Reducing over-reporting of deterministic co-occurrence patterns in biotic communities

Null models of species co-occurrence are widely used to infer the existence of various ecological processes. Here we investigate the susceptibility of the most commonly used of these models (the C-score in conjunction with the sequential swap algorithm) to type 1 and type 2 errors. To do this we use simulated datasets with a range of numbers of sites, species and coefficients of variation (CV) in species abundance. We find that this model is particularly susceptible to type 1 errors when applied to large matrices and those with low CV in species abundance. As expected, type 2 error rates decrease with increasing numbers of sites and species, although they increase with increasing CV in species abundance. Despite this, power remains acceptable over a wide range of parameter combinations. The susceptibility of this analytical method to type 1 errors indicates that many previous studies may have incorrectly reported the existence of deterministic patterns of species co-occurrence. We demonstrate that in order to overcome the problem of high type 1 error rates, the number of swaps used to generate null distributions for smaller matrices needs to be increased to over 50,000 swaps (well beyond the 5000 commonly used in published analyses and the 30,000 suggested by Lehsten and Harmand, 2006). We also show that this approach reduces type 1 error rates in real datasets. However, even using this solution, larger datasets still suffer from high type 1 error rates. Such datasets therefore require the use of very large numbers of swaps, which calls for improvements in the most commonly used software. In general, users of this powerful analytical method must be aware that they need surprisingly large numbers of swaps to obtain unbiased estimates of structuring in biotic communities.     

Hierarchical Bayesian Spatial Models for Multispecies Conservation Planning and Monitoring

Abstract: Biologists who develop and apply habitat models are often familiar with the statistical challenges posed by their data's spatial structure but are unsure of whether the use of complex spatial models will increase the utility of model results in planning. We compared the relative performance of nonspatial and hierarchical Bayesian spatial models for three vertebrate and invertebrate taxa of conservation concern (Church's sideband snails [Monadenia churchi], red tree voles [Arborimus longicaudus], and Pacific fishers [Martes pennanti pacifica]) that provide examples of a range of distributional extents and dispersal abilities. We used presence–absence data derived from regional monitoring programs to develop models with both landscape and site‐level environmental covariates. We used Markov chain Monte Carlo algorithms and a conditional autoregressive or intrinsic conditional autoregressive model framework to fit spatial models. The fit of Bayesian spatial models was between 35 and 55% better than the fit of nonspatial analogue models. Bayesian spatial models outperformed analogous models developed with maximum entropy (Maxent) methods. Although the best spatial and nonspatial models included similar environmental variables, spatial models provided estimates of residual spatial effects that suggested how ecological processes might structure distribution patterns. Spatial models built from presence–absence data improved fit most for localized endemic species with ranges constrained by poorly known biogeographic factors and for widely distributed species suspected to be strongly affected by unmeasured environmental variables or population processes. By treating spatial effects as a variable of interest rather than a nuisance, hierarchical Bayesian spatial models, especially when they are based on a common broad‐scale spatial lattice (here the national Forest Inventory and Analysis grid of 24 km² hexagons), can increase the relevance of habitat models to multispecies conservation planning.     

牛磺熊脱氧胆酸在棕榈酸诱导的INS-1细胞凋亡中的作用（Effects of Tauroursodeoxycholic Acid on the Apoptosis of INS-1 Cells Cultured by Palmitate）

为观察牛磺熊脱氧胆酸(Tauroursodeoxycholic acid,TUDCA)对棕榈酸(Palmitate)诱导的INS-1细胞凋亡的影响,分别用不同浓度棕榈酸(0.25mmol&#183;L-1、0.5mmol&#183;L-1、1.0mmol&#183;L-1),棕榈酸(0.5mmol&#183;L-1)+不同浓度TUDCA(25μmol&#183;L-1、50μmol&#183;L-1、100μmol&#183;L-1)培养INS-1细胞12h,用MTT法检测细胞毒性作用,流式细胞术检测细胞凋亡,RT-PCR技术检测凋亡相关基因Bax/Bcl-2的表达.结果表明,与空白对照组比较,棕榈酸组(浓度≥0.5mmol&#183;L-1)INS-1细胞凋亡率显著上升(p<0.05);加TUDCA培养组,当浓度≥50μmol&#183;L-1时,与棕榈酸组相比,INS-1细胞凋亡率显著下降(p<0.05),呈剂量-效应关系.此外,棕榈酸组(浓度≥0.5mmol&#183;L-1)INS-1细胞凋亡相关基因Bax表达显著上升(p<0.05),Bcl-2则明显下降;加TUDCA后,Bax基因表达显著下降(p<0.05),而Bcl-2则明显上升(p<0.05),并呈剂量-效应关系.以上结果表明,TUDCA能够减少游离脂肪酸引起的INS-1细胞凋亡,对INS-1细胞发挥保护作用.而凋亡促进基因Bax的表达下调,凋亡抑制基因Bcl-2的表达上调可能是其作用机制之一.     

