A representative pond net sample: Fiction or reality?

The occurrence of chironomids in a standard pond net sample was studied. The standard pond net sample is quite biased; its qualitative to semi-quantitive character should always be taken into account. It is advised to transform abundances (log-normal) of chironomids when collected with the standard pond net. Despite disadvantages the pond net can be used in water quality surveys because of their general objectives.     

Estimating the Population Mean Using Extreme Ranked Set Sampling

Precision of the estimate of the population mean using ranked set sample (RSS) relative to using simple random sample (SRS), with the same number of quantified units, depends upon the population and success in ranking. In practice, even ranking a sample of moderate size and observing the ith ranked unit (other than the extremes) is a difficult task. Therefore, in this paper we introduce a variety of extreme ranked set sample (ERSSs) to estimate the population mean. ERSSs is more practical than the ordinary ranked set sampling, since in case of even sample size we need to identify successfully only the first and/or the last ordered unit or in case of odd sample size the median unit. We show that ERSSs gives an unbiased estimate of the population mean in case of symmetric populations and it is more efficient than SRS, using the same number of quantified units. Example using real data is given. Also, parametric examples are given.     

Serving science and conservation: The biological materials request protocol of the New York Zoological Society

Biological materials obtained during routine veterinary treatment and necropsies on zoo and aquarium animals provide opportunities to study a wide variety of phenomena, many of which have important implications for wildlife conservation and captive animal management. Collection and shipment of biological materials require extensive coordination, and few zoological institutions have developed detailed, standardized protocols to facilitate these efforts. The value of using biological materials is reviewed and a set of policies and guidelines are outlined for their collection, preservation, and shipment. Several related issues are discussed, including health hazards and liability issues, permit requirements, and animal welfare considerations.     

Factors influencing the distribution of aquatic plant communities in Irish canals

Terrestrial tardigrades are often found in the lichens and mosses growing on trees and rocks. The assertion that tardigrades in these habitats are very patchy in their distribution has rarely been backed by quantitative sampling. This study assesses spatial variability in tardigrade populations inhabiting small patches (0.1 cm² to over 5 cm²) of moss and lichen on trees and rocks at three sites in the United States of America. Tardigrades were collected from four replicate rocks in the Ouachita Mountains of Arkansas, with 30 lichen patches collected on two adjacent boulders and 20 moss patches on a second pair of boulders. In Fort Myers and in Citrus Springs, Florida, 30 lichen patches per tree were collected from two pairs of trees. The tardigrades in each sample were extracted, mounted, identified, and counted. The variation in tardigrade abundance among lichen or moss patches within rocks or trees was very high; the only consistent pattern was that very small patches usually lacked tardigrades. Tardigrade diversity and abundance also varied greatly within sites when lichens and mosses of the same species from different rocks and trees were compared (in the most extreme case one tree had numerous individuals of two tardigrade species present while the other had almost no tardigrades). The results of this quantitative sampling support the assertion that tardigrades are very patchy in distribution. Given the considerable time investment required for the quantitative processing of tardigrade samples, this high spatial variability in tardigrade diversity and abundance requires that researches testing ecological hypotheses about tardigrade abundance check variability before deciding how many samples to take.     

吉林蛟河42 hm2针阔混交林样地植物种-面积关系

 种-面积关系是生态学中的基本问题, 其构建方式对种-面积关系的影响以及最优种-面积模型的选择仍然存在争议。该文利用吉林蛟河42 hm²针阔混交林样地数据, 分别采用巢式样方法和随机样方法建立对数模型、幂函数模型和逻辑斯蒂克模型, 并通过赤池信息量准则(AIC)检验种-面积模型优度。结果表明, 种-面积关系受到取样方法的影响, 随机样方法的拟合效果优于巢式样方法。采用随机样方法构建的幂指数模型(AIC = 89.11)和逻辑斯蒂克模型(AIC = 71.21)优于对数模型(AIC = 113.81)。根据AIC值可知, 随机样方法构建的逻辑斯蒂克模型是拟合42 hm²针阔混交林样地种-面积关系的最优模型。该研究表明: 在分析种-面积关系时不仅应考虑尺度效应, 还需注意生境变化及群落演替的影响。     

