precise interpretation in the electropherogram. In this study, we explored the potential of poly(ethyleneoxide)‐poly(propyleneoxide)‐poly(ethyleneoxide) (PEO‐PPO‐PEO) triblock copolymer as a sieving matrix for CE‐SSCP analysis on a microdevice. To demonstrate the superior resolving power of PEO‐PPO‐PEO copolymers, 255‐bp PCR amplicons obtained from 16S ribosomal RNA genes of four bacterial species, namely Proteus mirabilis, Haemophilus ducreyi, Pseudomonas aeruginosa, and Neisseria meningitidis, were analyzed in the PEO‐PPO‐PEO matrix in comparison with 5% linear polyacrylamide and commercial GeneScan? gel. Due to enhanced dynamic coating and sieving ability, PEO‐PPO‐PEO copolymer displayed fourfold enhancement of resolving power in the CE‐SSCP to separate same‐sized DNA molecules. Fivefold input of genomic DNA of P. aeruginosa and/or N. meningitidis produced proportionally increased corresponding amplicon peaks, enabling correct quantitative analysis in the pathogen detection. Besides the high‐resolution sieving capability, a facile loading and replenishment of gel in the microchannel due to thermally reversible gelation property makes PEO‐PPO‐PEO triblock copolymer an excellent matrix in the CE‐SSCP analysis on the microdevice.     

CE‐MS analysis of heroin and its basic impurities using a charged polymer‐protected gold nanoparticle‐coated capillary

The first application of charged polymer‐protected gold nanoparticles (Au NPs) as semi‐permanent capillary coating in CE‐MS was presented. Poly(diallyldimethylammonium chloride) (PDDA) was the only reducing and stabilizing agent for Au NPs preparation. Stable and repeatable coating with good tolerance to 0.1 M HCl, methanol, and ACN was obtained via a simple rinsing procedure. Au NPs enhanced the coating stability toward flushing by methanol, improved the run‐to‐run and capillary‐to‐capillary repeatabilities, and improved the separation efficiency of heroin and its basic impurities for tracing geographical origins of illicit samples. Baseline resolution of eight heroin‐related alkaloids was achieved on the PDDA‐protected Au NPs‐coated capillary under the optimum conditions: 120 mM ammonium acetate (pH 5.2) with addition of 13% methanol, separation temperature 20°C, applied voltage ?20 kV, and capillary effective length 60.0 cm. CE‐MS analysis with run‐to‐run RSDs (n=5) of migration time in the range of 0.43–0.62% and RSDs (n=5) of peak area in the range of 1.49–4.68% was obtained. The established CE‐MS method would offer sensitive detection and confident identification of heroin and related compounds and provide an alternative to LC‐MS and GC‐MS for illicit drug control.     

Thermo‐responsive shape memory behavior of poly(styrene‐b‐isoprene‐b‐styrene)/ethylene‐1‐octene copolymer thermoplastic elastomer blends

Thermally‐triggered shape memory polymers (SMPs) are smart materials, which are capable of changing their shapes when they are exposed a heat stimulant. Blending semi‐crystalline and elastomeric polymers is an easy and low‐cost way to obtain thermo‐responsive SMPs. In this work, novel poly(ethylene‐co‐1‐octene) (PEO) and poly(styrene‐b‐isoprene‐b‐styrene) (SIS) thermoplastic elastomer blends were prepared via melt blending method. The morphological, mechanical, rheological properties and shape memory behaviours of the blends were investigated in detail. In morphological analysis, co‐continuous morphology was found for 50 wt% PEO/50 wt% SIS and 60 wt% PEO/40 wt% SIS (60PEO/40SIS) blends. The shape memory analysis performing by dynamic mechanical analyzer showed that the 60PEO/40SIS blend also exhibited the optimum shape memory performance with 95.74% shape fixing and 98.98% shape recovery. Qualitatively shape memory analysis in hot‐water pointed out that the amount of semi‐crystalline PEO promotes shape fixing ability of the blends whereas SIS content enhances shape recovery capability. Although the SIS and PEO are immiscible polymers, the blends of them were exhibited good elastomeric properties with regard to tensile strength, toughness, and elongation at break.     

