基于功能性状的生态系统服务研究框架

功能性状通过影响生态系统的属性和过程及其维持来影响生态系统服务。功能多样性-生态系统功能关系的研究有助于深入探讨生态系统服务形成机制, 也为生态系统服务研究提供了一个切入点。该文对目前的功能性状和生态系统服务研究框架进行了介绍, 回顾了功能多样性-生态系统功能关系的研究现状, 总结了目前功能性状在生态系统服务研究中的应用, 提出了基于功能性状的生态系统服务研究框架。在这个研究框架中, 首先选取对生态系统功能影响显著的非生物因子和功能多样性指数, 然后量化非生物因子和功能多样性与生态系统功能, 以及生态系统功能-生态系统服务之间的关系, 进而构建功能多样性与生态系统服务的数量关系。与此同时, 利用群落构建理论和物种共存机制分析功能多样性-生态系统功能变化的机制联系, 以研究生态系统服务形成和变化机制, 为生态系统服务管理决策提供科学依据。     

基于功能一致性和网络拓扑属性预测冠心病致病基因

基于功能一致性利用蛋白质互作网络挖掘潜在的疾病致病基因,对于了解疾病致病机理和改进临床治疗至关重要．基于基因功能一致性和其在蛋白质互作网络中的拓扑属性将基因与疾病之间建立关联,对疾病风险位点内的基因进行了致病风险预测,并通过GO及KEGG功能富集分析方法进一步筛选,预测出新的致病基因．预测出了51个新的冠心病致病基因,分析发现大部分基因参与了冠心病的致病过程．为疾病基因的挖掘提出一个新的思路,从而有助于复杂疾病致病机理的研究．     

Functional gene networks based on the gene neighborhood in metagenomes

The gene neighborhood in prokaryotic genomes has been effectively utilized in inferring co-functional networks in various organisms. Previously, such genomic context information has been sought among completely assembled prokaryotic genomes. Here, we present a method to infer functional gene networks according to the gene neighborhood in metagenome contigs, which are incompletely assembled genomic fragments. Given that the amount of metagenome sequence data has now surpassed that of completely assembled prokaryotic genomes in the public domain, we expect benefits of inferring networks by the metagenome-based gene neighborhood. We generated co-functional networks for diverse taxonomical species using metagenomics contigs derived from the human microbiome and the ocean microbiome. We found that the networks based on the metagenome gene neighborhood outperformed those based on 1748 completely assembled prokaryotic genomes. We also demonstrated that the metagenome-based gene neighborhood could predict genes related to virulence-associated phenotypes in a bacterial pathogen, indicating that metagenome-based functional links could be sufficiently predictive for some phenotypes of medical importance. Owing to the exponential growth of metagenome sequence data in public repositories, metagenome-based inference of co-functional networks will facilitate understanding of gene functions and pathways in diverse species.     

Trait‐based ecology of terrestrial arthropods

In focusing on how organisms' generalizable functional properties (traits) interact mechanistically with environments across spatial scales and levels of biological organization, trait‐based approaches provide a powerful framework for attaining synthesis, generality and prediction. Trait‐based research has considerably improved understanding of the assembly, structure and functioning of plant communities. Further advances in ecology may be achieved by exploring the trait–environment relationships of non‐sessile, heterotrophic organisms such as terrestrial arthropods, which are geographically ubiquitous, ecologically diverse, and often important functional components of ecosystems. Trait‐based studies and trait databases have recently been compiled for groups such as ants, bees, beetles, butterflies, spiders and many others; however, the explicit justification, conceptual framework, and primary‐evidence base for the burgeoning field of ‘terrestrial arthropod trait‐based ecology’ have not been well established. Consequently, there is some confusion over the scope and relevance of this field, as well as a tendency for studies to overlook important assumptions of the trait‐based approach. Here we aim to provide a broad and accessible overview of the trait‐based ecology of terrestrial arthropods. We first define and illustrate foundational concepts in trait‐based ecology with respect to terrestrial arthropods, and justify the application of trait‐based approaches to the study of their ecology. Next, we review studies in community ecology where trait‐based approaches have been used to elucidate how assembly processes for terrestrial arthropod communities are influenced by niche filtering along environmental gradients (e.g. climatic, structural, and land‐use gradients) and by abiotic and biotic disturbances (e.g. fire, floods, and biological invasions). We also review studies in ecosystem ecology where trait‐based approaches have been used to investigate biodiversity–ecosystem function relationships: how the functional diversity of arthropod communities relates to a host of ecosystem functions and services that they mediate, such as decomposition, pollination and predation. We then suggest how future work can address fundamental assumptions and limitations by investigating trait functionality and the effects of intraspecific variation, assessing the potential for sampling methods to bias the traits and trait values observed, and enhancing the quality and consolidation of trait information in databases. A roadmap to guide observational trait‐based studies is also presented. Lastly, we highlight new areas where trait‐based studies on terrestrial arthropods are well positioned to advance ecological understanding and application. These include examining the roles of competitive, non‐competitive and (multi‐)trophic interactions in shaping coexistence, and macro‐scaling trait–environment relationships to explain and predict patterns in biodiversity and ecosystem functions across space and time. We hope this review will spur and guide future applications of the trait‐based framework to advance ecological insights from the most diverse eukaryotic organisms on Earth.     