ABI sequencing analysis

The ABI Sequencing Analysis application is designed specifically for the analysis of data produced by the ABI DNA Sequencer. The ABI sequencer is a laser-based instrument that utilizes fluorescent labels to analyze the products of a sequencing reaction as they migrate through a gel. After the data are collected from a sequencing run, the Analysis program identifies and tracks the sample lanes of the gel and subsequently normalizes and integrates the raw data into a chromatogram of the final sequence. For the use, there are basically two types of files that can be manipulated to potentially improve the analysis results. The Gel File consists of a computer generated image of the sequencing gel with the fluorescent DNA banding patterns. This image allows the user to view and edit the tracking lines generated and used by Analysis to collect data points for each sample. Individual Sample Files are stored for each of the samples analyzed and include the chromatogram, raw data, and annotations and information regarding the sample and sequence run. Generally, the products of a sequencing reaction are easily resolved and the Analysis software interprets the correct nucleotide sequence. Ambiguous base calls tend to occur near the end of the sequence and may be either edited or deleted by the user before exporting the data for further comparisons or alignments. Occasionally the tracking lines within the gel image may need to be adjusted or moved. The sample data are then reextracted from the Gel File and analyzed again. This review explains the general operation of Analysis in terms of viewing and editing a chromatogram, retracking the lanes of a Gel File, and analyzing the final sample data. The three versions 1.2.1, 2.1.2, and 3.3 are discussed.     

Suspension trapping (STrap) sample preparation method for bottom‐up proteomics analysis

Despite recent developments in bottom‐up proteomics, the need still exists in a fast, uncomplicated, and robust method for comprehensive sample processing especially when applied to low protein amounts. The suspension trapping method combines the advantage of efficient SDS‐based protein extraction with rapid detergent removal, reactor‐type protein digestion, and peptide cleanup. Proteins are solubilized in SDS. The sample is acidified and introduced into the suspension trapping tip incorporating the depth filter and hydrophobic compartments, filled with the neutral pH methanolic solution. The instantly formed fine protein suspension is trapped in the depth filter stack—this crucial step is aimed at separating the particulate matter in space. SDS and other contaminants are removed in the flow‐through, and a protease is introduced. Following the digestion, the peptides are cleaned up using the tip's hydrophobic part. The methodology allows processing of protein loads down to the low microgram/submicrogram levels. The detergent removal takes about 5 min, whereas the tryptic proteolysis of a cellular lysate is complete in as little as 30 min. We have successfully utilized the method for analysis of cellular lysates, enriched membrane preparations, and immunoprecipitates. We expect that due to its robustness and simplicity, the method will become an essential proteomics tool.     

Determination of alosetron in human plasma or serum by high-performance liquid chromatography with robotic sample preparation

A method of analysis for the determination of alosetron in human plasma or serum has been developed. The method was fully automated using a laboratory robot in order to improve analytical precision, efficiency and safety. The assay involved solid-phase extraction with reversed-phase HPLC separation and fluorescence detection. A validation exercise over the concentration range of 0.1 to 20 ng/ml demonstrated the selectivity, linearity, sensitivity, accuracy, precision, extraction efficiency, ruggedness and stability of the method. The method has been applied in support of numerous human pharmacokinetic/biopharmaceutic studies over the last five years.     

Reduction of Total Sample Size and Cost of Sampling in Tests of Hypothesis by Using Unequal Group Sizes

The standard approach in calculating the appropriate sample size required to detect a specified difference in the means of two populations for given type I and II errors assumes equal sample sizes in each group. It is shown here that equal sample sizes are usually sub-optimal with respect to total sample size and with respect to total cost of the experiment. This is may be important in experiments involving animals when costs are measured not only in monetary terms but also in terms of animal suffering or inconvenience.     