Effect of temperature gradients on single-strand conformation polymorphism analysis in a capillary electrophoresis system using Pluronic polymer matrix

Capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) analysis is a prominent bioseparation method based on the mobility diversity caused by sequence-induced conformational differences of single-stranded DNA. The use of Pluronic polymer matrix has opened up new opportunities for CE-SSCP, because it improved the resolution for various genetic analyses. However, there still exists a challenge in optimizing Pluronic-based CE-SSCP, because the physical properties of Pluronic solutions are sensitive to temperature, particularly near the gelation temperature, where the viscoelasticity of Pluronic F108 solutions sharply changes from that of a Newtonian fluid to a hydrogel upon heating. We have focused on a set of experiments to control the ambient temperature of the CE system with the aim of enhancing the reliability of the CE-SSCP analysis by using the Applied Biosystems ABI 3130xl genetic analyzer with Pluronic F108 solution matrix. The ambient temperature control allowed us to vary the inlet and outlet portion of the capillary column, while the temperature of the column was kept at 35 °C. The resolution to separate 2 single-base-pair-differing DNA fragments was significantly enhanced by changing the temperature from 19 to 30 °C. The viscoelastic properties of the F108 solution matrix upon heating were also investigated by ex situ rheological experiments with an effort to reveal how the development of gels in Pluronic solutions affects the resolution of CE-SSCP. We found that the column inlet and outlet temperatures of the capillary column have to be controlled to optimize the resolution in CE-SSCP by using the Pluronic matrix.     

Robust and high‐resolution simulations of nonlinear electrokinetic processes in variable cross‐section channels

We present a model and an associated numerical scheme to simulate complex electrokinetic processes in channels with nonuniform cross‐sectional area. We develop a quasi‐1D model based on local cross‐sectional area averaging of the equations describing unsteady, multispecies, electromigration‐diffusion transport. Our approach uses techniques of lubrication theory to approximate electrokinetic flows in channels with arbitrary variations in cross‐section; and we include chemical equilibrium calculations for weak electrolytes, Taylor–Aris type dispersion due of nonuniform bulk flow, and the effects of ionic strength on species mobility and on acid–base equilibrium constants. To solve the quasi‐1D governing equations, we provide a dissipative finite volume scheme that adds numerical dissipation at selective locations to ensure both unconditional stability and high accuracy. We couple the numerical scheme with a novel adaptive grid refinement algorithm that further improves the accuracy of simulations by minimizing numerical dissipation. We benchmark our numerical scheme with existing numerical schemes by simulating nonlinear electrokinetic problems, including ITP and electromigration dispersion in CZE. Simulation results show that our approach yields fast, stable, and high‐resolution solutions using an order of magnitude less grid points compared to the existing dissipative schemes. To highlight our model's capabilities, we demonstrate simulations that predict increase in detection sensitivity of ITP in converging cross‐sectional area channels. We also show that our simulations of ITP in variable cross‐sectional area channels have very good quantitative agreement with published experimental data.     

Two‐way multi‐shape memory properties of peroxide crosslinked ethylene vinyl‐acetate copolymer (EVA)/polycaprolactone (PCL) blends

Rare studies have investigated on the 2‐way shape memory crosslinked blends with multiple shape memory behavior up to date. To consider the merit of commercial cost‐competitive crystalline polymers, ethylene vinyl‐acetate copolymer (EVA) / polycaprolactone (PCL) blends (60/40 and 30/70) were peroxide‐cured to form the 2‐way multi‐shape memory crosslinked blends using a melt‐blending method. Both resins were selected to have a similar controlled crosslinking degree, which allowed us to distinctly evaluate their actuation contributions from the cooling‐induced elongation (crystallization) and from the entropy‐driven elongation during cooling process, respectively. In the 2‐way process for the 60/40 system, 2 respective peaks contributed from the cooling‐induced crystallization of EVA and PCL in the cooling curves based on the strain derivate rates at various temperatures were observed. After the cooling process under the loading stress of 150 kPa, the 2‐step heating‐induced contraction process with increasing temperature started at 54.1°C above the melting temperature of PCL at 52.3°C and EVA at 78.3°C, demonstrating 2‐way multi‐shape memory behavior. The multi‐step behavior was more prominent at higher PCL composition and higher load for the 30/70 system. It was found that the entropy‐driven contribution to the overall actuation magnitude increased with increasing nominal loads due to the increased orientation of molecular networks in the blends. The current approach offers numerous possibilities in preparing 2‐way multi‐shape memory crosslinked blends.     

