Two methods for detecting landscape associations based on a landscape map

Landscape association refers to relations among landscape elements. Two methods, landscape juxtaposition and landscape region, for detecting landscape associations are described. Sampling transects across a landscape map were used to collect data. A series of equidistant points is located along each transect, and the landscape element in which each point falls is identified and recorded. These data are easy to collect and analyze by the two techniques. The first method considers the frequency of juxtaposition of landscape elements and tests whether this frequency is significantly greater than or less than a random expectation. The second method divides each transect into regions and tests whether the number of occurrences of each landscape element within the regions of occurrence of each other element is significantly greater than or less than that outside those regions. These two methods were applied to the analysis of landscape associations for Shaanxi vegetation landscape, and they provided rational and meaningful results. These methods made detecting landscape associations considerably easier.     

Comparison of methods for detecting bottlenecks from microsatellite loci

This paper describes simulation tests to compare methods for detecting recent bottlenecks using microsatellite data. This study considers both type I error (detecting a bottleneck when there wasn’t one) and type II error (failing to detect a bottleneck when there was one) under a variety of scenarios. The two most promising methods were the range in allele size conditioned on the number of alleles, M _k , and heterozygosity given the number of alleles, H _k , under a two-phase mutation model; in most of the simulations one of these two methods had the lowest type I and type II error relative to other methods. M _k was the method most likely to correctly identify a bottleneck when a bottleneck lasted several generations, the population had made a demographic recovery, and mutation rates were high or pre-bottleneck population sizes were large. On the other hand H _k was most likely to correctly identify a bottleneck when a bottleneck was more recent and less severe and when mutation rates were low or pre-bottleneck population sizes were small. Both methods were prone to type I errors when assumptions of the model were violated, but it may be easier to design a conservative heterozygosity test than a conservative ratio test.     

Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations

Identifying adaptive loci can provide insight into the mechanisms underlying local adaptation. Genotype–environment association (GEA) methods, which identify these loci based on correlations between genetic and environmental data, are particularly promising. Univariate methods have dominated GEA, despite the high dimensional nature of genotype and environment. Multivariate methods, which analyse many loci simultaneously, may be better suited to these data as they consider how sets of markers covary in response to environment. These methods may also be more effective at detecting adaptive processes that result in weak, multilocus signatures. Here, we evaluate four multivariate methods and five univariate and differentiation‐based approaches, using published simulations of multilocus selection. We found that Random Forest performed poorly for GEA. Univariate GEAs performed better, but had low detection rates for loci under weak selection. Constrained ordinations, particularly redundancy analysis (RDA), showed a superior combination of low false‐positive and high true‐positive rates across all levels of selection. These results were robust across the demographic histories, sampling designs, sample sizes and weak population structure tested here. The value of combining detections from different methods was variable and depended on the study goals and knowledge of the drivers of selection. Re‐analysis of genomic data from grey wolves highlighted the unique, covarying sets of adaptive loci that could be identified using RDA. Although additional testing is needed, this study indicates that RDA is an effective means of detecting adaptation, including signatures of weak, multilocus selection, providing a powerful tool for investigating the genetic basis of local adaptation.     

Comparison of novel and existing methods for detecting differentially methylated regions

Background

Single-probe analyses in epigenome-wide association studies (EWAS) have identified associations between DNA methylation and many phenotypes, but do not take into account information from neighboring probes. Methods to detect differentially methylated regions (DMRs) (clusters of neighboring probes associated with a phenotype) may provide more power to detect associations between DNA methylation and diseases or phenotypes of interest.

Results

We proposed a novel approach, GlobalP, and perform comparisons with 3 methods—DMRcate, Bumphunter, and comb-p—to identify DMRs associated with log triglycerides (TGs) in real GAW20 data before and after fenofibrate treatment. We applied these methods to the summary statistics from an EWAS performed on the methylation data. Comb-p, DMRcate, and GlobalP detected very similar DMRs near the gene CPT1A on chromosome 11 in both the pre- and posttreatment data. In addition, GlobalP detected 2 DMRs before fenofibrate treatment in the genes ETV6 and ABCG1. Bumphunter identified several DMRs on chromosomes 1 and 20, which did not overlap with DMRs detected by other methods.

Conclusions

Our novel method detected the same DMR identified by two existing methods and detected two additional DMRs not identified by any of the existing methods we compared.