Generalized reliability based on distances

The intraclass correlation coefficient (ICC) is a classical index of measurement reliability. With the advent of new and complex types of data for which the ICC is not defined, there is a need for new ways to assess reliability. To meet this need, we propose a new distance‐based ICC (dbICC), defined in terms of arbitrary distances among observations. We introduce a bias correction to improve the coverage of bootstrap confidence intervals for the dbICC, and demonstrate its efficacy via simulation. We illustrate the proposed method by analyzing the test‐retest reliability of brain connectivity matrices derived from a set of repeated functional magnetic resonance imaging scans. The Spearman‐Brown formula, which shows how more intensive measurement increases reliability, is extended to encompass the dbICC.     

基于叶片水势的内蒙古典型草原植物水分适应特征研究

水分是限制草原生态系统植物生存、繁殖和扩散最重要的生态因子,植物通过多样的水分适应策略适应干旱环境。为了解典型草原植物水势特征及其影响因素,在2017年和2018年的生长季对内蒙古典型草原71种植物的叶片黎明水势、午后水势、叶片和根系功能性状进行了测定与分析。结果表明:测定的71种植物叶片的黎明水势分布于-2.67—-0.63 MPa,午后水势分布于-4.67—-1.01 MPa;一年生植物的叶片具有最高的黎明水势、午后水势和最小的水势日差值(叶片的黎明水势与午后水势的差值),多年生禾草的叶片具有最低的黎明水势、午后水势和最大的水势日差值;71种植物对水分的适应策略可分为高水势保持型、低水势忍耐型和变水势波动型;叶片午后水势与叶片干物质含量和根系深度呈极显著的负相关关系(P<0.01),但与比叶面积呈极显著的正相关关系(P<0.01)。本研究有助于从植物生理学的角度上准确认识典型草原植物的水分适应性及水分生态特征。     

基于双聚类挖掘癌症共享的基因功能模块

基因多效性是癌症遗传机制中的普遍现象, 但罕见系统性的分析。文章提出采用双聚类挖掘基因功能模块的新思路探索癌症的共享分子机制和不同癌症间的关系。获取20种癌症的基因表达数据, 应用改良t检验和倍数法筛选出至少在两种癌症中差异表达的基因, 得到10417×20的数据矩阵; 采用双聚类方法获得22个癌症共享的基因簇; 进一步富集分析得到17个基因功能模块(Bonferroni校正后P<0.05), 主要参与有丝分裂染色单体分离的调控、细胞分化、免疫和炎症反应、胶原纤维组织等生物过程; 主要执行ATP结合和微管活动、MHCⅡ类受体活性、肽链内切酶抑制活性等分子功能; 活动区域主要在细胞骨架、染色体、MHCⅡ蛋白质复合体、中间丝蛋白、胶原纤维等。基于模块构建癌症相关网络, 显示胃癌、卵巢腺癌、宫颈鳞癌和间皮瘤等之间相关程度较高, 而两种血液系统癌症(急性髓细胞性白血病与多发性骨髓瘤)分子机制与其他癌症存在较大差异。可见癌症共享的基因功能模块与多种生物机制有关, 癌症之间相似性可能与组织起源、共同的致癌机制等有关。文章提出的基因多效性分析方法有助于解释人类复杂性疾病的共享分子机制。     

