Traceable phosphorus measurements by ICP-OES and HPLC for the quantitation of DNA

Measurement of the phosphorus content of nucleotides and deoxyribonucleic acid (DNA) offers an approach to the quantitation of nucleic acids that is traceable to the SI. Such measurements can be an alternative to the commonly used spectroscopic tools that are not traceable. Phosphorus measurements of thymidine 5'-monophosphate (TMP) and acid-digested plasmid and genomic DNA preparations were made using high-performance inductively coupled plasma optical emission spectroscopy (HP-ICP-OES) and high-performance liquid chromatography (HPLC) and compared for bias and uncertainty. A prerequisite for quality measurement is the purity of the materials. Quantitation with the two platforms was comparable for the TMP. However, the HPLC values had larger uncertainties and were all statistically different from the gravimetric values at the 95% confidence level. When using ICP-OES, the digestion of the nucleotide monophosphate can be eliminated, thus simplifying the procedure. The differences between the results obtained by using the two platforms, when measuring genomic or plasmid DNA, were dependent on the mass fraction of the digest. ICP-OES measurement of phosphorus provides a highly accurate quantitation for both nucleotide monophosphates and DNA with expanded uncertainties of less than 0.1%. Currently, ICP-OES requires a significant sample size restricting its usefulness for the quantitation of DNA but represents a valuable tool for certification of reference materials. HPLC requires smaller amounts of material to perform the analysis but is less useful for certification of reference materials because of lower accuracy and 10-fold higher expanded uncertainties.     

高通量测序DNA文库定量质控技术研究

DNA文库定量的准确与否直接影响测序数据质量的好坏,因此,开展文库定量质控技术研究非常重要。针对Illumina高通量测序平台的DNA文库定量,建立了基于SYBR Green荧光染料嵌合的高特异性数字PCR绝对定量方法,用于DNA文库定量标准物质的定值;并对制备的文库定量标准物质的适用性进行了验证。结果表明制备的5个水平的文库定量标准物质线性良好,可以作为Illumina平台DNA文库定量的标准曲线。     

Quantifying limits to detection of early warning for critical transitions

Catastrophic regime shifts in complex natural systems may be averted through advanced detection. Recent work has provided a proof-of-principle that many systems approaching a catastrophic transition may be identified through the lens of early warning indicators such as rising variance or increased return times. Despite widespread appreciation of the difficulties and uncertainty involved in such forecasts, proposed methods hardly ever characterize their expected error rates. Without the benefits of replicates, controls or hindsight, applications of these approaches must quantify how reliable different indicators are in avoiding false alarms, and how sensitive they are to missing subtle warning signs. We propose a model-based approach to quantify this trade-off between reliability and sensitivity and allow comparisons between different indicators. We show these error rates can be quite severe for common indicators even under favourable assumptions, and also illustrate how a model-based indicator can improve this performance. We demonstrate how the performance of an early warning indicator varies in different datasets, and suggest that uncertainty quantification become a more central part of early warning predictions.     

Development of isotope dilution cold vapor inductively coupled plasma mass spectrometry and its application to the certification of mercury in NIST standard reference materials

An isotope dilution cold vapor inductively coupled plasma mass spectrometry (ID-CV-ICPMS) method featuring gaseous introduction of mercury via tin chloride reduction has been developed and applied to the quantification and certification of mercury in various NIST standard reference materials: SRM 966 Toxic Metals in Bovine Blood (30 ng x mL(-1)); SRM 1641d Mercury in Water (1.6 microg x mL(-1)); and SRM 1946 Lake Superior Fish Tissue (436 ng x g(-1)). Complementary mercury data were generated for SRMs and NIST quality control standards using cold vapor atomic absorption spectroscopy (CVAAS). Certification results for the determination of mercury in SRM 1641d using two independent methods (ID-CV-ICPMS and CVAAS) showed a degree of agreement of 0.3% between the methods. Gaseous introduction of mercury into the ICPMS resulted in a single isotope sensitivity of 2 x 10(6) counts x s(-1)/ng x g(-1) for 201Hg and significantly reduced the memory and washout effects traditionally encountered in solution nebulization ICPMS. Figures of merit for isotope ratio accuracy and precision were evaluated at dwell times of 10, 20, 40, 80, and 160 ms using SRM 3133 Mercury Spectrometric Solution. The optimum dwell time of 80 ms yielded a measured 201Hg/202Hg isotope ratio within 0.13% of the theoretical natural value and a measurement precision of 0.34%, on the basis of three replicate injections of SRM 3133.     

Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry

Herein we report a novel method for determining genomic DNA methylation that utilizes liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to measure 5-methyl-2'-deoxycytidine levels following enzymatic hydrolysis of genomic DNA. LC separation of 5-methyl-2'-deoxycytidine from the four deoxyribonucleosides, the four ribonucleosides, and 5-methyl-2'-cytidine, a RNA methylation product, has been achieved within 15 min. In combination with ESI-MS/MS detection, the reported method is highly specific and extremely sensitive with a limit of detection (LOD) of 0.2 fmol and a quantification linearity range from 1 fmol to 20 pmol. Genomic DNA methylation was expressed as the ratio of 5-methyl-2'-deoxycytidine to 2'-deoxyguanosine and was determined directly using 2'-deoxyguanosine as the internal standard. Because deoxycytidine methylation typically ranges from 2 to 6% in mammalian genomes, and pharmacological or genetic manipulations have not achieved levels lower than 0.1%, we validated the assay for methylation levels ranging from 0.05 to 10%. Importantly, both RNA contamination and incomplete DNA hydrolysis had no appreciable effect on 5-methyl-2'-deoxycytidine quantification. LOD studies indicate that only 4 ng of DNA is required for this assay. This LOD should permit the use of this method for applications having limiting amounts of DNA that were not previously candidates for global genomic DNA methylation analysis, e.g., clinical trial samples, or cells collected by laser capture microdissection.     

Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip

In this paper, digital quantitative detection of nucleic acids was achieved at the single-molecule level by chemical initiation of over one thousand sequence-specific, nanoliter isothermal amplification reactions in parallel. Digital polymerase chain reaction (digital PCR), a method used for quantification of nucleic acids, counts the presence or absence of amplification of individual molecules. However, it still requires temperature cycling, which is undesirable under resource-limited conditions. This makes isothermal methods for nucleic acid amplification, such as recombinase polymerase amplification (RPA), more attractive. A microfluidic digital RPA SlipChip is described here for simultaneous initiation of over one thousand nL-scale RPA reactions by adding a chemical initiator to each reaction compartment with a simple slipping step after instrument-free pipet loading. Two designs of the SlipChip, two-step slipping and one-step slipping, were validated using digital RPA. By using the digital RPA SlipChip, false-positive results from preinitiation of the RPA amplification reaction before incubation were eliminated. End point fluorescence readout was used for "yes or no" digital quantification. The performance of digital RPA in a SlipChip was validated by amplifying and counting single molecules of the target nucleic acid, methicillin-resistant Staphylococcus aureus (MRSA) genomic DNA. The digital RPA on SlipChip was also tolerant to fluctuations of the incubation temperature (37-42 °C), and its performance was comparable to digital PCR on the same SlipChip design. The digital RPA SlipChip provides a simple method to quantify nucleic acids without requiring thermal cycling or kinetic measurements, with potential applications in diagnostics and environmental monitoring under resource-limited settings. The ability to initiate thousands of chemical reactions in parallel on the nanoliter scale using solvent-resistant glass devices is likely to be useful for a broader range of applications.     

Qualitative and quantitative analyses of ginkgo terpene trilactones by liquid chromatography/sonic spray ionization ion trap mass spectrometry

A liquid chromatography/sonic spray ionization mass spectrometry method (LC/SSI-MS) was developed for qualitative and quantitative analyses of ginkgo terpene trilactones. Five ginkgo terpene trilactones were successfully protonated for qualitative and quantitative analyses under the study conditions. The typical ion adducts were identified as (M + H)+, (M + NH4)+, and (M + Na)+. The limits of detection were achieved between 2.5 and 10 ng with RSD of 0.173-4.82% and a linear range of 10-80 ng with R2 = 0.991-0.999. This method was used to identify and quantify ginkgo terpene trilactones in extractions of ginkgo biloba leaves obtained from three different extraction methods. This is the first completely validated LC/MS method for quantification of ginkgo terpene trilactones. The factors that contributed to reduce the errors of identification and quantification of ginkgo terpene trilactones are systematically reported, and the advantages and disadvantages of LC/MS method in quantitative analysis are also discussed.     