     

A covering method for detecting genetic associations between rare variants and common phenotypes

Genome wide association (GWA) studies, which test for association between common genetic markers and a disease phenotype, have shown varying degrees of success. While many factors could potentially confound GWA studies, we focus on the possibility that multiple, rare variants (RVs) may act in concert to influence disease etiology. Here, we describe an algorithm for RV analysis, RareCover. The algorithm combines a disparate collection of RVs with low effect and modest penetrance. Further, it does not require the rare variants be adjacent in location. Extensive simulations over a range of assumed penetrance and population attributable risk (PAR) values illustrate the power of our approach over other published methods, including the collapsing and weighted-collapsing strategies. To showcase the method, we apply RareCover to re-sequencing data from a cohort of 289 individuals at the extremes of Body Mass Index distribution (NCT00263042). Individual samples were re-sequenced at two genes, FAAH and MGLL, known to be involved in endocannabinoid metabolism (187Kbp for 148 obese and 150 controls). The RareCover analysis identifies exactly one significantly associated region in each gene, each about 5 Kbp in the upstream regulatory regions. The data suggests that the RVs help disrupt the expression of the two genes, leading to lowered metabolism of the corresponding cannabinoids. Overall, our results point to the power of including RVs in measuring genetic associations.     

基因芯片筛选差异表达基因方法比较

摘要: 使用计算机模拟数据和真实的芯片数据, 对8种筛选差异表达基因的方法进行了比较分析, 旨在比较不同方法对基因芯片数据的筛选效果。模拟数据分析表明, 所使用的8种方法对均匀分布的差异表达基因有很好的识别、检出作用。算法方面, SAM和Wilcoxon秩和检验方法较好; 数据分布方面, 正态分布的识别效果较好, 卡方分布和指数分布的识别效果较差。杨树cDNA芯片分析表明, SAM、Samroc和回归模型方法相近, 而Wilcoxon秩和检验方法与它们有较大差异。     

两种用于测定A/C群脑膜炎球菌多糖疫苗中乳糖含量方法的比较分析

为探索一个灵敏、简便、快速的定量检测A/C群脑膜炎球菌多糖疫苗中乳糖含量的方法,对两种化学法进行了分析和比较。两种化学方法分别采用间苯二酚显色法和苦味酸显色法。间苯二酚显色法为套用唾液酸测定法,苦味酸显色法是对乳制品中乳糖含量检测方法的改良。两种方法的相关系数均大于0.99,线性良好。用间苯二酚法测定样品的回收试验检测结果平均值和变异系数分别为100.4%和3.09%,用苦味酸法测定样品的回收试验检测平均值和变异系数分别为99.9%和1.43%。这两种方法可以初步应用于疫苗中乳糖含量检测。     

Comparison of three immunological methods for detecting staphylococcal enterotoxins from food

AIMS: Immunologically based assays for the detection of staphylococcal enterotoxins are numerous. These techniques include radio immunosorbent assays and enzyme-linked immunosorbent assays (ELISA), some of which are available as commercial kits. The purpose of this study was to compare the performances of three commercial immunoassays. METHODS AND RESULTS: Two automated detection systems, VIDAS SET bioMèrieux, VIDAS SET2 bioMérieux and an ELISA method, TRANSIA PLATE Staphylococcal Enterotoxins Diffchamb were compared for detecting different quantities of purified staphylococcal enterotoxins (A, B, C2, D and E) added to food. CONCLUSIONS: VIDAS SET2 had a greater specificity (100%) and sensitivity than VIDAS SET and TRANSIA PLATE Staphylococcal Enterotoxins. More precisely, VIDAS SET2 could detect <0.5 ng g(-1) of toxins A and B, <1 ng g(-1) of toxins C2 and E and 1 ng g(-1) of toxins D and E. SIGNIFICANCE AND IMPACT OF THE STUDY: Because staphylococcal food poisoning (resulting from ingestion of low levels of staphylococcal enterotoxins) is one of the most common forms of foodborne illness there is a need for specific and sensitive methods for detecting these enterotoxins. VIDAS SET2 appears to be suitable for detecting staphylococcal enterotoxins from food.     

