后丽盲蝽属作为属级分类单元的DNA分子证据

用蛋白酶K消化法提取并正反链双向测得半翅目盲蝽科盲蝽族(Mirini)中后丽盲蝽属(Apolygus)和草盲蝽属(Lygus)9个种的线粒体DNA细胞色素b基因片段的序列,应用Mega计算该两个属7个种11个Cyt b 432 bp片段序列的碱基组成、核苷酸的种间变异率、所编码的144个氨基酸的变异率。其核苷酸变异率：后丽盲蝽属内小于0．02,草盲蝽属内小于0．08(个别种例外);两个属种类之间平均变异率都大于0．10,平均为0．15。氨基酸变异率：后丽盲蝽属内种间无变异,而草盲蝽属内只有L．gemellatus与其他种间有13个氨基酸变异,仅占9．03％;两属各种类间却存在8～11个氨基酸的变异。表明在分子水平上两属之间较之于属内种间具有明显的差异,支持将后丽盲蝽从亚属提升为属级分类单元的分类观点。     

Advances in the Chromosome-Centric Human Proteome Project: looking to the future

Introduction: The mission of the Chromosome-Centric Human Proteome Project (C-HPP), is to map and annotate the entire predicted human protein set (~20,000 proteins) encoded by each chromosome. The initial steps of the project are focused on ‘missing proteins (MPs)’, which lacked documented evidence for existence at protein level. In addition to remaining 2,579 MPs, we also target those annotated proteins having unknown functions, uPE1 proteins, alternative splice isoforms and post-translational modifications. We also consider how to investigate various protein functions involved in cis-regulatory phenomena, amplicons lncRNAs and smORFs.

Areas covered: We will cover the scope, historic background, progress, challenges and future prospects of C-HPP. This review also addresses the question of how we can best improve the methodological approaches, select the optimal biological samples, and recommend stringent protocols for the identification and characterization of MPs. A new strategy for functional analysis of some of those annotated proteins having unknown function will also be discussed.

Expert commentary: If the project moves well by reshaping the original goals, the current working modules and team work in the proposed extended planning period, it is anticipated that a progressively more detailed draft of an accurate chromosome-based proteome map will become available with functional information.     

Open‐access platform to synthesize knowledge of ape conservation across sites

Despite the large body of literature on ape conservation, much of the data needed for evidence‐based conservation decision‐making is still not readily accessible and standardized, rendering cross‐site comparison difficult. To support knowledge synthesis and to complement the IUCN SSC Ape Populations, Environments and Surveys database, we created the A.P.E.S. Wiki ( https://apeswiki.eva.mpg.de ), an open‐access platform providing site‐level information on ape conservation status and context. The aim of this Wiki is to provide information and data about geographical ape locations, to curate information on individuals and organizations active in ape research and conservation, and to act as a tool to support collaboration between conservation practitioners, scientists, and other stakeholders. To illustrate the process and benefits of knowledge synthesis, we used the momentum of the update of the conservation action plan for western chimpanzees (Pan troglodytes verus) and began with this critically endangered taxon. First, we gathered information on 59 sites in West Africa from scientific publications, reports, and online sources. Information was compiled in a standardized format and can thus be summarized using a web scraping approach. We then asked experts working at those sites to review and complement the information (20 sites have been reviewed to date). We demonstrate the utility of the information available through the Wiki, for example, for studying species distribution. Importantly, as an open‐access platform and based on the well‐known wiki layout, the A.P.E.S. Wiki can contribute to direct and interactive information sharing and promote the efforts invested by the ape research and conservation community. The Section on Great Apes and the Section on Small Apes of the IUCN SSC Primate Specialist Group will guide and support the expansion of the platform to all small and great ape taxa. Similar collaborative efforts can contribute to extending knowledge synthesis to all nonhuman primate species.     

An investigation of adequate volume for the diagnosis of malignancy in pleural fluids

S. C. Thomas, L. R. R. Davidson and M. E. McKean An investigation of adequate volume for the diagnosis of malignancy in pleural fluids Objective: The cytological examination of pleural effusions is an important investigation in the diagnosis of malignancy. Maximizing the chances of identifying malignant effusions is therefore desirable. Recent Royal College of Pathologists guidelines, based on the British Society for Clinical Cytology codes of practice, have suggested that a minimum of 20 ml of pleural fluid is required for diagnostic purposes. Methods & Results: We examined 2155 pleural fluids received over a 6‐year period in order to define a minimum required volume for adequacy. By examining the plateau phase of a graph of threshold volumes for initial samples received for each patient (n = 1584) we determine that a minimum fluid volume of 25 ml is required and that more than 50 ml does not improve sensitivity. Conclusion: Between 25 and 50 ml of fluid are required for the adequate assessment of pleural effusions for malignancy.     