ICP-OES不确定度评定模型的探讨

不确定度的大小是评定一种测量方法能力优劣的指征。等离子发射光谱(ICP—OES)在化学计量领域和分析测试领域均有广泛的应用,对于申请CNAL认证认可的实验室而言．校准实验室和检测实验室在不确定度评定的模型选用原则上存在很大的区别,本文采用国家一级或二级标准物质对仪器进行校准和检测试验,并根据需要拟订出校准实验室的检出限不确定度评定模型和检测实验室中检测结果不确定度评定模型。经过对大量数据的统计分析给出输入量的A类或B类不确定度评定实例．并按照国际通行方法进行不确定度的合成与扩展,最终得到ICP-OES在2种实验室中不确定度的判断。     

Uncertainty analysis of elastostatic problems incorporating a new hybrid stochastic-spectral finite element method

This article aims to present a combination of stochastic finite element and spectral finite element methods as a new numerical tool for uncertainty quantification. One of the well-established numerical methods for reliability analysis of engineering systems is the stochastic finite element method. In this article, a commonly used version of the stochastic finite element method is combined with the spectral finite element method. Furthermore, the spectral finite element method is a numerical method employing special orthogonal polynomials (e.g., Lobatto) and quadrature schemes (e.g., Gauss-Lobatto-Legendre), leading to suitable accuracy, and much less domain discretization with excellent convergence as well. The proposed method of this article is a hybrid method utilizing efficiencies of both methods for analysis of stochastically linear elastostatic problems. Moreover, a spectral finite element method is proposed for numerical solution of a Fredholm integral equation followed by the present method, to provide further efficiencies to accelerate stochastic computations. Numerical examples indicate the efficiency and accuracy of the proposed method.     

Differential effect of three base modifications on DNA thermostability revealed by high resolution melting

High resolution melting (HRM) can detect and quantify the presence of 5-methylcytosine (5mC) in DNA samples, but the ability of HRM to diagnose other DNA modifications remains unexplored. The DNA bases N6-methyladenine and 5-hydroxymethylcytosine occur across almost all phyla. While their function remains controversial, their presence perturbs DNA structure. Such modifications could affect gene regulation, chromatin condensation and DNA packaging. Here, we reveal that DNA containing N6-methyladenine or 5-hydroxymethylcytosine exhibits reduced thermal stability compared to cytosine-methylated DNA. These thermostability changes are sufficiently divergent to allow detection and quantification by HRM analysis. Thus, we report that HRM distinguishes between sequence-identical DNA differing only in the modification type of one base. This approach is also able to distinguish between two DNA fragments carrying both N6-methyladenine and 5-methylcytosine but differing only in the distance separating the modified bases. This finding provides scope for the development of new methods to characterize DNA chemically and to allow for low cost screening of mutant populations of genes involved in base modification. More fundamentally, contrast between the thermostabilizing effects of 5mC on dsDNA compared with the destabilizing effects of N6-methyladenine (m6A) and 5-hydroxymethylcytosine (5hmC) raises the intriguing possibility of an antagonistic relationship between modification types with functional significance.     

基于子成分分解的脑电信号去噪方法比较研究

脑电信号包含了丰富的时间和空间信息,为了获得实时性好且抗干扰的生理信号,大量的微弱脑电信号提取技术被应用研究。针对实际生理脑电信号易受无关噪声影响等问题,对最大分量分析法和独立成分分析法在去除脑电信号所包含伪迹上的分离性能以及处理的实时性进行对比,从散点图分析、相关性指标对比、计算速度3个方面对其解混效果进行评价。结果表明,两种方法对噪声信号均具有分离效果,且都可以保证实时性,但最大分量分析法比独立成分分析法具有分离效果更好、相关性指标更高、分离相似度高、相似度值浮动小更稳定等优点,具有更广泛的应用前景。     

Reliability performance of safety instrumented systems: A common approach for both low- and high-demand mode of operation

Safety instrumented systems (SISs) are usually divided into two modes of operation, low-demand and high-demand. Unfortunately, this classification is not easy to justify and the available formulas that are used to quantify the reliability performance in these two modes of operation are unable to capture combined effects of functional testing, spurious activations, and successful responses to demands. This article discusses some important modeling issues for SIS reliability performance quantification, and demonstrates their implementation in a Markov model. The accuracy of the Markov model for a simple case study of a pressure transmitter is verified through comparison with a scenario-based formula, and it is shown that the Markov approach gives a sufficiently accurate result for all demand rates, covering both low- and high-demand modes of operation.     