Comparison of methods for detecting vulnerability of xylem embolism in Robinia pseudoacacia

在全球变暖的背景下, 植物木质部栓塞脆弱性是林木死亡率升高的重要生理学因素。然而不同方法在长导管树种上建立的栓塞脆弱性曲线存在较大差异。该研究以长导管树种刺槐(Robinia pseudoacacia)为研究对象, 利用自然干燥法、Cochard Cavitron离心机法以及Sperry离心机法建立了栓塞脆弱性曲线, 旨在探讨不同检测方法的合理性。在Sperry离心法中, 使用了两种规格的转子, 从而对“开口导管假象”学说进行了检验。研究结果表明: 自然干燥法建立的栓塞脆弱性曲线为“s”形, 而Cochard Cavitron离心机法和Sperry离心机法建立的栓塞脆弱性曲线为“r”形; 自然干燥法与离心机法建立的曲线存在显著性差异, 且两种离心机法建立的曲线也具有显著性差异。尽管刺槐枝条的导管长度分布表明14.4 cm长的刺槐枝条具有更高比例的开放导管, 但用Sperry离心机法在27.4 cm和14.4 cm长茎段上建立的栓塞脆弱性曲线相似, 表明Sperry离心机法检测刺槐脆弱性曲线时未产生“开口导管假象”, 具有更为可靠的检测结果。     

刺槐木质部栓塞脆弱性检测的方法比较

在全球变暖的背景下, 植物木质部栓塞脆弱性是林木死亡率升高的重要生理学因素。然而不同方法在长导管树种上建立的栓塞脆弱性曲线存在较大差异。该研究以长导管树种刺槐(Robinia pseudoacacia)为研究对象, 利用自然干燥法、Cochard Cavitron离心机法以及Sperry离心机法建立了栓塞脆弱性曲线, 旨在探讨不同检测方法的合理性。在Sperry离心法中, 使用了两种规格的转子, 从而对“开口导管假象”学说进行了检验。研究结果表明: 自然干燥法建立的栓塞脆弱性曲线为“s”形, 而Cochard Cavitron离心机法和Sperry离心机法建立的栓塞脆弱性曲线为“r”形; 自然干燥法与离心机法建立的曲线存在显著性差异, 且两种离心机法建立的曲线也具有显著性差异。尽管刺槐枝条的导管长度分布表明14.4 cm长的刺槐枝条具有更高比例的开放导管, 但用Sperry离心机法在27.4 cm和14.4 cm长茎段上建立的栓塞脆弱性曲线相似, 表明Sperry离心机法检测刺槐脆弱性曲线时未产生“开口导管假象”, 具有更为可靠的检测结果。     

Comparison of media and methods for detecting and enumerating Listeria monocytogenes in refrigerated cabbage

Direct plating, selective enrichment, and cold enrichment followed by secondary selective enrichment procedures were compared for detecting and enumerating Listeria monocytogenes in chopped cabbage stored at 5 degrees C for up to 64 days. Addition of Fe3+ to solid media enhanced detection of the organism. Cold enrichment (5 degrees C) in nutrient broth and brain heart infusion broth followed by secondary enrichment (48 h, 30 degrees C) in Trypticase soy-yeast extract-antibiotic broth and thiocyanate-nalidixic acid broth and plating on selective agar media (Doyle and Schoeni selective enrichment agar [minus acriflavin hydrochloride, supplemented with 5 micrograms of Fe3+/ml] and McBride Listeria agar) resulted in the detection of highest populations.     

花斑裸鲤年龄鉴定材料的比较与年龄判别

鱼类年龄的准确鉴定是研究鱼类生态学和保护生物学的基础。本文对黄河上游花斑裸鲤(Gymnocypris eckloni)耳石、背鳍条和臀鳞等3种年龄材料的年龄解释一致性以及最佳年龄材料的选择进行了比较和分析,并首次建立了花斑裸鲤低龄个体年龄判别方程。结果表明:花斑裸鲤3种年龄材料上年轮可读性依次是耳石背鳍条臀鳞,最大鉴定年龄分别为25龄、17龄和16龄;对于6龄及以下个体,背鳍条作为年龄鉴定材料更有优势;对7龄及以上个体,耳石效果最佳;同时对6龄及以下个体以全长、体长、体重和空壳重为自变量,采用逐步选择法进行判别分析,最终提取全长和体重建立年龄的分类函数;全部样本正判率和交叉验证正判率显示,该年龄判别模型的正确区分度较高,可用于6龄及以下个体(全长93~259 mm;体重6.25~177.10 g)的年龄判别。     

