Real-time polymerase chain reaction-based exponential sample amplification for microarray gene expression profiling

Conventional approaches to target labeling for gene expression analysis using microarray technology typically require relatively large amounts of RNA, a serious limitation when the available sample is limited. Here we describe an alternative exponential sample amplification method by using quantitative real-time polymerase chain reaction (QRT-PCR) to follow the amplification and eliminate the overamplified cDNA which could distort the quantitative ratio of the starting mRNA population. Probes generated from nonamplified, PCR-amplified, and real-time-PCR-amplified cDNA samples were generated from lipopolysaccharide-treated and nontreated mouse macrophages and hybridized to mouse cDNA microarrays. Signals obtained from the three protocols were compared. Reproducibility and reliability of the methods were determined. The Pearson correlation coefficients for replica experiments were r=0.927 and r=0.687 for QRT-PCR-amplification and PCR-overamplification protocols, respectively. Chi2 test showed that overamplification resulted in major biases in expression ratios, while these alterations could be eliminated by following the cycling status with QRT-PCR. Our exponential sample amplification protocol preserves the original expression ratios and allows unbiased gene expression analysis from minute amounts of starting material.     

Blinded sample size recalculation in multiple composite population designs with normal data and baseline adjustments

The increasing interest in subpopulation analysis has led to the development of various new trial designs and analysis methods in the fields of personalized medicine and targeted therapies. In this paper, subpopulations are defined in terms of an accumulation of disjoint population subsets and will therefore be called composite populations. The proposed trial design is applicable to any set of composite populations, considering normally distributed endpoints and random baseline covariates. Treatment effects for composite populations are tested by combining p-values, calculated on the subset levels, using the inverse normal combination function to generate test statistics for those composite populations while the closed testing procedure accounts for multiple testing. Critical boundaries for intersection hypothesis tests are derived using multivariate normal distributions, reflecting the joint distribution of composite population test statistics given no treatment effect exists. For sample size calculation and sample size, recalculation multivariate normal distributions are derived which describe the joint distribution of composite population test statistics under an assumed alternative hypothesis. Simulations demonstrate the absence of any practical relevant inflation of the type I error rate. The target power after sample size recalculation is typically met or close to being met.     

Analysis of tissue cadmium distribution in chronic cadmium-exposed mice using in-air micro-PIXE

This study undertook the analysis of tissue cadmium (Cd) distribution using in-air micro-particle-induced X-ray emission (PIXE) and the examination of the involvement of metal ions in parenteral Cd toxicity. A mouse was injected intraperitoneally with 3 mg/kg body weight of CdCl₂ thrice weekly. After 27 wk, the liver and kidney were excised and fixed in 10% formalin solution for 4 h and then embedded in paraffin. Thin paraffin sections were used to analyze trace elements with in-air micro-PIXE and to examine metallothionein protein and histological changes. Cd distribution was determined by micro-PIXE in the liver and renal cortex of the Cd-exposed mouse, and the net Cd count was higher in the liver than in the renal cortex. The net iron (Fe) count was higher in the liver of the Cd-exposed mouse compared to the control, and an opposite tendency was observed in the renal cortex. Wide cellular Cd distribution was demonstrated in the liver and renal cortex of the chronic Cd-exposed mouse compared to the control. Metallothionein staining was increased by chronic exposure to Cd both in the liver and kidney, and nephrotoxicity was more apparent than hepatotoxicity. The modification of tissue Fe and calcium distribution by an intraperitoneal injection of Cd might be involved in Cd-induced toxicity.     

Simultaneous analysis of artemisinin and flavonoids of several extracts of Artemisia annua L. obtained from a commercial sample and a selected cultivar

Artemisia annua L. (Qinghao) is a promising and potent antimalarial herbal drug. This activity has been ascribed to its component artemisinin, a sesquiterpene lactone that is very effective against drug-resistant Plasmodium species with a low toxicity. Our studies indicate that several flavonoids of A. annua can promote and enhance the reaction of artemisinin with hemin. These data are in good agreement with previous investigations on the in vitro potentiation of antimalarial activity of artemisinin by such flavonoids. As a consequence, in view of a possible use of the phytocomplex rather than pure artemisinin, an HPLC/DAD/MS method is proposed for the simultaneous detection and quantification of both flavonoids and artemisinin. Different extracts, obtained from two different herbal drugs, a commercial sample and a selected cultivar, were analyzed in order to determine which solvents provide the best yields of both artemisinin and flavonoids. Qualitative and quantitative results obtained using an HPLC method are described, which will be useful for developing highly effective herbal drug preparations.     

Raising the bar for the next generation of biological atlases: using existing data to inform the design and implementation of atlas monitoring

Selecting a sampling design to monitor multiple species across a broad geographical region can be a daunting task and often involves tradeoffs between limited resources and the accurate estimation of population abundance and occurrence. Since the 1950s, biological atlases have been implemented in various regions to document the occurrence of plant and animal species. As next‐generation atlases repeat original surveys, investigators often seek to raise the rigour of atlases by incorporating species abundances. We present a repeatable framework that incorporates existing monitoring data, hierarchical modelling and sampling simulations to augment existing atlas occurrence and breeding status maps with a secondary sampling of species abundances. Using existing information on three bird species with varying abundance and detectability, we evaluated several sampling scenarios for the 2nd Wisconsin Breeding Bird Atlas. In general, we found that most sampling schemes produced accurate mean statewide abundance estimates for species with medium to high abundance and detection probability, but estimates varied significantly for species with low abundance and low detection probability. Our approach provided a statewide point‐count sampling design that: provided precise and unbiased abundance estimates for species of varied prevalence and detectability; ensured suitable spatial coverage across the state and its habitats; and reduced spending on total survey costs. Our framework could benefit investigators conducting atlases and other broad‐scale avian surveys that seek to add systematic, multi‐species sampling for estimating density and abundance across broad geographical regions.     