Rapidly Shifting Baselines in Yangtze Fishing Communities and Local Memory of Extinct Species

Abstract: Local ecological knowledge can provide a unique source of data for conservation, especially in efforts to investigate the status of rare or possibly extinct species, but it is unlikely to remain constant over time. Loss of perspective about past ecological conditions caused by lack of communication between generations may create “shifting baseline syndrome,” in which younger generations are less aware of local species diversity or abundance in the recent past. This phenomenon has been widely discussed, but has rarely been examined quantitatively. We present new evidence of shifting baselines in local perception of regional species declines and on the duration of “community memory” of extinct species on the basis of extensive interviews with fishers in communities across the middle‐lower Yangtze basin. Many Yangtze species have experienced major declines in recent decades, and the Yangtze River dolphin or baiji (Lipotes vexillifer) and Yangtze paddlefish (Psephurus gladius) may have become extinct during the 21^st century. Although informants across all age classes were strongly aware of the Yangtze ecosystem's escalating resource depletion and environmental degradation, older informants were more likely to recognize declines in two commercially important fish species, Reeves’ shad (Tenualosa reevesii) and Yangtze pufferfish (Takifugu fasciatus), and to have encountered baiji and paddlefish in the past. Age was also a strong predictor of whether informants had even heard of baiji or paddlefish, with younger informants being substantially less likely to recognize either species. A marked decrease in local knowledge about the Yangtze freshwater megafauna matched the time of major population declines of these species from the 1970s onwards, and paddlefish were already unknown to over 70% of all informants below the age of 40 and to those who first started fishing after 1995. This rapid rate of cultural baseline shift suggests that once even megafaunal species cease to be encountered on a fairly regular basis, they are rapidly forgotten by local communities.     

Cl-BDE-208和BDE-209诱导LINE-1基因低甲基化和ESR1基因高甲基化

十溴联苯醚(BDE-209)是使用最多的一种多溴阻燃剂,由于具有高亲脂性和低挥发性,容易蓄积在生物体内,在人体血清、母乳、肝脏等组织中均有检出;其环境脱溴产物九溴一氯联苯醚(Cl-BDE-208)也在血清样品和环境样品中被频频检出,而目前对这种化合物的毒理学研究,特别是对人体早期健康效应的研究较少。为了评估Cl-BDE-208和BDE-209的早期健康效应,以人乳腺癌细胞MCF-7为模型,环境相关浓度(0.375~3μmol·L-1)为暴露浓度,检测Cl-BDE-208和BDE-209对重复序列LINE-1、全基因组DNA甲基化(GDM)和雌激素受体基因(包括ESR1和ESR2)甲基化水平的改变。结果表明,Cl-BDE-208和BDE-209都可能通过降低DNA甲基化转移酶(DNMTs)活性而诱导了LINE-1和GDM的低甲基化,8-羟基脱氧鸟苷(8-OHd G)水平的升高可能参与了BDE-209引起的低甲基化过程;同时通过促进雌激素受体α(ESR1)基因的高甲基化而显著下调了ESR1基因的表达,而对雌激素受体β(ESR2)基因甲基化水平并没有显著影响。Cl-BDE-208和BDE-209都可能通过改变DNA甲基化水平而影响人体的早期健康效应,同时ESR1基因的高甲基化可能是Cl-BDE-208和BDE-209引起内分泌毒性的机制之一。     

零价铁对污泥厌氧消化过程中四环素抗性基因水平转移的作用影响

细菌抗药性问题已成为全球生态环境安全和人体健康领域的一个关注焦点.污水处理剩余污泥是抗生素抗性基因（ARGs）的一个重要储存库和排放源,采用荧光定量PCR方法检测分析了四环素抗性基因（TC-ARGs,包括tetA、tetC、tetG、tetM、tetO、tetW和tetX）及第一类整合子 intI1基因丰度在污泥厌氧消化过程中的变化特征,考察了不同投加量零价铁（Fe⁰）对目标基因的消长影响,初步分析了质粒DNA接合作用对TC-ARGs水平转移的作用影响,并探讨了TC-ARGs与 intI1基因之间的相关关系.结果表明,污泥厌氧消化过程对TC-ARGs和intI1基因丰度具有不同程度的削减作用,其中tetX基因丰度降幅可达2.4个数量级.Fe⁰的加入对TC-ARGs和intI1基因丰度削减不显著,并且随着Fe⁰投加量的增加,TC-ARGs和intI1基因丰度相比对照组出现逐渐升高的趋势.通过对质粒组DNA所携带的TC-ARGs基因丰度进行检测分析发现,质粒DNA接合作用对TC-ARGs的水平转移具有促进作用.相关性分析结果显示,tetG与intI1基因之间具有显著正相关关系,表明intI1基因在污泥厌氧消化过程中可能对tetG基因的演变过程具有重要影响.     