Diversity and classification of mycorrhizal associations

Most mycorrhizas are 'balanced' mutualistic associations in which the fungus and plant exchange commodities required for their growth and survival. Myco-heterotrophic plants have 'exploitative' mycorrhizas where transfer processes apparently benefit only plants. Exploitative associations are symbiotic (in the broad sense), but are not mutualistic. A new definition of mycorrhizas that encompasses all types of these associations while excluding other plant-fungus interactions is provided. This definition recognises the importance of nutrient transfer at an interface resulting from synchronised plant-fungus development. The diversity of interactions between mycorrhizal fungi and plants is considered. Mycorrhizal fungi also function as endophytes, necrotrophs and antagonists of host or non-host plants, with roles that vary during the lifespan of their associations. It is recommended that mycorrhizal associations are defined and classified primarily by anatomical criteria regulated by the host plant. A revised classification scheme for types and categories of mycorrhizal associations defined by these criteria is proposed. The main categories of vesicular-arbuscular mycorrhizal associations (VAM) are 'linear' or 'coiling', and of ectomycorrhizal associations (ECM) are 'epidermal' or 'cortical'. Subcategories of coiling VAM and epidermal ECM occur in certain host plants. Fungus-controlled features result in 'morphotypes' within categories of VAM and ECM. Arbutoid and monotropoid associations should be considered subcategories of epidermal ECM and ectendomycorrhizas should be relegated to an ECM morphotype. Both arbuscules and vesicles define mycorrhizas formed by glomeromycotan fungi. A new classification scheme for categories, subcategories and morphotypes of mycorrhizal associations is provided.     

Comparison of media and methods for detecting and enumerating Listeria monocytogenes in refrigerated cabbage.

Direct plating, selective enrichment, and cold enrichment followed by secondary selective enrichment procedures were compared for detecting and enumerating Listeria monocytogenes in chopped cabbage stored at 5 degrees C for up to 64 days. Addition of Fe3+ to solid media enhanced detection of the organism. Cold enrichment (5 degrees C) in nutrient broth and brain heart infusion broth followed by secondary enrichment (48 h, 30 degrees C) in Trypticase soy-yeast extract-antibiotic broth and thiocyanate-nalidixic acid broth and plating on selective agar media (Doyle and Schoeni selective enrichment agar [minus acriflavin hydrochloride, supplemented with 5 micrograms of Fe3+/ml] and McBride Listeria agar) resulted in the detection of highest populations.     

Comparison of three different methods for automated classification of cervical cells.

Over 4600 exfoliated squamous cervical cells taken from appropriate Papanicolaou samples were classified as normal, mildly dysplastic, moderately dysplastic and severely dysplastic by an experienced cytopathologist. The slides were de-stained and subsequently re-stained with Feulgen Thionin-SO2 stain. Images of the nuclei were then captured, recorded and processed employing an image cytometry device. Automated classification of the cells was carried out using three different methods--discriminant function analysis, a decision tree classifier and a neutral network classifier. The discriminant function analysis method, which combined all dysplastic cells into an abnormal group, achieved a combined error rate of less than 0.4% for moderate and severe dysplastic cells, and less than 40% for mildly dysplastic cells. All three methods yielded comparable results, which approached those of human performance.     

Power for detecting genetic divergence: differences between statistical methods and marker loci

Information on statistical power is critical when planning investigations and evaluating empirical data, but actual power estimates are rarely presented in population genetic studies. We used computer simulations to assess and evaluate power when testing for genetic differentiation at multiple loci through combining test statistics or P values obtained by four different statistical approaches, viz. Pearson's chi-square, the log-likelihood ratio G-test, Fisher's exact test, and an F(ST)-based permutation test. Factors considered in the comparisons include the number of samples, their size, and the number and type of genetic marker loci. It is shown that power for detecting divergence may be substantial for frequently used sample sizes and sets of markers, also at quite low levels of differentiation. The choice of statistical method may be critical, though. For multi-allelic loci such as microsatellites, combining exact P values using Fisher's method is robust and generally provides a high resolving power. In contrast, for few-allele loci (e.g. allozymes and single nucleotide polymorphisms) and when making pairwise sample comparisons, this approach may yield a remarkably low power. In such situations chi-square typically represents a better alternative. The G-test without Williams's correction frequently tends to provide an unduly high proportion of false significances, and results from this test should be interpreted with great care. Our results are not confined to population genetic analyses but applicable to contingency testing in general.     

Unhatched eggs: methods for discriminating between infertility and early embryo mortality

Unhatched eggs are a common phenomenon in birds and are often referred to as being 'infertile', which (confusingly) can mean at least two things: (1) that the ovum has not been fertilized or (2) that the embryo has died during development. These two broad categories of hatching failure can be difficult to distinguish, particularly in the early stages of embryo development. We describe methods to distinguish between infertility (due to insufficient sperm) and early embryo mortality in passerine eggs using the Zebra Finch Taeniopygia guttata as a model. We also describe how we successfully adapted these methods for use on eggs from a wild species, the Tree Sparrow Passer montanus , collected after the incubation period, and show that sperm can be visualized on the perivitelline layer of unhatched eggs even several weeks after laying.