基于功能性状的中亚热带岩溶常绿落叶阔叶混交林物种多样性维持研究

理解植物功能性状和功能实体在森林群落的分布,有助于探讨物种丧失对森林生态系统功能、冗余和恢复力的影响。为了解脆弱的岩溶石山森林在应对生物多样性丧失的生态系统反馈,对桂林岩溶石山两块1hm²的常绿落叶阔叶混交林的木本植物数据进行了分析。包括基于功能性状计算功能多样性、构建功能实体计算功能冗余以及采用Pearson相关分析和Mantel检验评估物种多样性指标在生态系统的维持机制。结果显示:(1)青冈+大叶榉树群落的功能多样性指标均低于鱼骨木+青冈+圆叶乌桕群落,且两个群落间功能均匀度不相关(P ＞ 0.05),功能丰富度、功能离散度和Rao''s二次熵呈现极显著相关性(P ＜ 0.001),功能分散度呈现显著相关性(P ＜ 0.05)。(2)两个群落的物种丰富度与功能冗余指标表现出相似的线性关系,即物种丰富度与功能实体等级、功能冗余、功能超冗余呈正相关,与功能脆弱性呈负相关关系。(3)不同植物功能性状间、不同功能多样性指标间和不同功能冗余指标间的相关性较强,功能多样性指标和功能冗余指标间无显著相关性,但功能性状与功能多样性指标、功能性状与功能冗余指标均存在不同程度的相关性。而在功能实体与物种多样性指标的相关性方面,呈现出同物种丰富度与物种多样性指标相似的显著度。另外,物种多度与物种丰富度、功能分散度、功能离散度、Rao''s二次熵及功能脆弱性均显著相关。总之,在岩溶石山常绿落叶阔叶混交林中,高功能多样性的群落存在高功能冗余的现象,但功能多样性和功能冗余是相互独立的因素;物种丰富度高的群落所提供的保险效应无法抵消其生态系统的脆弱性。因此,不能仅通过保护物种丰富度来维持生态系统的特有功能,还应充分考虑多度对生态系统功能的贡献,以更有效地实现对岩溶石山森林生态系统的保护。     

基于CiteSpace植物功能性状的研究进展

植物功能性状不仅反映植物对生存环境的适应和响应,而且能够强烈影响生态系统功能,是生态学重要研究领域。利用CiteSpace软件,全面系统梳理植物功能性状的研究成果,分析当前国际研究现状,挖掘其知识基础,归纳研究热点和发展趋势。研究发现:(1)国际上植物功能性状研究领域的发文数量经历了缓慢增长—波动增长—平稳增长—快速增长4个阶段;(2)植物功能性状研究分为探索阶段、发展阶段、平稳阶段和扩展阶段,各阶段均由相应的关键文献引领发展。4个阶段的研究热点不同,当前研究热点为"叶性状"、"经济谱"、"植物功能多样性"、"性状生态位";(3)植物功能性状研究内容从大尺度、单一生境、单个性状扩展到小尺度、多生境、多性状组合的演变趋势;(4)美国、德国、法国和中国是该领域贡献最多的国家,中国科学院是发文量最多的机构;Sandra Lavorel,Peter B Reich,Johannes H C Cornelissen等科学家奠定了植物功能性状的研究基础;(5)今后应运用先进技术手段,结合植物不同器官和系统发育信息,研究植物功能性状在不同空间和时间尺度的变化。     

