不同样本中甲螨的分离方法

采用电热分离法、清水漂浮法和振动分离法对不同样本中甲螨的分离时间、数量,样本的放置时间及电热分离所用热光源作了比较,结果证明,分离土壤甲螨时,土壤放置7d与立即分离所获甲螨数无差别,少量土样宜用清水漂浮法,大量土样宜用电热分离法,而植被样本宜用振动分离法。     

Determination of nitrie in human blood by combination of a specific sample preparation with high-performance anion-exchange chromatography and electrochemical detection

All photometric or HPLC methods described to date have been unable to detect nitrite, a reliable marker of NO synthase activity, in human blood because of its rapid metabolism within the erythrocytes. We now elaborate on method to prevent nitrite degradation during sample preparation which in combination with high-performance anion-exchange chromatography and electrochemical detection allows a sensitive measurement of nitrite. A linear current response in the concentration range of 10–1000 nmol/l nitrite was observed yielding a correlation coefficient of 0.99. In addition, the combination of the electrochemical with a UV detector allowed us to simultaneously quantify nitrate one analytical run, which is the end product of NO/nitrite metabolism. Basal levels for nitrate and nitrite in human blood were determined with 25±4 μmol/l and 578±116 nmol/l (n=8), respectively and thus were in the same concentration range as expected from NO measurement in saline perfused isolated organs or cultured endothelial cells. Therefore, the presented method may be used to assess activity of endothelial constitutive NO synthase in humans under physiological and pathophysiological conditions.     

Inconstancy of Taylor'sb: Simulated sampling with different quadrat sizes and spatial distributions

Taylor 's power law, s²=am^b, provides a precise summary of the relationship between sample variance (s²) and sample mean (m) for many organisms. The coefficient b has been interpreted as an index of aggregation, with a characteristic value for a given species in a particular environment, and has been thought to be independent of the sample unit. Simulation studies were conducted that demonstrate that the value of b may vary with the size of the sample unit in quadrat sampling, and this relationship, in turn, depends on the underlying spatial distribution of the population. For example, simulated populations with hierarchical aggregation on a large scale produced values of b that increased with the size of the sample unit. In contrast, for a simulated population with randomly distributed clusters of individuals, the value of b eventually decreased with increasing quadrat size, as sample counts became more uniform. A single value ofTaylor 's b, determined with a particular sample unit, provides neither a fixed index of aggregation nor a complete picture of a species' spatial distribution. Rather, it describes a consistent relationship between sample variance and sample mean over a range of densities, on a spatial scale related to the size of the sample unit. This relationship may reflect, but not uniquely define, density-dependent population and behavioral processes governing the spatial distribution of the organism. Interpretation ofTaylor 'sb for a particular organism should be qualified by reference to the sample unit, and comparisons should not be made between cases in which different sample units were used. Whenever possible, a range of sample units should be used to provide information about the pattern of distribution of a population on various spatial scales.     

The effects of dominance,species ranking and species matching on some similarity indices

Abstract. The performance of certain indices of sample similarity was explored with respect to variation in species matching, species ranking and dominance of simulated samples. An index of similarity is suggested which accounts for variation in species matching and ranking rather than for differences in dominance.     

Semi-automated liquid--liquid back-extraction in a 96-well format to decrease sample preparation time for the determination of dextromethorphan and dextrorphan in human plasma

A semi-automated, 96-well based liquid-liquid back-extraction (LLE) procedure was developed and used for sample preparation of dextromethorphan (DEX), an active ingredient in many over-the-counter cough formulations, and dextrorphan (DOR), an active metabolite of DEX, in human plasma. The plasma extracts were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS-MS). The analytes were isolated from human plasma using an initial ether extraction, followed by a back extraction from the ether into a small volume of acidified water. The acidified water isolated from the back extraction was analyzed directly by LC-MS-MS, eliminating the need for a dry down step. A liquid handling system was utilized for all aspects of liquid transfers during the LLE procedure including the transfer of samples from individual tubes into a 96-well format, preparation of standards, addition of internal standard and the addition and transfer of the extraction solvents. The semi-automated, 96-well based LLE procedure reduced sample preparation time by a factor of four versus a comparable manually performed LLE procedure.     

