Group screening for rare events based on incomplete block designs

Fields such as, diagnostic testing, biotherapeutics, drug development, and toxicology among others, center on the premise of searching through many specimens for a rare event. Scientists in the business of “searching for a needle in a haystack” may greatly benefit from the use of group screening design strategies. Group screening, where specimens are composited into pools with each pool being tested for the presence of the event, can be much more cost-efficient than testing each individual specimen. A number of group screening designs have been proposed in the literature. Incomplete block screening designs are described here and compared with other group screening designs. It is shown under certain conditions, that incomplete block screening designs can provide nearly a 90% cost saving compared to other group screening designs such as when prevalence is 0.001 and screening 3876 specimens with an ICB-sequential design vs. a Dorfman design. In other cases, previous group screening designs are shown to be most efficient. Overall, when prevalence is small (≤0.05) group screening designs are shown to be quite cost effective at screening a large number of specimens and in general there is no one design that is best in all situations. © 2018 American Institute of Chemical Engineers Biotechnol Progress, 35: e2770, 2019.     

黄河下游农业景观中景观结构和生境特征对林表生蜘蛛多样性的影响

以捕食者来进行"自上而下"的生物防治是有效而经济的。蜘蛛作为农业景观中重要的捕食者,在不同的尺度上研究景观和环境要素对其多样性的影响是十分必要的。目前,有关黄河下游农业景观研究中,关于蜘蛛多样性的研究报道较少。针对黄河下游农业景观中林地生境的蜘蛛多样性展开研究,于2014年4月和7月采用陷阱法调查林地生境中蜘蛛种群的分布及其多样性,分析了对蜘蛛多样性影响最强烈的环境因子,以及不同蜘蛛种群对草本植被盖度的不同选择。结果发现:研究区林地生境内蜘蛛的优势种群为星豹蛛(Pardosa astrigena)、单带希托蛛(Hitobia unifascigera)、类水狼蛛(Pirata piratoides)和陕西近狂蛛(Drassyllus shaanxiensis)。不同尺度上的景观要素和环境要素(解释变量)对蜘蛛多样性的影响存在差异,且在不同的季节均为100 m尺度上的解释变量对蜘蛛多样性的影响最大。在100 m尺度上,不同的解释变量对蜘蛛多样性的影响也不同,春季林地中的植被盖度对其影响最大,路距和林地面积也有较为明显的影响,夏季林地中的植被高度和植被盖度对其影响最大,其余解释变量的影响则极小。不同的蜘蛛种群对草本植被盖度大小的偏好不同,多数蜘蛛偏好高的植被盖度,如星豹蛛和白纹舞蛛(Alopecosa albostriata)等,也有部分蜘蛛种群偏好中、低植被盖度,如赫氏花蟹蛛(Xysticus hedini Schenkel)、白斑猎蛛(Evarcha albaria)和皮雄红螯蛛(Araneae)。研究表明,黄河下游农业景观林地生境中,不同的景观要素和环境要素在不同尺度和不同季节上对蜘蛛多样性的影响具有显著的差异,草本植被对蜘蛛多样性的影响极为显著。因此在研究区内合理规划林地的建设,加强草本植被的保护,提高林地捕食者的数量,有助于生物防治工作的发展和生物多样性保护工作的进行。     

Micro-colony array based high throughput platform for enzyme library screening

Enzymes are becoming increasingly important tools for synthesizing and modifying fine and bulk chemicals. The availability of biocatalysts which fulfil the requirements of industrial processes is often limited. Recruiting suited enzymes from natural (e.g. metagenomes) and artificial (e.g. directed evolution) biodiversity is based on screening libraries of microbial clones expressing enzyme variants. However, exploring the complex diversity of such libraries needs efficient screening methods. Overcoming the "screening bottleneck" requires rapid high throughput technology allowing the analysis of a large diversity of different enzymes and applying different screening conditions. Facing these facts an efficient and cost effective method for high throughput screening of large enzyme libraries at the colony level was developed. Therefore, ordered high density micro-colony arrays were combined with optical sensor technology and automated image analysis. The system generally allows the simultaneous monitoring of enzyme activities reflected by up to 7000 micro-colonies spotted on a filter in the size of a micro-titer plate. A developed replica option also allows the analysis of clones under varying external conditions. The method was verified by a model screening using esterases and was proved to provide reliable enzyme activity measurements within single micro-colonies allowing the discrimination of activity differences in the range of 10-20%.     