基于蛋白质互作评价差异表达基因的重复性

利用高通量基因表达谱数据可以识别在肿瘤与正常组织中差异表达的基因,为研究癌机理提供重要的线索。目前,在研究同种癌型的不同实验中发现的差异表达基因的交叠比例很低。这种高通量基因表达谱数据低重复性的现象严重制约了基因芯片在癌症研究中的应用。然而,已有研究表明从研究同种癌型的不同实验数据中得到的不交叠的差异表达基因倾向于扰动相同的功能。因此,在评价差异表达基因重复性时,应考虑其在生物学功能上的一致性。本文结合基因共表达和蛋白质互作关系,设计了功能重复性指标来评价差异表达基因列表的可重复性。通过分析两套卵巢癌数据,发现对同种癌型得到的差异表达基因具有很高的功能一致性(p<0.0001)。结果表明,在功能水平上评估差异表达基因的一致性具有合理性。     

Synthesis and photophysical studies on a new fluorescent phenothiazine‐based derivative

A new typical phenothiazine compound functionalized with thienyl‐indandione derivative (PTZTID) was synthesized and characterized using spectral analysis (ultraviolet–visible (UV–vis) light, infrared (IR), ¹H nuclear magnetic resonance (NMR) and ¹³C NMR tools). The UV–vis absorption spectra of the PTZTID solution in 1,4‐dioxane showed two absorption bands attributed to localized aromatic π–π* transitions of conjugated aromatic moieties and intramolecular charge transfer with the characteristics of a π–π* transition. The fluorescence spectra exhibited a maximum emission wavelength at 580 nm. The effect of concentration on photophysical properties took the form of a minor hypsochromic shift, which was attributed to some extent to the occurrence of H‐type aggregation of the PTZTID derivative. Binary solvent effects on the spectroscopic behaviour of PTZTID were measured at different H₂O/1,4‐dioxane ratios. Similarly, when increasing the water content, a hypsochromic shift was observed that resulted from H‐type aggregation. Furthermore, geometry and electronic configurations of PTZTID were studied at density functional theory /B3LYP level and indicated that the compound had a nonplanar (butterfly structure).     

基于知识图谱的植物功能性状与环境研究前沿态势分析

为系统了解国际上植物功能性状与环境的研究进展,该研究基于Web of Science数据来源,采用Web of Science数据库分析工具和Thomson Data Analysis(TDA)进行数据清理和统计分析,并利用Ucinet和Netdraw、Excel等软件进行可视化作图。结果表明:(1)近26年来,植物功能性状与环境研究论文数量呈持续稳步增长态势,尤其近9年来呈加速增长态势。(2)近9年来,研究主题主要围绕比叶面积、叶面积(指数)、光合作用(性能)、叶厚度、叶形态、叶氮含量、叶绿素、叶绿素荧光、比根长等功能指标,及光照、温度、水(水分利用效率、干旱等)、肥(氮、磷为主)、CO2等环境因子展开;化学计量学在该领域应用广泛。(3)2009—2017年间,欧美等发达国家是该领域研究的主要力量。美国发文数量和文献质量均为世界领先。中国在该领域的发文量居第二位,仅次于美国,但文献篇均被引和H指数较低。中国科学院发文量以绝对优势居第一位,但文献质量有待进一步提升。(4)该领域载文量Top10期刊8种为JCR分区Q1区、2种为Q2区。其中,Plant and Soil和Plant Ecology载文量分居第一位和第二位。(5) Top10高被引论文发表于8种期刊,其第一作者分别来自美国、荷兰、加拿大、德国和法国。     

基于系统发育及功能性状的不同坡向荒漠植物群落构建研究——以博湖县沙化封禁保护区为例

荒漠植物群落构建机制的研究有助于荒漠生态系统植物资源的保护及系统平衡稳定的维持。基于系统发育与功能性状相结合的方法,以博湖县沙化封禁保护区植物群落为研究对象,在研究区内纵向沙垄的不同坡向上(丘间、阴坡、阳坡)设置样方,进行植物群落物种功能性状和土壤因子的调查与测定,通过检验植物群落物种功能性状的系统发育信号,分析不同坡向植物群落物种系统发育结构和功能结构的表现模式,利用主成分分析(PCA)和线性回归模型(Linear regression model)筛选出影响物种共存的环境因子,进而揭示研究区干旱荒漠生态系统植物群落物种共存的驱动因素。结果表明：(1)研究区植被主要以耐旱的灌木和藜科草本植物为优势种;不同坡向土壤因子具有异质性,丘间、阴坡土壤养分、水分更为丰富。(2)研究区样地植物群落物种10个功能性状指标的系统发育信号K值均小于1,说明物种功能性状受系统进化影响较小,物种功能性状未表现出系统发育保守性。(3)不同坡向系统发育结构均趋于发散,限制相似性在植物分布中占主导作用;丘间和阴坡上较丰富的土壤肥力是物种功能结构发散的主要原因,阳坡物种功能结构表现为聚集效应,生境过滤为其驱动因素...     