Effect of different sample pretreatment methods on the concentrations of excitatory amino acids in cerebrospinal fluid determined by high-performance liquid chromatography

Using high-performance liquid chromatography (HPLC), the effect of different sample pretreatment methods on the concentrations of excitatory amino acids (EAAs, glutamate and aspartate) measured in cerebrospinal fluid (CSF) was investigated. The results showed that the measured values of glutamate and aspartate were constant when the samples were stored at -80 degrees C and then methanol was used for CSF deproteinization before assay; the values of glutamate (Glu) increased when 0.3 M perchloric acid was used for CSF deproteinization with the CSF subsequently being stored at -20 degrees C; the values of Glu changed when the samples were stored at -20 degrees C over 8 weeks with methanol subsequently being used for CSF deproteinization before assay. This reference data suggested that the CSF sample would be better stored at -80 degrees C. If the sample is stored at -20 degrees C over 8 weeks, the Glu values change with the storage time. If strong acidic reagents are used for precipitation of protein in the CSF sample and then stored at -20 degrees C, Glu values are abnormally increased. From this study, an accurate and sensitive reversed-phase high-performance liquid chromatographic method has been developed for anti-excitotoxicity therapy and thorough study of EAAs in a clinical setting.     

Sample Variances for Several MINQ-Estimators in the One-way Classification

A generalization of Ahrens' (1965) formulas for sample variances is done, considering the case of MINQ-Estimators which may be biased. The formulas are generally valid, but are restricted for the sake of simplicity to those of the one-way classification. Some MINQ-Estimators are considered and their sample variances calculated.     

SASI-Seq: sample assurance Spike-Ins,and highly differentiating 384 barcoding for Illumina sequencing

Background

A minor but significant fraction of samples subjected to next-generation sequencing methods are either mixed-up or cross-contaminated. These events can lead to false or inconclusive results. We have therefore developed SASI-Seq; a process whereby a set of uniquely barcoded DNA fragments are added to samples destined for sequencing. From the final sequencing data, one can verify that all the reads derive from the original sample(s) and not from contaminants or other samples.

Results

By adding a mixture of three uniquely barcoded amplicons, of different sizes spanning the range of insert sizes one would normally use for Illumina sequencing, at a spike-in level of approximately 0.1%, we demonstrate that these fragments remain intimately associated with the sample. They can be detected following even the tightest size selection regimes or exome enrichment and can report the occurrence of sample mix-ups and cross-contamination.As a consequence of this work, we have designed a set of 384 eleven-base Illumina barcode sequences that are at least 5 changes apart from each other, allowing for single-error correction and very low levels of barcode misallocation due to sequencing error.

Conclusion

SASI-Seq is a simple, inexpensive and flexible tool that enables sample assurance, allows deconvolution of sample mix-ups and reports levels of cross-contamination between samples throughout NGS workflows.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-110) contains supplementary material, which is available to authorized users.     

Recent advances in DNA sequencing methods - general principles of sample preparation

DNA sequencing has revolutionized biomedicine, and progress in the field has been unrelenting since it was invented over 30 years ago. The complete DNA sequence of the human genome was obtained as the culmination of a decade of work by a large number of scientists. Less than ten years later, so-called ‘next-generation’ instruments now make it possible for a single lab to produce the same amount of data in a week. But while the instruments are increasingly automated, upstream sample processing remains a challenge. Here I review the current state of the art in preparing genomic and RNA samples for high throughput sequencing.     

Sample size calculations for noninferiority trials with Poisson distributed count data

Clinical trials with Poisson distributed count data as the primary outcome are common in various medical areas such as relapse counts in multiple sclerosis trials or the number of attacks in trials for the treatment of migraine. In this article, we present approximate sample size formulae for testing noninferiority using asymptotic tests which are based on restricted or unrestricted maximum likelihood estimators of the Poisson rates. The Poisson outcomes are allowed to be observed for unequal follow‐up schemes, and both the situations that the noninferiority margin is expressed in terms of the difference and the ratio are considered. The exact type I error rates and powers of these tests are evaluated and the accuracy of the approximate sample size formulae is examined. The test statistic using the restricted maximum likelihood estimators (for the difference test problem) and the test statistic that is based on the logarithmic transformation and employs the maximum likelihood estimators (for the ratio test problem) show favorable type I error control and can be recommended for practical application. The approximate sample size formulae show high accuracy even for small sample sizes and provide power values identical or close to the aspired ones. The methods are illustrated by a clinical trial example from anesthesia.     

Randomized Blocks Analysis for the Exponential Distribution

A procedure for analyzing randomized blocks experiments for uncensored exponential random variables is presented. Its small sample behavior is studied in several simulations. Sample size requirements are given.     