Microsatellite marker development,mapping and applications in rice genetics and breeding

Microsatellites are simple, tandemly repeated di- to tetra-nucleotide sequence motifs flanked by unique sequences. They are valuable as genetic markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase chain reaction (PCR). Results from screening a rice genomic library suggest that there are an estimated 5700-10 000 microsatellites in rice, with the relative frequency of different repeats decreasing with increasing size of the motif. A map consisting of 120 microsatellite markers demonstrates that they are well distributed throughout the 12 chromosomes of rice. Five multiple copy primer sequences have been identified that could be mapped to independent chromosomal locations. The current level of genome coverage provided by these simple sequence length polymorphisms (SSLPs) in rice is sufficient to be useful for genotype identification, gene and quantitative trait locus (QTL) analysis, screening of large insert libraries, and marker-assisted selection in breeding. Studies of allelic diversity have documented up to 25 alleles at a single locus in cultivated rice germplasm and provide evidence that amplification in wild relatives of Oryza sativa is generally reliable. The availability of increasing numbers of mapped SSLP markers can be expected to complement existing RFLP and AFLP maps, increasing the power and resolution of genome analysis in rice.     

Development and application of a 6.5 million feature affymetrix genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

ABSTRACT: BACKGROUND: High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). RESULTS: We developed a 6.5 million feature Affymetrix GeneChip? for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip? and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. CONCLUSION: By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise.     

社会经济因素对上海市居住区植物多样性的影响

居住区是城市地区主要的土地利用类型之一,也是城市生物的重要生境之一,在生物多样性保护中发挥着重要作用.前人研究发现,国外城市居住区的植物多样性受到社会经济水平的影响,在中国的城市管理体制下,上述结论是否成立有待证明.本研究对上海市39个居住区进行植物多样性调查,选取人口密度、房价、房龄、绿化率4个社会经济指标,利用单因素分析和偏最小二乘回归分析方法,探讨社会经济因素对上海市居住区植物多样性的影响.结果表明: 社会经济因素会影响城市居住区的植物多样性,人口密度、房价、房龄和绿化率对不同分类群的物种多样性的影响各异.其中,房龄对大多数分类群的影响效果最大,其次是人口密度、绿化率和房价.本研究证明,“奢侈效应”和“遗产效应”假说在上海城市居住区只适用于一部分植物类群.研究结果可为上海的城市植物多样性的维持、保护、管理以及城市和景观规划提供参考.     

Culture-dependent and culture-independent diversity surveys target different bacteria: a case study in a freshwater sample

Compared with culture-independent approaches, traditionally used culture-dependent methods have a limited capacity to characterize water microbiota. Nevertheless, for almost a century the latter have been optimized to detect and quantify relevant bacteria. A pertinent question is if culture-independent diversity surveys give merely an extended perspective of the bacterial diversity or if, even with a higher coverage, focus on a different set of organisms. We compared the diversity and phylogeny of bacteria in a freshwater sample recovered by currently used culture-dependent and culture-independent methods (DGGE and 454 pyrosequencing). The culture-dependent diversity survey presented lower coverage than the other methods. However, it allowed bacterial identifications to the species level, in contrast with the other procedures that rarely produced identifications below the order. Although the predominant bacterial phyla detected by both approaches were the same (Proteobacteria, Actinobacteria, Bacteroidetes), sequence similarity analysis showed that, in general, different operational taxonomical units were targeted by each method. The observation that culture-dependent and independent approaches target different organisms has implications for the use of the latter for studies in which taxonomic identification has a predictive value. In comparison to DGGE, 454 pyrosequencing method had a higher capacity to explore the bacterial richness and to detect cultured organisms, being also less laborious.     

半自然农田边界与相邻农田步甲和蜘蛛的时空分布

分别于小麦、玉米收获前后,采用陷阱法调查了华北地区典型农业景观中具有不同植被结构的农田边界及其相邻农田中两类重要天敌类群步甲和蜘蛛的多样性.通过比较农田生境及相邻农田边界间两类天敌群落的时空分布格局及其与相邻半自然生境植被群落的相关关系,探讨半自然农田边界对两类天敌类群的保护作用.结果表明: 整个取样季节农田边界处蜘蛛的多度显著高于农田内部;而步甲多样性在农田与边界间无显著性差异,仅呈现不同的群落结构;作物收获后蜘蛛分科数在边界处的增加以及在农田的减少,显示了蜘蛛在农田和边界之间的迁移活动.边界植被结构对蜘蛛和步甲多样性有不同影响:边界较高的草本层盖度和较低的乔木层盖度有利于增加农田中某些步甲优势种的多样性;而较高的草本层盖度有利于增加皿蛛科蜘蛛的多样性.因此,半自然生境的存在可以通过天敌在农田和边界之间的迁移运动促进农田天敌多样性的维持;但不同类型半自然生境植被群落结构可能影响其对不同天敌群落多样性的维持和保护作用.为促进农业景观对天敌的保护作用,提高其害虫控制功能,需要深入了解不同天敌的生境需求及食物需求,精心设计有利于天敌多样性维持的半自然生境.     