Phylogeny of sea skaters, Halobates Eschscholtz (Hemiptera, Gerridae), based on mtDNA sequence and morphology

We examined phylogenetic relationships among halobatine water striders (Hemiptera, Gerridae) using molecular and morphological data. The molecular data set was 780 bp DNA sequence data from the 3' half of the mitochondria! gene encoding cytochrome oxidase subunit I from 19 species of sea skaters, Halobates , and one species from each of three related genera, Asclepios annandalei, Austrobates rivularis , and Eurymetra natalensis. The morphological data set was a slightly modified version of a previously published data set. Unweighted parsimony analyses of the molecular data set gave one tree with weak support for most branches. Maximum likelihood analysis of the same data set gave a tree with slightly different topology, but reveiled many of the clades found in parsimony analyses of the morphological data set. Parsimony analyses of the combined molecular + morphology data sets gave a better resolved and better supported tree than did analyses of any single data set. The phytogeny of Halobates presented here allows a more rigorous evaluation of several prior hypotheses about evolutionary processes in marine water striders. In particular, it supports the hypothesis of at least two separate transitions from coastal to oceanic environments.     

A forest‐specialist carnivore in the middle of the desert?Comments on Anabalon et al. 2019

We present comments on an article recently published in Ecology and Evolution (“High‐resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the Lycalopex genus in Chile”) by Anabalon et al. that reported the presence of Darwin's fox (Lycalopex fulvipes), a temperate forest specialist, in the hyperarid Atacama Desert of northern Chile. We argue that this putative record lacks ecological support in light of ongoing research on this endangered species, and contains numerous methodological flaws and omissions related to the molecular identification of the species. Based on these issues, we suggest the scientific community and conservation decision‐makers disregard the alleged presence of the Darwin's fox in the Atacama Desert.     

Forensic Ecotoxicology: Establishing Causality between Contaminants and Biological Effects in Field Studies

Twelve papers in this series were derived from two conference sessions focusing on causality in field studies. Eight of these papers involve case studies examining biological effects of chemical contaminants in field situations. Using a weight-of-evidence approach, these case studies were evaluated against seven proposed criteria for establishing causality. The seven criteria were: strength of association; consistency of association; specificity of association; time order; biological gradient; experimental evidence; and biological plausibility. One of these seven criteria, ‘specificity of association’ was found to be of little utility for establishing causality in these field studies. The case studies are presented in approximate order of increasing levels of biological organization (i.e., going from endpoints at the suborganismal level to endpoints at the population or community level). In case studies examining higher levels of biological organization, it appears that the ‘biological gradient’ criterion was also not useful in establishing causality. These results, together with suggestions from other papers in the series, are used to recommend a set of modified criteria for establishing causality in field studies of the biological effects of chemical contaminants.     

Cancer de la prostate : les niveaux de preuve des biomarqueurs de la détection précoce

As part of an overall review on the role of PSA and other emerging biomarkers in the detection, diagnosis and treatment of prostate cancer, we present here a part of a review of the literature made by the working group Biologie de la Prostate (AFU, CNBH, SFBC, SFMN) on the use of PSA and other biomarkers in the early detection of prostate cancer with an assessment of the level of evidence.     

Accumulating evidence in ecology: Once is not enough

Many published studies in ecological science are viewed as stand‐alone investigations that purport to provide new insights into how ecological systems behave based on single analyses. But it is rare for results of single studies to provide definitive results, as evidenced in current discussions of the “reproducibility crisis” in science. The key step in science is the comparison of hypothesis‐based predictions with observations, where the predictions are typically generated by hypothesis‐specific models. Repeating this step allows us to gain confidence in the predictive ability of a model, and its corresponding hypothesis, and thus to accumulate evidence and eventually knowledge. This accumulation may occur via an ad hoc approach, via meta‐analyses, or via a more systematic approach based on the anticipated evolution of an information state. We argue the merits of this latter approach, provide an example, and discuss implications for designing sequences of studies focused on a particular question. We conclude by discussing current data collection programs that are preadapted to use this approach and argue that expanded use would increase the rate of learning in ecology, as well as our confidence in what is learned.