Novel strategy for the determination of illegal adulterants in health foods and herbal medicines using high‐performance liquid chromatography with high‐resolution mass spectrometry

The detection, confirmation, and quantification of multiple illegal adulterants in health foods and herbal medicines by using a single analytical method are a challenge. This paper reports on a new strategy to meet this challenge by employing high‐performance liquid chromatography coupled with high‐resolution mass spectrometry and a mass spectral tree similarity filter technique. This analytical method can rapidly collect high‐resolution, high‐accuracy, optionally multistage mass data for compounds in samples. After a preliminary screening by retention time and high‐resolution mass spectral data, known illegal adulterants can be detected. The mass spectral tree similarity filter technique has been applied to rapidly confirm these adulterants and simultaneously discover unknown ones. By using full‐scan mass spectra as stem and data‐dependent subsequent stage mass spectra to form branches, mass spectrometry data from detected compounds are converted into mass spectral trees. The known or unknown illegal adulterants in the samples are confirmed or discovered based on the similarity between their mass spectral trees and those of the references in a library, and they are finally quantified against standard curves. This new strategy has been tested by using 50 samples, and the illegal adulterants were rapidly and effectively detected, confirmed and quantified.     

Combining targeted and nontargeted data analysis for liquid chromatography/high‐resolution mass spectrometric analyses

Increasing importation of food and the diversity of potential contaminants have necessitated more analytical testing of these foods. Historically, mass spectrometric methods for testing foods were confined to monitoring selected ions (SIM or MRM), achieving sensitivity by focusing on targeted ion signals. A limiting factor in this approach is that any contaminants not included on the target list are not typically identified and retrospective data mining is limited. A potential solution is to utilize high‐resolution MS to acquire accurate mass full‐scan data. Based on the instrumental resolution, these data can be correlated to the actual mass of a contaminant, which would allow for identification of both target compounds and compounds that are not on a target list (nontargets). The focus of this research was to develop software algorithms to provide rapid and accurate data processing of LC/MS data to identify both targeted and nontargeted analytes. Software from a commercial vendor was developed to process LC/MS data and the results were compared to an alternate, vendor‐supplied solution. The commercial software performed well and demonstrated the potential for a fully automated processing solution.     

Characterization of stress‐strain behavior for binary blends of isotactic polypropylene with ethylene‐α‐olefin copolymer

The characterization of the mechanical nonlinear behavior of isotactic polypropylene/ethylene‐1‐hexene copolymer blends with various kinds of morphology was carried out using a nonlinear constitutive equation in which the plastic deformation and the anharmonicity of elastic response are taken into account. It was found that the mechanical nonlinearity of the incompatible blends showing phase separation is much greater than that of the compatible blends having rubbery components in the interlamellar regions. Moreover, the mechanical behavior is governed by the plastic deformation for the incompatible blends, whereas the anharmonicity strongly affects the mechanical behavior for the compatible blends. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1513–1521, 1999     

Comparison of a new high‐resolution monolithic column with core‐shell and fully porous columns for the analysis of retinol and α‐tocopherol in human serum and breast milk by ultra‐high‐performance liquid chromatography†

The reduction of analysis time, cost, and improvement of separation efficiency are the main requirements in the development of high‐throughput assay methods in bioanalysis. It can be achieved either by ultra‐high‐performance liquid chromatography (UHPLC) using stationary phases with small particles (<2 μm) at high back pressures or by using opposite direction—monolithic stationary phases with low back pressures. The application of new types of monolithic stationary phases for UHPLC is a novel idea combining these two different paths. The aim of this work was to test the recently introduced second‐generation of monolithic column Chromolith® HighResolution for UHPLC analysis of liposoluble vitamins in comparison with core‐shell and fully porous sub‐2 μm columns with different particle sizes, column lengths, and shapes. The separation efficiency, peak shape, resolution, time of analysis, consumption of mobile phase, and lifetime of columns were calculated and compared. The main purpose of the study was to find a new, not only economical option of separation of liposoluble vitamins for routine practice.     