Prospecting for hyperaccumulators of trace elements: a review

Specific plant species that can take up and accumulate abnormally high concentrations of elements in their aboveground tissues are referred to as “hyperaccumulators”. The use of this term is justified in the case of enormous element-binding capacity of plants growing in their natural habitats and showing no toxicity symptoms. An increasing interest in the study of hyperaccumulators results from their potential applications in environmental biotechnology (phytoremediation, phytomining) and their emerging role in nanotechnology. The highest number of plant species with confirmed hyperaccumulative properties has been reported for hyperaccumulators of nickel, cadmium, zinc, manganese, arsenic and selenium. More limited data exist for plants accumulating other elements, including common pollutants (chromium, lead and boron) or elements of commercial value, such as copper, gold and rare earth elements. Different approaches have been used for the study of hyperaccumulators – geobotanical, chemical, biochemical and genetic. The chemical approach is the most important in screening for new hyperaccumulators. This article presents and critically reviews current trends in new hyperaccumulator research, emphasizing analytical methodology that is applied in identification of new hyperaccumulators of trace elements and its future perspectives.     

一种提取动物基因组总DNA的野外样品保存方法

为了确定一种方便的野外动物样品保存方法,以新鲜材料作对照,从-20℃冰箱、70%乙醇、含50mmol/L EDTA的70%乙醇、95%乙醇、液氮处理的高原鼠肌肉和肝脏组织中提取基因组总DNA。通过琼脂糖凝胶电泳和紫外分光光度计对提取的基因组总DNA质量进行检测。结果显示:相同处理的肝脏DNA产量大,肌肉组织提取的DNA质量好;各种保存方法提取的DNA降解程度依次为,-20℃冰箱、70%乙醇>含50mmol/L EDTA的70%乙醇、95%乙醇>液氮>新鲜。选择新鲜肌肉和95%酒精处理的肌肉样品提取的总DNA作模板,进行微卫星PCR扩增,均可获得清晰的电泳带。将该方法用于高原鼢鼠,进行线粒体12S rRNA、Cytb和D-loop区测序,结果显示该方法保存的样品与新鲜样品没有差别。因此,在野外用95%乙醇固定肌肉样品是一种可行的样品保存方法。     

不同冰冻保存时间对淡水硝酸盐浓度测定的影响(连续流动分析法)

采用AA3连续流动分析仪对不同冰冻时间的标准浓度水样和自然水样的硝酸盐含量进行了测定.结果表明,标准水样在-20℃条件下冰冻30d的硝酸盐浓度稳定,而自然水样冰冻2d的硝酸盐浓度较原始值高,此后时间越长,硝酸盐含量越低.     

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.     

Extraction of Cysts and Eggs of Heterodera schachtii from Soil with an Assessment of Extraction Efficiency

Techniques are described for the extraction and enumeration of cysts and contained eggs from soil samples. The average recovery of cysts from seeded soil samples of differing soil texture was 82.7 ± 2.1%. Recovery from sandy clay soil samples seeded at 1 cyst/100 g soil was 63.4 ± 5.5%; at 4.2 cysts/100 g soil recovery was 89.6 ± 1.8%. Recovery of cysts from naturally infested clay soil was 88.3 ± 2.05%. Egg extraction efficiency for seeded samples was calculated as 78%, and for naturally infested soil was estimated as 83%.     

血液蛋白质组学的研究技术及进展

人血液含有来源于几乎所有细胞、组织、器官的蛋白质,可以直接反映病理、生理状态,是各种疾病诊断、生物标志物发现的最有价值的标本。因此,长期以来,血浆蛋白质组一直是人们研究的热点,并被人类蛋白质组组织(HUPO)列为首批启动的重大国际合作研究项目。血浆蛋白质含量动态范围非常广、成分极其复杂,血浆蛋白质组的研究极富挑战性。近年来,血浆高丰度蛋白质去除、蛋白质/肽段分离、质谱鉴定、数据处理等多种相关技术都取得了很大的进展。本文简要综述了上述技术领域的研究和应用进展。     

A density-based proteomics sample fractionation technology: folate deficiency induced oxidative stress response in liver and brain.