A Fast and Economical Sample Preparation Protocol for Interaction Proteomics Analysis

A simple and fast immunoprecipitation (IP) protocol is designed with the sample preparation incorporated, applicable to both low and high throughput. This new protocol combines two procedures based on magnetic beads in 96‐well plate format. Protein complexes are captured by antibodies and magnetic beads conjugated with protein A. Proteins are washed and on‐bead digested by using Single‐Pot solid‐phase sample preparation (SP3). The whole IP‐SP3 approach can be completed in one day, which is considerably faster compared to the classical approach. No major quantitative differences are found between SP3 and FASP (filter‐aided sample preparation) or a longer incubation protocol. Taken together, the IP‐SP3 protocol is a fast and economical approach easily applicable for large‐scale protein interactome analysis.     

样本量对云南松幼苗生物量模型构建及预估精度的影响

为探究不同样本量对生物量模型构建及建模精度的影响,以实际调查的20个家系,共615株云南松幼苗为例,通过编写计算机程序建立进行简单随机抽样,构建不同样本量云南松幼苗各器官及单株生物量异速生长方程。利用决定系数（R²）、估计值标准误（SEE）、均方根误差（RMSE）、总相对误差（RS）及平均误差绝对值（MAB）,对模型拟合优度与精度进行比较分析。结果表明：幂函数方程可较好地用于估测云南松幼苗生物量;随着样本量的增加模型精度评估指数MAB呈幂函数形式逐渐减小;当样本数量小于200时MAB较为敏感,模型精度较差,样本量大于200时,其精度随样本量逐渐增加,但变化幅度逐步减小并趋于稳定。因此,根据MAB的变化趋势,样本量达到200时可以构建精度较高且稳定模型。     

Factor scoring models of the Pittsburgh Sleep Quality Index: a comparative confirmatory factor analysis

The Pittsburgh Sleep Quality Index (PSQI) is a rigorously validated questionnaire with extensive use in sleep assessment. Findings from numerous factor analytic studies of the PSQI have been interpreted to support a heterogeneous factor structure model for the test. Nevertheless, the literature continues to lack a focused evaluation of whether this heterogeneous factor structure is justified. A consideration of this issue led to a conclusion that a closer analysis of the PSQI’s factor structure was merited. To address this need a comparative confirmatory factor analysis for assessing the performance of the accepted factors models of the PSQI was conducted. A sample of university students (n = 418), age = 20.92 ± 1.81 years, BMI = 23.30 ± 2.57 kg/m² completed the multi-structured sleep survey at Jamia Millia Islamia, New Delhi, India. Seventeen putative factor structures (three 1-Factor, eight 2-Factor, and six 3-Factor) of the PSQI from the existing literature were selected for analysis. Fourteen models (82.35%) had almost similar values for model fit indices. Two models were misfits, and one model was a poor fit. The two misfit models incorporated gender and age as covariates. The third poor fit model was used to produce a unique path diagram, which made it distinct from the remaining 16 models. The overlapping values in the fit range of the model fit indices did not support the often projected heterogeneous factor structures of the PSQI for the vast majority of the models.     

A Critical Review of Discrete Soil Sample Data Reliability: Part 1—Field Study Results

Part 1 of this study summarizes data for a field investigation of contaminant concentration variability within individual, discrete soil samples (intra-sample variability) and between closely spaced, “co-located” samples (inter-sample variability). Hundreds of discrete samples were collected from three sites known respectively to be contaminated with arsenic, lead, and polychlorinated biphenyls. Intra-sample variability was assessed by testing soil from ten points within a minimally disturbed sample collected at each of 24 grid points. Inter-sample variability was assessed by testing five co-located samples collected within a 0.5-m diameter of each grid point. Multi Increment soil samples (triplicates) were collected at each study site for comparison. The study data demonstrate that the concentration of a contaminant reported for a given discrete soil sample is largely random within a relatively narrow (max:min <2X) to a very wide (max:min >100X) range of possibilities at any given sample collection point. The magnitude of variability depends in part on the contaminant type and the nature of the release. The study highlights the unavoidable randomness of contaminant concentrations reported in discrete soil samples and the unavoidable error and inefficiency associated with the use of discrete soil sample data for decision making in environmental investigations.     

土壤样品中DNA提取方法的比较

对土壤样品中提取DNA方法的有效性进行了比较研究。如果以细胞有效裂解和DNA产率为标准,用冻融进行预处理再结合SDS和溶菌酶的化学裂解方法,是效果最佳的DNA抽提方法,细胞裂解率为82%,DNA产率达20.8μg/g。为了去除PCR抑制物,将DNA样品进一步用柱纯化,回收率为80%。纯化后的DNA样品可用于16SrDNA扩增及其他分子操作。