Protein quantification by isotope dilution mass spectrometry of proteolytic fragments: cleavage rate and accuracy

The practice of quantifying proteins by peptide fragments from enzymatic proteolysis (digestion) was assessed regarding accuracy, reliability, and uncertainty of the results attainable. Purified recombinant growth hormone (rhGH, 22 kDa isoform) was used as a model analyte. Two tryptic peptides from hGH, T6 and T12, were chosen to determine the amount of the protein in the original sample. Reference solutions of T6 and T12 (isotopically labeled forms), value assigned by quantitative amino acid analysis (AAA) after complete hydrolysis, were used as internal standards. The accuracy of protein quantification by fragments T6 and T12 was evaluated by comparison of peptide results to those obtained for the same rhGH sample by AAA. The rate of cleavage (and thus the experimental protocol used) turned out to be crucial to the quality of results in protein quantification using enzymatic fragments. Applying a protocol customarily found in (qualitative) bottom-up proteomics gave results significantly higher than the target value from AAA (+11% with T6 and +6% with T12). In contrast, using a modified protocol optimized for fast and complete hydrolysis, results were unbiased within the limits of uncertainty, while the time needed for completion of proteolysis was considerably reduced (30 min as compared to 1080-1200 min). The method assessed highlighted three important criteria deemed necessary for successful protein quantification using proteolysis-based mass spectrometry methods. These are the following: the requirement for both the selected peptides and labeled internal standard to be stable throughout digestion; the correct purity assignment to the selected peptide standards; the proof of equimolar release of the selected peptides. The combined (overall) uncertainty for protein quantification was established by combination of estimates obtained for individual components and found to be U = 4% for this example. This uncertainty is of the same order as that typically attainable in quantification of "small" organic molecules using liquid chromatography/isotope dilution mass spectrometry.     

Development, validation, and application of a method for quantification of methylmercury in biological marine materials using gas chromatography atomic emission detection

A gas chromatographic method was developed for the quantification of alkylmercury species using microwave-induced plasma atomic emission detection (GC-AED). The column conditioning and analyte derivatization required for previous methods were found to be unnecessary for stable, accurate, and sensitive element-specific detection using GC-AED. Chromatographic and detection parameters such as stationary phase type, stationary phase film thickness, GC column dimensions, helium mobile phase column head pressure, detector makeup gas flow rate, and detector reagent gas type and flow rate were found to significantly affect analyte response. The detection limit for the optimized GC-AED conditions was 0.8 pg (0.1 pg/s) of methylmercury chloride (as mercury). A solid-liquid extraction procedure with preparative gel permeation chromatography cleanup and GC-AED analysis was used to quantify methylmercury in a variety of complex matrix marine materials. The methylmercury quantification method was validated with four marine certified reference materials (CRMs). The method was then applied to 13 standard reference materials, CRMs, and control materials for which no certified reference values for methylmercury have been determined. Four National Institute of Standards and Technology Standard Reference Materials and one control material, which were analyzed using the GC-AED method, were also analyzed by two other laboratories using independent methods to further validate the method.     