豚草入侵对新疆伊犁河谷林下本地草本植物群落结构的影响

为探究外来入侵植物豚草（Ambrosia artemisiifolia）对本地植物群落结构的影响,结合区内林下草本植物调查和室内分析方法,分析了豚草不同入侵压力下（无入侵、轻度入侵、中度入侵、重度入侵）本地草本植物丰富度、盖度等特征,探讨了地形、气候、土壤、光照、人口密度等外部因素与豚草种群特征、本地植物群落结构之间的关系。结果表明：豚草种群盖度与其高度、密度、生物量显著正相关。与对照相比,轻度入侵下本土草本植物Shannon-Wiener多样性指数和Pielou均匀度指数显著增加,丰富度、盖度未出现显著差异。随着豚草入侵程度加剧,本地草本植物物种丰富度、盖度极显著降低,样方Shannon-Wiener多样性指数先升高再降低,本土草本植物Pielou均匀度指数差异不显著。冗余分析（RDA）表明,土壤全氮、与道路距离、土壤全磷、郁闭度对研究区植物群落结构影响最大,土壤全氮含量随豚草盖度和生物量增加而减少,距道路越近或光照越强,豚草盖度和生物量越高。增强伊犁河谷地区交通往来货物豚草检验检疫力度、增加林内植被郁闭度或是抑制区内豚草入侵的有效手段。     

Diversity & tractability revisited in collaborative small molecule phenotypic screening library design

Identification of purposeful chemical matter on a broad range of drug targets is of high importance to the pharmaceutical industry. However, disease-relevant but more complex hit-finding plans require flexibility regarding the subset of the compounds that we screen. Herein we describe a strategy to design high-quality small molecule screening subsets of two different sizes to cope with a rapidly changing early discovery portfolio. The approach taken balances chemical tractability, chemical diversity and biological target coverage. Furthermore, using surveys, we actively involved chemists within our company in the selection process of the diversity decks to ensure current medicinal chemistry principles were incorporated. The chemist surveys revealed that not all published PAINS substructure alerts are considered productive by the medicinal chemistry community and in agreement with previously published results from other institutions, QED scores tracked quite well with chemists’ notions of chemical attractiveness.     

The “dehesa”, a key ecosystem in maintaining the diversity of Mediterranean saproxylic insects (Coleoptera and Diptera: Syrphidae)

The “dehesa” is a traditional Iberian agrosilvopastoral ecosystem characterized by the presence of old scattered trees that are considered as “keystone-structures”, which favor the presence of a wide range of biodiversity. We show the high diversity of saproxylic beetles and syrphids (Diptera) in this ecosystem, including red-listed species. We analyzed whether saproxylic species distribution in the “dehesa” was affected by tree density per hectare, dominant tree species or vegetation coverage. Species diversity did not correlate with tree density; however, it was affected by tree species and shrub coverage but in a different way for each taxon. The highest beetle diversity was linked to Quercus pyrenaica, the most managed tree species, with eight indicator species. In contrast, Q. rotundifolia hosted more species of saproxylic syrphids. Regarding vegetation coverage, shrub coverage was the only variable that affected insect richness, again in a different way for both taxa. In contrast, beetle species composition was only affected by dominant tree species whereas syrphid species composition was not affected by tree species or shrub coverage. We concluded that the high diversity of saproxylic insects in the “dehesa” is related to its long history of agrosilvopastoral management, which has generated landscape heterogeneity and preserved old mature trees. However, the richness and composition of different taxa of insects respond in different ways to tree species and vegetation coverage. Consequently, conservation strategies should try to maintain traditional management, and different saproxylic taxa should be used to monitor the effect of management on saproxylic diversity.     