Folate deficiency (FD) alters hepatic methionine metabolism and is associated with increased hepatocellular apoptosis. Additionally, mice deprived of folate showed increased oxidative damage in brain tissue, leading to cognitive impairment. Most previous studies have focused independently on either liver, the main tissue of folate storage and metabolism, or brain, where folate regulates neurogenesis and programs cell death. The aim of this study was to apply a powerful, rapid proteomics approach to understand potential subcellular correlations of folate deficiency in both brain and liver of the same rat. This approach combined a new density-based sample fractionation technology (enhanced density gradient extraction = Edge technology) with other conventional proteomics techniques, such as western blot analysis, 2DE, and mass spectrometry. The brain and the liver from individual rats, fed normal or FD diets for 6 wks, were homogenized and then fractionated using the Edge 200 Separation System. Subsequently, all fractions from brain and liver, from control and treated rats, were analyzed by western blot using two markers of oxidative stress: glutathione peroxidase 1 (GPx1) and glucose-regulated protein 75 (GRP75). certain fractions were selected based on western blot analysis and were further analyzed by 2DE. protein spots of interest were identified by MALDI-TOF/TOF. The results demonstrated that edge technology provides a powerful density based separation and enrichment method for rapid screening of potential FD markers and their possible correlations to both liver and brain diseases.     

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.     

Skinfold thicknesses in a national probability sample of U.S. males and females aged 6 through 17 years

Cycles II and III of the Health Examination Survey included measurements of the skinfolds of over 14,000 individuals 6 through 17 years of age, statistically weighted to provide an accurate national probability sample. Analyses of the triceps and subscapular skinfolds of Negroes and whites are reported here, utilizing the median in preference to the mean. Females of either racial group have thicker skinfolds at all ages studied. Whites have greater median triceps thicknesses than Negroes of the same sex and age, but there are no differences between the two racial groups in the subscapular. Since, between all but one pair of adjacent ages in males, from 12 years on, the median triceps fold decreases, but the estimated cross-sectional are of fat increases, it is strongly recommended that reductions in triceps thickness not be automatically interpreted as meaning a loss of subcutaneous fat. Since greater skewness is found in the subscapular distributions in whites, but not in the triceps, it is suggested that racial differences in triceps thickness at these ages occurs from the operation of hereditary factors, while differences in the subscapular skinfold arise from environmental causes.     

A Critical Review of Discrete Soil Sample Data Reliability: Part 2—Implications

Part 2 of this study investigates the implications of random, small-scale contaminant concentration variability in soil for reliance on discrete soil sample data to guide environmental investigations. Random variability around an individual point limits direct comparison of discrete sample data to risk-based screening levels. “False negatives” can lead to premature termination of an investigation or remedial action. Small-scale distributional heterogeneity of contaminants in soil is expressed as artificial, seemingly isolated “hot spots” and “cold spots” in isoconcentration maps. Surgical removal of hot spots can lead to erroneous conclusions regarding the magnitude of remaining contamination. The field precision of an individual discrete sample data set for estimation of means for a contaminant in a risk assessment is not directly testable. Omission of “outlier” data in order to force data to fit a geostatistical model distorts estimates of mean concentrations and introduces error into a risk assessment. The potential for such errors was pointed out in early USEPA guidance but largely ignored or misunderstood. Decision Unit and Multi Increment sample investigation methods, long known to the agricultural and mining industries, were specifically developed to overcome these inherent shortcomings of discrete sampling methods and provide more reliable and defensible data for environmental investigations.