The effects of saliva collection,handling and storage on salivary testosterone measurement

Several endocrine parameters commonly measured in plasma, such as steroid hormones, can be measured in the oral fluid. However, there are several technical aspects of saliva sampling and processing that can potentially bias the validity of salivary testosterone measurement. The aim of this study was to evaluate the effects caused by repeated sampling; 5 min centrifugation (at 2000, 6000 or 10,000g); the stimulation of saliva flow by a cotton swab soaked in 2% citric acid touching the tongue; different storage times and conditions as well as the impact of blood contamination on salivary testosterone concentration measured using a commercially available ELISA kit. Fresh, unprocessed, unstimulated saliva samples served as a control. Salivary testosterone concentrations were influenced neither by repeated sampling nor by stimulation of salivary flow. Testosterone levels determined in samples stored in various laboratory conditions for time periods up to 1 month did not differ in comparison with controls. For both genders, salivary testosterone levels were substantially reduced after centrifugation (men F = 29.1; women F = 56.17, p < 0.0001). Blood contamination decreased salivary testosterone levels in a dose-dependent manner (men F = 6.54, p < 0.01, F = 5.01, p < 0.05). Salivary testosterone can be considered A robust and stable marker. However, saliva processing and blood leakage can introduce bias into measurements of salivary testoterone using ELISA. Our observations should be considered in studies focusing on salivary testosterone.     

Evaluation of saliva as a source of human DNA for population and association studies

A simple noninvasive procedure for saliva sample collection and DNA extraction was developed. On average, the amount of human DNA (as measured by a TaqMan-based assay) was about 11.4 microg/mL saliva, which is more than can be obtained from other noninvasive samples such as cheek swabs. However, the presence of large amounts of nonhuman DNA (up to 90% of the total extracted DNA) in saliva samples does necessitate DNA quantitation methods that are specific for human DNA. We were able to reliably and accurately type different genetic markers (mDNA sequences, Y-chromosomal single-nucleotide polymorphisms, and autosomal microsatellite loci) from saliva samples stored for up to 30 days at 37 degrees C, making this method well-suited for field conditions and convenient transportation of samples back to the laboratory. Thus, saliva can be considered a reliable source of DNA for a wide variety of genetic studies.     

Techniques of preparing plant material for chromatographic separation and analysis

This paper discusses preparation techniques of samples of plant material for chromatographic analysis. Individual steps of the procedures used in sample preparation, including sample collection from the environment or from tissue cultures, drying, comminution, homogenization, leaching, extraction, distillation and condensation, analyte enrichment, and obtaining the final extracts for chromatographic analysis are discussed. The techniques most often used for isolation of analytes from homogenized plant material, i.e., Soxhlet extraction, ultrasonic solvent extraction (sonication), accelerated solvent extraction, microwave-assisted extraction, supercritical-fluid extraction, steam distillation, as well as membrane processes are emphasized. Sorptive methods of sample enrichment and removal of interferences, i.e., solid-phase extraction, and solid-phase micro-extraction are also discussed.     

Sample preparation and digestion for proteomic analyses using spin filters

We describe the use of commercially available microcentrifugation devices (spin filters) for cleanup and digestion of protein samples for mass spectrometry analyses. The protein sample is added to the upper chamber of a spin filter with a > or = 3000 molecular weight cutoff membrane and then washed prior to resuspension in ammonium bicarbonate. The protein is then reduced, alkylated, and digested with trypsin in the upper chamber and the peptides are recovered by centrifugation through the membrane. The method provides digestion efficiencies comparable to standard in-solution digests, avoids lengthy dialysis steps, and allows rapid cleanup of samples containing salts, some detergents, and acidic or basic buffers.     

箭毒木种子蛋白质样品制备及双向电泳改良方法

建立箭毒木（Antiaris toxicaria）种子总蛋白的提取方法,以及可以对其蛋白质组进行分析的双向电泳条件。通过各种条件的优化与组合,建立了以TCA-丙酮为基础的Tris—HCl提取法提取总蛋白,第1向电泳为固相pH梯度等电聚焦,第2向电泳为垂直平板SDS-PAGE的双向电泳体系。通过对样品制备、样品溶解、等电聚焦电泳、SDS-聚丙烯酰胺凝胶电泳以及染色方法等关键步骤进行分析,获得了满意的双向电泳图谱。在探索适合箭毒木种子蛋白质组学研究双向电泳方法中,比较了三氯乙酸-丙酮沉淀法、和Tris—HCl法,以及对双向电泳过程中的关键步骤的改良,认为Tris—HCl法为最适方法,所得图谱背景清晰,蛋白质信息量最大,为箭毒木属植物的差异蛋白质组学的后续研究打下了坚实的基础。     

微生物代谢组学的前处理及分析技术

微生物代谢组学主要研究细胞生长或生长周期某一时刻细胞内外所有低分子量代谢物。分析技术的不断发展促进了微生物代谢组学研究的进展。本文结合微生物样品前处理方法, 综述了目前研究中所采用的各种分析技术的特点与应用, 并展望微生物代谢组学研究中分析技术的发展趋势。