基于功能类群分析呼兰河口湿地浮游植物群落结构特征

浮游植物对水环境条件变化敏感,其群落演替特征被广泛应用于指示水环境变化。基于3种浮游植物功能类群方法,对呼兰河口湿地浮游植物群落结构进行研究。于2018年春季（4、5月）、夏季（6、7、8月）和秋季（9、10月）三季,在呼兰河口湿地共设置11个采样点,通过ASNOSIM和SIMPER分析探索FG、MFG和MBFG功能类群的演替特征,基于RDA分析阐述功能类群对环境因子的响应模式。研究期间共鉴定浮游植物243个分类单位,隶属于7门9纲18目32科75属;其种类组成主要以绿藻门（46.09%）、裸藻门（19.34%）和硅藻门（18.52%）为主。共划分FG功能类群25个,MFG功能类群20个,MBFG功能类群6个;ANOSIM分析表明不同季节之间FG和MFG功能类群结构差异显著;SIMPER分析表明S1/Lo/W1/P/J/Y、9b/5a/11b/6a/2c/2d/1c和Ⅲ/Ⅰ类群是影响不同季节之间功能类群变化的主要类群;RDA分析表明,FG、MFG和MBFG功能类群的演替受多种环境因素共同影响,其中pH、BOD₅、Tur.和COD_Mn与功能类群演替关系密切。相较于MBFG功能类群,FG和MFG功能类群能更好的响应呼兰河口湿地水环境的空间异质性。     

Functional annotations in bacterial genomes based on small RNA signatures

One of the key challenges in computational genomics is annotating coding genes and identification of regulatory RNAs in complete genomes. An attempt is made in this study which uses the regulatory RNA locations and their conserved flanking genes identified within the genomic backbone of template genome to search for similar RNA locations in query genomes. The search is based on recently reported coexistence of small RNAs and their conserved flanking genes in related genomes. Based on our study, 54 additional sRNA locations and functions of 96 uncharacterized genes are predicted in two draft genomes viz., Serratia marcesens Db1 and Yersinia enterocolitica 8081. Although most of the identified additional small RNA regions and their corresponding flanking genes are homologous in nature, the proposed anchoring technique could successfully identify four non-homologous small RNA regions in Y. enterocolitica genome also. The KEGG Orthology (KO) based automated functional predictions confirms the predicted functions of 65 flanking genes having defined KO numbers, out of the total 96 predictions made by this method. This coexistence based method shows more sensitivity than controlled vocabularies in locating orthologous gene pairs even in the absence of defined Orthology numbers. All functional predictions made by this study in Y. enterocolitica 8081 were confirmed by the recently published complete genome sequence and annotations. This study also reports the possible regions of gene rearrangements in these two genomes and further characterization of such RNA regions could shed more light on their possible role in genome evolution.     

Transferability of trait‐based species distribution models

The need for reliable prediction of species distributions dependent upon traits has been hindered by a lack of model transferability testing. We tested the predictive capacity of trait‐SDMs by fitting hierarchical generalised linear models with three trait and four environmental predictors for 20 eucalypt taxa in a reference region. We used these models to predict occurrence for a much larger set of taxa and target areas (82 taxa across 18 target regions) in south‐eastern Australia. Median predictive performance for new species in target regions was 0.65 (area under receiver operating curve) and 1.24 times random (area under precision recall curve). Prediction in target regions did not worsen with increasing geographic, environmental or community compositional distance from the reference region, and was improved with reliable trait–environment relationships. Transfer testing also identified trait–environment relationships that did not transfer. These results give confidence that traits and transfer testing can assist in the hard problem of predicting environmental responses for new species, environmental conditions and regions.