Development of Crude Oil Reference Material Certified for the Concentrations of Sulfur,Iron, Nickel,Vanadium and Magnesium

Crude oil quality and uses are largely affected by the presence of sulfur and some other elements. Controlling the risk associated with these elements in crude oil depends on their accurate determination which is crucially governed by the use of certified reference materials (CRMs). This paper describes the development of a natural-matrix reference material for quantification of sulfur, iron, nickel, vanadium and magnesium in crude oil. The crude oil was homogenized and bottled to prepare the candidate material. Homogeneity and stability of the prepared reference material were investigated and characterization of sulfur content was carried out using wavelength-dispersive X-ray fluorescence (WD-XRF) spectrometry and gravimetric methods. Meanwhile, characterization of iron, nickel, vanadium and magnesium content was carried out using atomic absorption spectrometry (AAS) and inductively coupled plasma-optical emission spectrometry (ICP-OES) techniques. Statistical evaluation of the data showed good homogeneity and stability of the candidate reference material. Sufficiently good agreement between methods of characterization was achieved which allowed certification. The certified values and their associated uncertainties were statistically derived using the approach of combining data from two or more independent analytical methods developed by National Institute for Standards and Technology (NIST, Gaithersburg, USA).     

Comparison of MALDI to ESI on a triple quadrupole platform for pharmacokinetic analyses

This present work describes the systematic experimental comparison of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) for pharmacokinetic (PK) analysis of two drug candidates from rat plasma using single reaction monitoring (SRM) on a triple quadrupole mass spectrometer. The electrospray assay is an established method using a fast liquid chromatography (LC) separation of the sample extracts prior to mass spectrometry analysis. The novel MALDI assays measured the concentration levels of the drug candidates directly from the spotted sample extracts. Importantly, for both LC-ESI and MALDI the same solid-phase sample extraction protocol, internal standards, triple quadrupole mass analyzer platform, and SRM conditions were used, thus effectively standardizing all experimental parameters of the two assays. Initially, analytical figures of merit such as linearity, limit of quantitation, precision, and accuracy were determined from the calibration curves, indicating very similar performance for both LC-ESI and MALDI. Moreover, the LC-ESI rat plasma concentration time profiles of the drug candidates after orally dosing the animals were accurately reproduced by the MALDI assay, giving virtually identical PK results. The direct MALDI assay, however, was able to generate the data at least 50 x faster than the LC-ESI assay. It is shown in this study that analyzing the entire PK curve for one animal took less than 2 min using MALDI (with five replicate analyses per sample), whereas the corresponding LC-ESI assay required 80 min, however, allowing only two replicate measurements in that time frame.     

ICP-OES法测定铁矿中的MFe

本文采电感耦合等离子体发射光谱法测定铁矿石中MFe的含量。加入混酸溶解样品,提高了溶解温度,并且使溶解更完全。结果表明,本法溶解速度快,分析精确度高,稳定性好,成本低,适合铁矿石中的MFe测定。     

Effect of Lamina Thickness of Prepreg on the Surface Accuracy of Carbon Fiber Composite Space Mirrors

Composite space mirror can completely replicate the high-precision surface of mould by replication process, but the actual surface accuracy of the replication composite mirror always decreases. Lamina thickness of prepreg affects the layers and layup sequence of composite space mirror, and which would affect surface accuracy of space mirror. In our research, two groups of contrasting cases through finite element analyses (FEA) and comparative experiments were studied; the effect of different lamina thicknesses of prepreg and corresponding lay-up sequences was focused as well. We describe a special analysis model, validated process and result analysis. The simulated and measured surface figures both get the same conclusion. Reducing lamina thickness of prepreg used in replicating composite space mirror is propitious to optimal design of layup sequence for fabricating composite mirror, and could improve its surface accuracy.     

Determination of the fraction and stoichiometry of femtomolar levels of biomolecular complexes in an excess of monomer using single-molecule, two-color coincidence detection

We have extended the method of single-molecule fluorescence, two-color coincidence detection (TCCD) to detect coincident events due to a low fraction of a complex against a background of chance coincident events, due to monomers. We developed two complementary methods to determine the number of chance coincident events using the experimental data and without the need for additional experiments. We show that the subtraction of the chance coincidence level is essential for accurate quantification of the relative number of complexes and their stoichiometry. By performing experiments on model samples made from fluorophore-labeled duplex DNA and free dye, a linear dependence on the fraction of duplex DNA was found, independent of the level or ratio of free dye, with quantification down to a level of 0.5% and 500 fM duplex DNA. The method was then used to measure the equilibrium dissociation constant and offrate of a 9-mer duplex DNA, demonstrating the application of this method to systems with nanomolar dissociation constants. These improvements to the method of TCCD analysis significantly extend the application of TCCD to weakly bound complexes and large multicomponent biomolecular systems.