MUCT短程硝化和反硝化除磷系统中Candidatus Accu- mulibacter的代谢活性和菌群结构

采用实现亚硝酸型硝化的MUCT工艺处理低C/N实际生活污水,在短程硝化的基础上实现反硝化除磷.研究短程硝化建立与破坏过程中,亚硝酸盐积累率的变化对系统除磷性能及Candidatus Accumulibacter菌群结构的影响.结果表明:MUCT除磷以反硝化除磷为主,平均反硝化除磷率高达88%.磷去除率与亚硝酸盐积累率具有很好的正相关性.短程硝化阶段磷的平均去除率比全程硝化阶段高30%以上,证明了亚硝酸盐更适合作为低C/N比污水反硝化除磷的电子受体.以多聚磷酸盐激酶基因(ppk1)作为遗传标记,采用实时荧光定量PCR方法考察不同亚硝酸盐积累率下Accumulibacter的丰度、各主要进化分支的菌群结构和相对丰度.当系统处于全程硝化状态时,存在少量以硝酸盐为电子受体的Acc-I型反硝化聚磷菌,低于总Accumulibacter的5%;当系统进入短程硝化状态后,Acc-I逐渐消失.运行期间以亚硝酸盐作为电子受体进行反硝化除磷的Acc-IID始终是优势聚磷菌,达到总Accumulibacter的92%以上,甚至接近100%,保证了亚硝酸型反硝化除磷的稳定运行,亚硝酸盐浓度是影响其丰度变化的重要因素.     

不同硝化负荷MBR去除类固醇雌激素的研究

以雌酮(E1)和17α-乙炔基雌二醇(EE2)2种典型类固醇雌激素为研究对象,考察了不同硝化负荷好氧MBR对其的去除特性.结果表明,硝化负荷为6.19,0.35,10.58mg/(gMLSS·d)的MBR对E1平均去除率分别为72.33%、64.06%和71.77%,去除负荷分别为29.98,23.06,27.66mg/(gMLSS·d);对EE2平均去除率分别为55.40%、42.87%和58.90%,去除负荷分别为22.39,16.54,23.58mg/(gMLSS·d).E1去除效果均优于EE2.MBR硝化负荷与氨氧化细菌之间有较好的线性关系;而SEs去除负荷与氨氧化细菌及硝化负荷之间不满足线性关系.硝化负荷为0.35mg/(gMLSS·d)时,SEs去除负荷较低,硝化负荷达到6.19mg/(gMLSS·d)时,SEs的去除负荷显著提高,而当硝化负荷增加到10.58mg/(gMLSS·d)时,SEs去除负荷不再有效提高.     

An improved index for monitoring metal pollutants in surface sediments

An approach for defining the quality of surface sediments of limited areas in terms of heavy metal contents is proposed. Sediments were taken on a bi‐dimensional mapping, for checking possible different sources of pollution in the case study, a harbour zone. Non residual metals were determined by ICP‐AES in cold diluted hydrochloric acid leachates of sediments. An “enrichment factor”;, r, can be computed for each metal: metals with r values exceeding unity can be considered as indicators of metal pollution. A “total enrichment factor”;, R, was proposed in order to assess the degree of pollution of sediments for each site. R is an adimensional value that accounts for the presence of metals that exceed threshold values determined by background concentrations.     

Plant extract reduces tobacco smoke harmful effects on alveolar macrophage immune responses

Tobacco smoke is a major factor responsible for lung cancer and chronic obstructive pulmonary disease. Although the best solution to reduce the incidence of these diseases is to quit smoking, there are still a large number of smokers. Thus, given the immunoregulatory properties of plant extracts, their capacity to reduce tobacco smoke harmful effects on alveolar macrophage (AM) functions was investigated. AM were treated with tobacco smoke extract and parenchymata tissue extract (PTE), or mesophyll cell extract (MCE) of Spinacia oleacea. The effects of tobacco smoke extract from PTE and MCE-treated cigarette filters were also investigated. AM production of tumor necrosis factor (TNF), interleukin-10 (IL-10) and macrophage chemoattractant protein-1 (MCP-1), and AM cytotoxicity were measured. Tobacco smoke extract significantly inhibited TNF, IL-10, and MCP-1 release, and AM cytotoxicity. The addition of PTE and MCE to tobacco smoke extract abrogated the inhibition of AM mediator release. However, only MCE restored AM cytotoxicity. Interestingly, tobacco smoke extract of PTE and MCE-treated cigarette filters showed reduced effects on AM functions. Tobacco smoke extract from MCE-treated (0.25%) cigarette filters did not inhibit TNF, IL-10, and MCP-1 release in contrast to tobacco smoke extract from buffer-treated cigarette filters. AM cytotoxic activity was not inhibited by the treatment with tobacco smoke extract from MCE-treated cigarette filters. Our data suggest that the presence of plant extract in cigarette filters reduces the inhibitory effects of cigarette smoke on AM functions. Thus, MCE-treated cigarette filters may help reducing lung diseases associated with smoking.