内蒙古贺兰山啮齿动物群落多样性及其与环境因子关系

啮齿动物群落结构可以反映生态环境特征。本研究对处于阿拉善荒漠区呈“孤岛”状态的内蒙古贺兰山国家级自然保护区内啮齿动物的种类、分布型及群落多样性进行系统研究。将内蒙古贺兰山划分为五种生境类型,于2013年春、夏、秋3季共布设有效铗日18748个,捕获啮齿动物235只,分属2目5科11属13种。在整体研究区域,阿拉善黄鼠（Spermophilus alashanicus）为优势种。明确了喜湿型是本研究区域的主要分布型,占捕获啮齿动物的54%,并且在中低海拔区域,随着海拔的升高,喜湿型所占比例增加。受“边缘效应”的影响,山地荒漠和荒漠草原生境以及山地草原灌丛生境的啮齿动物群落多样性指数高于其他生境,除环境因素外,啮齿动物群落的多样性受两种因素的影响,既可随群落内物种数量的增加而增大,同时又受制于群落内部物种分布的均匀程度。冗余分析结果表明,植被高度、植被盖度、灌木（乔木）高度和海拔4个环境因子是决定啮齿动物群落结构最主要的环境因子,其中植被盖度与群落多样性呈负相关,随着植被盖度的增加,多样性指数随之减低。     

The effects of encoding data in diversity studies and the applicability of the weighting index approach for data analysis from different molecular markers

The use of molecular markers to study genetic diversity represents a breakthrough in this area, because of the increase in polymorphism levels and phenotypic neutrality. Codominant markers, such as microsatellites (SSR), are sensitive enough to distinguish the heterozygotes in genetic studies. Despite this advantage, there are some studies that ignore this feature and work with encoded data because of the simplicity of the evaluation, existence of polyploids and need for the combined analysis of different types of molecular markers. Thus, our study aims to investigate the consequences of these encodings on simulated and real data. In addition, we suggest an alternative analysis for genetic evaluations using different molecular markers. For the simulated data, we proposed the following two scenarios: the first uses SNP markers, and the second SSR markers. For real data, we used the SSR genotyping data from Coffea canephora accessions maintained in the Embrapa Germplasm Collection. The genetic diversity was studied using cluster analysis, the dissimilarity index, and the Bayesian approach implemented in the STRUCTURE software. For the simulated data, we observed a loss of genetic information to the encoded data in both scenarios. The same result was observed in the coffee studies. This loss of information was discussed in the context of a plant-breeding program, and the consequences were weighted to germplasm evaluations and the selection of parents for hybridization. In the studies that involved different types of markers, an alternative to the combined analysis is discussed, where the informativeness, coverage and quality of markers are weighted in the genetic diversity studies.     

A conceptual guide to measuring species diversity

Three metrics of species diversity – species richness, the Shannon index and the Simpson index – are still widely used in ecology, despite decades of valid critiques leveled against them. Developing a robust diversity metric has been challenging because, unlike many variables ecologists measure, the diversity of a community often cannot be estimated in an unbiased way based on a random sample from that community. Over the past decade, ecologists have begun to incorporate two important tools for estimating diversity: coverage and Hill diversity. Coverage is a method for equalizing samples that is, on theoretical grounds, preferable to other commonly used methods such as equal-effort sampling, or rarefying datasets to equal sample size. Hill diversity comprises a spectrum of diversity metrics and is based on three key insights. First, species richness and variants of the Shannon and Simpson indices are all special cases of one general equation. Second, richness, Shannon and Simpson can be expressed on the same scale and in units of species. Third, there is no way to eliminate the effect of relative abundance from estimates of any of these diversity metrics, including species richness. Rather, a researcher must choose the relative sensitivity of the metric towards rare and common species, a concept which we describe as ‘leverage.' In this paper we explain coverage and Hill diversity, provide guidelines for how to use them together to measure species diversity, and demonstrate their use with examples from our own data. We show why researchers will obtain more robust results when they estimate the Hill diversity of equal-coverage samples, rather than using other methods such as equal-effort sampling or traditional sample rarefaction.     

三峡库区移民区和淹没区植物群落物种多样性的空间分布格局

为研究三峡库区移民安置区和淹没区植物群落物种多样性的空间分布格局, 在从坝区到重庆的长江南北两岸各设置了7条样带, 从海拔70 m到610 m每上升50 m设置一个样方, 共调查了129个样方。采用物种数和基于盖度的Shannon-Wiener指数作为物种多样性指标, 分析了不同海拔、样带、坡向与南北岸位置的植物群落物种多样性的空间分布特点; 采用DCCA 排序阐明物种多样性与环境因子的相互关系, 并进一步分析了造成上述空间分布格局的环境因子。结果表明: 南岸的物种多样性高于北岸; 物种多样性随海拔升高而增加, 但趋势不显著; 从坝区到重庆物种多样性变化没有明显的规律性, 在坝区和万州最高, 重庆和巫山最低。DCCA排序结果表明, 影响物种多样性变化的外在环境因子最主要的是南北岸位置, 其次为海拔; 而增加物种多样性的主导生境因子是群落乔木层的盖度, 灌木层的盖度则对物种多样性具有抑制作用, 说明群落自身的结构特点决定着物种多样性。总之, 研究区域由水热条件组合影响的物种多样性空间分布格局的规律性由于人为活动的异质性干扰发生了改变, 而干扰后群落自身的结构特点, 特别是群落冠层的盖度, 决定着群落自身的物种多样性。     

Print news coverage of cancer: What prevention messages are conveyed when screening is newsworthy?