Accurate identification of dimers from α‐pinene oxidation using high‐resolution collision‐induced dissociation mass spectrometry

Interest in mass spectrometry of highly oxidized dimers from α‐pinene oxidation has increased in the atmospheric chemistry field. Here, we apply high‐resolution collision‐induced dissociation mass spectrometry (HR‐CID‐MS) with an atmospheric pressure ionization source to investigate in detail how α‐pinene‐derived dimers are detected and identified by MS. The resulting HR‐CID spectra and specific fragmentation patterns suggest that a large fraction of dimer ions detected in full‐scan mass spectra can be hydrogen‐bonded artifact clusters and the residual small fraction includes covalently bonded actual dimers. We also show how individual fractions of the artifact clusters and actual dimers are calculated using the HR‐CID spectra.     

Application of high‐resolution ESI and MALDI mass spectrometry to metabolite profiling of small interfering RNA duplex

We investigated the application of a high‐resolution Orbitrap mass spectrometer equipped with an electrospray ionization (ESI) source and a matrix‐assisted laser desorption/ionization‐time‐of‐flight (MALDI‐TOF) mass spectrometer to the metabolite profiling of a model small interfering RNA (siRNA) duplex TSR#34 and compared their functions and capabilities. TSR#34 duplex was incubated in human serum in vitro, and the duplex and its metabolites were then purified by ion exchange chromatography in order to remove the biological matrices. The fraction containing the siRNA duplex and its metabolites was collected and desalted and then subjected to high‐performance liquid chromatography (HPLC) equipped with a reversed phase column. The siRNA and its metabolites were separated into single strands by elevated chromatographic temperature and analyzed using the ESI‐Orbitrap or the MALDI‐TOF mass spectrometer. Using this method, the 5' and/or 3' truncated metabolites of each strand were detected in the human serum samples. The ESI‐Orbitrap mass spectrometer enabled differentiation between two possible RNA‐based sequences, a monoisotopic molecular mass difference which was less than 2 Da, with an intrinsic mass resolving power. In‐source decay (ISD) analysis using a MALDI‐TOF mass spectrometer allowed the sequencing of the RNA metabolite with characteristic fragment ions, using 2,4‐dihydroxyacetophenone (2,4‐DHAP) as a matrix. The ESI‐Orbitrap mass spectrometer provided the highest mass accuracy and the benefit of on‐line coupling with HPLC for metabolite profiling. Meanwhile, the MALDI‐TOF mass spectrometer, in combination with 2,4‐DHAP, has the potential for the sequencing of RNA by ISD analysis. The combined use of these methods will be beneficial to characterize the metabolites of therapeutic siRNA compounds. Copyright © 2012 John Wiley & Sons, Ltd.     

Effect of PEO‐PPO‐PEO copolymer on the mechanical and thermal properties and morphological behavior of biodegradable poly (L‐lactic acid) (PLLA) and poly (butylene succinate‐co‐L‐lactate) (PBSL) blends

A blend of two biodegradable and semi‐crystalline polymers, poly (L‐lactic acid) (PLLA; 70 wt%) and poly (butylene succinate‐co‐L‐lactate) (PBSL; 30 wt%), was prepared in the presence of various polyethylene oxide‐polypropylene oxide‐polyethylene oxide (PEO‐PPO‐PEO) triblock copolymer contents (0.5, 1, 2 wt%). Mechanical, thermal properties, and Fourier transform infrared (FTIR) analysis of the blends were investigated. It was found that the addition of copolymer to PLLA/PBSL improved the fracture toughness of the blends as shown by mode I fracture energies. It was supported by morphological analysis where the brittle deformation behavior of PLLA changed to ductile deformation with the presence of elongated fibril structure in the blend with copolymer system. The glass transition temperature (T_g), melting temperature (T_m) of PLLA, and PBSL shift‐closed together indicated that some compatibility exists in the blends. In short, PEO‐PPO‐PEO could be used as compatibilizer to improve the toughness and compatibility of the PLLA/PBSL blends. Copyright © 2010 John Wiley & Sons, Ltd.