Background: Americans are generally favorable towards cancer screening, but fatalistic about cancer prevention. News coverage shapes perceptions of cancer control in meaningful ways, but there is little consensus as to the impact of news on our understanding of and engagement in cancer screening practices. Our analysis of cancer screening-related print news coverage during a four month period in 2005 suggests that the newsworthiness of new screening technologies may undermine public confidence in currently available and effective secondary prevention programs, while promoting tests whose effectiveness is debated or not yet established. Methods and results: We conducted a structured text analysis of 517 cancer-related news articles from 15 leading daily newspapers and a subsequent qualitative analysis of the 79 screening news articles. Screening articles were analyzed for content related to criteria for screening effectiveness. Content patterns for each type of screening and cancer were also noted. News coverage consistently conveyed screening as important and highlighted the need to protect and expand access to screening. At the same time, to the extent that story content was framed by the newsworthiness of new tests and technologies this often indirectly called into question effective and established protocols and programs without providing any actionable alternative. Conclusion: This analysis revealed unexpected messages about screening that are potentially problematic for cancer control. The cancer control community should continue efforts to understand and shape news coverage of screening in order to promote balanced and action-oriented content. Research has shown that Americans hold conflicting views regarding cancer—having a favorable opinion of screening while simultaneously feeling fatalistic about prevention. Our analysis of print news stories on cancer screening suggests that the determination of screening's “newsworthiness” is related to newly developed tests and protocols, which may create demand for new tests whose effectiveness is unknown and undermine confidence in established and effective screening programs.     

Analysis of the non-thermophilic Crenarchaeota phylogeny in the swamp soil of Zoige plateau wetland

Zoige wetland of Tibetan plateau is a model low temperature ecosystem in a low latitude (33°56′N, 102°52′E) and high altitude region. Its organism has a unique phylogeny. To better evaluate the resource of the non-thermophilic Crenarchaeota in such an ecosystem, both restriction fragment length polymorphism (RFLP) and clone techniques were employed to study the diversity and phylogenetics of the non-thermophilic Crenarchaeota in the wetland soil. Archaeal 16S rRNA genes were amplified with the archaea-specific primers, and a library consisting of 240 clones was established. The non-thermophilic Crenarchaeota phylogenetic tree was constructed using the ARB phylogenetic analysis software. Based on the results of the RFLP experiments, the clones of all three Zoige wetland swamp soil samples were grouped into 16 different restriction cleavage patterns, all the clone coverage indices were above 91%, showing high library coverage. The correlations analysis indicated that the biodiversity of the non-thermophilic Crenarchaeota be positively correlated with soil moisture. The phylogenetic analysis revealed that all of the 16 Crenarchaeota sequences were clustered into two groups: 13 sequences in the Group 1.1b and 3 in the Group 1.3, similar to those archaeal sequences obtained from grassland soil, freshwater reservoirs, and seawater above boreholes, and radioactive groundwater and hot springs.     

Joint analysis for genome-wide association studies in family-based designs

In family-based data, association information can be partitioned into the between-family information and the within-family information. Based on this observation, Steen et al. (Nature Genetics. 2005, 683-691) proposed an interesting two-stage test for genome-wide association (GWA) studies under family-based designs which performs genomic screening and replication using the same data set. In the first stage, a screening test based on the between-family information is used to select markers. In the second stage, an association test based on the within-family information is used to test association at the selected markers. However, we learn from the results of case-control studies (Skol et al. Nature Genetics. 2006, 209-213) that this two-stage approach may be not optimal. In this article, we propose a novel two-stage joint analysis for GWA studies under family-based designs. For this joint analysis, we first propose a new screening test that is based on the between-family information and is robust to population stratification. This new screening test is used in the first stage to select markers. Then, a joint test that combines the between-family information and within-family information is used in the second stage to test association at the selected markers. By extensive simulation studies, we demonstrate that the joint analysis always results in increased power to detect genetic association and is robust to population stratification.